# Format: 201 Warning "Message"
# 1st field: integer message number
# 2nd field: message type: Output Note Warning or an error type (most
#            Python exception types, plus ModellerError, FileFormatError,
#            StatisticsError, SequenceMismatchError)
# 3rd field: The message text
#
# Arguments to the messages, as defined in CALL WRTMSG():
#
#   @I1   ... integer scalar 1, etc.
#   @i1   ... integer array 1, etc.
#
#   @R1   ... real scalar 1, etc.
#   @r1   ... real array 1, etc.
#
#   @S1   ... string scalar 1, etc.
#   @s1   ... string array 1, etc.
#
#   @L1   ... logical scalar 1, etc.
#   @l1   ... logical array 1, etc.
#

201 ModellerError
"'optimization_method' is out of range."
 
202 NotImplementedError
"Not implemented."
 
203 ModellerError
"CHARMM atom type is out of range;
Probably because model.generate_topology() was not called.
Atom index, atom type: @I1 @I2"
 
204 Warning
"Atomic radius very small; 'dynamic_sphere' term will be ignored for this atom.
Atom index, atom type, atom radius: @I1 @S1 @R1"
 
205 Warning
"'lennard_jones_switch[1]' reset to 'lennard_jones_switch[0]'+0.5.
'lennard_jones_switch[1]': @R1"
 
206 Warning
"'coulomb_switch[1]' reset to 'coulomb_switch[0]'+0.5.
'coulomb_switch[1]': @R1"
 
207 Warning
"A or B too big, or MAXIT too small."
 
208 ModellerError
"X < 0."
 
209 Warning
"A too large or ITMAX too small."
 
210 ModellerError
"A or X less than 0."
 
211 ModellerError
"Bad argument, X < 0 or X > 1."
 
212 ModellerError
"Too many iterations: @I1"
 
213 ZeroDivisionError
"Division by zero; divisor = @R1"

214 IndexError
"Index @I1 out of range @I2 to @I3"
 
215 MemoryError
"Dynamic memory allocation failed.
Routine, variable, status: @S1 @S2 @I1"

216 ValueError
"Self-guided molecular dynamics requested
(guide_factor is non-zero) but guide_time
is zero! Please specify a non-zero guide
time, in fs, or set guide_factor to zero
to request regular MD."

217 ModellerError
"Single-character residue type @S1
is not a standard residue type (one
of the first @I1 residues in restyp.lib)."
 
218 ValueError
"'n_subopt' out of range (must be 0 or more): @I1"

219 ModellerError
"No DEFATM line found in the first @I1
residues in restyp.lib."
 
220 ModellerError
"One-letter residue type @S1 is not a
'standard' residue type (one of the
first @I1 residues in restyp.lib)."

221 ModellerError
"Beginning of schedule not found."
 
222 Warning
"Missing columns in schedule file at step: @I1
automatically added scaling factors of 1.0."
 
223 ModellerError
"Internal error: array too small: @S1
current maximum, current need: @I2 @I1"
 
224 Note
"Open @I1 @S1 @S2 @S3"
 
225 IOError
"File does not exist: @S1"
 
226 IOError
"File already exists: @S1"

227 ModellerError
"Default residue type@S1 must be one of the
first @I1 residue types."
 
228 IOError
"Error opening file: @S1"
 
229 IndexError
"Solvent model index @I1 out of range:
must be between 1 and @I2."

230 Warning
"Alignment code@S1 is present multiple times in the
alignment file! Only the first entry will be read.
Suggest you remove the duplicate(s) to avoid confusion."

231 ModellerError
"CHARMM atom type is not recognized (not in RADII_LIB): @S1"
 
232 Note
"parameters    BONDS   ANGLS  DIHEDS IMPROPS    MODE
@S1"
 
233 ModellerError
"No keyword before contents."

234 ModellerError
"Atom @I1 (type @I2) has GB/SA radius @R1.
Radii must all be greater than zero. Please edit
the library file (e.g. modlib/solv.lib) to set
a correct radius for this atom type."
 
235 ModellerError
"SELECT identifier out of range: @I1"
 
236 ModellerError
"Atom class is out of range: @S1"
 
237 ModellerError
"Residue type undefined: @I1"
 
238 Note
"Reading CHARMM residue topology file version: @S1"
 
239 ModellerError
"Opt,dih,res mean out of range: @I1 @I2 @S1 @R1 @R2 @R3"
 
240 ModellerError
"Include residue type in RESTYP_LIB: @S1"
 
241 ModellerError
"Residue type defined multiple times: @S1"
 
242 ModellerError
"Numbers of dihedral angle entries and types not the same: @I1 @I2"
 
243 Warning
"This DELE keyword is not supported: @S1"
 
244 Warning
"Incorrect number of tokens: @I1"
 
245 Warning
"Number of atoms in MODEL2 <> MODEL: @I1 @I2"
 
246 Warning
"MODEL atom <> MODEL2 atom, atom index: @S1 @S2 @I1"
 
247 ModellerError
"Internal error: @I1 @I2"
 
248 Warning
"OFF_DIAGONAL <= OVERHANG: @I1 @I2"

249 FileFormatError
"@S1 record without a preceding @S2 record."
 
250 Warning
"Use OVERHANG=0 with local alignment."
 
251 ModellerError
"MATRIX_OFFSET probably has an invalid value: @R1"

252 FileFormatError
"Incorrectly formatted residue line: @S1
RESI or PRES lines must contain exactly three tokens:
RESI or PRES, the name of the residue, and the total charge."
 
253 ModellerError
"Singular matrix."
 
254 ModellerError
"Incorrect dimensions for matrix multiplication."
 
255 ModellerError
"PDB residue type unrecognized: @S1"
 
256 ModellerError
"Dihedral angle correlation coeff. out of bounds (+-1): $I1 $I2 $R1"
 
257 Note
"Number of classes: @I1"

258 Warning
"Group restraint on atom groups @S1, @S2 duplicated
(original restraint was @I1, this one is @I2)
Original restraint will be ignored!"
 
259 FileFormatError
"Incorrect number of items in a line: @S1"
 
260 ModellerError
"CHARMM residue type unrecognized: @S1"
 
261 EOFError
"Premature end of file: @S1"

262 ModellerError
"Central bond in dihedral too short: @R1
Perhaps atoms @I1 and @I2 have very similar coordinates?"
 
263 Note
"Number of dihedral angle types         : @I1
Maximal number of dihedral angle optima: @I2
Dihedral angle names                   : @s1"
 
264 ModellerError
"Weights sum to (almost) zero: @R1 @I1 @I2"
 
265 ModellerError
"Weights do not sum to 1: @R1 @I1 @I2
Old weights: @r1"
 
266 Note
"Number of residue groups: @I1"
 
267 FileFormatError
"First line not #DISTANCE or #SIMILARITY.
Line: @S1"
 
268 Note
"Number of residue types: @I1"
 
269 ModellerError
"Single character residue type unrecognized: @S1"
 
270 ModellerError
"Error reading/processing file: @S1"
 
271 ModellerError
"Mainchain class code not recognized: @S1"
 
272 FileFormatError
"Missing mainchain conformation class data for some
residues in MNCHDEF_LIB, @S1"
 
273 FileFormatError
"Incorrect format or empty line in RESTYP_LIB: @S1"
 
274 Note
"Mainchain residue conformation classes: @S1"
 
275 ModellerError
"E_o > 0: @R1"
 
276 Note
"'align_block' changed to 1."
 
277 ModellerError
"Residue identifier not found: @S1"
 
278 ModellerError
"No \":\" in ATOM:RESID[:CHAINID] atom identifier: @S1"
 
279 Warning
"IUPAC atom @S1 not found in topology library for residue
type @S2, index @I1.
Possible reasons are a non-standard PDB file, or new residue/atom
types. Compare the offending residue in the PDB file with its
definition in the topology library."
 
280 Warning
"No topology library in memory or assigning a BLK residue.
Default CHARMM atom type assigned: @S1 --> @S2
This message is written only for the first such atom."
 
281 ModellerError
"Probably RADII_LIB and MODELS_LIB are inconsistent with topology library.
Residue_type, Atom_type_IUPAC, Atom_type_CHARMM: @I1 @S1 @S2"

282 ModellerError
"Unable to read structural information for alignment
sequence: @I1 @S1
This command requires structures."
 
283 ModellerError
"Too few patched residues for this patching residue type: @I1 @I2"
 
284 ModellerError
"Beginning atom index for a residue out of bounds: @I1 @I2"
 
285 Warning
"Only @I1 residues out of @I2 contain atoms of type @S1
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)"
 
286 Warning
"MODEL atom not classified: @S1 @S2"
 
287 ModellerError
"No \":\" in RESID:CHAINID residue identifier: @S1"
 
288 Warning
"Protein not accepted: @I1 @S1"
 
289 Note
"Proteins (all/accepted): @I1 @I2"
 
290 ModellerError
"Number of residues in the alignment and @S1 files are different: @I1 @I2
For alignment entry: @I3 @S2"
 
291 SequenceMismatchError
"Sequence difference between alignment and @S1 :"
 
292 Warning
"Too many neighbors; overflow ignored: @I1 @I2"
 
293 Warning
"Reported @I1 warnings for this file;
further warnings will be suppressed."
 
294 ModellerError
"Probably cannot use SDCH=.T. here because of the atom order."
 
295 ModellerError
"Strange eigenvalues of matrix p: @r1"
 
296 ModellerError
"Number of equivalent positions < 3: @I1"
 
297 Note
"Segments, residues, atoms: @I1 @I2 @I3"
 
298 Note
"Segment: @I1 @S1 @S2 @I2"
 
299 ModellerError
"Atom index is out of bounds: @I1 @I2"
 
300 Note
"Number of pseudo atoms: @I1"
 
301 Warning
"File:@S1, Line@I1
Undefined input atom coordinates."
 
302 Note
"This file probably contains only Calpha atoms: @S1"
 
303 ModellerError
"No atoms were read from the specified input@S1 file, since the
starting residue number and/or chain id in MODEL_SEGMENT (or
the alignment file header) was not found;
requested starting position: residue number \"@S2\", chain \"@S3\";
atom file name: @S4"
 
304 Note
"Restraints in memory, selected restraints: @I1 @I2
Explicitly excluded atom pairs in memory : @I3
Pseudo atoms in memory                   : @I4"
 
305 FileFormatError
"Incorrect record identifier in restraint file; card: @S1"
 
306 ModellerError
"Atom identifier not found: @S1"
 
307 Note
"Number of restraints read    : @I1
Number of excluded pairs read: @I2
Number of pseudo atoms read  : @I3"

308 ValueError
"subopt_offset must be non-zero when n_subopt > 0"
 
309 ModellerError
"Mathematical form out of bounds; iform, icsr: @I1 @I2"
 
310 ModellerError
"Feature type out of bounds; iftyp, icsr: @I1 @I2"
 
311 ModellerError
"Restraint group out of bounds; group, icsr: @I1 @I2"
 
312 ModellerError
"Wrong number of parameters (@I1) for
@I2-dimensional cubic spline; should be 6 parameters per
dimension, plus the product of the modalities (i.e. @I3).
Restraint ID: @I4. Modalities are: @i1"
 
313 Note
"The overhangs in the alignment have been cut. You have to
re-read the alignment from a file to use it after this."
 
314 Warning
"Only integer residue numbers are allowed: @S1"
 
315 Warning
"There should be two sequences in the alignment: @I1"
 
316 ModellerError
"OFF_DIAGONAL <= OVERHANG: @I1 @I2"
 
317 Warning
"M. Levitt suggests 'gap_penalties_3d' should be 0 10: @R1 @R2"
 
318 Note
"I,NEQVCUT,NEQV,RMSCUT,RMS,RMSROT: @I1 @I2 @I3 @R1 @R2 @R3"
 
319 ModellerError
"Not two structures in alignment; nothing done."
 
320 Warning
"Alignment not refined."

321 ModellerError
"You cannot call libraries.read_restyp() while topologies are in memory; either
delete them first, or call libraries.read_restyp() before topology.read()"
 
322 Note
"Sequences start-points aligned initially: @I1"
 
323 Note
"Sequences end-points aligned initially: @I1"
 
324 Note
"Sequences mid-points aligned initially: @I1"
 
325 Warning
"A very bad case with no defined positions: @I1"
 
326 Warning
"No selected atoms for frw position: @I1"
 
327 Warning
"Only one structure; nothing done."
 
328 Note
"Initial framework positions: @I1"
 
329 Warning
"Insufficient overlap; nothing done."
 
330 Note
"Framework, Cycles, RMS_frw(i-1,i): @I1 @I2 @R1"
 
331 ModellerError
"Framework did not converge."
 
332 Note
"Framework: @I1"
 
333 ModellerError
"Atom index @I1 is out of range, for restraint @I2.
(Atom indices should be between 1 and NATOM.)"
 
334 ModellerError
"Alignment did not converge."
 
335 ModellerError
"No alignment."
 
336 ModellerError
"No template structures."

337 ModellerError
"For transfer_xyz with cluster_cut > 0, all template structures
must have the same topology as the model
(i.e. @I1 atoms, @I4 residues)"
 
338 Note
"Both ATOM_FILES and ALIGN_CODES are empty for entry: @I1"
 
339 Warning
"Model residue @I1 (type @I2, code @S1) does not match
that in alignment (type @I3, code @S2)."
 
340 ModellerError
"Number of residues in model (@I1) does not match
that in alignment (@I2)."
 
341 Warning
"Check the N-terminus numbering."
 
342 Warning
"Same residue numbers: @I1 @I2 @S1"
 
343 Note
">> BEGINNING OF COMMAND @S1"
 
344 Note
"<< END OF COMMAND @S1"
 
345 ModellerError
"Alignment with two proteins is needed."
 
346 ModellerError
"Reference structure and MODEL have different lengths: @I1 @I2"
 
347 ModellerError
"Reference structure and MODEL are different: @I1 @I2 @I3"
 
348 ModellerError
"RMS_CUTOFFS does not have the right number of elements: @I1 @I2
Probably because the number of dihedral angle types changed."
 
349 Warning
"Some residues are without DISTANCE_ATOMS[1] atom. NALN, position: @I1 @I2"
 
350 ModellerError
"Sequences different; seq;pos;types: @I1 @I2 @I3"
 
351 ModellerError
"Lengths of sequences different; seq;lens: @I1 @I2 @I3"
 
352 ModellerError
"Number of sequences in the two alignments is different: @I1 @I2"
 
353 Warning
"All distances are equal. Number of objects clustered: @I1"
 
354 ModellerError
"Incorrect ID1, ID2 range: @i1"
 
355 ModellerError
"Too many models for alignment.expand(): @I1 @I2"
 
356 Note
"Coordinates swapped in residue: @I1 @S1 @R1 @R2"
 
357 Warning
"atm1nam <> atm2nam, ia, ires (no swap): @S1 @S2 @I1 @I2"
 
358 Warning
"iatmr1 <> katmr2, ires (no swap): @I1 @I2 @I3"
 
359 Note
"Swapping atoms to minimize RMS in residues: @S1"
 
360 Warning
"nres1<>nres2 or natm1<>natm2 (no swap): @I1 @I2 @I3 @I4"
 
361 ModellerError
"nbound <> 2*nblk: @I1 @I2"
 
362 ModellerError
"Not a similarity matrix."
 
363 ModellerError
"Not correct segm/loops."
 
364 ModellerError
"Not correct segm/nnnshft."
 
365 ModellerError
"Not correct segm/nncshft."
 
366 ModellerError
"Target sequence length is 0."
 
367 ModellerError
"Sequence not found; code: @S1"
 
368 ModellerError
"Search sequence length = 0; code: @S1"
 
369 ModellerError
"Internal error. LOWLIM or UPLIM are out of range: @I1 @I2"
 
370 Note
"Group added to ALIGNMENT: @S1"
 
371 Warning
"Not adding group to alignment (not found in groups file): @S1"
 
372 FileFormatError
"No PDB code in field 2 for structure: @S1
Card: @S2"
 
373 ModellerError
"Protein specified in ALIGN_CODES(i) was not found
in the alignment file; ALIGN_CODES(@I1) = @S1"
 
374 Note
"Non-standard residue type,position,sequence: @S1 @I1 @I2"
 
375 ModellerError
"Unknown residue type,position,sequence: @S1 @I1 @I2"

376 FileFormatError
"Garbage after expected end of @I1 tokens;
file @S1, line @I2, column @I3"
 
377 FileFormatError
"Incorrectly formatted MASS line: @S1
MASS lines must contain exactly five tokens:
MASS, an integer atom type (ignored by MODELLER),
the CHARMM atom name, the atomic mass, and the
element name."

378 ModellerError
"Error reading sequence from PDB file: @I1"
 
379 ModellerError
"Alignment sequence not found in PDB file: @I1 @S1"
 
380 FileFormatError
"Incorrect format in the PAP alignment file (no code): @S1"
 
381 FileFormatError
"Error reading the PAP alignment file (no non-empty line): @S1"
 
382 FileFormatError
"No : in Insight alignment file: @S1"
 
383 FileFormatError
"Couldn't read the alignment code from an Insight file: @S1"
 
384 ModellerError
"First sequence longer than MODEL: @I1 @I2 @I3 @S1"

385 ModellerError
"No primary sequence was read from PDB file \"@S1\",
since the starting residue number \"@S2\"
and/or chain id \"@S3\" given in the alignment file header
were not found in the PDB."
 
386 Warning
"A potential that relies on two proteins is used, yet you only have
an unknown in the alignment. Library, not MDT, potential is used."
 
387 Warning
"Model has multiple chains, and they do not all have a unique
chain ID. Suggest you relabel them as A, B, C, etc."

388 ModellerError
"indhash() out of range: @I1 @I2"
 
389 ModellerError
"MDT table range is too small.
MDT should be derived with the full range of possible values for
the independent variables."

390 Warning
"File:@S1, Line@I1
This line contains at least one tab character, and is thus
invalid PDB format. Each tab character has been replaced with
a space. It is recommended that remove tabs from your PDB
files to avoid running into other problems."

391 ModellerError
"SALIGN features 2, 3, 4, and 5 are distance features,
so cannot be used with similarity_flag=True.
Set similarity_flag to False, or set weights for
all features except feature 1 to zero."
 
392 ModellerError
"Your library requires all bins zero; nbinx: @I1"
 
393 Warning
"Sum of p(x/a,b,...,c) < tenm4: @R1
This is due to a bug or a very sparse pseudo-potential.
Pdf arbitrarily set to even distribution."
 
394 ModellerError
"NRESFEAT is incorrect: @I1"
 
395 Warning
"w(i) < 0; check a_i: @R1"
 
396 ModellerError
"SIMTOT < 1E-5: @R1"
 
397 Warning
"Atoms were not swapped because of the uncertainty of how to handle the H atom."
 
398 ModellerError
"SUM = 0: @R1"
 
399 ModellerError
"Incorrect number of parameters."

400 ModellerError
"PROFILE alignments currently work only with feature 1.
Set weights for all features except feature 1 to zero,
or set align_what to BLOCK to request a block rather
than profile alignment."
 
401 Note
"USER SYMMETRY, SYMMETRY: @I1 @L1
SYMMETRIC = .T. ==> NALN*NALN/2
SYMMETRIC = .F. ==> NALN*NALN
All protein pairs always generated."
 
402 Warning
"ires, irestp: @I1 @I2"

403 Warning
"Treating residue type @S1 as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file."

404 Warning
"At least one template is aligned with model residue @S1
but no coordinates could be transferred. This usually
occurs when your input files do not use the official
PDBv3 atom names. Please check your templates."

405 ModellerError
"HBONDS data can only be written to files, not to Biso, but
you did not specify a file name."

406 Warning
"Could not align @S1 with @S2, so will place these
sequences in separate clusters; MATRIX_OFFSET (@R1)
may have an invalid value. This message will be printed a maximum
of 20 times per call of sequence_db.filter()."

407 ValueError
"Only one-dimensional mathematical forms can be splined.
This form is defined on @I1 features."

408 Warning
"DISU patches are designed to be applied to exactly two CYS
residues; you have asked to patch residues
of types @S1 and @S2."

409 ModellerError
"Input distance matrix is of size zero: cannot calculate dendrogram."

410 Warning
"Residue index @I1 in model contains multiple selected
atoms with the same name (@S1). Only the first will be used."

411 ModellerError
"Cannot write a binary format sequence_db to another binary format
file. Copy the file instead (this is more efficient anyway)."

412 ValueError
"align code (@S1)
too long; length @I1 is greater than max length @I2."

413 IndexError
"Feature index out of range: @I1"
 
414 ModellerError
"Error in the format/contents of mdt1.ini."

415 Warning
"Sum of p(ijk) (@R1) is not equal to 1.0"
 
416 Warning
"Align code too long (@I1 characters); it has been
truncated to @I2 characters.
Align code: @S1."

417 Note
"Restraint type to be calculated: @S1"
 
418 ModellerError
"NPHYCNS from $FEATS_LIB <> size(RESTRAINTS_FILTER): @I1 @I2"
 
419 ModellerError
"No topology library is in memory. Use topology.read() to read one."
 
420 ModellerError
"No parameter library is in memory. Use parameters.read() to read one."
 
421 ModellerError
"No model topology; run model.generate_topology() first."
 
422 Note
"Number of previous, current restraints         : @I1 @I2"
 
423 Note
"Number of previous, current selected restraints: @I1 @I2"
 
424 Warning
"CIS peptide: @I1 - @I2 @S1 - @S2 @S3 - @S4 @i1"
 
425 Note
"Unselected all O C +N +CA dihedrals: @I1
(This is to avoid clashes between STEREO
and OMEGA_DIHEDRAL restraints)"
 
426 ModellerError
"Need 2 atoms in ATOM_IDS for RESTRAINT_TYPE = 'SHEET': @I1"

427 Note
"@I1 redundant cosine dihedral restraints were unselected."
 
428 ModellerError
"Alpha class undefined: @S1"
 
429 Note
"Restraining segment to strand: @I1 @I2"
 
430 ModellerError
"Strand class undefined: @S1"
 
431 ModellerError
"Proline beta class undefined: @S1"
 
432 ModellerError
"Atoms for the first H-bond not found: @S1 @S2 @I1 @I2 @I3 @I4"
 
433 ModellerError
"First H-bond cannot be a MC H-bond: : @S1 @S2"
 
434 Output
"Restraining segments to parallel sheet, H-bonds: @S1 @S2 @I1"
 
435 Output
"Restraining segments to anti-parallel sheet, H-bonds: @S1 @S2 @I1"
 
436 Output
"Number of user distances added: @I1
Total number of restraints before, now: @I2 @I3"
 
437 Warning
"Standard deviation is very small: @R1"
 
438 Warning
"Force constant is very small: @R1"
 
439 ModellerError
"No MODEL in memory."
 
440 Warning
"Adding params (mean,force,period): @R1 @R2 @I1
For atoms: @s1"
 
441 Output
"Number of restraints unselected: @I1"
 
442 ModellerError
"One or more atoms absent from MODEL: @s1"
 
443 Output
"Restraints marked for deletion were removed.
Total number of restraints before, now: @I1 @I2"
 
444 ModellerError
"Incorrect number of parameters; expected, specified: @I1 @I2"
 
445 ModellerError
"Excluded atom @S1 absent from MODEL."
 
446 Warning
"A potential that relies on one protein is used, yet you have at
least one known structure available. MDT, not library, potential is used."
 
447 ModellerError
"MNCH bins from MDT <> LIB: @I1 @I2"
 
448 ModellerError
"indatm, wght < 0: @I1 @R1"
 
449 Warning
"No atoms selected; no restraints will be selected."
 
450 ModellerError
"Probably because no MODEL is in memory; use model.read()."
 
451 Warning
"Requested schedule step not available: @I1
schedule.step set to len(schedule)."
 
452 ModellerError
"Probably because no schedule was read/made; use schedule.read()/schedule.make()."
 
453 Warning
"No fixed restraints selected; there may be some dynamic ones."
 
454 Warning
"Restraints file was probably not read; use restraints.append()."
 
455 Warning
"None of the non-bonded terms selected."
 
456 Warning
"Both soft sphere and Lennard-Jones terms selected."
 
457 Warning
"Both soft sphere and statistical potential terms selected."
 
458 Warning
"Both Lennard-Jones and statistical potential terms selected."

459 Warning
"Residue type @S1 not recognized. 'automodel' model building
will treat this residue as a rigid body.
To use real parameters, add the residue type to ${LIB}/restyp.lib,
its topology to ${LIB}/top_*.lib, and suitable forcefield
parameters to ${LIB}/par.lib."
 
460 ModellerError
"Center residue not found: @S1"
 
461 ModellerError
"Center atom not found: @S1"
 
462 Note
"Number of selected atoms            : @I1"
 
463 Note
"Number of splined restraints: @I1"
 
464 Warning
"Inventing the MODEL coordinates."
 
465 Warning
"No seed atoms can be found in MODEL."
 
466 Warning
"Some coordinates in MODEL not assigned."
 
467 Warning
"All coordinates in MODEL have been assigned."
 
468 Warning
"Some coordinates in MODEL are still undefined."

469 Warning
"At least one residue number in the model is duplicated.
(First duplication is residue \"@S1\", chain \"@S2\".)
Suggest you renumber the residues and/or chains to
avoid selecting the wrong residues (e.g. with model_segment)."
 
470 Warning
"Atoms I-J-K are co-linear; L not built: @I1 @I2 @I3 @I4"
 
471 ModellerError
"Number of bonds/atom incorrect; possibly increase MAXBAT.
Atom indices in bond: ', @I1 @I2
Their bonds         : ', @I3 @I4"
 
472 ModellerError
"No template residues; number of templates: @I1"
 
473 ModellerError
"Atom indices for seed atoms are duplicated: @I1 @I2 @I3"
 
474 Warning
"Some IC values are zero for seed atoms.
I,J,K,RIJ,RJK,THETA: @I1 @I2 @I3 @R1 @R2 @R3"
 
475 Warning
"Could not find parameters in the parameters library: @S1 @S2 @S3 @S4"

476 Warning
"Residue @S1, name @S2 contains a mixture of HETATM and ATOM
lines. Modeller will treat this residue as ATOM. To treat it
as HETATM, modify the PDB and mark all atoms in this residue
as HETATM."
 
477 ModellerError
"No templates in the alignment.
Number of sequences in the alignment: @I1"

478 Warning
"Residue @S1, name @S2 is marked as ATOM in restyp.lib but
as HETATM in the PDB file. Modeller will treat this residue
as a HETATM (BLK) residue. To treat it as ATOM, modify the
PDB and mark at least one atom in this residue as ATOM."
 
479 ModellerError
"Must not use patching residues here.
Residue type index, residue type: @I1 @S1"
 
480 Warning
"Residue type ignored (aln position, sequence, type): @I1 @I2 @S1"
 
481 Warning
"This disulfide was already patched."
 
482 ModellerError
"Patching residue identifier not found: @S1"
 
483 Note
"CD1/2 CE1/2 swapped: @R1 @I1 @S1"
 
484 Warning
"Dihedral still outside +-90: @R1"
 
485 Note
"OD1/2 will be swapped: @R1 @I1 @S1"
 
486 Note
"OE1/2 will be swapped: @R1 @I1 @S1"
 
487 Note
"NH1/2 swapped: @R1 @I1 @S1"
 
488 Warning
"CHARMM LIB atom not found in MODEL: @I1 @S1 @S2"
 
489 ModellerError
"CHARMM LIB atom not found in MODEL: @I1 @S1 @S2"
 
490 ModellerError
"MODEL residue does not have the same number of atoms as
CHARMM topology library residue: @I1 @S1 @I2 @I3"
 
491 Note
"MODEL residue changed: @I1 @S1 @S2 @S3"
 
492 Warning
"Are you sure you want to calculate a normalized energy profile!"
 
493 ModellerError
"MODEL atom not found in MODEL2: @I1 @S1 @S2"
 
494 ModellerError
"MODEL residue does not have the same number of atoms as
MODEL2 residue: @I1 @S1 @I2 @I3"
 
495 Warning
"MODEL residue type not in MODEL2: @I1 @S1"
 
496 Note
"Amplitude is > 0; randomization is done."
 
497 Note
"Amplitude is < 0; random coordinates are assigned."
 
498 Note
"Atoms,selected atoms,random_seed,amplitude: @I1 @I2 @I3 @R1"
 
499 Note
"Amplitude is 0; no randomization will be done."
 
500 ModellerError
"Numbers of MODEL and MODEL2 residues not equal: @I1 @I2"
 
501 Note
"Gravity center of MODEL: @R1 @R2 @R3"
 
502 ModellerError
"Order of RESI/ATOM/PRES is incorrect."
 
503 ModellerError
"Number of atoms in topology library > MODEL; residue: @I1 @I2 @S1"

504 Warning
"Sequence database contains no sequences. No profile will be built."
 
505 Note
"MODEL is an average of the largest cluster: @R1"
 
506 Note
"MODEL is an average of all templates."
 
507 ModellerError
"Number of residues in alignment different from that in MODEL: @I1 @I2
(Did you call clear_topology() before generate_topology() ?)"
 
508 Warning
"Residue type in ALIGNMENT different from that in MODEL.
MODEL position, ALIGNMENT type, MODEL type: @I1 @I2 @I3"

509 ValueError
"by_chain mode works only on a single edited sequence.
You have selected @I1."

510 ModellerError
"by_chain mode works only on edited sequences that
do not have structural information."
 
511 Note
"Number of templates for coordinate transfer: @I1
After transferring coordinates of the equivalent template atoms,
there are defined, undefined atoms in MODEL: @I2 @I3"
 
512 ModellerError
"Dihedral undefined: @i1"
 
513 Warning
"Local optimization without restraints selected.
Thus, no change to structure at all."
 
514 ModellerError
"Bad restraints; undefined mean."
 
515 Note
"Residues,dihedral type,all-selected,optimized: @I1 @I2 @I3 @I4"
 
516 Note
"Residues, dihedral type, randomized: @I1 @I2 @I3"
 
517 Note
"Local optimization around @S1"
 
518 Note
"Local randomization around @S1 for @R1"
 
519 Warning
"Amplitude is 0; no randomization."
 
520 Warning
"Normalization of charges failed: @I1 @R1 @R2"
 
521 Note
"Reducing the topology to @I1"
 
522 Output
"Number of disulfides patched in MODEL: @I1"
 
523 ModellerError
"The same SG atom occurs in more than one disulfide.
Thus, the model is incorrect."
 
524 ModellerError
"An SG atom is bonded to itself. Thus, the model is incorrect."

525 Warning
"@I1 mainchain (N or C) atoms were approximately placed
based on CA atom coordinates."

526 Warning
"Inventing the mainchain model coordinates."

527 Warning
"align_block is ignored for PROGRESSIVE alignments.
Perhaps you meant alignment_type='PAIRWISE' ?"

528 ModellerError
"Density map must be cubic; actual dimensions
@I1 @I2 @I3"
 
529 Note
"MODELLER, EXIT(0)."
 
540 TypeError
"Numbers of expected, actual arguments are different: @I1 @I2
Command line: @S1"
 
541 Note
"Number of reals,integers,strings,logicals: @i1"
 
553 IOError
"I/O stream not opened: @I1"
 
554 ModellerError
"I/O stream out of range: @I1"
 
565 ModellerError
"Restraint index out of bounds (NCSR,NICSR,IC,I): @I1 @I2 @I3 @I4"
 
566 Note
"Residues, atoms, charge: @I1 @I2 @R1"
 
567 Note
"Residues, atoms: @I1 @I2"
 
568 Note
"Residues, atoms, selected atoms: @I1 @I2 @I3"
 
569 ModellerError
"Incorrect type of the non-bonded pair routine: @I1"
 
570 Warning
"Unknown atom type for atom: @I1"
 
571 Warning
"Unspecified restraint for atoms, types: @I1 @I2 @I3 @I4"
 
572 Warning
"Unknown atom types for atoms: @I1 @I2 @I3 @I4"
 
573 Warning
"OBJFUNC() <> Sum FEATPDF: @R1 @R2"
 
576 ModellerError
"Environment variable for application directory undefined.
Program probably not installed correctly."
 
578 Note
"Initializing application @S1"
 
580 Warning
"Weird SELECTION_STATUS: both initialization and removing selected."
 
581 ModellerError
"Defining a pseudo atom with an undefined real atom: @I1 @I2"
 
582 ModellerError
"Run model.transfer_xyz(), model.read() or model.build() first."
 
583 ModellerError
"Run topology.read() and model.generate_topology() first."
 
584 ModellerError
"Number of sequences in the alignment is 0."
 
585 ModellerError
"Wrong number of topology models (@I1) in MODELS_LIB:
was expecting @I2 (to match RADII_LIB)"
 
587 ModellerError
"This command needs a non-empty alignment.
Run alignment.append() or make alignment first."
 
588 ModellerError
"Run model.generate_topology() and parameters.read() first."
 
589 ModellerError
"Run topology.read() first."
 
590 ModellerError
"No topology generated for sequence: @S1
Possibly because incorrect topology library is used."
 
592 ModellerError
"There is no such CODE in the alignment: @S1"
 
594 ModellerError
"No atoms in memory. Run model.read() or model.build()"
 
595 ModellerError
"Number of selected atoms in sets 2 & 3 is not the same: @I1 @I2"
 
596 ModellerError
"Atom index is out of range (iatm,natm): @I1 @I2"
 
597 ModellerError
"Atom type(s) out of range: @I1 @I2"
 
598 Output
"Number of user atom restraints added  : @I1
Total number of restraints before, now: @I2 @I3"
 
599 Warning
"Atom type not found; restraint ignored: @S1 @S2"
 
600 ModellerError
"Restraint for atom type not found."
 
601 ModellerError
"Not one atom in restraint."
 
602 ModellerError
"Incorrect physical restraint type: @I1"
 
603 ModellerError
"Impropers must have periodicity 0: @I1"
 
604 ModellerError
"Torsions must have periodicity 1,2,3,4,5,6: @I1"
 
605 ModellerError
"Force constant cannot be less than 0."
 
606 Note
"Stereochemical restraints were constructed from RTF & PRMF.
Added bond,angle,dihedral,improper restraints  : @i1
Total number of restraints before, now         : @I1 @I2"
 
607 Warning
"Cannot find params in params file:
CHARMM atoms : @s1
IUPAC atoms  : @s2
Atom indices : @i1
Residues     : @s3"
 
609 ModellerError
"Delta time too small: @R1"
 
610 Warning
"Precision problem; starting from scratch."
 
611 Warning
"Precision problem; starting from scratch.
Last such message in this model.optimize()."
 
612 Note
"Number of MODEL atoms, selected restraints; @I1 @I2"
 
613 Warning
"No selected restraints remain!"
 
615 Warning
"SEGMENT_IDS length < number of segments: @I1 @I2
Segment ids set to blank for missing SEGMENT_IDS."
 
616 Warning
"SEGMENT_IDS length > number of segments: @I1 @I2
Additional SEGMENT_IDS are ignored."
 
617 Note
"End of the function/derivatives test; no discrepancies
were found to be above given cutoffs."
 
618 Warning
"Derivatives of@S1 disagree:
analytic, numeric, absolute&fractional error:
@R1 @R2 @R3 @R4"
 
621 Note
"Testing the objective function and derivatives code by comparison
of numerical and analytical derivatives. Any discrepancies with
absolute and relative errors larger than the two cutoffs are
written out.
Derivatives for individual restraints evaluated : @L1
Absolute error cutoff for whole function        : @R1
Fractional cutoff for whole function            : @R2
Absolute error cutoff for restraints            : @R3
Fractional cutoff for restraints                : @R4
This test does not work for splines of periodic features!"
 
622 ModellerError
"H must be nonzero."
 
624 Warning
"Restraint @I1 derivatives disagree for
@S1: analytic, numeric, abs&frac error:
@R1 @R2 @R3 @R4"
 
627 ModellerError
"No undefined atom type in RADII_LIB"
 
628 ModellerError
"Wrong number of atom types (@I1) in @S1:
was expecting @I2 (to match RADII_LIB)"
 
629 ModellerError
"Wrong number of topology models (@I1) in @S1:
was expecting @I2 (to match RADII_LIB)"
 
630 ModellerError
"Atom types differ in RADII_LIB and @S3
(@S1 versus @S2)
Atom types (and their order) must be the same
in both files."
 
631 ModellerError
"No aligned template residues for BLK residue;
number of templates: @I1
Make sure that each BLK residue in your target
sequence is aligned with your templates.
(This can also be caused by a lack of structural
information. Make sure you are using a PIR, not
FASTA, alignment file, and that the template
headers use 'structureX' not 'sequence'.)"

632 ModellerError
"Number of mnch. conf. classes not the same in
Ramachandran LIB and MNCH LIB: @I1 @I2"
 
633 ModellerError
"Number of mnch. conf. classes not the same in
Ramachandran LIB and MNCH1 LIB: @I1 @I2"
 
634 ModellerError
"Number of mnch. conf. classes not the same in
Ramachandran LIB and MNCH2 LIB: @I1 @I2"
 
635 ModellerError
"Number of mnch. conf. classes not the same in
Ramachandran LIB and MNCH3 LIB: @I1 @I2"
 
636 ModellerError
"Must be a distance residue-residue weight matrix: @R1"
 
637 Warning
"No residue topology library is in memory.
Better radii would be used if topology.read() is called first."

638 Note
"Missing atoms in a dihedral, residue index, residue type: @I1 @I2 @S1"

639 Note
"Atoms are labeled incorrectly; swapped: @I1 @I2 @S1"

640 Note
"Bond is too long (bond, dih.type, ires, resnam): @I1 @I2 I3 @S1"

641 Note
"At least one atom has undefined XYZ (dih. type, residue index, residue type): @I1 @I2 @S1"

642 Note
"SIZE1*SIZE2 = 0: (dih. type, residue index, residue type): @I1 @I2 @S1"

643 Note
"Protein accepted: @S1"

644 Warning
"Two basis restraints have means too far apart:
ICSR  MEAN1   MEAN2   STDEV1  STDEV2  R.VIOL1 R.VIOL2 NEW_SD1 NEW_SD2
@S1"

645 Warning
"New number of symmetry segments, atom pairs: @I1 @I2"

646 Output
"REGION_SIZE, seed atom index, total_area: @I1 @I2 @R1"

647 ModellerError
"Not enough exposed atoms given the requested size of the patch: @I1 @I2"

648 SequenceMismatchError
"Alignment sequence does not match that in@S1 file: @I1 @S2
(You didn't specify the starting and ending residue numbers and
chain IDs in the alignment, so Modeller tried to guess these from
the PDB file.)
Suggestion: put in the residue numbers and chain IDs (see the
manual) and run again for more detailed diagnostics.
You could also try running with allow_alternates=True to accept
alternate one-letter code matches (e.g. B to N, Z to Q)."

649 Warning
"Chain names are identical; chn ids, names: @I1 @I2 @S1 @S2
  2nd chain automatically renamed."

650 ModellerError
"Inconsistency in the sequence database contents. 
Numbers of residues do not match: @I1 @I2"

652 Warning
"At least one residue type in the profile is non-standard.
Non-standard residues will be mapped to standard residues
as defined in modlib/restyp.lib."

655 Note
"If Weights Type ('SIMILAR' or 'DISTANCE') is not specified it is assumed to be 'SIMILAR'."

656 Warning
"Number of bins for histogram too small - results maybe unreliable, nbins: @I1"

657 StatisticsError
"Not enough bins in histogram - cannot calculate statistics, nbins: @I1"

658 Output
"Percentage of alignments from previous iterations still significant, [iter, perc]: @I1, @R1"

659 Warning
"Profile appears to be diverging. The observed/expected distributions do not fit.
Kolmogov-Smirnov statistic for the fit: @R1"

660 Output
"Quality of the fit between observed/expected score distributions.
[Iteration, Chi2, nbins, KS-Stat, nscores ] = @I1, @R1, @I2, @R2, @I3"

661 ModellerError
"Internal error - no possible choices given for variable@S1"

662 ValueError
"Invalid choice@S1 for variable@S2: can choose
@S3 from the following:@S4"

663 ValueError
"Variable@S1 cannot be blank: you can choose
@S2 from the following:@S3"

664 ModellerError
"Internal error - cannot call num_optvar on the single-choice optvar@S1"

665 ModellerError
"Internal error - option@S1 is not a valid choice from
@S2"

666 ModellerError
"Cannot calculate multiple iterations when 'score_statistics' = True"

667 ModellerError
"Cannot continue - no alignment in memory!"

668 ModellerError
"There is no second model in memory!"

669 Note
"Uncompressing compressed file with system command:
@S1"

670 ModellerError
"Feature value @R1 is outside defined range for closed cubic spline: @R2 @R3"

672 FileFormatError
"Reached end of alignment file: @S1
Please check the file to make sure your sequences end with
the '*' character."

673 ModellerError
"Request for invalid restraint global array: @I1
Valid range is 1 through @I2."

674 ModellerError
"Inconsistency detected; the number of profiles in
the PSSMDB (@I1) does not match that in your profile
list file (@I2)."

676 Warning
"No topology library in memory, so using default submodel:@I1"

677 ModellerError
"Exactly one sequence must be present in the alignment."

678 Warning
"No file units available for output - no output written"

679 ModellerError
"No group restraints loaded for this model - cannot make ONE_ATOM restraints"

680 ModellerError
"Cannot read topology.submodel from topology file, line: @S1"

681 Output
"topology.submodel read from topology file: @I1"

683 TypeError
"Variable@S1 should be a sequence of length@I1 (the number of
physical restraint types). Got@I2."

684 Note
"Compressing file with system command:
@S1"

685 ModellerError
"System command failed."

686 Warning
"Residue @S1 contains multiple C alpha atoms; only the first
will be used for restraint derivation. Check the structure file
@S2 for residues with unmarked alternate location atoms."

687 ModellerError
"PSSMs should be read in from a database to calculate
significance scores."

688 ModellerError
"Incorrect range for open cubic spline @I1,
dimension @I2: xlow (@R1) should be less than
xhigh (@R2), and the range should be equal to the
delta (@R3) times the modality (@I3) minus 1."

689 ModellerError
"Incorrect range for closed cubic spline @I1,
dimension @I2: xlow (@R1) should be less than
xhigh (@R2), and the range should be equal to the
delta (@R3) times the modality (@I3)."

690 ModellerError
"Atom index@I1 is in multiple rigid bodies!"

691 ModellerError
"Inconsistent parameters: the number of features,
modalities, atom groups must all be the same."

692 ModellerError
"Was expecting@S1 at position@I1 in
the string: @S2"

693 ModellerError
"Rigid body atom index @I1 is out of range.
(Atom indices should be between 1 and NATOM = @I2.)"

694 ModellerError
"Rigid body contains no atoms!"

695 ModellerError
"Cannot perform alignment - zero length sequence:@S1
(Check to make sure you read in the alignment correctly.)"

696 ModellerError
"Residue @I1 in model @I2 is lacking at least
one of the needed 4 backbone (C, CA, N, O) atoms."

697 ModellerError
"The two models must have the same number of residues!"

698 Note
"Only some atoms in the rigid bodies are selected
(the first NONselected atom is index@I1)
Each whole body will move, but only restraints
involving the selected atoms will be enforced.
Selecting all atoms in the body is recommended."

699 TypeError
"Optimizer state should be a sequence of length@I1 (the number of
degrees of freedom). Got@I2."

700 ModellerError
"Cannot perform profile-profile alignment, since no sequence
profile information is available and smooth_prof_weight = 0.
(This occurs when there is no variability in your input
sequences, for example if you have only one sequence in each of
your alignment blocks. Increase smooth_prof_weight to use the
background information.)"

701 Warning
"Insufficient system memory to allocate storage for cell-based
(NlogN) nonbond list algorithm; falling back to N*N method.
Warning @I1 of @I2; further warnings will be suppressed."

702 FileFormatError
"File:@S1, Line@I1
Could not parse data from file; file is probably corrupt."

703 ModellerError
"USER restraints format is no longer supported."

704 Warning
"At least one non-standard residue was found in the profile and 
was converted to a standard residue to calculate sensible values
for sequence weights. The non-standard residues in the alignment
will be unchanged. The following corrections are made: ASX -> ASN,
GLX -> GLN, UNK -> ALA, BRK -> GAP, MSE -> MET and all other
non-standard residues to GLY."

705 ModellerError
"saxs_computepr in saxs_routines stopped - increase number of points
for P(r) (now nr=@I1 ). Alter in ini_saxs."

706 Warning
"BLK ('.') residue type in alignment will force 'automodel'
model building to treat residue type @S1 as a rigid body,
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, use 1-letter code '@S2' in the alignment."

707 ModellerError
"Inconsistency in chi-square calculation: @R1 @R2"

708 Warning
"There are zero degrees of freedom;
chi-square calculation is meaningless."

709 ValueError
"'dimensions' is @I1; it must be either 1 or 2,
and not more than the dimensionality of this MDT, @I2"

710 ModellerError
"For feature @I1 new start @I2 and size @I3
are out of range."

711 ModellerError
"Structures must be available for every sequence
in the alignment for output='QUALITY'."

712 FileFormatError
"Invalid line in class file; expected it to start
with either @S1 or @S2:
@S3"

714 ModellerError
"Number of bins in MDT table (@I1) does not
match that in bin file (@I2) for feature
number @I3, feature type @I4."

716 NotImplementedError
"MDT feature @I1 not implemented."

717 ModellerError
"Unable to get template coordinates for BLK residue
number @I1, as the alignment contains only @I2
positions. This is likely caused because your
alignment does not match your model, or you forgot
to call clear_topology() before generate_topology()."

718 FileFormatError
"Could not find all required fields in the atom_site loop."

719 FileFormatError
"Found @S1 in an mmCIF loop over a different category.
mmCIF files do not allow loops to contain fields from
multiple categories."