Fri May 2 14:32:27 BST 2014 ############### You are running ARP/wARP 7.4, patch 2 ############### Working directory /data1/jmht/ensemble_arpwarp/1BYZ/All_atom_trunc_0.00843_rad_1 Job ID is set to . X-ray data file /data1/jmht/ensemble_arpwarp/1BYZ/1BYZ-cad.mtz Sequence file /data1/jmht/ensemble_arpwarp/1BYZ/1BYZ_1.pir Input PDB file /data1/jmht/ensemble_arpwarp/1BYZ/All_atom_trunc_0.00843_rad_1/shelxe_phaser_loc0_ALL_All_atom_trunc_0.00843_rad_1_UNMOD.pdb Tracing mode WARPNTRACEMODEL Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: freelabin=FREE mtz labels taken: FP SIGFP FREE Parameter file /data1/jmht/ensemble_arpwarp/1BYZ/All_atom_trunc_0.00843_rad_1/arp_warp_tracing.par Job launched in /data1/jmht/ensemble_arpwarp/1BYZ/All_atom_trunc_0.00843_rad_1 ############### You are running ARP/wARP 7.4, patch 2 ############### ================================================================================== | Please cite at least one of the publications below for | | the ARP/wARP application you are using: | | | | Langer G, Cohen SX, Lamzin VS, Perrakis A. (2008) Automated macromolecular | | model building for x-ray crystallography using ARP/wARP version 7. | | Nat. Protoc. 3, 1171-1179 | | | | Perrakis A, Morris RM, Lamzin VS. (1999) Automated protein model building | | combined with iterative structure refinement. Nature Struct. Biol. 6, 458-463 | | | | Wiegels T. & Lamzin, V.S. (2012) Use of noncrystallographic symmetry for | | automated model building at medium to low resolution. Acta Crystallogr D Biol | | Crystallogr. 68, 446-453 | | | | Use of Refmac is an essential part of model building with ARP/wARP. | | Please acknowledge the use of Refmac by citing the following publication: | | | | Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, | | Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular | | crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 | ================================================================================== Fri May 2 14:32:41 BST 2014 You are running ARP/wARP version 7.4 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory is: /data1/jmht/ensemble_arpwarp/1BYZ/All_atom_trunc_0.00843_rad_1 ARP/wARP software version is: 7.4 The parameter file is: /data1/jmht/ensemble_arpwarp/1BYZ/All_atom_trunc_0.00843_rad_1/arp_warp_tracing.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 46 and 0 Target number of residues in the AU: 46 Target solvent content: 0.3606 Checking the provided sequence file Detected sequence length: 12 Number of NCS-related molecules: 4 Adjusted target number of residues: 48 Adjusted target solvent content: 0.33 Input MTZ file is: 1BYZ-cad.mtz.cad Column labels for model refinement: FP SIGFP FREE Rfree value for free reflections: 0 Space group number is: 1 Cell parameters: 20.846 20.909 27.057 102.400 95.330 119.620 Input sequence file is: 1BYZ_1.pir_lf Input PDB file is: shelxe_phaser_loc0_ALL_All_atom_trunc_0.00843_rad_1_UNMOD.pdb_lf Setting PDB header to reflect the MTZ header content Number of atoms in the PDB file: 260 ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 1 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling, No bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 0 Loops will be built when appropriate and at the last cycle Resolution range: 25.690 0.904 Wilson plot Bfac: 3.75 Checking whether input PDB contains ligands unknown to the Refmac library 22467 reflections ( 85.86 % complete ) and 256 restraints for refining 260 atoms. Observations/parameters ratio is 21.60 ------------------------------------------------------ Starting model: R = 0.4486 (Rfree = 0.480). ------------------------------------------------------ Cycle 0: After refmac, R = 0.4199 (Rfree = 0.452) for 260 atoms. Cycle 0: After refmac, R = 0.4102 (Rfree = 0.443) for 260 atoms. Cycle 0: After refmac, R = 0.4045 (Rfree = 0.438) for 260 atoms. Cycle 0: After refmac, R = 0.4011 (Rfree = 0.434) for 260 atoms. Cycle 0: After refmac, R = 0.3989 (Rfree = 0.433) for 260 atoms. Cycle 0: After refmac, R = 0.3974 (Rfree = 0.432) for 260 atoms. Cycle 0: After refmac, R = 0.3964 (Rfree = 0.431) for 260 atoms. Cycle 0: After refmac, R = 0.3956 (Rfree = 0.430) for 260 atoms. Cycle 0: After refmac, R = 0.3949 (Rfree = 0.430) for 260 atoms. Found 85 (85 requested) and removed 6 (42 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 0.48 0.58 Round 1: 45 peptides, 4 chains. Longest chain 13 peptides. Score 0.890 Round 2: 45 peptides, 4 chains. Longest chain 13 peptides. Score 0.890 Round 3: 45 peptides, 4 chains. Longest chain 13 peptides. Score 0.890 Round 4: 45 peptides, 4 chains. Longest chain 13 peptides. Score 0.890 Round 5: 45 peptides, 4 chains. Longest chain 13 peptides. Score 0.890 Taking the results from Round 5 Chains 4, Residues 41, Estimated correctness of the model 99.9 % 2 chains (23 residues) have been docked in sequence 4 chains (41 residues) following loop building 2 chains (23 residues) in sequence following loop building ------------------------------------------------------ 22467 reflections ( 85.86 % complete ) and 570 restraints for refining 378 atoms. 310 conditional restraints added. Observations/parameters ratio is 14.86 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3723 (Rfree = 0.390) for 378 atoms. Found 86 (124 requested) and removed 3 (62 requested) atoms. Cycle 2: After refmac, R = 0.3082 (Rfree = 0.354) for 461 atoms. Found 52 (151 requested) and removed 6 (75 requested) atoms. Cycle 3: After refmac, R = 0.2556 (Rfree = 0.297) for 501 atoms. Found 37 (166 requested) and removed 9 (83 requested) atoms. Cycle 4: After refmac, R = 0.2202 (Rfree = 0.263) for 526 atoms. Found 33 (174 requested) and removed 1 (87 requested) atoms. Cycle 5: After refmac, R = 0.2170 (Rfree = 0.265) for 551 atoms. Found 24 (183 requested) and removed 2 (91 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 0.47 0.57 Round 1: 48 peptides, 4 chains. Longest chain 12 peptides. Score 0.907 Round 2: 45 peptides, 4 chains. Longest chain 13 peptides. Score 0.890 Round 3: 48 peptides, 4 chains. Longest chain 12 peptides. Score 0.907 Round 4: 44 peptides, 4 chains. Longest chain 13 peptides. Score 0.883 Round 5: 45 peptides, 4 chains. Longest chain 13 peptides. Score 0.890 Taking the results from Round 3 Chains 4, Residues 44, Estimated correctness of the model 99.9 % 4 chains (44 residues) have been docked in sequence 4 chains (44 residues) following loop building 4 chains (44 residues) in sequence following loop building ------------------------------------------------------ 22467 reflections ( 85.86 % complete ) and 584 restraints for refining 495 atoms. 212 conditional restraints added. Observations/parameters ratio is 11.35 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2504 (Rfree = 0.283) for 495 atoms. Found 43 (163 requested) and removed 5 (81 requested) atoms. Cycle 7: After refmac, R = 0.2022 (Rfree = 0.238) for 533 atoms. Found 29 (175 requested) and removed 5 (87 requested) atoms. Cycle 8: After refmac, R = 0.1851 (Rfree = 0.222) for 552 atoms. Found 19 (183 requested) and removed 5 (91 requested) atoms. Cycle 9: After refmac, R = 0.1713 (Rfree = 0.216) for 562 atoms. Found 19 (186 requested) and removed 6 (93 requested) atoms. Cycle 10: After refmac, R = 0.1668 (Rfree = 0.210) for 569 atoms. Found 18 (189 requested) and removed 7 (94 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 0.45 0.54 Round 1: 48 peptides, 4 chains. Longest chain 12 peptides. Score 0.907 Round 2: 45 peptides, 4 chains. Longest chain 13 peptides. Score 0.890 Round 3: 48 peptides, 4 chains. Longest chain 12 peptides. Score 0.907 Round 4: 48 peptides, 4 chains. Longest chain 12 peptides. Score 0.907 Round 5: 48 peptides, 4 chains. Longest chain 12 peptides. Score 0.907 Taking the results from Round 5 Chains 4, Residues 44, Estimated correctness of the model 99.9 % 4 chains (44 residues) have been docked in sequence 4 chains (44 residues) following loop building 4 chains (44 residues) in sequence following loop building ------------------------------------------------------ 22467 reflections ( 85.86 % complete ) and 597 restraints for refining 500 atoms. 225 conditional restraints added. Observations/parameters ratio is 11.23 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2278 (Rfree = 0.255) for 500 atoms. Found 46 (164 requested) and removed 2 (82 requested) atoms. Cycle 12: After refmac, R = 0.1906 (Rfree = 0.236) for 544 atoms. Found 28 (179 requested) and removed 5 (89 requested) atoms. Cycle 13: After refmac, R = 0.1753 (Rfree = 0.222) for 564 atoms. Found 32 (186 requested) and removed 9 (93 requested) atoms. Cycle 14: After refmac, R = 0.1707 (Rfree = 0.220) for 580 atoms. Found 24 (193 requested) and removed 12 (96 requested) atoms. Cycle 15: After refmac, R = 0.1642 (Rfree = 0.210) for 590 atoms. Found 33 (194 requested) and removed 9 (97 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 0.44 0.53 Round 1: 48 peptides, 4 chains. Longest chain 12 peptides. Score 0.907 Round 2: 48 peptides, 4 chains. Longest chain 12 peptides. Score 0.907 Round 3: 48 peptides, 4 chains. Longest chain 12 peptides. Score 0.907 Round 4: 48 peptides, 4 chains. Longest chain 12 peptides. Score 0.907 Round 5: 45 peptides, 4 chains. Longest chain 13 peptides. Score 0.890 Taking the results from Round 4 Chains 4, Residues 44, Estimated correctness of the model 99.9 % 4 chains (44 residues) have been docked in sequence 4 chains (44 residues) following loop building 4 chains (44 residues) in sequence following loop building ------------------------------------------------------ 22467 reflections ( 85.86 % complete ) and 626 restraints for refining 508 atoms. 254 conditional restraints added. Observations/parameters ratio is 11.06 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2231 (Rfree = 0.257) for 508 atoms. Found 43 (167 requested) and removed 3 (83 requested) atoms. Cycle 17: After refmac, R = 0.2010 (Rfree = 0.246) for 548 atoms. Found 24 (180 requested) and removed 3 (90 requested) atoms. Cycle 18: After refmac, R = 0.1906 (Rfree = 0.246) for 563 atoms. Found 30 (187 requested) and removed 4 (93 requested) atoms. Cycle 19: After refmac, R = 0.1840 (Rfree = 0.247) for 587 atoms. Found 22 (193 requested) and removed 6 (96 requested) atoms. Cycle 20: After refmac, R = 0.1787 (Rfree = 0.244) for 597 atoms. Found 30 (198 requested) and removed 9 (99 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 0.42 0.51 Round 1: 48 peptides, 4 chains. Longest chain 12 peptides. Score 0.907 Round 2: 45 peptides, 4 chains. Longest chain 13 peptides. Score 0.890 Round 3: 45 peptides, 4 chains. Longest chain 13 peptides. Score 0.890 Round 4: 45 peptides, 4 chains. Longest chain 13 peptides. Score 0.890 Round 5: 45 peptides, 4 chains. Longest chain 13 peptides. Score 0.890 Taking the results from Round 1 Chains 4, Residues 44, Estimated correctness of the model 99.9 % 4 chains (44 residues) have been docked in sequence 4 chains (44 residues) following loop building 4 chains (44 residues) in sequence following loop building ------------------------------------------------------ 22467 reflections ( 85.86 % complete ) and 622 restraints for refining 507 atoms. 250 conditional restraints added. Observations/parameters ratio is 11.08 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2126 (Rfree = 0.245) for 507 atoms. Found 41 (166 requested) and removed 1 (83 requested) atoms. Cycle 22: After refmac, R = 0.1815 (Rfree = 0.228) for 547 atoms. Found 31 (180 requested) and removed 2 (90 requested) atoms. Cycle 23: After refmac, R = 0.1776 (Rfree = 0.226) for 573 atoms. Found 27 (189 requested) and removed 6 (94 requested) atoms. Cycle 24: After refmac, R = 0.1766 (Rfree = 0.220) for 590 atoms. Found 21 (195 requested) and removed 8 (97 requested) atoms. Cycle 25: After refmac, R = 0.1717 (Rfree = 0.232) for 599 atoms. Found 21 (198 requested) and removed 7 (99 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 0.42 0.51 Round 1: 48 peptides, 4 chains. Longest chain 12 peptides. Score 0.907 Round 2: 45 peptides, 4 chains. Longest chain 13 peptides. Score 0.890 Round 3: 48 peptides, 4 chains. Longest chain 12 peptides. Score 0.907 Round 4: 48 peptides, 4 chains. Longest chain 12 peptides. Score 0.907 Round 5: 45 peptides, 4 chains. Longest chain 13 peptides. Score 0.890 Taking the results from Round 4 Chains 4, Residues 44, Estimated correctness of the model 99.9 % 4 chains (44 residues) have been docked in sequence 4 chains (44 residues) following loop building 4 chains (44 residues) in sequence following loop building ------------------------------------------------------ 22467 reflections ( 85.86 % complete ) and 636 restraints for refining 511 atoms. 264 conditional restraints added. Observations/parameters ratio is 10.99 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2278 (Rfree = 0.268) for 511 atoms. Found 48 (168 requested) and removed 3 (84 requested) atoms. Cycle 27: After refmac, R = 0.2039 (Rfree = 0.254) for 556 atoms. Found 27 (183 requested) and removed 3 (91 requested) atoms. Cycle 28: After refmac, R = 0.1939 (Rfree = 0.249) for 578 atoms. Found 26 (191 requested) and removed 4 (95 requested) atoms. Cycle 29: After refmac, R = 0.1873 (Rfree = 0.250) for 594 atoms. Found 21 (197 requested) and removed 2 (98 requested) atoms. Cycle 30: After refmac, R = 0.1827 (Rfree = 0.249) for 606 atoms. Found 24 (201 requested) and removed 5 (100 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 0.44 0.53 Round 1: 48 peptides, 4 chains. Longest chain 12 peptides. Score 0.907 Round 2: 45 peptides, 4 chains. Longest chain 13 peptides. Score 0.890 Round 3: 48 peptides, 4 chains. Longest chain 12 peptides. Score 0.907 Round 4: 45 peptides, 4 chains. Longest chain 13 peptides. Score 0.890 Round 5: 48 peptides, 4 chains. Longest chain 12 peptides. Score 0.907 Taking the results from Round 5 Chains 4, Residues 44, Estimated correctness of the model 99.9 % 4 chains (44 residues) have been docked in sequence 4 chains (44 residues) following loop building 4 chains (44 residues) in sequence following loop building ------------------------------------------------------ 22467 reflections ( 85.86 % complete ) and 620 restraints for refining 507 atoms. 248 conditional restraints added. Observations/parameters ratio is 11.08 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2422 (Rfree = 0.273) for 507 atoms. Found 48 (166 requested) and removed 5 (83 requested) atoms. Cycle 32: After refmac, R = 0.1975 (Rfree = 0.247) for 550 atoms. Found 34 (181 requested) and removed 3 (90 requested) atoms. Cycle 33: After refmac, R = 0.1922 (Rfree = 0.248) for 577 atoms. Found 24 (191 requested) and removed 3 (95 requested) atoms. Cycle 34: After refmac, R = 0.1853 (Rfree = 0.246) for 593 atoms. Found 17 (196 requested) and removed 4 (98 requested) atoms. Cycle 35: After refmac, R = 0.1811 (Rfree = 0.237) for 602 atoms. Found 15 (199 requested) and removed 2 (99 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 0.44 0.53 Round 1: 48 peptides, 4 chains. Longest chain 12 peptides. Score 0.907 Round 2: 48 peptides, 4 chains. Longest chain 12 peptides. Score 0.907 Round 3: 48 peptides, 4 chains. Longest chain 12 peptides. Score 0.907 Round 4: 48 peptides, 4 chains. Longest chain 12 peptides. Score 0.907 Round 5: 48 peptides, 4 chains. Longest chain 12 peptides. Score 0.907 Taking the results from Round 5 Chains 4, Residues 44, Estimated correctness of the model 99.9 % 4 chains (44 residues) have been docked in sequence 4 chains (44 residues) following loop building 4 chains (44 residues) in sequence following loop building ------------------------------------------------------ 22467 reflections ( 85.86 % complete ) and 669 restraints for refining 513 atoms. 297 conditional restraints added. Observations/parameters ratio is 10.95 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2334 (Rfree = 0.267) for 513 atoms. Found 44 (168 requested) and removed 1 (84 requested) atoms. Cycle 37: After refmac, R = 0.2127 (Rfree = 0.266) for 556 atoms. Found 27 (183 requested) and removed 1 (91 requested) atoms. Cycle 38: After refmac, R = 0.2023 (Rfree = 0.256) for 579 atoms. Found 16 (191 requested) and removed 1 (95 requested) atoms. Cycle 39: After refmac, R = 0.1928 (Rfree = 0.250) for 590 atoms. Found 19 (195 requested) and removed 0 (97 requested) atoms. Cycle 40: After refmac, R = 0.1866 (Rfree = 0.251) for 607 atoms. Found 15 (200 requested) and removed 4 (100 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 0.43 0.52 Round 1: 48 peptides, 4 chains. Longest chain 12 peptides. Score 0.907 Round 2: 48 peptides, 4 chains. Longest chain 12 peptides. Score 0.907 Round 3: 48 peptides, 4 chains. Longest chain 12 peptides. Score 0.907 Round 4: 48 peptides, 4 chains. Longest chain 12 peptides. Score 0.907 Round 5: 48 peptides, 4 chains. Longest chain 12 peptides. Score 0.907 Taking the results from Round 5 Chains 4, Residues 44, Estimated correctness of the model 99.9 % 4 chains (44 residues) have been docked in sequence 4 chains (44 residues) following loop building 4 chains (44 residues) in sequence following loop building ------------------------------------------------------ 22467 reflections ( 85.86 % complete ) and 653 restraints for refining 514 atoms. 281 conditional restraints added. Observations/parameters ratio is 10.93 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2647 (Rfree = 0.299) for 514 atoms. Found 44 (169 requested) and removed 0 (84 requested) atoms. Cycle 42: After refmac, R = 0.2083 (Rfree = 0.263) for 558 atoms. Found 32 (183 requested) and removed 3 (91 requested) atoms. Cycle 43: After refmac, R = 0.1995 (Rfree = 0.264) for 585 atoms. Found 24 (193 requested) and removed 3 (96 requested) atoms. Cycle 44: After refmac, R = 0.1914 (Rfree = 0.257) for 603 atoms. Found 15 (199 requested) and removed 3 (99 requested) atoms. Cycle 45: After refmac, R = 0.1840 (Rfree = 0.253) for 611 atoms. Found 17 (202 requested) and removed 5 (101 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 0.43 0.52 Round 1: 45 peptides, 4 chains. Longest chain 13 peptides. Score 0.890 Round 2: 45 peptides, 4 chains. Longest chain 13 peptides. Score 0.890 Round 3: 48 peptides, 4 chains. Longest chain 12 peptides. Score 0.907 Round 4: 48 peptides, 4 chains. Longest chain 12 peptides. Score 0.907 Round 5: 45 peptides, 4 chains. Longest chain 13 peptides. Score 0.890 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 4, Residues 44, Estimated correctness of the model 99.9 % 4 chains (44 residues) have been docked in sequence Sequence coverage is 97 % All DUM atoms will be removed 4 chains (44 residues) following loop building 4 chains (44 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 22467 reflections ( 85.86 % complete ) and 372 restraints for refining 377 atoms. Observations/parameters ratio is 14.90 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3146 (Rfree = 0.327) for 377 atoms. Found 48 (124 requested) and removed 0 (124 requested) atoms. Cycle 47: After refmac, R = 0.2513 (Rfree = 0.270) for 377 atoms. Found 16 (139 requested) and removed 0 (69 requested) atoms. Cycle 48: After refmac, R = 0.2248 (Rfree = 0.252) for 377 atoms. Found 6 (145 requested) and removed 1 (72 requested) atoms. Cycle 49: After refmac, R = 0.2157 (Rfree = 0.242) for 377 atoms. Found 2 (146 requested) and removed 2 (73 requested) atoms. Writing map files covering molecule ... Normal termination of warpNtrace Fri May 2 15:41:41 BST 2014 Job finished.