Tue Feb 3 13:43:39 GMT 2015 ############### You are running ARP/wARP 7.5 ############### Working directory /opt/ample-dev1.testset/examples/toxd-example/ROSETTA_MR_4/MRBUMP/search_c1_tl100_r2_polya_mrbump/data/loc0_ALL_c1_tl100_r2_polya/unmod/mr/phaser/build/shelxe/rebuild/arpwarp Job ID is set to . X-ray data file /opt/ample-dev1.testset/examples/toxd-example/ROSETTA_MR_4/MRBUMP/search_c1_tl100_r2_polya_mrbump/data/loc0_ALL_c1_tl100_r2_polya/unmod/mr/phaser/build/shelxe/shelxe_phaser_loc0_ALL_c1_tl100_r2_polya_UNMOD.mtz Sequence file /opt/ample-dev1.testset/examples/toxd-example/ROSETTA_MR_4/MRBUMP/search_c1_tl100_r2_polya_mrbump/input/toxd_.fasta Input PDB file /opt/ample-dev1.testset/examples/toxd-example/ROSETTA_MR_4/MRBUMP/search_c1_tl100_r2_polya_mrbump/data/loc0_ALL_c1_tl100_r2_polya/unmod/mr/phaser/build/shelxe/shelxe_phaser_loc0_ALL_c1_tl100_r2_polya_UNMOD.pdb Tracing mode WARPNTRACEMODEL Accepted label: fp=F Accepted label: sigfp=SIGF Accepted label: phibest=PHI_SHELXE Accepted label: fom=FOM_SHELXE Accepted label: freelabin=FreeR_flag mtz labels taken: F SIGF PHI_SHELXE FOM_SHELXE FreeR_flag Parameter file /opt/ample-dev1.testset/examples/toxd-example/ROSETTA_MR_4/MRBUMP/search_c1_tl100_r2_polya_mrbump/data/loc0_ALL_c1_tl100_r2_polya/unmod/mr/phaser/build/shelxe/rebuild/arpwarp/arp_warp_tracing.par Job launched in /opt/ample-dev1.testset/examples/toxd-example/ROSETTA_MR_4/MRBUMP/search_c1_tl100_r2_polya_mrbump/data/loc0_ALL_c1_tl100_r2_polya/unmod/mr/phaser/build/shelxe/rebuild/arpwarp ############### You are running ARP/wARP 7.5 ############### ================================================================================== | 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 | ================================================================================== Tue Feb 3 13:43:45 GMT 2015 You are running ARP/wARP version 7.5 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /opt/ample-dev1.testset/examples/toxd-example/ROSETTA_MR_4/MRBUMP/search_c1_tl100_r2_polya_mrbump/data/loc0_ALL_c1_tl100_r2_polya/unmod/mr/phaser/build/shelxe/rebuild/arpwarp ARP/wARP software version: 7.5 The parameter file: /opt/ample-dev1.testset/examples/toxd-example/ROSETTA_MR_4/MRBUMP/search_c1_tl100_r2_polya_mrbump/data/loc0_ALL_c1_tl100_r2_polya/unmod/mr/phaser/build/shelxe/rebuild/arpwarp/arp_warp_tracing.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Target number of residues in the AU: 59 Target solvent content: 0.5198 Checking the provided sequence file Detected sequence length: 59 Number of NCS-related molecules: 1 Adjusted target number of residues: 59 Adjusted target solvent content: 0.52 Input MTZ file: shelxe_phaser_loc0_ALL_c1_tl100_r2_polya_UNMOD.mtz.cad Column labels for model refinement: F SIGF FreeR_flag Rfree value for free reflections: 0 Space group number: 19 Cell parameters: 73.530 39.060 23.150 90.000 90.000 90.000 Input sequence file: toxd_.fasta_lf Input PDB file: shelxe_phaser_loc0_ALL_c1_tl100_r2_polya_UNMOD.pdb_lf Setting PDB header to reflect the MTZ header content Number of atoms in the PDB file: 230 ARP/wARP will be iterated with REFMAC5 25 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 1 Loops will be built when appropriate and at the last cycle Resolution range: 36.765 2.201 Wilson plot Bfac: 16.45 Checking whether input PDB contains ligands unknown to the Refmac library 3497 reflections ( 98.81 % complete ) and 227 restraints for refining 230 atoms. Observations/parameters ratio is 3.80 ------------------------------------------------------ Starting model: R = 0.5255 (Rfree = 0.504). ------------------------------------------------------ Cycle 0: After refmac, R = 0.4896 (Rfree = 0.488) for 230 atoms. Cycle 0: After refmac, R = 0.4835 (Rfree = 0.494) for 230 atoms. Cycle 0: After refmac, R = 0.4737 (Rfree = 0.488) for 230 atoms. Cycle 0: After refmac, R = 0.4702 (Rfree = 0.485) for 230 atoms. Cycle 0: After refmac, R = 0.4685 (Rfree = 0.484) for 230 atoms. Cycle 0: After refmac, R = 0.4683 (Rfree = 0.480) for 230 atoms. Cycle 0: After refmac, R = 0.4685 (Rfree = 0.480) for 230 atoms. Found 5 (5 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.01 1.96 Round 1: 42 peptides, 2 chains. Longest chain 29 peptides. Score 0.834 Round 2: 45 peptides, 2 chains. Longest chain 30 peptides. Score 0.858 Round 3: 46 peptides, 2 chains. Longest chain 30 peptides. Score 0.865 Round 4: 46 peptides, 2 chains. Longest chain 30 peptides. Score 0.865 Round 5: 46 peptides, 2 chains. Longest chain 30 peptides. Score 0.865 Taking the results from Round 5 Chains 2, Residues 44, Estimated correctness of the model 97.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3497 reflections ( 98.81 % complete ) and 429 restraints for refining 250 atoms. 255 conditional restraints added. Observations/parameters ratio is 3.50 ------------------------------------------------------ Cycle 1: After refmac, R = 0.4573 (Rfree = 0.506) for 250 atoms. Found 6 (6 requested) and removed 2 (3 requested) atoms. Cycle 2: After refmac, R = 0.4294 (Rfree = 0.528) for 254 atoms. Found 6 (6 requested) and removed 1 (3 requested) atoms. Cycle 3: After refmac, R = 0.4132 (Rfree = 0.498) for 259 atoms. Found 6 (6 requested) and removed 1 (3 requested) atoms. Cycle 4: After refmac, R = 0.4023 (Rfree = 0.493) for 264 atoms. Found 6 (6 requested) and removed 0 (3 requested) atoms. Cycle 5: After refmac, R = 0.3953 (Rfree = 0.481) for 270 atoms. Found 7 (7 requested) and removed 0 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.90 1.85 Round 1: 43 peptides, 3 chains. Longest chain 18 peptides. Score 0.795 Round 2: 45 peptides, 3 chains. Longest chain 18 peptides. Score 0.814 Round 3: 41 peptides, 2 chains. Longest chain 28 peptides. Score 0.826 Round 4: 43 peptides, 2 chains. Longest chain 29 peptides. Score 0.843 Round 5: 44 peptides, 2 chains. Longest chain 29 peptides. Score 0.851 Taking the results from Round 5 Chains 2, Residues 42, Estimated correctness of the model 97.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3497 reflections ( 98.81 % complete ) and 488 restraints for refining 289 atoms. 322 conditional restraints added. Observations/parameters ratio is 3.03 ------------------------------------------------------ Cycle 6: After refmac, R = 0.4191 (Rfree = 0.500) for 289 atoms. Found 7 (7 requested) and removed 3 (3 requested) atoms. Cycle 7: After refmac, R = 0.3925 (Rfree = 0.489) for 293 atoms. Found 7 (7 requested) and removed 3 (3 requested) atoms. Cycle 8: After refmac, R = 0.3820 (Rfree = 0.489) for 297 atoms. Found 2 (7 requested) and removed 3 (3 requested) atoms. Cycle 9: After refmac, R = 0.3736 (Rfree = 0.497) for 296 atoms. Found 5 (7 requested) and removed 2 (3 requested) atoms. Cycle 10: After refmac, R = 0.3673 (Rfree = 0.492) for 298 atoms. Found 5 (7 requested) and removed 1 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.91 1.86 Round 1: 41 peptides, 3 chains. Longest chain 15 peptides. Score 0.773 Round 2: 40 peptides, 2 chains. Longest chain 25 peptides. Score 0.817 Round 3: 40 peptides, 4 chains. Longest chain 21 peptides. Score 0.700 Round 4: 40 peptides, 4 chains. Longest chain 15 peptides. Score 0.700 Round 5: 44 peptides, 4 chains. Longest chain 16 peptides. Score 0.751 Taking the results from Round 2 Chains 2, Residues 38, Estimated correctness of the model 95.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3497 reflections ( 98.81 % complete ) and 510 restraints for refining 307 atoms. 360 conditional restraints added. Observations/parameters ratio is 2.85 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3753 (Rfree = 0.514) for 307 atoms. Found 7 (8 requested) and removed 4 (4 requested) atoms. Cycle 12: After refmac, R = 0.3642 (Rfree = 0.503) for 310 atoms. Found 4 (8 requested) and removed 4 (4 requested) atoms. Cycle 13: After refmac, R = 0.3593 (Rfree = 0.497) for 310 atoms. Found 6 (8 requested) and removed 1 (4 requested) atoms. Cycle 14: After refmac, R = 0.3503 (Rfree = 0.526) for 315 atoms. Found 6 (8 requested) and removed 2 (4 requested) atoms. Cycle 15: After refmac, R = 0.3459 (Rfree = 0.524) for 319 atoms. Found 8 (8 requested) and removed 1 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.91 1.86 Round 1: 38 peptides, 3 chains. Longest chain 15 peptides. Score 0.737 Round 2: 40 peptides, 3 chains. Longest chain 15 peptides. Score 0.762 Round 3: 41 peptides, 3 chains. Longest chain 18 peptides. Score 0.773 Round 4: 41 peptides, 2 chains. Longest chain 30 peptides. Score 0.826 Round 5: 41 peptides, 2 chains. Longest chain 30 peptides. Score 0.826 Taking the results from Round 5 Chains 2, Residues 39, Estimated correctness of the model 96.1 % 1 chains (29 residues) have been docked in sequence ------------------------------------------------------ 3497 reflections ( 98.81 % complete ) and 491 restraints for refining 392 atoms. 206 conditional restraints added. Observations/parameters ratio is 2.23 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3812 (Rfree = 0.539) for 392 atoms. Found 11 (11 requested) and removed 5 (5 requested) atoms. Cycle 17: After refmac, R = 0.3647 (Rfree = 0.538) for 398 atoms. Found 10 (10 requested) and removed 5 (5 requested) atoms. Cycle 18: After refmac, R = 0.3469 (Rfree = 0.534) for 403 atoms. Found 5 (10 requested) and removed 5 (5 requested) atoms. Cycle 19: After refmac, R = 0.3363 (Rfree = 0.529) for 403 atoms. Found 8 (10 requested) and removed 5 (5 requested) atoms. Cycle 20: After refmac, R = 0.3283 (Rfree = 0.503) for 406 atoms. Found 9 (10 requested) and removed 3 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.92 1.87 Round 1: 39 peptides, 2 chains. Longest chain 29 peptides. Score 0.807 Round 2: 43 peptides, 2 chains. Longest chain 32 peptides. Score 0.843 Round 3: 44 peptides, 2 chains. Longest chain 33 peptides. Score 0.851 Round 4: 44 peptides, 2 chains. Longest chain 33 peptides. Score 0.851 Round 5: 44 peptides, 2 chains. Longest chain 33 peptides. Score 0.851 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 2, Residues 42, Estimated correctness of the model 97.0 % 1 chains (32 residues) have been docked in sequence Sequence coverage is 74 % Consider running further cycles of model building using shelxe_phaser_loc0_ALL_c1_tl100_r2_polya_UNMOD_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3497 reflections ( 98.81 % complete ) and 513 restraints for refining 423 atoms. 207 conditional restraints added. Observations/parameters ratio is 2.07 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3495 (Rfree = 0.476) for 423 atoms. Found 0 (11 requested) and removed 2 (5 requested) atoms. Cycle 22: After refmac, R = 0.3325 (Rfree = 0.480) for 421 atoms. Found 0 (10 requested) and removed 1 (5 requested) atoms. Cycle 23: After refmac, R = 0.3264 (Rfree = 0.485) for 420 atoms. Found 0 (10 requested) and removed 0 (5 requested) atoms. Cycle 24: After refmac, R = 0.3248 (Rfree = 0.484) for 420 atoms. Found 0 (10 requested) and removed 0 (5 requested) atoms. Writing map files covering molecule ... Normal termination of warpNtrace Tue Feb 3 13:47:37 GMT 2015 Job finished.