Mon 24 Dec 00:57:42 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2oh1-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2oh1-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2oh1-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2oh1-3.2-parrot-mrncs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2oh1-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2oh1-3.2-parrot-mrncs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 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 ============================================================ Mon 24 Dec 00:57:47 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2oh1-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2oh1-3.2-parrot-mrncs/arp_warp_classic.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 546 and 0 Target number of residues in the AU: 546 Target solvent content: 0.6332 Checking the provided sequence file Detected sequence length: 179 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 716 Adjusted target solvent content: 0.52 Input MTZ file: 2oh1-3.2-parrot-mrncs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 19 Cell parameters: 65.646 99.855 122.905 90.000 90.000 90.000 Input sequence file: 2oh1-3.2-parrot-mrncs.fasta_lf Building free atoms model in initial map for 5728 target number of atoms Had to go as low as 0.75 sigma, to complete atoms search. 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 3 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 with 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 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 77.501 3.200 Wilson plot Bfac: 68.01 13772 reflections ( 99.14 % complete ) and 0 restraints for refining 6398 atoms. Observations/parameters ratio is 0.54 ------------------------------------------------------ Starting model: R = 0.3088 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2768 (Rfree = 0.000) for 6398 atoms. Found 57 (57 requested) and removed 65 (28 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.23 3.15 Search for helices and strands: 0 residues in 0 chains, 6522 seeds are put forward NCS extension: 0 residues added, 6522 seeds are put forward Round 1: 411 peptides, 67 chains. Longest chain 15 peptides. Score 0.468 Round 2: 459 peptides, 64 chains. Longest chain 26 peptides. Score 0.570 Round 3: 497 peptides, 60 chains. Longest chain 23 peptides. Score 0.650 Round 4: 509 peptides, 54 chains. Longest chain 36 peptides. Score 0.699 Round 5: 485 peptides, 51 chains. Longest chain 27 peptides. Score 0.687 Taking the results from Round 4 Chains 56, Residues 455, Estimated correctness of the model 65.0 % 4 chains (44 residues) have been docked in sequence ------------------------------------------------------ 13772 reflections ( 99.14 % complete ) and 10567 restraints for refining 5229 atoms. 8632 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2605 (Rfree = 0.000) for 5229 atoms. Found 27 (46 requested) and removed 42 (23 requested) atoms. Cycle 2: After refmac, R = 0.2406 (Rfree = 0.000) for 5147 atoms. Found 9 (46 requested) and removed 32 (23 requested) atoms. Cycle 3: After refmac, R = 0.2296 (Rfree = 0.000) for 5095 atoms. Found 7 (45 requested) and removed 25 (22 requested) atoms. Cycle 4: After refmac, R = 0.2260 (Rfree = 0.000) for 5049 atoms. Found 9 (45 requested) and removed 27 (22 requested) atoms. Cycle 5: After refmac, R = 0.2221 (Rfree = 0.000) for 5021 atoms. Found 6 (45 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.22 3.14 Search for helices and strands: 0 residues in 0 chains, 5138 seeds are put forward NCS extension: 43 residues added (25 deleted due to clashes), 5181 seeds are put forward Round 1: 437 peptides, 51 chains. Longest chain 34 peptides. Score 0.624 Round 2: 499 peptides, 54 chains. Longest chain 28 peptides. Score 0.687 Round 3: 496 peptides, 45 chains. Longest chain 27 peptides. Score 0.731 Round 4: 499 peptides, 50 chains. Longest chain 29 peptides. Score 0.709 Round 5: 512 peptides, 52 chains. Longest chain 36 peptides. Score 0.713 Taking the results from Round 3 Chains 53, Residues 451, Estimated correctness of the model 71.5 % 7 chains (106 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 88 A and 97 A 51 chains (457 residues) following loop building 6 chains (114 residues) in sequence following loop building ------------------------------------------------------ 13772 reflections ( 99.14 % complete ) and 9987 restraints for refining 5229 atoms. 7717 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2556 (Rfree = 0.000) for 5229 atoms. Found 34 (46 requested) and removed 39 (23 requested) atoms. Cycle 7: After refmac, R = 0.2383 (Rfree = 0.000) for 5203 atoms. Found 5 (45 requested) and removed 26 (23 requested) atoms. Cycle 8: After refmac, R = 0.2623 (Rfree = 0.000) for 5167 atoms. Found 30 (44 requested) and removed 37 (23 requested) atoms. Failed to save intermediate PDB Cycle 9: After refmac, R = 0.2339 (Rfree = 0.000) for 5151 atoms. Found 13 (43 requested) and removed 30 (23 requested) atoms. Cycle 10: After refmac, R = 0.2229 (Rfree = 0.000) for 5121 atoms. Found 6 (42 requested) and removed 25 (23 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.20 3.12 Search for helices and strands: 0 residues in 0 chains, 5230 seeds are put forward NCS extension: 40 residues added (20 deleted due to clashes), 5270 seeds are put forward Round 1: 436 peptides, 52 chains. Longest chain 24 peptides. Score 0.616 Round 2: 471 peptides, 45 chains. Longest chain 35 peptides. Score 0.704 Round 3: 488 peptides, 49 chains. Longest chain 33 peptides. Score 0.701 Round 4: 499 peptides, 50 chains. Longest chain 27 peptides. Score 0.709 Round 5: 501 peptides, 52 chains. Longest chain 27 peptides. Score 0.700 Taking the results from Round 4 Chains 52, Residues 449, Estimated correctness of the model 67.1 % 4 chains (79 residues) have been docked in sequence Building loops using Loopy2018 52 chains (449 residues) following loop building 4 chains (79 residues) in sequence following loop building ------------------------------------------------------ 13772 reflections ( 99.14 % complete ) and 10481 restraints for refining 5229 atoms. 8369 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2534 (Rfree = 0.000) for 5229 atoms. Found 22 (41 requested) and removed 55 (23 requested) atoms. Cycle 12: After refmac, R = 0.2328 (Rfree = 0.000) for 5183 atoms. Found 15 (40 requested) and removed 33 (23 requested) atoms. Cycle 13: After refmac, R = 0.2351 (Rfree = 0.000) for 5157 atoms. Found 11 (40 requested) and removed 30 (23 requested) atoms. Cycle 14: After refmac, R = 0.2282 (Rfree = 0.000) for 5134 atoms. Found 9 (39 requested) and removed 28 (23 requested) atoms. Cycle 15: After refmac, R = 0.2643 (Rfree = 0.000) for 5111 atoms. Found 37 (37 requested) and removed 31 (22 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.14 3.06 Search for helices and strands: 0 residues in 0 chains, 5274 seeds are put forward NCS extension: 21 residues added (4 deleted due to clashes), 5295 seeds are put forward Round 1: 453 peptides, 58 chains. Longest chain 24 peptides. Score 0.601 Round 2: 491 peptides, 57 chains. Longest chain 27 peptides. Score 0.660 Round 3: 490 peptides, 55 chains. Longest chain 24 peptides. Score 0.670 Round 4: 489 peptides, 51 chains. Longest chain 28 peptides. Score 0.692 Round 5: 492 peptides, 54 chains. Longest chain 29 peptides. Score 0.678 Taking the results from Round 4 Chains 53, Residues 438, Estimated correctness of the model 63.5 % 4 chains (80 residues) have been docked in sequence ------------------------------------------------------ 13772 reflections ( 99.14 % complete ) and 10426 restraints for refining 5229 atoms. 8358 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2506 (Rfree = 0.000) for 5229 atoms. Found 31 (37 requested) and removed 41 (23 requested) atoms. Cycle 17: After refmac, R = 0.2561 (Rfree = 0.000) for 5201 atoms. Found 37 (37 requested) and removed 38 (23 requested) atoms. Cycle 18: After refmac, R = 0.2309 (Rfree = 0.000) for 5187 atoms. Found 13 (37 requested) and removed 32 (23 requested) atoms. Cycle 19: After refmac, R = 0.2326 (Rfree = 0.000) for 5160 atoms. Found 25 (37 requested) and removed 35 (23 requested) atoms. Cycle 20: After refmac, R = 0.2098 (Rfree = 0.000) for 5148 atoms. Found 12 (37 requested) and removed 24 (23 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.20 3.12 Search for helices and strands: 0 residues in 0 chains, 5301 seeds are put forward NCS extension: 24 residues added (7 deleted due to clashes), 5325 seeds are put forward Round 1: 457 peptides, 61 chains. Longest chain 22 peptides. Score 0.587 Round 2: 479 peptides, 54 chains. Longest chain 27 peptides. Score 0.662 Round 3: 485 peptides, 55 chains. Longest chain 26 peptides. Score 0.664 Round 4: 477 peptides, 53 chains. Longest chain 25 peptides. Score 0.665 Round 5: 471 peptides, 50 chains. Longest chain 30 peptides. Score 0.675 Taking the results from Round 5 Chains 52, Residues 421, Estimated correctness of the model 59.7 % 6 chains (100 residues) have been docked in sequence ------------------------------------------------------ 13772 reflections ( 99.14 % complete ) and 10437 restraints for refining 5229 atoms. 8367 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2403 (Rfree = 0.000) for 5229 atoms. Found 14 (37 requested) and removed 47 (23 requested) atoms. Cycle 22: After refmac, R = 0.2225 (Rfree = 0.000) for 5182 atoms. Found 21 (37 requested) and removed 29 (23 requested) atoms. Cycle 23: After refmac, R = 0.2150 (Rfree = 0.000) for 5167 atoms. Found 5 (37 requested) and removed 26 (23 requested) atoms. Cycle 24: After refmac, R = 0.2098 (Rfree = 0.000) for 5136 atoms. Found 21 (37 requested) and removed 23 (23 requested) atoms. Cycle 25: After refmac, R = 0.2279 (Rfree = 0.000) for 5134 atoms. Found 19 (37 requested) and removed 25 (23 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.22 3.14 Search for helices and strands: 0 residues in 0 chains, 5269 seeds are put forward NCS extension: 14 residues added (4 deleted due to clashes), 5283 seeds are put forward Round 1: 434 peptides, 61 chains. Longest chain 22 peptides. Score 0.552 Round 2: 478 peptides, 56 chains. Longest chain 24 peptides. Score 0.649 Round 3: 475 peptides, 54 chains. Longest chain 25 peptides. Score 0.657 Round 4: 473 peptides, 56 chains. Longest chain 20 peptides. Score 0.642 Round 5: 460 peptides, 56 chains. Longest chain 25 peptides. Score 0.624 Taking the results from Round 3 Chains 56, Residues 421, Estimated correctness of the model 55.5 % 6 chains (83 residues) have been docked in sequence ------------------------------------------------------ 13772 reflections ( 99.14 % complete ) and 10437 restraints for refining 5228 atoms. 8461 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2349 (Rfree = 0.000) for 5228 atoms. Found 25 (37 requested) and removed 36 (23 requested) atoms. Cycle 27: After refmac, R = 0.2147 (Rfree = 0.000) for 5207 atoms. Found 11 (37 requested) and removed 29 (23 requested) atoms. Cycle 28: After refmac, R = 0.2063 (Rfree = 0.000) for 5184 atoms. Found 13 (37 requested) and removed 23 (23 requested) atoms. Cycle 29: After refmac, R = 0.1907 (Rfree = 0.000) for 5163 atoms. Found 3 (37 requested) and removed 23 (23 requested) atoms. Cycle 30: After refmac, R = 0.1864 (Rfree = 0.000) for 5140 atoms. Found 1 (37 requested) and removed 23 (23 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.23 3.15 Search for helices and strands: 0 residues in 0 chains, 5254 seeds are put forward NCS extension: 35 residues added (2 deleted due to clashes), 5289 seeds are put forward Round 1: 436 peptides, 57 chains. Longest chain 28 peptides. Score 0.583 Round 2: 463 peptides, 49 chains. Longest chain 28 peptides. Score 0.671 Round 3: 468 peptides, 53 chains. Longest chain 25 peptides. Score 0.654 Round 4: 473 peptides, 50 chains. Longest chain 27 peptides. Score 0.678 Round 5: 458 peptides, 57 chains. Longest chain 23 peptides. Score 0.615 Taking the results from Round 4 Chains 51, Residues 423, Estimated correctness of the model 60.4 % 4 chains (80 residues) have been docked in sequence ------------------------------------------------------ 13772 reflections ( 99.14 % complete ) and 10465 restraints for refining 5229 atoms. 8483 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2258 (Rfree = 0.000) for 5229 atoms. Found 28 (37 requested) and removed 36 (23 requested) atoms. Cycle 32: After refmac, R = 0.2090 (Rfree = 0.000) for 5216 atoms. Found 16 (37 requested) and removed 24 (23 requested) atoms. Cycle 33: After refmac, R = 0.2020 (Rfree = 0.000) for 5204 atoms. Found 5 (37 requested) and removed 23 (23 requested) atoms. Cycle 34: After refmac, R = 0.1997 (Rfree = 0.000) for 5181 atoms. Found 7 (37 requested) and removed 23 (23 requested) atoms. Cycle 35: After refmac, R = 0.1894 (Rfree = 0.000) for 5164 atoms. Found 6 (37 requested) and removed 24 (23 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.23 3.15 Search for helices and strands: 0 residues in 0 chains, 5264 seeds are put forward NCS extension: 12 residues added (15 deleted due to clashes), 5276 seeds are put forward Round 1: 404 peptides, 64 chains. Longest chain 19 peptides. Score 0.478 Round 2: 441 peptides, 54 chains. Longest chain 29 peptides. Score 0.610 Round 3: 438 peptides, 60 chains. Longest chain 19 peptides. Score 0.565 Round 4: 435 peptides, 56 chains. Longest chain 21 peptides. Score 0.588 Round 5: 423 peptides, 51 chains. Longest chain 27 peptides. Score 0.604 Taking the results from Round 2 Chains 55, Residues 387, Estimated correctness of the model 43.7 % 4 chains (65 residues) have been docked in sequence ------------------------------------------------------ 13772 reflections ( 99.14 % complete ) and 10841 restraints for refining 5229 atoms. 9062 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2156 (Rfree = 0.000) for 5229 atoms. Found 29 (37 requested) and removed 34 (23 requested) atoms. Cycle 37: After refmac, R = 0.2008 (Rfree = 0.000) for 5218 atoms. Found 9 (37 requested) and removed 23 (23 requested) atoms. Cycle 38: After refmac, R = 0.1987 (Rfree = 0.000) for 5198 atoms. Found 5 (37 requested) and removed 23 (23 requested) atoms. Cycle 39: After refmac, R = 0.1979 (Rfree = 0.000) for 5180 atoms. Found 8 (37 requested) and removed 23 (23 requested) atoms. Cycle 40: After refmac, R = 0.1917 (Rfree = 0.000) for 5163 atoms. Found 6 (37 requested) and removed 23 (23 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.25 3.16 Search for helices and strands: 0 residues in 0 chains, 5273 seeds are put forward NCS extension: 22 residues added (17 deleted due to clashes), 5295 seeds are put forward Round 1: 378 peptides, 58 chains. Longest chain 29 peptides. Score 0.478 Round 2: 422 peptides, 57 chains. Longest chain 39 peptides. Score 0.561 Round 3: 418 peptides, 56 chains. Longest chain 25 peptides. Score 0.561 Round 4: 407 peptides, 57 chains. Longest chain 27 peptides. Score 0.536 Round 5: 408 peptides, 55 chains. Longest chain 22 peptides. Score 0.553 Taking the results from Round 3 Chains 57, Residues 362, Estimated correctness of the model 30.1 % 7 chains (87 residues) have been docked in sequence ------------------------------------------------------ 13772 reflections ( 99.14 % complete ) and 10746 restraints for refining 5229 atoms. 8994 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2232 (Rfree = 0.000) for 5229 atoms. Found 26 (37 requested) and removed 38 (23 requested) atoms. Cycle 42: After refmac, R = 0.2096 (Rfree = 0.000) for 5208 atoms. Found 11 (37 requested) and removed 23 (23 requested) atoms. Cycle 43: After refmac, R = 0.2063 (Rfree = 0.000) for 5187 atoms. Found 8 (37 requested) and removed 23 (23 requested) atoms. Cycle 44: After refmac, R = 0.2028 (Rfree = 0.000) for 5169 atoms. Found 6 (37 requested) and removed 23 (23 requested) atoms. Cycle 45: After refmac, R = 0.1940 (Rfree = 0.000) for 5144 atoms. Found 10 (37 requested) and removed 23 (23 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.21 3.13 Search for helices and strands: 0 residues in 0 chains, 5259 seeds are put forward NCS extension: 18 residues added (6 deleted due to clashes), 5277 seeds are put forward Round 1: 393 peptides, 62 chains. Longest chain 17 peptides. Score 0.474 Round 2: 402 peptides, 53 chains. Longest chain 31 peptides. Score 0.557 Round 3: 426 peptides, 56 chains. Longest chain 18 peptides. Score 0.574 Round 4: 407 peptides, 51 chains. Longest chain 22 peptides. Score 0.579 Round 5: 389 peptides, 52 chains. Longest chain 25 peptides. Score 0.543 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 55, Residues 356, Estimated correctness of the model 35.3 % 5 chains (37 residues) have been docked in sequence Sequence coverage is 10 % Consider running further cycles of model building using 2oh1-3_warpNtrace.pdb as input Building loops using Loopy2018 55 chains (356 residues) following loop building 5 chains (37 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 13772 reflections ( 99.14 % complete ) and 11324 restraints for refining 5228 atoms. 9824 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2144 (Rfree = 0.000) for 5228 atoms. Found 0 (37 requested) and removed 23 (23 requested) atoms. Cycle 47: After refmac, R = 0.2110 (Rfree = 0.000) for 5196 atoms. Found 0 (37 requested) and removed 7 (23 requested) atoms. Cycle 48: After refmac, R = 0.2058 (Rfree = 0.000) for 5185 atoms. Found 0 (37 requested) and removed 10 (23 requested) atoms. Cycle 49: After refmac, R = 0.2063 (Rfree = 0.000) for 5170 atoms. TimeTaking 67.58