Mon 24 Dec 00:57:22 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 1vm8-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vm8-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vm8-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vm8-4.0-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/1vm8-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vm8-4.0-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 00:57:26 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/1vm8-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vm8-4.0-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 762 and 0 Target number of residues in the AU: 762 Target solvent content: 0.6677 Checking the provided sequence file Detected sequence length: 534 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 1068 Adjusted target solvent content: 0.53 Input MTZ file: 1vm8-4.0-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: 4 Cell parameters: 80.094 73.402 107.132 90.000 99.827 90.000 Input sequence file: 1vm8-4.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 8544 target number of atoms Had to go as low as 0.65 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: 105.560 4.000 Wilson plot Bfac: 90.76 Failed to save intermediate PDB 10439 reflections ( 98.84 % complete ) and 0 restraints for refining 9406 atoms. Observations/parameters ratio is 0.28 ------------------------------------------------------ Starting model: R = 0.3285 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3271 (Rfree = 0.000) for 9406 atoms. Found 44 (44 requested) and removed 82 (22 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.80 3.65 Search for helices and strands: 0 residues in 0 chains, 9540 seeds are put forward NCS extension: 0 residues added, 9540 seeds are put forward Round 1: 349 peptides, 69 chains. Longest chain 15 peptides. Score 0.285 Round 2: 413 peptides, 74 chains. Longest chain 13 peptides. Score 0.347 Round 3: 454 peptides, 77 chains. Longest chain 15 peptides. Score 0.385 Round 4: 452 peptides, 69 chains. Longest chain 20 peptides. Score 0.429 Round 5: 475 peptides, 73 chains. Longest chain 19 peptides. Score 0.435 Taking the results from Round 5 Chains 73, Residues 402, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 10439 reflections ( 98.84 % complete ) and 18753 restraints for refining 7711 atoms. 17195 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2431 (Rfree = 0.000) for 7711 atoms. Found 35 (36 requested) and removed 69 (18 requested) atoms. Cycle 2: After refmac, R = 0.2229 (Rfree = 0.000) for 7534 atoms. Found 34 (36 requested) and removed 73 (18 requested) atoms. Cycle 3: After refmac, R = 0.2204 (Rfree = 0.000) for 7408 atoms. Found 35 (35 requested) and removed 52 (17 requested) atoms. Cycle 4: After refmac, R = 0.2017 (Rfree = 0.000) for 7329 atoms. Found 33 (35 requested) and removed 64 (17 requested) atoms. Cycle 5: After refmac, R = 0.2102 (Rfree = 0.000) for 7245 atoms. Found 34 (34 requested) and removed 57 (17 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.76 3.61 Search for helices and strands: 0 residues in 0 chains, 7476 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 7494 seeds are put forward Round 1: 418 peptides, 81 chains. Longest chain 17 peptides. Score 0.312 Round 2: 481 peptides, 78 chains. Longest chain 19 peptides. Score 0.415 Round 3: 490 peptides, 79 chains. Longest chain 13 peptides. Score 0.421 Round 4: 484 peptides, 71 chains. Longest chain 18 peptides. Score 0.458 Round 5: 500 peptides, 75 chains. Longest chain 18 peptides. Score 0.456 Taking the results from Round 4 Chains 71, Residues 413, Estimated correctness of the model 0.0 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 10439 reflections ( 98.84 % complete ) and 17094 restraints for refining 7340 atoms. 15460 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2088 (Rfree = 0.000) for 7340 atoms. Found 30 (34 requested) and removed 85 (17 requested) atoms. Cycle 7: After refmac, R = 0.1911 (Rfree = 0.000) for 7233 atoms. Found 34 (34 requested) and removed 57 (17 requested) atoms. Cycle 8: After refmac, R = 0.1824 (Rfree = 0.000) for 7166 atoms. Found 34 (34 requested) and removed 48 (17 requested) atoms. Cycle 9: After refmac, R = 0.1656 (Rfree = 0.000) for 7117 atoms. Found 26 (33 requested) and removed 44 (16 requested) atoms. Cycle 10: After refmac, R = 0.1295 (Rfree = 0.000) for 7087 atoms. Found 5 (33 requested) and removed 30 (16 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.79 3.64 Search for helices and strands: 0 residues in 0 chains, 7295 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 7318 seeds are put forward Round 1: 449 peptides, 85 chains. Longest chain 10 peptides. Score 0.332 Round 2: 497 peptides, 76 chains. Longest chain 17 peptides. Score 0.446 Round 3: 497 peptides, 77 chains. Longest chain 18 peptides. Score 0.441 Round 4: 481 peptides, 77 chains. Longest chain 14 peptides. Score 0.421 Round 5: 500 peptides, 73 chains. Longest chain 15 peptides. Score 0.466 Taking the results from Round 5 Chains 73, Residues 427, Estimated correctness of the model 0.0 % 6 chains (41 residues) have been docked in sequence ------------------------------------------------------ 10439 reflections ( 98.84 % complete ) and 17312 restraints for refining 7612 atoms. 15533 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1922 (Rfree = 0.000) for 7612 atoms. Found 33 (36 requested) and removed 95 (18 requested) atoms. Cycle 12: After refmac, R = 0.1893 (Rfree = 0.000) for 7489 atoms. Found 35 (35 requested) and removed 73 (17 requested) atoms. Cycle 13: After refmac, R = 0.1797 (Rfree = 0.000) for 7410 atoms. Found 35 (35 requested) and removed 53 (17 requested) atoms. Cycle 14: After refmac, R = 0.1387 (Rfree = 0.000) for 7368 atoms. Found 14 (35 requested) and removed 29 (17 requested) atoms. Cycle 15: After refmac, R = 0.1327 (Rfree = 0.000) for 7337 atoms. Found 2 (34 requested) and removed 26 (17 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.84 3.69 Search for helices and strands: 0 residues in 0 chains, 7528 seeds are put forward NCS extension: 26 residues added (0 deleted due to clashes), 7554 seeds are put forward Round 1: 435 peptides, 76 chains. Longest chain 15 peptides. Score 0.366 Round 2: 451 peptides, 72 chains. Longest chain 15 peptides. Score 0.410 Round 3: 481 peptides, 75 chains. Longest chain 19 peptides. Score 0.432 Round 4: 473 peptides, 69 chains. Longest chain 20 peptides. Score 0.455 Round 5: 486 peptides, 69 chains. Longest chain 23 peptides. Score 0.471 Taking the results from Round 5 Chains 70, Residues 417, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 10439 reflections ( 98.84 % complete ) and 18087 restraints for refining 7715 atoms. 16451 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1989 (Rfree = 0.000) for 7715 atoms. Found 36 (36 requested) and removed 92 (18 requested) atoms. Cycle 17: After refmac, R = 0.1822 (Rfree = 0.000) for 7621 atoms. Found 36 (36 requested) and removed 66 (18 requested) atoms. Cycle 18: After refmac, R = 0.1777 (Rfree = 0.000) for 7555 atoms. Found 36 (36 requested) and removed 55 (18 requested) atoms. Cycle 19: After refmac, R = 0.1726 (Rfree = 0.000) for 7508 atoms. Found 35 (35 requested) and removed 39 (17 requested) atoms. Cycle 20: After refmac, R = 0.1791 (Rfree = 0.000) for 7486 atoms. Found 35 (35 requested) and removed 43 (17 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.78 3.63 Search for helices and strands: 0 residues in 0 chains, 7709 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 7726 seeds are put forward Round 1: 376 peptides, 75 chains. Longest chain 13 peptides. Score 0.288 Round 2: 442 peptides, 75 chains. Longest chain 14 peptides. Score 0.381 Round 3: 459 peptides, 68 chains. Longest chain 23 peptides. Score 0.443 Round 4: 443 peptides, 73 chains. Longest chain 15 peptides. Score 0.394 Round 5: 441 peptides, 68 chains. Longest chain 17 peptides. Score 0.420 Taking the results from Round 3 Chains 73, Residues 391, Estimated correctness of the model 0.0 % 6 chains (56 residues) have been docked in sequence ------------------------------------------------------ 10439 reflections ( 98.84 % complete ) and 17694 restraints for refining 7715 atoms. 16038 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1822 (Rfree = 0.000) for 7715 atoms. Found 30 (36 requested) and removed 73 (18 requested) atoms. Cycle 22: After refmac, R = 0.1684 (Rfree = 0.000) for 7600 atoms. Found 27 (36 requested) and removed 47 (18 requested) atoms. Cycle 23: After refmac, R = 0.1677 (Rfree = 0.000) for 7540 atoms. Found 31 (36 requested) and removed 36 (18 requested) atoms. Cycle 24: After refmac, R = 0.1688 (Rfree = 0.000) for 7508 atoms. Found 35 (35 requested) and removed 49 (17 requested) atoms. Cycle 25: After refmac, R = 0.1667 (Rfree = 0.000) for 7471 atoms. Found 35 (35 requested) and removed 30 (17 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.81 3.66 Search for helices and strands: 0 residues in 0 chains, 7701 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 7724 seeds are put forward Round 1: 400 peptides, 78 chains. Longest chain 11 peptides. Score 0.304 Round 2: 437 peptides, 76 chains. Longest chain 12 peptides. Score 0.368 Round 3: 432 peptides, 74 chains. Longest chain 12 peptides. Score 0.373 Round 4: 447 peptides, 79 chains. Longest chain 17 peptides. Score 0.364 Round 5: 447 peptides, 72 chains. Longest chain 18 peptides. Score 0.405 Taking the results from Round 5 Chains 74, Residues 375, Estimated correctness of the model 0.0 % 2 chains (16 residues) have been docked in sequence ------------------------------------------------------ 10439 reflections ( 98.84 % complete ) and 18275 restraints for refining 7715 atoms. 16794 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2132 (Rfree = 0.000) for 7715 atoms. Found 36 (36 requested) and removed 68 (18 requested) atoms. Cycle 27: After refmac, R = 0.1918 (Rfree = 0.000) for 7621 atoms. Found 36 (36 requested) and removed 48 (18 requested) atoms. Failed to save intermediate PDB Cycle 28: After refmac, R = 0.1928 (Rfree = 0.000) for 7552 atoms. Found 36 (36 requested) and removed 41 (18 requested) atoms. Cycle 29: After refmac, R = 0.1380 (Rfree = 0.000) for 7514 atoms. Found 7 (35 requested) and removed 23 (17 requested) atoms. Cycle 30: After refmac, R = 0.1644 (Rfree = 0.000) for 7478 atoms. Found 35 (35 requested) and removed 30 (17 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.82 3.67 Search for helices and strands: 0 residues in 0 chains, 7696 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 7713 seeds are put forward Round 1: 339 peptides, 67 chains. Longest chain 10 peptides. Score 0.283 Round 2: 387 peptides, 63 chains. Longest chain 15 peptides. Score 0.378 Round 3: 394 peptides, 68 chains. Longest chain 13 peptides. Score 0.357 Round 4: 404 peptides, 68 chains. Longest chain 17 peptides. Score 0.371 Round 5: 417 peptides, 66 chains. Longest chain 14 peptides. Score 0.401 Taking the results from Round 5 Chains 66, Residues 351, Estimated correctness of the model 0.0 % 3 chains (17 residues) have been docked in sequence ------------------------------------------------------ 10439 reflections ( 98.84 % complete ) and 18194 restraints for refining 7652 atoms. 16804 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1834 (Rfree = 0.000) for 7652 atoms. Found 36 (36 requested) and removed 81 (18 requested) atoms. Cycle 32: After refmac, R = 0.1784 (Rfree = 0.000) for 7566 atoms. Found 36 (36 requested) and removed 51 (18 requested) atoms. Cycle 33: After refmac, R = 0.1726 (Rfree = 0.000) for 7522 atoms. Found 35 (35 requested) and removed 40 (17 requested) atoms. Cycle 34: After refmac, R = 0.1291 (Rfree = 0.000) for 7489 atoms. Found 17 (35 requested) and removed 38 (17 requested) atoms. Cycle 35: After refmac, R = 0.1179 (Rfree = 0.000) for 7446 atoms. Found 5 (35 requested) and removed 20 (17 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.80 3.65 Search for helices and strands: 0 residues in 0 chains, 7650 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 7669 seeds are put forward Round 1: 328 peptides, 69 chains. Longest chain 10 peptides. Score 0.253 Round 2: 382 peptides, 71 chains. Longest chain 10 peptides. Score 0.322 Round 3: 415 peptides, 71 chains. Longest chain 12 peptides. Score 0.368 Round 4: 419 peptides, 72 chains. Longest chain 20 peptides. Score 0.368 Round 5: 399 peptides, 65 chains. Longest chain 15 peptides. Score 0.382 Taking the results from Round 5 Chains 65, Residues 334, Estimated correctness of the model 0.0 % 6 chains (34 residues) have been docked in sequence ------------------------------------------------------ 10439 reflections ( 98.84 % complete ) and 18039 restraints for refining 7621 atoms. 16679 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1883 (Rfree = 0.000) for 7621 atoms. Found 36 (36 requested) and removed 80 (18 requested) atoms. Cycle 37: After refmac, R = 0.1846 (Rfree = 0.000) for 7544 atoms. Found 36 (36 requested) and removed 41 (18 requested) atoms. Cycle 38: After refmac, R = 0.1809 (Rfree = 0.000) for 7510 atoms. Found 35 (35 requested) and removed 36 (17 requested) atoms. Cycle 39: After refmac, R = 0.1811 (Rfree = 0.000) for 7482 atoms. Found 35 (35 requested) and removed 39 (17 requested) atoms. Cycle 40: After refmac, R = 0.1848 (Rfree = 0.000) for 7447 atoms. Found 35 (35 requested) and removed 37 (17 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.81 3.66 Search for helices and strands: 0 residues in 0 chains, 7731 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 7745 seeds are put forward Round 1: 298 peptides, 65 chains. Longest chain 10 peptides. Score 0.232 Round 2: 358 peptides, 69 chains. Longest chain 14 peptides. Score 0.299 Round 3: 371 peptides, 68 chains. Longest chain 12 peptides. Score 0.324 Round 4: 371 peptides, 68 chains. Longest chain 12 peptides. Score 0.324 Round 5: 358 peptides, 62 chains. Longest chain 12 peptides. Score 0.343 Taking the results from Round 5 Chains 62, Residues 296, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10439 reflections ( 98.84 % complete ) and 17540 restraints for refining 7354 atoms. 16418 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1960 (Rfree = 0.000) for 7354 atoms. Found 34 (34 requested) and removed 73 (17 requested) atoms. Cycle 42: After refmac, R = 0.1845 (Rfree = 0.000) for 7256 atoms. Found 34 (34 requested) and removed 44 (17 requested) atoms. Cycle 43: After refmac, R = 0.1766 (Rfree = 0.000) for 7207 atoms. Found 34 (34 requested) and removed 47 (17 requested) atoms. Cycle 44: After refmac, R = 0.1818 (Rfree = 0.000) for 7178 atoms. Found 34 (34 requested) and removed 41 (17 requested) atoms. Cycle 45: After refmac, R = 0.1843 (Rfree = 0.000) for 7156 atoms. Found 34 (34 requested) and removed 42 (17 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.79 3.64 Search for helices and strands: 0 residues in 0 chains, 7381 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 7396 seeds are put forward Round 1: 254 peptides, 56 chains. Longest chain 9 peptides. Score 0.221 Round 2: 326 peptides, 65 chains. Longest chain 12 peptides. Score 0.276 Round 3: 330 peptides, 63 chains. Longest chain 13 peptides. Score 0.296 Round 4: 329 peptides, 64 chains. Longest chain 12 peptides. Score 0.288 Round 5: 313 peptides, 58 chains. Longest chain 12 peptides. Score 0.303 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 58, Residues 255, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence Sequence coverage is 2 % Consider running further cycles of model building using 1vm8-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 10439 reflections ( 98.84 % complete ) and 16789 restraints for refining 7103 atoms. 15804 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1932 (Rfree = 0.000) for 7103 atoms. Found 0 (33 requested) and removed 16 (16 requested) atoms. Cycle 47: After refmac, R = 0.1826 (Rfree = 0.000) for 7060 atoms. Found 0 (33 requested) and removed 16 (16 requested) atoms. Cycle 48: After refmac, R = 0.1717 (Rfree = 0.000) for 7024 atoms. Found 0 (33 requested) and removed 16 (16 requested) atoms. Cycle 49: After refmac, R = 0.1688 (Rfree = 0.000) for 6992 atoms. Found 0 (33 requested) and removed 16 (16 requested) atoms. Writing output files ... TimeTaking 85.95