Mon 24 Dec 01:01:49 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 1vm8-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vm8-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vm8-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vm8-3.4-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/1vm8-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vm8-3.4-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 01:01:54 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/1vm8-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vm8-3.4-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 846 and 0 Target number of residues in the AU: 846 Target solvent content: 0.6311 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: 1vm8-3.4-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: 1vm8-3.4-parrot-mrncs.fasta_lf Building free atoms model in initial map for 8544 target number of atoms Had to go as low as 0.60 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 3.400 Wilson plot Bfac: 67.13 16970 reflections ( 99.23 % complete ) and 0 restraints for refining 9424 atoms. Observations/parameters ratio is 0.45 ------------------------------------------------------ Starting model: R = 0.3223 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2894 (Rfree = 0.000) for 9424 atoms. Found 71 (71 requested) and removed 174 (35 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.29 3.16 Search for helices and strands: 0 residues in 0 chains, 9506 seeds are put forward NCS extension: 0 residues added, 9506 seeds are put forward Round 1: 465 peptides, 82 chains. Longest chain 16 peptides. Score 0.371 Round 2: 525 peptides, 80 chains. Longest chain 19 peptides. Score 0.459 Round 3: 552 peptides, 79 chains. Longest chain 25 peptides. Score 0.496 Round 4: 576 peptides, 74 chains. Longest chain 28 peptides. Score 0.548 Round 5: 578 peptides, 78 chains. Longest chain 23 peptides. Score 0.531 Taking the results from Round 4 Chains 77, Residues 502, Estimated correctness of the model 10.8 % 5 chains (46 residues) have been docked in sequence ------------------------------------------------------ 16970 reflections ( 99.23 % complete ) and 17491 restraints for refining 7767 atoms. 15409 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2367 (Rfree = 0.000) for 7767 atoms. Found 45 (58 requested) and removed 56 (29 requested) atoms. Cycle 2: After refmac, R = 0.2214 (Rfree = 0.000) for 7687 atoms. Found 21 (58 requested) and removed 46 (29 requested) atoms. Cycle 3: After refmac, R = 0.2184 (Rfree = 0.000) for 7622 atoms. Found 27 (57 requested) and removed 49 (28 requested) atoms. Cycle 4: After refmac, R = 0.2127 (Rfree = 0.000) for 7583 atoms. Found 17 (57 requested) and removed 35 (28 requested) atoms. Cycle 5: After refmac, R = 0.2091 (Rfree = 0.000) for 7550 atoms. Found 22 (57 requested) and removed 38 (28 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.29 3.16 Search for helices and strands: 0 residues in 0 chains, 7801 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 7821 seeds are put forward Round 1: 498 peptides, 80 chains. Longest chain 18 peptides. Score 0.426 Round 2: 560 peptides, 77 chains. Longest chain 24 peptides. Score 0.516 Round 3: 565 peptides, 79 chains. Longest chain 21 peptides. Score 0.511 Round 4: 576 peptides, 76 chains. Longest chain 27 peptides. Score 0.538 Round 5: 594 peptides, 79 chains. Longest chain 32 peptides. Score 0.543 Taking the results from Round 5 Chains 87, Residues 515, Estimated correctness of the model 9.0 % 9 chains (97 residues) have been docked in sequence ------------------------------------------------------ 16970 reflections ( 99.23 % complete ) and 16984 restraints for refining 7768 atoms. 14693 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2309 (Rfree = 0.000) for 7768 atoms. Found 48 (58 requested) and removed 59 (29 requested) atoms. Cycle 7: After refmac, R = 0.2185 (Rfree = 0.000) for 7718 atoms. Found 20 (58 requested) and removed 51 (29 requested) atoms. Cycle 8: After refmac, R = 0.2131 (Rfree = 0.000) for 7667 atoms. Found 33 (58 requested) and removed 51 (29 requested) atoms. Cycle 9: After refmac, R = 0.2058 (Rfree = 0.000) for 7623 atoms. Found 20 (57 requested) and removed 38 (28 requested) atoms. Cycle 10: After refmac, R = 0.2036 (Rfree = 0.000) for 7590 atoms. Found 23 (57 requested) and removed 32 (28 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.29 3.16 Search for helices and strands: 0 residues in 0 chains, 7866 seeds are put forward NCS extension: 24 residues added (2 deleted due to clashes), 7890 seeds are put forward Round 1: 522 peptides, 88 chains. Longest chain 18 peptides. Score 0.412 Round 2: 597 peptides, 79 chains. Longest chain 26 peptides. Score 0.546 Round 3: 586 peptides, 76 chains. Longest chain 20 peptides. Score 0.549 Round 4: 579 peptides, 78 chains. Longest chain 22 peptides. Score 0.532 Round 5: 564 peptides, 73 chains. Longest chain 27 peptides. Score 0.540 Taking the results from Round 3 Chains 79, Residues 510, Estimated correctness of the model 11.2 % 8 chains (91 residues) have been docked in sequence ------------------------------------------------------ 16970 reflections ( 99.23 % complete ) and 16943 restraints for refining 7768 atoms. 14673 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2263 (Rfree = 0.000) for 7768 atoms. Found 53 (58 requested) and removed 44 (29 requested) atoms. Cycle 12: After refmac, R = 0.2135 (Rfree = 0.000) for 7734 atoms. Found 22 (58 requested) and removed 38 (29 requested) atoms. Cycle 13: After refmac, R = 0.2093 (Rfree = 0.000) for 7698 atoms. Found 23 (58 requested) and removed 35 (29 requested) atoms. Cycle 14: After refmac, R = 0.2098 (Rfree = 0.000) for 7673 atoms. Found 23 (58 requested) and removed 30 (29 requested) atoms. Cycle 15: After refmac, R = 0.2076 (Rfree = 0.000) for 7657 atoms. Found 18 (57 requested) and removed 29 (28 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.31 3.18 Search for helices and strands: 0 residues in 0 chains, 7884 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 7901 seeds are put forward Round 1: 508 peptides, 86 chains. Longest chain 14 peptides. Score 0.405 Round 2: 566 peptides, 79 chains. Longest chain 22 peptides. Score 0.512 Round 3: 578 peptides, 79 chains. Longest chain 21 peptides. Score 0.526 Round 4: 570 peptides, 76 chains. Longest chain 18 peptides. Score 0.532 Round 5: 578 peptides, 80 chains. Longest chain 22 peptides. Score 0.521 Taking the results from Round 4 Chains 76, Residues 494, Estimated correctness of the model 4.9 % 5 chains (40 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 16970 reflections ( 99.23 % complete ) and 17628 restraints for refining 7768 atoms. 15602 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2219 (Rfree = 0.000) for 7768 atoms. Found 42 (58 requested) and removed 42 (29 requested) atoms. Cycle 17: After refmac, R = 0.2057 (Rfree = 0.000) for 7731 atoms. Found 17 (58 requested) and removed 39 (29 requested) atoms. Cycle 18: After refmac, R = 0.2051 (Rfree = 0.000) for 7690 atoms. Found 34 (58 requested) and removed 35 (29 requested) atoms. Cycle 19: After refmac, R = 0.1992 (Rfree = 0.000) for 7667 atoms. Found 19 (58 requested) and removed 34 (29 requested) atoms. Cycle 20: After refmac, R = 0.1984 (Rfree = 0.000) for 7639 atoms. Found 16 (57 requested) and removed 35 (28 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.30 3.17 Search for helices and strands: 0 residues in 0 chains, 7857 seeds are put forward NCS extension: 12 residues added (4 deleted due to clashes), 7869 seeds are put forward Round 1: 478 peptides, 83 chains. Longest chain 15 peptides. Score 0.383 Round 2: 555 peptides, 87 chains. Longest chain 20 peptides. Score 0.458 Round 3: 551 peptides, 81 chains. Longest chain 20 peptides. Score 0.485 Round 4: 557 peptides, 83 chains. Longest chain 20 peptides. Score 0.482 Round 5: 537 peptides, 85 chains. Longest chain 18 peptides. Score 0.447 Taking the results from Round 3 Chains 82, Residues 470, Estimated correctness of the model 0.0 % 8 chains (54 residues) have been docked in sequence ------------------------------------------------------ 16970 reflections ( 99.23 % complete ) and 17372 restraints for refining 7766 atoms. 15414 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2140 (Rfree = 0.000) for 7766 atoms. Found 38 (58 requested) and removed 44 (29 requested) atoms. Cycle 22: After refmac, R = 0.2026 (Rfree = 0.000) for 7734 atoms. Found 26 (58 requested) and removed 36 (29 requested) atoms. Cycle 23: After refmac, R = 0.1989 (Rfree = 0.000) for 7703 atoms. Found 25 (58 requested) and removed 41 (29 requested) atoms. Cycle 24: After refmac, R = 0.1936 (Rfree = 0.000) for 7674 atoms. Found 18 (58 requested) and removed 32 (29 requested) atoms. Cycle 25: After refmac, R = 0.1897 (Rfree = 0.000) for 7649 atoms. Found 22 (57 requested) and removed 34 (28 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.29 3.16 Search for helices and strands: 0 residues in 0 chains, 7867 seeds are put forward NCS extension: 11 residues added (5 deleted due to clashes), 7878 seeds are put forward Round 1: 471 peptides, 88 chains. Longest chain 13 peptides. Score 0.344 Round 2: 539 peptides, 87 chains. Longest chain 18 peptides. Score 0.439 Round 3: 535 peptides, 84 chains. Longest chain 18 peptides. Score 0.450 Round 4: 546 peptides, 78 chains. Longest chain 20 peptides. Score 0.495 Round 5: 529 peptides, 86 chains. Longest chain 14 peptides. Score 0.432 Taking the results from Round 4 Chains 82, Residues 468, Estimated correctness of the model 0.0 % 6 chains (61 residues) have been docked in sequence ------------------------------------------------------ 16970 reflections ( 99.23 % complete ) and 17337 restraints for refining 7768 atoms. 15309 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2065 (Rfree = 0.000) for 7768 atoms. Found 40 (58 requested) and removed 51 (29 requested) atoms. Cycle 27: After refmac, R = 0.1950 (Rfree = 0.000) for 7721 atoms. Found 28 (58 requested) and removed 33 (29 requested) atoms. Cycle 28: After refmac, R = 0.1868 (Rfree = 0.000) for 7691 atoms. Found 22 (58 requested) and removed 30 (29 requested) atoms. Cycle 29: After refmac, R = 0.1776 (Rfree = 0.000) for 7661 atoms. Found 16 (58 requested) and removed 35 (29 requested) atoms. Cycle 30: After refmac, R = 0.1735 (Rfree = 0.000) for 7639 atoms. Found 9 (57 requested) and removed 34 (28 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.30 3.17 Search for helices and strands: 0 residues in 0 chains, 7857 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 7880 seeds are put forward Round 1: 499 peptides, 92 chains. Longest chain 15 peptides. Score 0.359 Round 2: 546 peptides, 87 chains. Longest chain 19 peptides. Score 0.447 Round 3: 557 peptides, 90 chains. Longest chain 24 peptides. Score 0.445 Round 4: 564 peptides, 88 chains. Longest chain 18 peptides. Score 0.464 Round 5: 572 peptides, 88 chains. Longest chain 18 peptides. Score 0.473 Taking the results from Round 5 Chains 91, Residues 484, Estimated correctness of the model 0.0 % 7 chains (55 residues) have been docked in sequence ------------------------------------------------------ 16970 reflections ( 99.23 % complete ) and 17377 restraints for refining 7768 atoms. 15345 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2059 (Rfree = 0.000) for 7768 atoms. Found 52 (58 requested) and removed 45 (29 requested) atoms. Failed to save intermediate PDB Cycle 32: After refmac, R = 0.1906 (Rfree = 0.000) for 7742 atoms. Found 33 (58 requested) and removed 34 (29 requested) atoms. Cycle 33: After refmac, R = 0.1876 (Rfree = 0.000) for 7721 atoms. Found 31 (58 requested) and removed 32 (29 requested) atoms. Cycle 34: After refmac, R = 0.1821 (Rfree = 0.000) for 7698 atoms. Found 24 (58 requested) and removed 34 (29 requested) atoms. Cycle 35: After refmac, R = 0.1775 (Rfree = 0.000) for 7674 atoms. Found 18 (58 requested) and removed 35 (29 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.28 3.15 Search for helices and strands: 0 residues in 0 chains, 7892 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 7917 seeds are put forward Round 1: 431 peptides, 79 chains. Longest chain 16 peptides. Score 0.342 Round 2: 507 peptides, 82 chains. Longest chain 18 peptides. Score 0.426 Round 3: 518 peptides, 80 chains. Longest chain 20 peptides. Score 0.451 Round 4: 498 peptides, 79 chains. Longest chain 18 peptides. Score 0.431 Round 5: 503 peptides, 78 chains. Longest chain 20 peptides. Score 0.443 Taking the results from Round 3 Chains 82, Residues 438, Estimated correctness of the model 0.0 % 7 chains (38 residues) have been docked in sequence ------------------------------------------------------ 16970 reflections ( 99.23 % complete ) and 17899 restraints for refining 7767 atoms. 16127 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1979 (Rfree = 0.000) for 7767 atoms. Found 42 (58 requested) and removed 39 (29 requested) atoms. Cycle 37: After refmac, R = 0.1909 (Rfree = 0.000) for 7747 atoms. Found 25 (58 requested) and removed 34 (29 requested) atoms. Cycle 38: After refmac, R = 0.1849 (Rfree = 0.000) for 7728 atoms. Found 19 (58 requested) and removed 34 (29 requested) atoms. Cycle 39: After refmac, R = 0.1822 (Rfree = 0.000) for 7708 atoms. Found 18 (58 requested) and removed 34 (29 requested) atoms. Cycle 40: After refmac, R = 0.1807 (Rfree = 0.000) for 7682 atoms. Found 23 (58 requested) and removed 29 (29 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.31 3.18 Search for helices and strands: 0 residues in 0 chains, 7932 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 7949 seeds are put forward Round 1: 421 peptides, 81 chains. Longest chain 16 peptides. Score 0.316 Round 2: 487 peptides, 82 chains. Longest chain 16 peptides. Score 0.400 Round 3: 457 peptides, 70 chains. Longest chain 19 peptides. Score 0.430 Round 4: 479 peptides, 74 chains. Longest chain 18 peptides. Score 0.435 Round 5: 468 peptides, 76 chains. Longest chain 17 peptides. Score 0.410 Taking the results from Round 4 Chains 77, Residues 405, Estimated correctness of the model 0.0 % 6 chains (48 residues) have been docked in sequence ------------------------------------------------------ 16970 reflections ( 99.23 % complete ) and 17771 restraints for refining 7766 atoms. 16074 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1950 (Rfree = 0.000) for 7766 atoms. Found 56 (58 requested) and removed 36 (29 requested) atoms. Cycle 42: After refmac, R = 0.1839 (Rfree = 0.000) for 7770 atoms. Found 26 (58 requested) and removed 31 (29 requested) atoms. Cycle 43: After refmac, R = 0.1805 (Rfree = 0.000) for 7756 atoms. Found 21 (58 requested) and removed 31 (29 requested) atoms. Cycle 44: After refmac, R = 0.1786 (Rfree = 0.000) for 7735 atoms. Found 36 (58 requested) and removed 30 (29 requested) atoms. Cycle 45: After refmac, R = 0.1726 (Rfree = 0.000) for 7732 atoms. Found 28 (58 requested) and removed 32 (29 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.29 3.16 Search for helices and strands: 0 residues in 0 chains, 7905 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 7928 seeds are put forward Round 1: 417 peptides, 82 chains. Longest chain 13 peptides. Score 0.304 Round 2: 449 peptides, 74 chains. Longest chain 18 peptides. Score 0.396 Round 3: 449 peptides, 73 chains. Longest chain 13 peptides. Score 0.402 Round 4: 439 peptides, 71 chains. Longest chain 15 peptides. Score 0.400 Round 5: 436 peptides, 69 chains. Longest chain 17 peptides. Score 0.408 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 71, Residues 367, Estimated correctness of the model 0.0 % 6 chains (34 residues) have been docked in sequence Sequence coverage is 9 % Consider running further cycles of model building using 1vm8-3_warpNtrace.pdb as input Building loops using Loopy2018 71 chains (367 residues) following loop building 6 chains (34 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 16970 reflections ( 99.23 % complete ) and 18161 restraints for refining 7766 atoms. 16684 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1898 (Rfree = 0.000) for 7766 atoms. Found 0 (58 requested) and removed 29 (29 requested) atoms. Cycle 47: After refmac, R = 0.1883 (Rfree = 0.000) for 7723 atoms. Found 0 (58 requested) and removed 12 (29 requested) atoms. Cycle 48: After refmac, R = 0.1866 (Rfree = 0.000) for 7696 atoms. Found 0 (58 requested) and removed 20 (29 requested) atoms. Cycle 49: After refmac, R = 0.1826 (Rfree = 0.000) for 7666 atoms. TimeTaking 76.1