Mon 24 Dec 00:11:22 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 1vm8-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vm8-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vm8-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vm8-3.2-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/1vm8-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vm8-3.2-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 00:11:27 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/1vm8-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vm8-3.2-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 870 and 0 Target number of residues in the AU: 870 Target solvent content: 0.6207 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: 1vm8-3.2-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: 4 Cell parameters: 80.094 73.402 107.132 90.000 99.827 90.000 Input sequence file: 1vm8-3.2-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 3.200 Wilson plot Bfac: 61.74 20337 reflections ( 99.36 % complete ) and 0 restraints for refining 9499 atoms. Observations/parameters ratio is 0.54 ------------------------------------------------------ Starting model: R = 0.3234 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2602 (Rfree = 0.000) for 9499 atoms. Found 77 (85 requested) and removed 125 (42 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.14 3.02 Search for helices and strands: 0 residues in 0 chains, 9651 seeds are put forward NCS extension: 0 residues added, 9651 seeds are put forward Round 1: 479 peptides, 87 chains. Longest chain 19 peptides. Score 0.361 Round 2: 582 peptides, 91 chains. Longest chain 22 peptides. Score 0.470 Round 3: 597 peptides, 82 chains. Longest chain 19 peptides. Score 0.532 Round 4: 618 peptides, 79 chains. Longest chain 25 peptides. Score 0.568 Round 5: 615 peptides, 79 chains. Longest chain 25 peptides. Score 0.565 Taking the results from Round 4 Chains 81, Residues 539, Estimated correctness of the model 32.1 % 5 chains (62 residues) have been docked in sequence ------------------------------------------------------ 20337 reflections ( 99.36 % complete ) and 16837 restraints for refining 7797 atoms. 14568 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2496 (Rfree = 0.000) for 7797 atoms. Found 70 (70 requested) and removed 73 (35 requested) atoms. Cycle 2: After refmac, R = 0.2415 (Rfree = 0.000) for 7697 atoms. Found 40 (69 requested) and removed 46 (34 requested) atoms. Cycle 3: After refmac, R = 0.2324 (Rfree = 0.000) for 7633 atoms. Found 28 (69 requested) and removed 41 (34 requested) atoms. Cycle 4: After refmac, R = 0.2272 (Rfree = 0.000) for 7593 atoms. Found 33 (68 requested) and removed 49 (34 requested) atoms. Cycle 5: After refmac, R = 0.2184 (Rfree = 0.000) for 7552 atoms. Found 33 (68 requested) and removed 39 (34 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.15 3.03 Search for helices and strands: 0 residues in 0 chains, 7776 seeds are put forward NCS extension: 42 residues added (2 deleted due to clashes), 7818 seeds are put forward Round 1: 527 peptides, 82 chains. Longest chain 19 peptides. Score 0.451 Round 2: 577 peptides, 75 chains. Longest chain 25 peptides. Score 0.544 Round 3: 589 peptides, 80 chains. Longest chain 25 peptides. Score 0.533 Round 4: 599 peptides, 78 chains. Longest chain 22 peptides. Score 0.553 Round 5: 612 peptides, 77 chains. Longest chain 23 peptides. Score 0.571 Taking the results from Round 5 Chains 80, Residues 535, Estimated correctness of the model 33.0 % 5 chains (38 residues) have been docked in sequence ------------------------------------------------------ 20337 reflections ( 99.36 % complete ) and 17166 restraints for refining 7760 atoms. 14982 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2452 (Rfree = 0.000) for 7760 atoms. Found 54 (69 requested) and removed 67 (34 requested) atoms. Cycle 7: After refmac, R = 0.2315 (Rfree = 0.000) for 7699 atoms. Found 24 (69 requested) and removed 42 (34 requested) atoms. Cycle 8: After refmac, R = 0.2282 (Rfree = 0.000) for 7655 atoms. Found 30 (68 requested) and removed 36 (34 requested) atoms. Cycle 9: After refmac, R = 0.2213 (Rfree = 0.000) for 7635 atoms. Found 21 (68 requested) and removed 39 (34 requested) atoms. Cycle 10: After refmac, R = 0.2162 (Rfree = 0.000) for 7596 atoms. Found 18 (68 requested) and removed 35 (34 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.14 3.02 Search for helices and strands: 0 residues in 0 chains, 7831 seeds are put forward NCS extension: 29 residues added (2 deleted due to clashes), 7860 seeds are put forward Round 1: 555 peptides, 87 chains. Longest chain 22 peptides. Score 0.458 Round 2: 590 peptides, 82 chains. Longest chain 33 peptides. Score 0.524 Round 3: 635 peptides, 88 chains. Longest chain 33 peptides. Score 0.544 Round 4: 618 peptides, 76 chains. Longest chain 31 peptides. Score 0.582 Round 5: 632 peptides, 74 chains. Longest chain 32 peptides. Score 0.605 Taking the results from Round 5 Chains 78, Residues 558, Estimated correctness of the model 42.4 % 6 chains (70 residues) have been docked in sequence ------------------------------------------------------ 20337 reflections ( 99.36 % complete ) and 16679 restraints for refining 7800 atoms. 14249 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2458 (Rfree = 0.000) for 7800 atoms. Found 64 (70 requested) and removed 59 (35 requested) atoms. Cycle 12: After refmac, R = 0.2251 (Rfree = 0.000) for 7778 atoms. Found 32 (70 requested) and removed 46 (35 requested) atoms. Cycle 13: After refmac, R = 0.2173 (Rfree = 0.000) for 7746 atoms. Found 12 (69 requested) and removed 39 (34 requested) atoms. Cycle 14: After refmac, R = 0.2119 (Rfree = 0.000) for 7703 atoms. Found 13 (69 requested) and removed 35 (34 requested) atoms. Cycle 15: After refmac, R = 0.2138 (Rfree = 0.000) for 7672 atoms. Found 12 (68 requested) and removed 34 (34 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.15 3.03 Search for helices and strands: 0 residues in 0 chains, 7879 seeds are put forward NCS extension: 48 residues added (3 deleted due to clashes), 7927 seeds are put forward Round 1: 542 peptides, 84 chains. Longest chain 28 peptides. Score 0.458 Round 2: 573 peptides, 77 chains. Longest chain 25 peptides. Score 0.530 Round 3: 589 peptides, 71 chains. Longest chain 32 peptides. Score 0.576 Round 4: 611 peptides, 74 chains. Longest chain 33 peptides. Score 0.584 Round 5: 605 peptides, 72 chains. Longest chain 28 peptides. Score 0.587 Taking the results from Round 5 Chains 76, Residues 533, Estimated correctness of the model 37.5 % 10 chains (98 residues) have been docked in sequence ------------------------------------------------------ 20337 reflections ( 99.36 % complete ) and 16419 restraints for refining 7800 atoms. 14004 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2384 (Rfree = 0.000) for 7800 atoms. Found 67 (70 requested) and removed 64 (35 requested) atoms. Cycle 17: After refmac, R = 0.2185 (Rfree = 0.000) for 7765 atoms. Found 29 (70 requested) and removed 50 (35 requested) atoms. Cycle 18: After refmac, R = 0.2160 (Rfree = 0.000) for 7718 atoms. Found 27 (69 requested) and removed 44 (34 requested) atoms. Cycle 19: After refmac, R = 0.2061 (Rfree = 0.000) for 7689 atoms. Found 16 (69 requested) and removed 35 (34 requested) atoms. Cycle 20: After refmac, R = 0.2021 (Rfree = 0.000) for 7661 atoms. Found 15 (68 requested) and removed 35 (34 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.14 3.02 Search for helices and strands: 0 residues in 0 chains, 7869 seeds are put forward NCS extension: 16 residues added (9 deleted due to clashes), 7885 seeds are put forward Round 1: 520 peptides, 85 chains. Longest chain 21 peptides. Score 0.426 Round 2: 591 peptides, 81 chains. Longest chain 25 peptides. Score 0.530 Round 3: 610 peptides, 79 chains. Longest chain 32 peptides. Score 0.560 Round 4: 591 peptides, 76 chains. Longest chain 23 peptides. Score 0.554 Round 5: 600 peptides, 74 chains. Longest chain 34 peptides. Score 0.573 Taking the results from Round 5 Chains 81, Residues 526, Estimated correctness of the model 33.6 % 8 chains (95 residues) have been docked in sequence ------------------------------------------------------ 20337 reflections ( 99.36 % complete ) and 16724 restraints for refining 7800 atoms. 14333 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2332 (Rfree = 0.000) for 7800 atoms. Found 64 (70 requested) and removed 60 (35 requested) atoms. Cycle 22: After refmac, R = 0.2148 (Rfree = 0.000) for 7778 atoms. Found 32 (70 requested) and removed 38 (35 requested) atoms. Cycle 23: After refmac, R = 0.2062 (Rfree = 0.000) for 7755 atoms. Found 14 (69 requested) and removed 34 (34 requested) atoms. Cycle 24: After refmac, R = 0.2018 (Rfree = 0.000) for 7723 atoms. Found 14 (69 requested) and removed 34 (34 requested) atoms. Cycle 25: After refmac, R = 0.2003 (Rfree = 0.000) for 7700 atoms. Found 13 (69 requested) and removed 34 (34 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.13 3.01 Search for helices and strands: 0 residues in 0 chains, 7897 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 7918 seeds are put forward Round 1: 536 peptides, 90 chains. Longest chain 22 peptides. Score 0.419 Round 2: 600 peptides, 80 chains. Longest chain 40 peptides. Score 0.545 Round 3: 596 peptides, 78 chains. Longest chain 26 peptides. Score 0.550 Round 4: 584 peptides, 81 chains. Longest chain 24 peptides. Score 0.522 Round 5: 603 peptides, 83 chains. Longest chain 29 peptides. Score 0.533 Taking the results from Round 3 Chains 86, Residues 518, Estimated correctness of the model 26.9 % 11 chains (99 residues) have been docked in sequence ------------------------------------------------------ 20337 reflections ( 99.36 % complete ) and 16911 restraints for refining 7799 atoms. 14579 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2285 (Rfree = 0.000) for 7799 atoms. Found 59 (70 requested) and removed 52 (35 requested) atoms. Failed to save intermediate PDB Cycle 27: After refmac, R = 0.2123 (Rfree = 0.000) for 7780 atoms. Found 26 (70 requested) and removed 42 (35 requested) atoms. Cycle 28: After refmac, R = 0.2118 (Rfree = 0.000) for 7746 atoms. Found 20 (69 requested) and removed 38 (34 requested) atoms. Cycle 29: After refmac, R = 0.2065 (Rfree = 0.000) for 7716 atoms. Found 20 (69 requested) and removed 34 (34 requested) atoms. Cycle 30: After refmac, R = 0.2043 (Rfree = 0.000) for 7685 atoms. Found 21 (69 requested) and removed 36 (34 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.11 2.99 Search for helices and strands: 0 residues in 0 chains, 7875 seeds are put forward NCS extension: 30 residues added (5 deleted due to clashes), 7905 seeds are put forward Round 1: 521 peptides, 83 chains. Longest chain 23 peptides. Score 0.438 Round 2: 570 peptides, 79 chains. Longest chain 24 peptides. Score 0.517 Round 3: 577 peptides, 81 chains. Longest chain 21 peptides. Score 0.515 Round 4: 582 peptides, 76 chains. Longest chain 29 peptides. Score 0.545 Round 5: 557 peptides, 72 chains. Longest chain 23 peptides. Score 0.537 Taking the results from Round 4 Chains 81, Residues 506, Estimated correctness of the model 25.4 % 7 chains (83 residues) have been docked in sequence ------------------------------------------------------ 20337 reflections ( 99.36 % complete ) and 16980 restraints for refining 7800 atoms. 14720 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2205 (Rfree = 0.000) for 7800 atoms. Found 64 (70 requested) and removed 50 (35 requested) atoms. Cycle 32: After refmac, R = 0.2053 (Rfree = 0.000) for 7799 atoms. Found 24 (70 requested) and removed 39 (35 requested) atoms. Cycle 33: After refmac, R = 0.2030 (Rfree = 0.000) for 7774 atoms. Found 32 (69 requested) and removed 36 (34 requested) atoms. Cycle 34: After refmac, R = 0.1961 (Rfree = 0.000) for 7753 atoms. Found 25 (69 requested) and removed 35 (34 requested) atoms. Cycle 35: After refmac, R = 0.1905 (Rfree = 0.000) for 7725 atoms. Found 22 (69 requested) and removed 35 (34 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.13 3.01 Search for helices and strands: 0 residues in 0 chains, 7914 seeds are put forward NCS extension: 15 residues added (5 deleted due to clashes), 7929 seeds are put forward Round 1: 497 peptides, 84 chains. Longest chain 20 peptides. Score 0.402 Round 2: 550 peptides, 77 chains. Longest chain 20 peptides. Score 0.504 Round 3: 535 peptides, 76 chains. Longest chain 20 peptides. Score 0.492 Round 4: 544 peptides, 75 chains. Longest chain 23 peptides. Score 0.508 Round 5: 543 peptides, 80 chains. Longest chain 24 peptides. Score 0.481 Taking the results from Round 4 Chains 80, Residues 469, Estimated correctness of the model 13.9 % 9 chains (84 residues) have been docked in sequence ------------------------------------------------------ 20337 reflections ( 99.36 % complete ) and 16990 restraints for refining 7800 atoms. 14883 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2110 (Rfree = 0.000) for 7800 atoms. Found 48 (70 requested) and removed 42 (35 requested) atoms. Cycle 37: After refmac, R = 0.2009 (Rfree = 0.000) for 7788 atoms. Found 26 (70 requested) and removed 40 (35 requested) atoms. Cycle 38: After refmac, R = 0.1980 (Rfree = 0.000) for 7757 atoms. Found 23 (69 requested) and removed 36 (34 requested) atoms. Cycle 39: After refmac, R = 0.1941 (Rfree = 0.000) for 7738 atoms. Found 19 (69 requested) and removed 34 (34 requested) atoms. Cycle 40: After refmac, R = 0.2244 (Rfree = 0.000) for 7717 atoms. Found 69 (69 requested) and removed 35 (34 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.11 2.99 Search for helices and strands: 0 residues in 0 chains, 7961 seeds are put forward NCS extension: 34 residues added (3 deleted due to clashes), 7995 seeds are put forward Round 1: 461 peptides, 81 chains. Longest chain 16 peptides. Score 0.372 Round 2: 502 peptides, 70 chains. Longest chain 20 peptides. Score 0.485 Round 3: 526 peptides, 71 chains. Longest chain 24 peptides. Score 0.508 Round 4: 528 peptides, 70 chains. Longest chain 34 peptides. Score 0.515 Round 5: 527 peptides, 71 chains. Longest chain 20 peptides. Score 0.509 Taking the results from Round 4 Chains 71, Residues 458, Estimated correctness of the model 16.1 % 6 chains (82 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 20337 reflections ( 99.36 % complete ) and 16839 restraints for refining 7800 atoms. 14728 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2131 (Rfree = 0.000) for 7800 atoms. Found 63 (70 requested) and removed 42 (35 requested) atoms. Cycle 42: After refmac, R = 0.1957 (Rfree = 0.000) for 7801 atoms. Found 25 (70 requested) and removed 36 (35 requested) atoms. Cycle 43: After refmac, R = 0.1927 (Rfree = 0.000) for 7779 atoms. Found 20 (69 requested) and removed 34 (34 requested) atoms. Cycle 44: After refmac, R = 0.1910 (Rfree = 0.000) for 7758 atoms. Found 22 (69 requested) and removed 35 (34 requested) atoms. Cycle 45: After refmac, R = 0.2237 (Rfree = 0.000) for 7739 atoms. Found 69 (69 requested) and removed 34 (34 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.12 3.00 Search for helices and strands: 0 residues in 0 chains, 7961 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 7983 seeds are put forward Round 1: 406 peptides, 68 chains. Longest chain 21 peptides. Score 0.374 Round 2: 464 peptides, 72 chains. Longest chain 28 peptides. Score 0.427 Round 3: 469 peptides, 69 chains. Longest chain 32 peptides. Score 0.450 Round 4: 462 peptides, 71 chains. Longest chain 19 peptides. Score 0.430 Round 5: 460 peptides, 63 chains. Longest chain 29 peptides. Score 0.472 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 63, Residues 397, Estimated correctness of the model 2.0 % 3 chains (37 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 63 chains (397 residues) following loop building 3 chains (37 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 20337 reflections ( 99.36 % complete ) and 17818 restraints for refining 7799 atoms. 16156 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2101 (Rfree = 0.000) for 7799 atoms. Found 0 (70 requested) and removed 35 (35 requested) atoms. Cycle 47: After refmac, R = 0.2094 (Rfree = 0.000) for 7750 atoms. Found 0 (69 requested) and removed 34 (34 requested) atoms. Cycle 48: After refmac, R = 0.2009 (Rfree = 0.000) for 7712 atoms. Found 0 (69 requested) and removed 21 (34 requested) atoms. Cycle 49: After refmac, R = 0.1949 (Rfree = 0.000) for 7682 atoms. TimeTaking 82.88