Sun 23 Dec 23:51:47 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 2pgc-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2pgc-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2pgc-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pgc-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/2pgc-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pgc-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 ============================================================ Sun 23 Dec 23:51:52 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/2pgc-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pgc-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 767 and 0 Target number of residues in the AU: 767 Target solvent content: 0.6446 Checking the provided sequence file Detected sequence length: 207 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 5 Adjusted target number of residues: 1035 Adjusted target solvent content: 0.52 Input MTZ file: 2pgc-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: 18 Cell parameters: 137.477 139.862 60.737 90.000 90.000 90.000 Input sequence file: 2pgc-3.4-parrot-mrncs.fasta_lf Building free atoms model in initial map for 8280 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: 98.043 3.400 Wilson plot Bfac: 74.58 16710 reflections ( 99.63 % complete ) and 0 restraints for refining 9111 atoms. Observations/parameters ratio is 0.46 ------------------------------------------------------ Starting model: R = 0.3244 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2913 (Rfree = 0.000) for 9111 atoms. Found 68 (68 requested) and removed 45 (34 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.39 3.30 Search for helices and strands: 0 residues in 0 chains, 9336 seeds are put forward NCS extension: 0 residues added, 9336 seeds are put forward Round 1: 525 peptides, 85 chains. Longest chain 19 peptides. Score 0.444 Round 2: 582 peptides, 76 chains. Longest chain 19 peptides. Score 0.561 Round 3: 637 peptides, 73 chains. Longest chain 24 peptides. Score 0.631 Round 4: 649 peptides, 74 chains. Longest chain 34 peptides. Score 0.638 Round 5: 676 peptides, 70 chains. Longest chain 29 peptides. Score 0.679 Taking the results from Round 5 Chains 72, Residues 606, Estimated correctness of the model 52.3 % 6 chains (87 residues) have been docked in sequence ------------------------------------------------------ 16710 reflections ( 99.63 % complete ) and 15502 restraints for refining 7526 atoms. 12833 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2574 (Rfree = 0.000) for 7526 atoms. Found 56 (56 requested) and removed 44 (28 requested) atoms. Cycle 2: After refmac, R = 0.2454 (Rfree = 0.000) for 7429 atoms. Found 32 (56 requested) and removed 35 (28 requested) atoms. Cycle 3: After refmac, R = 0.2399 (Rfree = 0.000) for 7387 atoms. Found 24 (56 requested) and removed 36 (28 requested) atoms. Cycle 4: After refmac, R = 0.2322 (Rfree = 0.000) for 7332 atoms. Found 24 (55 requested) and removed 31 (27 requested) atoms. Cycle 5: After refmac, R = 0.2242 (Rfree = 0.000) for 7308 atoms. Found 14 (55 requested) and removed 35 (27 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.36 3.27 Search for helices and strands: 0 residues in 0 chains, 7567 seeds are put forward NCS extension: 12 residues added (5 deleted due to clashes), 7579 seeds are put forward Round 1: 634 peptides, 82 chains. Longest chain 28 peptides. Score 0.588 Round 2: 684 peptides, 72 chains. Longest chain 34 peptides. Score 0.678 Round 3: 695 peptides, 73 chains. Longest chain 33 peptides. Score 0.684 Round 4: 699 peptides, 65 chains. Longest chain 42 peptides. Score 0.717 Round 5: 696 peptides, 65 chains. Longest chain 32 peptides. Score 0.715 Taking the results from Round 4 Chains 68, Residues 634, Estimated correctness of the model 62.1 % 4 chains (63 residues) have been docked in sequence Building loops using Loopy2018 68 chains (634 residues) following loop building 4 chains (63 residues) in sequence following loop building ------------------------------------------------------ 16710 reflections ( 99.63 % complete ) and 15524 restraints for refining 7529 atoms. 12811 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2438 (Rfree = 0.000) for 7529 atoms. Found 46 (56 requested) and removed 41 (28 requested) atoms. Cycle 7: After refmac, R = 0.2263 (Rfree = 0.000) for 7498 atoms. Found 16 (55 requested) and removed 30 (28 requested) atoms. Cycle 8: After refmac, R = 0.2146 (Rfree = 0.000) for 7469 atoms. Found 17 (54 requested) and removed 33 (28 requested) atoms. Cycle 9: After refmac, R = 0.2099 (Rfree = 0.000) for 7442 atoms. Found 22 (53 requested) and removed 29 (28 requested) atoms. Cycle 10: After refmac, R = 0.2040 (Rfree = 0.000) for 7427 atoms. Found 14 (52 requested) and removed 30 (28 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.37 3.28 Search for helices and strands: 0 residues in 0 chains, 7660 seeds are put forward NCS extension: 20 residues added (4 deleted due to clashes), 7680 seeds are put forward Round 1: 623 peptides, 82 chains. Longest chain 26 peptides. Score 0.576 Round 2: 672 peptides, 66 chains. Longest chain 26 peptides. Score 0.692 Round 3: 660 peptides, 64 chains. Longest chain 38 peptides. Score 0.690 Round 4: 668 peptides, 66 chains. Longest chain 32 peptides. Score 0.689 Round 5: 674 peptides, 64 chains. Longest chain 50 peptides. Score 0.701 Taking the results from Round 5 Chains 67, Residues 610, Estimated correctness of the model 58.1 % 7 chains (107 residues) have been docked in sequence Building loops using Loopy2018 67 chains (610 residues) following loop building 7 chains (107 residues) in sequence following loop building ------------------------------------------------------ 16710 reflections ( 99.63 % complete ) and 15253 restraints for refining 7528 atoms. 12475 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2318 (Rfree = 0.000) for 7528 atoms. Found 41 (50 requested) and removed 41 (28 requested) atoms. Cycle 12: After refmac, R = 0.2173 (Rfree = 0.000) for 7487 atoms. Found 24 (49 requested) and removed 32 (28 requested) atoms. Failed to save intermediate PDB Cycle 13: After refmac, R = 0.2080 (Rfree = 0.000) for 7454 atoms. Found 14 (48 requested) and removed 30 (28 requested) atoms. Cycle 14: After refmac, R = 0.2019 (Rfree = 0.000) for 7423 atoms. Found 16 (47 requested) and removed 28 (28 requested) atoms. Cycle 15: After refmac, R = 0.1959 (Rfree = 0.000) for 7401 atoms. Found 12 (45 requested) and removed 28 (27 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.39 3.30 Search for helices and strands: 0 residues in 0 chains, 7669 seeds are put forward NCS extension: 9 residues added (7 deleted due to clashes), 7678 seeds are put forward Round 1: 582 peptides, 85 chains. Longest chain 23 peptides. Score 0.515 Round 2: 640 peptides, 68 chains. Longest chain 36 peptides. Score 0.656 Round 3: 644 peptides, 70 chains. Longest chain 33 peptides. Score 0.651 Round 4: 633 peptides, 71 chains. Longest chain 36 peptides. Score 0.636 Round 5: 633 peptides, 74 chains. Longest chain 34 peptides. Score 0.623 Taking the results from Round 2 Chains 70, Residues 572, Estimated correctness of the model 45.9 % 4 chains (29 residues) have been docked in sequence ------------------------------------------------------ 16710 reflections ( 99.63 % complete ) and 16080 restraints for refining 7529 atoms. 13771 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2076 (Rfree = 0.000) for 7529 atoms. Found 35 (45 requested) and removed 31 (28 requested) atoms. Cycle 17: After refmac, R = 0.2002 (Rfree = 0.000) for 7514 atoms. Found 13 (45 requested) and removed 28 (28 requested) atoms. Cycle 18: After refmac, R = 0.1977 (Rfree = 0.000) for 7490 atoms. Found 15 (45 requested) and removed 28 (28 requested) atoms. Cycle 19: After refmac, R = 0.1946 (Rfree = 0.000) for 7458 atoms. Found 13 (45 requested) and removed 28 (28 requested) atoms. Cycle 20: After refmac, R = 0.1912 (Rfree = 0.000) for 7437 atoms. Found 10 (45 requested) and removed 28 (28 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.40 3.31 Search for helices and strands: 0 residues in 0 chains, 7701 seeds are put forward NCS extension: 26 residues added (10 deleted due to clashes), 7727 seeds are put forward Round 1: 552 peptides, 85 chains. Longest chain 24 peptides. Score 0.478 Round 2: 612 peptides, 69 chains. Longest chain 30 peptides. Score 0.625 Round 3: 615 peptides, 71 chains. Longest chain 24 peptides. Score 0.619 Round 4: 620 peptides, 72 chains. Longest chain 31 peptides. Score 0.619 Round 5: 632 peptides, 74 chains. Longest chain 29 peptides. Score 0.622 Taking the results from Round 2 Chains 69, Residues 543, Estimated correctness of the model 36.6 % 1 chains (29 residues) have been docked in sequence ------------------------------------------------------ 16710 reflections ( 99.63 % complete ) and 16369 restraints for refining 7527 atoms. 14136 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2091 (Rfree = 0.000) for 7527 atoms. Found 27 (45 requested) and removed 31 (28 requested) atoms. Cycle 22: After refmac, R = 0.2061 (Rfree = 0.000) for 7502 atoms. Found 23 (45 requested) and removed 30 (28 requested) atoms. Cycle 23: After refmac, R = 0.1962 (Rfree = 0.000) for 7489 atoms. Found 15 (45 requested) and removed 29 (28 requested) atoms. Cycle 24: After refmac, R = 0.1892 (Rfree = 0.000) for 7472 atoms. Found 12 (45 requested) and removed 28 (28 requested) atoms. Cycle 25: After refmac, R = 0.1890 (Rfree = 0.000) for 7453 atoms. Found 13 (45 requested) and removed 28 (28 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.36 3.27 Search for helices and strands: 0 residues in 0 chains, 7716 seeds are put forward NCS extension: 31 residues added (10 deleted due to clashes), 7747 seeds are put forward Round 1: 541 peptides, 87 chains. Longest chain 19 peptides. Score 0.454 Round 2: 593 peptides, 82 chains. Longest chain 18 peptides. Score 0.543 Round 3: 619 peptides, 76 chains. Longest chain 28 peptides. Score 0.600 Round 4: 591 peptides, 72 chains. Longest chain 27 peptides. Score 0.590 Round 5: 612 peptides, 70 chains. Longest chain 27 peptides. Score 0.620 Taking the results from Round 5 Chains 72, Residues 542, Estimated correctness of the model 35.1 % 4 chains (38 residues) have been docked in sequence ------------------------------------------------------ 16710 reflections ( 99.63 % complete ) and 16451 restraints for refining 7529 atoms. 14227 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2124 (Rfree = 0.000) for 7529 atoms. Found 23 (45 requested) and removed 28 (28 requested) atoms. Cycle 27: After refmac, R = 0.2026 (Rfree = 0.000) for 7495 atoms. Found 21 (45 requested) and removed 34 (28 requested) atoms. Failed to save intermediate PDB Cycle 28: After refmac, R = 0.1970 (Rfree = 0.000) for 7465 atoms. Found 16 (45 requested) and removed 29 (28 requested) atoms. Failed to save intermediate PDB Cycle 29: After refmac, R = 0.1837 (Rfree = 0.000) for 7446 atoms. Found 10 (45 requested) and removed 29 (28 requested) atoms. Cycle 30: After refmac, R = 0.1933 (Rfree = 0.000) for 7414 atoms. Found 23 (45 requested) and removed 31 (28 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.39 3.30 Search for helices and strands: 0 residues in 0 chains, 7673 seeds are put forward NCS extension: 16 residues added (15 deleted due to clashes), 7689 seeds are put forward Round 1: 539 peptides, 79 chains. Longest chain 22 peptides. Score 0.495 Round 2: 581 peptides, 74 chains. Longest chain 29 peptides. Score 0.569 Round 3: 602 peptides, 82 chains. Longest chain 29 peptides. Score 0.553 Round 4: 600 peptides, 79 chains. Longest chain 27 peptides. Score 0.566 Round 5: 582 peptides, 76 chains. Longest chain 29 peptides. Score 0.561 Taking the results from Round 2 Chains 79, Residues 507, Estimated correctness of the model 18.2 % 7 chains (54 residues) have been docked in sequence ------------------------------------------------------ 16710 reflections ( 99.63 % complete ) and 16484 restraints for refining 7529 atoms. 14365 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1965 (Rfree = 0.000) for 7529 atoms. Found 23 (45 requested) and removed 32 (28 requested) atoms. Cycle 32: After refmac, R = 0.1864 (Rfree = 0.000) for 7507 atoms. Found 15 (45 requested) and removed 29 (28 requested) atoms. Failed to save intermediate PDB Cycle 33: After refmac, R = 0.2131 (Rfree = 0.000) for 7487 atoms. Found 45 (45 requested) and removed 30 (28 requested) atoms. Cycle 34: After refmac, R = 0.1769 (Rfree = 0.000) for 7496 atoms. Found 12 (45 requested) and removed 28 (28 requested) atoms. Cycle 35: After refmac, R = 0.1761 (Rfree = 0.000) for 7476 atoms. Found 5 (45 requested) and removed 28 (28 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.35 3.26 Search for helices and strands: 0 residues in 0 chains, 7695 seeds are put forward NCS extension: 34 residues added (12 deleted due to clashes), 7729 seeds are put forward Round 1: 506 peptides, 77 chains. Longest chain 19 peptides. Score 0.465 Round 2: 564 peptides, 71 chains. Longest chain 30 peptides. Score 0.566 Round 3: 585 peptides, 75 chains. Longest chain 20 peptides. Score 0.569 Round 4: 603 peptides, 73 chains. Longest chain 29 peptides. Score 0.598 Round 5: 582 peptides, 70 chains. Longest chain 30 peptides. Score 0.590 Taking the results from Round 4 Chains 74, Residues 530, Estimated correctness of the model 28.0 % 5 chains (59 residues) have been docked in sequence ------------------------------------------------------ 16710 reflections ( 99.63 % complete ) and 16152 restraints for refining 7529 atoms. 13902 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1983 (Rfree = 0.000) for 7529 atoms. Found 36 (45 requested) and removed 35 (28 requested) atoms. Cycle 37: After refmac, R = 0.1879 (Rfree = 0.000) for 7514 atoms. Found 16 (45 requested) and removed 28 (28 requested) atoms. Cycle 38: After refmac, R = 0.1814 (Rfree = 0.000) for 7490 atoms. Found 17 (45 requested) and removed 28 (28 requested) atoms. Cycle 39: After refmac, R = 0.1747 (Rfree = 0.000) for 7472 atoms. Found 13 (45 requested) and removed 28 (28 requested) atoms. Failed to save intermediate PDB Cycle 40: After refmac, R = 0.1703 (Rfree = 0.000) for 7454 atoms. Found 12 (45 requested) and removed 28 (28 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.35 3.26 Search for helices and strands: 0 residues in 0 chains, 7689 seeds are put forward NCS extension: 42 residues added (0 deleted due to clashes), 7731 seeds are put forward Round 1: 504 peptides, 86 chains. Longest chain 13 peptides. Score 0.411 Round 2: 551 peptides, 71 chains. Longest chain 19 peptides. Score 0.551 Round 3: 579 peptides, 76 chains. Longest chain 31 peptides. Score 0.557 Round 4: 562 peptides, 74 chains. Longest chain 21 peptides. Score 0.548 Round 5: 575 peptides, 82 chains. Longest chain 26 peptides. Score 0.522 Taking the results from Round 3 Chains 76, Residues 503, Estimated correctness of the model 14.0 % 4 chains (25 residues) have been docked in sequence ------------------------------------------------------ 16710 reflections ( 99.63 % complete ) and 16654 restraints for refining 7529 atoms. 14645 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1908 (Rfree = 0.000) for 7529 atoms. Found 37 (45 requested) and removed 28 (28 requested) atoms. Failed to save intermediate PDB Cycle 42: After refmac, R = 0.1778 (Rfree = 0.000) for 7525 atoms. Found 19 (45 requested) and removed 28 (28 requested) atoms. Failed to save intermediate PDB Cycle 43: After refmac, R = 0.1758 (Rfree = 0.000) for 7515 atoms. Found 10 (45 requested) and removed 28 (28 requested) atoms. Cycle 44: After refmac, R = 0.1714 (Rfree = 0.000) for 7496 atoms. Found 12 (45 requested) and removed 28 (28 requested) atoms. Cycle 45: After refmac, R = 0.1675 (Rfree = 0.000) for 7476 atoms. Found 15 (45 requested) and removed 28 (28 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.36 3.27 Search for helices and strands: 0 residues in 0 chains, 7702 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 7716 seeds are put forward Round 1: 499 peptides, 78 chains. Longest chain 17 peptides. Score 0.450 Round 2: 546 peptides, 73 chains. Longest chain 24 peptides. Score 0.535 Round 3: 550 peptides, 75 chains. Longest chain 24 peptides. Score 0.529 Round 4: 537 peptides, 72 chains. Longest chain 19 peptides. Score 0.530 Round 5: 554 peptides, 71 chains. Longest chain 20 peptides. Score 0.554 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 72, Residues 483, Estimated correctness of the model 13.0 % 5 chains (39 residues) have been docked in sequence Sequence coverage is 8 % Consider running further cycles of model building using 2pgc-3_warpNtrace.pdb as input Building loops using Loopy2018 72 chains (483 residues) following loop building 5 chains (39 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 16710 reflections ( 99.63 % complete ) and 16961 restraints for refining 7528 atoms. 14973 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1982 (Rfree = 0.000) for 7528 atoms. Found 0 (45 requested) and removed 26 (28 requested) atoms. Cycle 47: After refmac, R = 0.1842 (Rfree = 0.000) for 7497 atoms. Found 0 (45 requested) and removed 7 (28 requested) atoms. Cycle 48: After refmac, R = 0.1789 (Rfree = 0.000) for 7482 atoms. Found 0 (45 requested) and removed 7 (28 requested) atoms. Cycle 49: After refmac, R = 0.1774 (Rfree = 0.000) for 7471 atoms. TimeTaking 98.47