Sun 23 Dec 22:22:46 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2pgc-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2pgc-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2pgc-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pgc-3.4-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/2pgc-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pgc-3.4-parrot-hancs ############### 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 22:22:56 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/hancs/ArpWArp/wArpResults/WorkingDir/2pgc-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pgc-3.4-parrot-hancs/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-hancs.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-hancs.fasta_lf Building free atoms model in initial map for 8280 target number of atoms Had to go as low as 0.80 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 9242 atoms. Observations/parameters ratio is 0.45 ------------------------------------------------------ Starting model: R = 0.3264 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3031 (Rfree = 0.000) for 9242 atoms. Found 69 (69 requested) and removed 48 (34 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.40 3.31 Search for helices and strands: 0 residues in 0 chains, 9465 seeds are put forward NCS extension: 0 residues added, 9465 seeds are put forward Round 1: 483 peptides, 76 chains. Longest chain 31 peptides. Score 0.441 Round 2: 615 peptides, 81 chains. Longest chain 36 peptides. Score 0.572 Round 3: 663 peptides, 79 chains. Longest chain 24 peptides. Score 0.630 Round 4: 687 peptides, 69 chains. Longest chain 25 peptides. Score 0.693 Round 5: 679 peptides, 70 chains. Longest chain 26 peptides. Score 0.682 Taking the results from Round 4 Chains 75, Residues 618, Estimated correctness of the model 56.1 % 7 chains (73 residues) have been docked in sequence ------------------------------------------------------ 16710 reflections ( 99.63 % complete ) and 15664 restraints for refining 7524 atoms. 12996 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2563 (Rfree = 0.000) for 7524 atoms. Found 54 (56 requested) and removed 41 (28 requested) atoms. Cycle 2: After refmac, R = 0.2440 (Rfree = 0.000) for 7436 atoms. Found 31 (56 requested) and removed 39 (28 requested) atoms. Cycle 3: After refmac, R = 0.2304 (Rfree = 0.000) for 7387 atoms. Found 20 (56 requested) and removed 39 (28 requested) atoms. Cycle 4: After refmac, R = 0.2286 (Rfree = 0.000) for 7343 atoms. Found 18 (55 requested) and removed 34 (27 requested) atoms. Cycle 5: After refmac, R = 0.2295 (Rfree = 0.000) for 7312 atoms. Found 21 (55 requested) and removed 31 (27 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.36 3.27 Search for helices and strands: 0 residues in 0 chains, 7602 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 7617 seeds are put forward Round 1: 610 peptides, 77 chains. Longest chain 31 peptides. Score 0.586 Round 2: 661 peptides, 71 chains. Longest chain 36 peptides. Score 0.662 Round 3: 671 peptides, 70 chains. Longest chain 34 peptides. Score 0.675 Round 4: 681 peptides, 66 chains. Longest chain 44 peptides. Score 0.699 Round 5: 670 peptides, 70 chains. Longest chain 36 peptides. Score 0.674 Taking the results from Round 4 Chains 69, Residues 615, Estimated correctness of the model 57.6 % 6 chains (97 residues) have been docked in sequence ------------------------------------------------------ 16710 reflections ( 99.63 % complete ) and 15542 restraints for refining 7529 atoms. 12827 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2457 (Rfree = 0.000) for 7529 atoms. Found 40 (56 requested) and removed 43 (28 requested) atoms. Cycle 7: After refmac, R = 0.2280 (Rfree = 0.000) for 7474 atoms. Found 18 (56 requested) and removed 37 (28 requested) atoms. Cycle 8: After refmac, R = 0.2233 (Rfree = 0.000) for 7431 atoms. Found 18 (56 requested) and removed 36 (28 requested) atoms. Failed to save intermediate PDB Cycle 9: After refmac, R = 0.2198 (Rfree = 0.000) for 7395 atoms. Found 16 (55 requested) and removed 33 (27 requested) atoms. Cycle 10: After refmac, R = 0.2252 (Rfree = 0.000) for 7373 atoms. Found 17 (55 requested) and removed 35 (27 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.35 3.26 Search for helices and strands: 0 residues in 0 chains, 7604 seeds are put forward NCS extension: 25 residues added (7 deleted due to clashes), 7629 seeds are put forward Round 1: 599 peptides, 74 chains. Longest chain 24 peptides. Score 0.589 Round 2: 669 peptides, 71 chains. Longest chain 32 peptides. Score 0.669 Round 3: 642 peptides, 74 chains. Longest chain 33 peptides. Score 0.632 Round 4: 642 peptides, 70 chains. Longest chain 26 peptides. Score 0.649 Round 5: 657 peptides, 70 chains. Longest chain 39 peptides. Score 0.663 Taking the results from Round 2 Chains 72, Residues 598, Estimated correctness of the model 49.6 % 5 chains (85 residues) have been docked in sequence ------------------------------------------------------ 16710 reflections ( 99.63 % complete ) and 15654 restraints for refining 7527 atoms. 13034 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2303 (Rfree = 0.000) for 7527 atoms. Found 36 (56 requested) and removed 33 (28 requested) atoms. Cycle 12: After refmac, R = 0.2232 (Rfree = 0.000) for 7516 atoms. Found 19 (56 requested) and removed 32 (28 requested) atoms. Cycle 13: After refmac, R = 0.2198 (Rfree = 0.000) for 7492 atoms. Found 21 (56 requested) and removed 30 (28 requested) atoms. Cycle 14: After refmac, R = 0.2100 (Rfree = 0.000) for 7475 atoms. Found 13 (56 requested) and removed 29 (28 requested) atoms. Cycle 15: After refmac, R = 0.1994 (Rfree = 0.000) for 7453 atoms. Found 12 (56 requested) and removed 29 (28 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.38 3.29 Search for helices and strands: 0 residues in 0 chains, 7701 seeds are put forward NCS extension: 29 residues added (13 deleted due to clashes), 7730 seeds are put forward Round 1: 614 peptides, 79 chains. Longest chain 27 peptides. Score 0.581 Round 2: 640 peptides, 66 chains. Longest chain 33 peptides. Score 0.664 Round 3: 650 peptides, 67 chains. Longest chain 33 peptides. Score 0.669 Round 4: 645 peptides, 68 chains. Longest chain 38 peptides. Score 0.660 Round 5: 654 peptides, 69 chains. Longest chain 33 peptides. Score 0.664 Taking the results from Round 3 Chains 70, Residues 583, Estimated correctness of the model 49.6 % 5 chains (86 residues) have been docked in sequence ------------------------------------------------------ 16710 reflections ( 99.63 % complete ) and 15699 restraints for refining 7528 atoms. 13136 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2261 (Rfree = 0.000) for 7528 atoms. Found 28 (56 requested) and removed 35 (28 requested) atoms. Cycle 17: After refmac, R = 0.2175 (Rfree = 0.000) for 7491 atoms. Found 21 (56 requested) and removed 34 (28 requested) atoms. Cycle 18: After refmac, R = 0.2157 (Rfree = 0.000) for 7461 atoms. Found 19 (56 requested) and removed 34 (28 requested) atoms. Cycle 19: After refmac, R = 0.2095 (Rfree = 0.000) for 7437 atoms. Found 12 (56 requested) and removed 29 (28 requested) atoms. Cycle 20: After refmac, R = 0.2081 (Rfree = 0.000) for 7416 atoms. Found 14 (56 requested) and removed 28 (28 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.38 3.29 Search for helices and strands: 0 residues in 0 chains, 7656 seeds are put forward NCS extension: 21 residues added (5 deleted due to clashes), 7677 seeds are put forward Round 1: 561 peptides, 78 chains. Longest chain 17 peptides. Score 0.527 Round 2: 631 peptides, 69 chains. Longest chain 31 peptides. Score 0.643 Round 3: 636 peptides, 66 chains. Longest chain 35 peptides. Score 0.661 Round 4: 626 peptides, 67 chains. Longest chain 28 peptides. Score 0.647 Round 5: 630 peptides, 69 chains. Longest chain 26 peptides. Score 0.642 Taking the results from Round 3 Chains 70, Residues 570, Estimated correctness of the model 47.3 % 6 chains (87 residues) have been docked in sequence ------------------------------------------------------ 16710 reflections ( 99.63 % complete ) and 15975 restraints for refining 7528 atoms. 13480 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2229 (Rfree = 0.000) for 7528 atoms. Found 47 (56 requested) and removed 36 (28 requested) atoms. Cycle 22: After refmac, R = 0.2101 (Rfree = 0.000) for 7512 atoms. Found 12 (56 requested) and removed 34 (28 requested) atoms. Cycle 23: After refmac, R = 0.2049 (Rfree = 0.000) for 7475 atoms. Found 15 (56 requested) and removed 30 (28 requested) atoms. Cycle 24: After refmac, R = 0.2044 (Rfree = 0.000) for 7451 atoms. Found 11 (56 requested) and removed 28 (28 requested) atoms. Cycle 25: After refmac, R = 0.2458 (Rfree = 0.000) for 7427 atoms. Found 56 (56 requested) and removed 36 (28 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.35 3.26 Search for helices and strands: 0 residues in 0 chains, 7696 seeds are put forward NCS extension: 19 residues added (8 deleted due to clashes), 7715 seeds are put forward Round 1: 540 peptides, 79 chains. Longest chain 31 peptides. Score 0.496 Round 2: 601 peptides, 72 chains. Longest chain 31 peptides. Score 0.600 Round 3: 615 peptides, 71 chains. Longest chain 28 peptides. Score 0.619 Round 4: 613 peptides, 69 chains. Longest chain 25 peptides. Score 0.626 Round 5: 605 peptides, 69 chains. Longest chain 20 peptides. Score 0.618 Taking the results from Round 4 Chains 71, Residues 544, Estimated correctness of the model 36.9 % 4 chains (59 residues) have been docked in sequence ------------------------------------------------------ 16710 reflections ( 99.63 % complete ) and 16287 restraints for refining 7526 atoms. 13985 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2208 (Rfree = 0.000) for 7526 atoms. Found 30 (56 requested) and removed 30 (28 requested) atoms. Cycle 27: After refmac, R = 0.2105 (Rfree = 0.000) for 7508 atoms. Found 10 (56 requested) and removed 33 (28 requested) atoms. Cycle 28: After refmac, R = 0.2058 (Rfree = 0.000) for 7468 atoms. Found 18 (56 requested) and removed 31 (28 requested) atoms. Cycle 29: After refmac, R = 0.2488 (Rfree = 0.000) for 7449 atoms. Found 56 (56 requested) and removed 38 (28 requested) atoms. Cycle 30: After refmac, R = 0.2053 (Rfree = 0.000) for 7448 atoms. Found 35 (56 requested) and removed 30 (28 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.38 3.29 Search for helices and strands: 0 residues in 0 chains, 7707 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 7720 seeds are put forward Round 1: 552 peptides, 82 chains. Longest chain 25 peptides. Score 0.495 Round 2: 598 peptides, 71 chains. Longest chain 25 peptides. Score 0.602 Round 3: 589 peptides, 74 chains. Longest chain 26 peptides. Score 0.578 Round 4: 590 peptides, 71 chains. Longest chain 29 peptides. Score 0.594 Round 5: 585 peptides, 69 chains. Longest chain 26 peptides. Score 0.598 Taking the results from Round 2 Chains 72, Residues 527, Estimated correctness of the model 29.3 % 1 chains (18 residues) have been docked in sequence ------------------------------------------------------ 16710 reflections ( 99.63 % complete ) and 16739 restraints for refining 7529 atoms. 14639 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2126 (Rfree = 0.000) for 7529 atoms. Found 43 (56 requested) and removed 33 (28 requested) atoms. Cycle 32: After refmac, R = 0.2049 (Rfree = 0.000) for 7523 atoms. Found 23 (56 requested) and removed 30 (28 requested) atoms. Cycle 33: After refmac, R = 0.1987 (Rfree = 0.000) for 7509 atoms. Found 18 (56 requested) and removed 32 (28 requested) atoms. Cycle 34: After refmac, R = 0.1970 (Rfree = 0.000) for 7490 atoms. Found 23 (56 requested) and removed 28 (28 requested) atoms. Cycle 35: After refmac, R = 0.1955 (Rfree = 0.000) for 7483 atoms. Found 25 (56 requested) and removed 28 (28 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.39 3.30 Search for helices and strands: 0 residues in 0 chains, 7712 seeds are put forward NCS extension: 38 residues added (4 deleted due to clashes), 7750 seeds are put forward Round 1: 521 peptides, 86 chains. Longest chain 13 peptides. Score 0.433 Round 2: 560 peptides, 77 chains. Longest chain 21 peptides. Score 0.531 Round 3: 569 peptides, 71 chains. Longest chain 22 peptides. Score 0.571 Round 4: 553 peptides, 73 chains. Longest chain 24 peptides. Score 0.543 Round 5: 543 peptides, 70 chains. Longest chain 23 peptides. Score 0.547 Taking the results from Round 3 Chains 72, Residues 498, Estimated correctness of the model 18.9 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 16710 reflections ( 99.63 % complete ) and 17003 restraints for refining 7529 atoms. 15053 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2115 (Rfree = 0.000) for 7529 atoms. Found 35 (56 requested) and removed 30 (28 requested) atoms. Cycle 37: After refmac, R = 0.2065 (Rfree = 0.000) for 7505 atoms. Found 29 (56 requested) and removed 31 (28 requested) atoms. Cycle 38: After refmac, R = 0.1971 (Rfree = 0.000) for 7491 atoms. Found 24 (56 requested) and removed 31 (28 requested) atoms. Cycle 39: After refmac, R = 0.1942 (Rfree = 0.000) for 7481 atoms. Found 16 (56 requested) and removed 28 (28 requested) atoms. Cycle 40: After refmac, R = 0.1946 (Rfree = 0.000) for 7468 atoms. Found 16 (56 requested) and removed 29 (28 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.39 3.30 Search for helices and strands: 0 residues in 0 chains, 7675 seeds are put forward NCS extension: 16 residues added (4 deleted due to clashes), 7691 seeds are put forward Round 1: 463 peptides, 75 chains. Longest chain 15 peptides. Score 0.420 Round 2: 507 peptides, 71 chains. Longest chain 21 peptides. Score 0.499 Round 3: 529 peptides, 71 chains. Longest chain 22 peptides. Score 0.526 Round 4: 519 peptides, 71 chains. Longest chain 23 peptides. Score 0.514 Round 5: 526 peptides, 71 chains. Longest chain 18 peptides. Score 0.522 Taking the results from Round 3 Chains 71, Residues 458, Estimated correctness of the model 2.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 16710 reflections ( 99.63 % complete ) and 17566 restraints for refining 7529 atoms. 15805 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2157 (Rfree = 0.000) for 7529 atoms. Found 31 (56 requested) and removed 30 (28 requested) atoms. Cycle 42: After refmac, R = 0.2085 (Rfree = 0.000) for 7516 atoms. Found 23 (56 requested) and removed 30 (28 requested) atoms. Cycle 43: After refmac, R = 0.2011 (Rfree = 0.000) for 7500 atoms. Found 10 (56 requested) and removed 30 (28 requested) atoms. Cycle 44: After refmac, R = 0.1980 (Rfree = 0.000) for 7474 atoms. Found 19 (56 requested) and removed 30 (28 requested) atoms. Cycle 45: After refmac, R = 0.1936 (Rfree = 0.000) for 7453 atoms. Found 19 (56 requested) and removed 28 (28 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.39 3.30 Search for helices and strands: 0 residues in 0 chains, 7690 seeds are put forward NCS extension: 13 residues added (6 deleted due to clashes), 7703 seeds are put forward Round 1: 451 peptides, 80 chains. Longest chain 20 peptides. Score 0.373 Round 2: 514 peptides, 77 chains. Longest chain 23 peptides. Score 0.475 Round 3: 507 peptides, 71 chains. Longest chain 22 peptides. Score 0.499 Round 4: 520 peptides, 69 chains. Longest chain 23 peptides. Score 0.526 Round 5: 514 peptides, 71 chains. Longest chain 20 peptides. Score 0.508 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 70, Residues 451, Estimated correctness of the model 2.7 % 2 chains (21 residues) have been docked in sequence Sequence coverage is 4 % Consider running further cycles of model building using 2pgc-3_warpNtrace.pdb as input Building loops using Loopy2018 70 chains (451 residues) following loop building 2 chains (21 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 16710 reflections ( 99.63 % complete ) and 17357 restraints for refining 7529 atoms. 15553 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2178 (Rfree = 0.000) for 7529 atoms. Found 0 (56 requested) and removed 28 (28 requested) atoms. Cycle 47: After refmac, R = 0.2146 (Rfree = 0.000) for 7490 atoms. Found 0 (56 requested) and removed 28 (28 requested) atoms. Cycle 48: After refmac, R = 0.2119 (Rfree = 0.000) for 7453 atoms. Found 0 (56 requested) and removed 28 (28 requested) atoms. Cycle 49: After refmac, R = 0.2020 (Rfree = 0.000) for 7415 atoms. TimeTaking 98.48