Mon 24 Dec 07:37:55 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2pgc-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2pgc-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2pgc-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2pgc-3.4-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2pgc-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2pgc-3.4-parrot-noncs ############### 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 07:37:59 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/noncs/ArpWArp/wArpResults/WorkingDir/2pgc-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2pgc-3.4-parrot-noncs/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-noncs.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-noncs.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 9181 atoms. Observations/parameters ratio is 0.46 ------------------------------------------------------ Starting model: R = 0.3381 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3109 (Rfree = 0.000) for 9181 atoms. Found 69 (69 requested) and removed 46 (34 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.40 3.31 Search for helices and strands: 0 residues in 0 chains, 9407 seeds are put forward NCS extension: 0 residues added, 9407 seeds are put forward Round 1: 427 peptides, 74 chains. Longest chain 14 peptides. Score 0.376 Round 2: 572 peptides, 87 chains. Longest chain 16 peptides. Score 0.492 Round 3: 581 peptides, 78 chains. Longest chain 19 peptides. Score 0.549 Round 4: 619 peptides, 73 chains. Longest chain 27 peptides. Score 0.614 Round 5: 621 peptides, 75 chains. Longest chain 27 peptides. Score 0.607 Taking the results from Round 4 Chains 76, Residues 546, Estimated correctness of the model 33.2 % 5 chains (77 residues) have been docked in sequence ------------------------------------------------------ 16710 reflections ( 99.63 % complete ) and 16051 restraints for refining 7528 atoms. 13623 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2592 (Rfree = 0.000) for 7528 atoms. Found 40 (56 requested) and removed 40 (28 requested) atoms. Cycle 2: After refmac, R = 0.2500 (Rfree = 0.000) for 7414 atoms. Found 27 (56 requested) and removed 37 (28 requested) atoms. Cycle 3: After refmac, R = 0.2412 (Rfree = 0.000) for 7363 atoms. Found 28 (55 requested) and removed 38 (27 requested) atoms. Cycle 4: After refmac, R = 0.2314 (Rfree = 0.000) for 7333 atoms. Found 13 (55 requested) and removed 38 (27 requested) atoms. Cycle 5: After refmac, R = 0.2287 (Rfree = 0.000) for 7300 atoms. Found 16 (55 requested) and removed 33 (27 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.43 3.34 Search for helices and strands: 0 residues in 0 chains, 7563 seeds are put forward NCS extension: 22 residues added (6 deleted due to clashes), 7585 seeds are put forward Round 1: 581 peptides, 83 chains. Longest chain 16 peptides. Score 0.524 Round 2: 605 peptides, 70 chains. Longest chain 40 peptides. Score 0.614 Round 3: 619 peptides, 76 chains. Longest chain 25 peptides. Score 0.600 Round 4: 644 peptides, 72 chains. Longest chain 30 peptides. Score 0.642 Round 5: 650 peptides, 72 chains. Longest chain 27 peptides. Score 0.648 Taking the results from Round 5 Chains 74, Residues 578, Estimated correctness of the model 43.6 % 3 chains (39 residues) have been docked in sequence ------------------------------------------------------ 16710 reflections ( 99.63 % complete ) and 16494 restraints for refining 7527 atoms. 14107 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2535 (Rfree = 0.000) for 7527 atoms. Found 45 (56 requested) and removed 36 (28 requested) atoms. Cycle 7: After refmac, R = 0.2341 (Rfree = 0.000) for 7493 atoms. Found 21 (56 requested) and removed 43 (28 requested) atoms. Cycle 8: After refmac, R = 0.2202 (Rfree = 0.000) for 7450 atoms. Found 13 (56 requested) and removed 31 (28 requested) atoms. Cycle 9: After refmac, R = 0.2180 (Rfree = 0.000) for 7418 atoms. Found 18 (56 requested) and removed 33 (28 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.2119 (Rfree = 0.000) for 7388 atoms. Found 11 (55 requested) and removed 28 (27 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.39 3.30 Search for helices and strands: 0 residues in 0 chains, 7625 seeds are put forward NCS extension: 9 residues added (4 deleted due to clashes), 7634 seeds are put forward Round 1: 565 peptides, 87 chains. Longest chain 18 peptides. Score 0.484 Round 2: 608 peptides, 76 chains. Longest chain 25 peptides. Score 0.589 Round 3: 614 peptides, 76 chains. Longest chain 22 peptides. Score 0.595 Round 4: 628 peptides, 74 chains. Longest chain 30 peptides. Score 0.618 Round 5: 633 peptides, 72 chains. Longest chain 30 peptides. Score 0.632 Taking the results from Round 5 Chains 74, Residues 561, Estimated correctness of the model 38.8 % 4 chains (38 residues) have been docked in sequence ------------------------------------------------------ 16710 reflections ( 99.63 % complete ) and 16448 restraints for refining 7526 atoms. 14159 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2400 (Rfree = 0.000) for 7526 atoms. Found 51 (56 requested) and removed 33 (28 requested) atoms. Cycle 12: After refmac, R = 0.2346 (Rfree = 0.000) for 7490 atoms. Found 25 (56 requested) and removed 32 (28 requested) atoms. Cycle 13: After refmac, R = 0.2239 (Rfree = 0.000) for 7457 atoms. Found 17 (56 requested) and removed 35 (28 requested) atoms. Cycle 14: After refmac, R = 0.2194 (Rfree = 0.000) for 7421 atoms. Found 16 (56 requested) and removed 31 (28 requested) atoms. Cycle 15: After refmac, R = 0.2128 (Rfree = 0.000) for 7394 atoms. Found 13 (55 requested) and removed 30 (27 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.34 3.25 Search for helices and strands: 0 residues in 0 chains, 7627 seeds are put forward NCS extension: 17 residues added (4 deleted due to clashes), 7644 seeds are put forward Round 1: 553 peptides, 83 chains. Longest chain 16 peptides. Score 0.491 Round 2: 599 peptides, 69 chains. Longest chain 46 peptides. Score 0.612 Round 3: 586 peptides, 73 chains. Longest chain 19 peptides. Score 0.580 Round 4: 599 peptides, 68 chains. Longest chain 46 peptides. Score 0.617 Round 5: 605 peptides, 77 chains. Longest chain 25 peptides. Score 0.581 Taking the results from Round 4 Chains 71, Residues 531, Estimated correctness of the model 34.1 % 5 chains (34 residues) have been docked in sequence ------------------------------------------------------ 16710 reflections ( 99.63 % complete ) and 16576 restraints for refining 7529 atoms. 14423 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2258 (Rfree = 0.000) for 7529 atoms. Found 40 (56 requested) and removed 39 (28 requested) atoms. Cycle 17: After refmac, R = 0.2161 (Rfree = 0.000) for 7510 atoms. Found 16 (56 requested) and removed 32 (28 requested) atoms. Cycle 18: After refmac, R = 0.2511 (Rfree = 0.000) for 7487 atoms. Found 56 (56 requested) and removed 43 (28 requested) atoms. Cycle 19: After refmac, R = 0.2050 (Rfree = 0.000) for 7482 atoms. Found 31 (56 requested) and removed 34 (28 requested) atoms. Cycle 20: After refmac, R = 0.1914 (Rfree = 0.000) for 7464 atoms. Found 19 (56 requested) and removed 32 (28 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.33 3.24 Search for helices and strands: 0 residues in 0 chains, 7710 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 7732 seeds are put forward Round 1: 514 peptides, 84 chains. Longest chain 16 peptides. Score 0.435 Round 2: 579 peptides, 81 chains. Longest chain 21 peptides. Score 0.532 Round 3: 614 peptides, 85 chains. Longest chain 20 peptides. Score 0.551 Round 4: 597 peptides, 76 chains. Longest chain 23 peptides. Score 0.577 Round 5: 587 peptides, 77 chains. Longest chain 23 peptides. Score 0.561 Taking the results from Round 4 Chains 78, Residues 521, Estimated correctness of the model 21.0 % 3 chains (27 residues) have been docked in sequence ------------------------------------------------------ 16710 reflections ( 99.63 % complete ) and 16493 restraints for refining 7529 atoms. 14409 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2148 (Rfree = 0.000) for 7529 atoms. Found 32 (56 requested) and removed 33 (28 requested) atoms. Cycle 22: After refmac, R = 0.2003 (Rfree = 0.000) for 7492 atoms. Found 24 (56 requested) and removed 33 (28 requested) atoms. Cycle 23: After refmac, R = 0.1918 (Rfree = 0.000) for 7467 atoms. Found 12 (56 requested) and removed 34 (28 requested) atoms. Failed to save intermediate PDB Cycle 24: After refmac, R = 0.1884 (Rfree = 0.000) for 7441 atoms. Found 14 (56 requested) and removed 32 (28 requested) atoms. Cycle 25: After refmac, R = 0.1821 (Rfree = 0.000) for 7416 atoms. Found 6 (56 requested) and removed 29 (28 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.35 3.26 Search for helices and strands: 0 residues in 0 chains, 7662 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 7685 seeds are put forward Round 1: 526 peptides, 85 chains. Longest chain 23 peptides. Score 0.445 Round 2: 572 peptides, 81 chains. Longest chain 19 peptides. Score 0.524 Round 3: 588 peptides, 76 chains. Longest chain 23 peptides. Score 0.567 Round 4: 564 peptides, 75 chains. Longest chain 20 peptides. Score 0.545 Round 5: 560 peptides, 69 chains. Longest chain 25 peptides. Score 0.571 Taking the results from Round 5 Chains 70, Residues 491, Estimated correctness of the model 18.9 % 3 chains (26 residues) have been docked in sequence ------------------------------------------------------ 16710 reflections ( 99.63 % complete ) and 16853 restraints for refining 7529 atoms. 14886 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2152 (Rfree = 0.000) for 7529 atoms. Found 40 (56 requested) and removed 34 (28 requested) atoms. Cycle 27: After refmac, R = 0.2035 (Rfree = 0.000) for 7513 atoms. Found 21 (56 requested) and removed 28 (28 requested) atoms. Cycle 28: After refmac, R = 0.1986 (Rfree = 0.000) for 7499 atoms. Found 11 (56 requested) and removed 28 (28 requested) atoms. Cycle 29: After refmac, R = 0.2315 (Rfree = 0.000) for 7471 atoms. Found 56 (56 requested) and removed 30 (28 requested) atoms. Cycle 30: After refmac, R = 0.1896 (Rfree = 0.000) for 7490 atoms. Found 20 (56 requested) and removed 30 (28 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.35 3.26 Search for helices and strands: 0 residues in 0 chains, 7701 seeds are put forward NCS extension: 35 residues added (1 deleted due to clashes), 7736 seeds are put forward Round 1: 504 peptides, 81 chains. Longest chain 22 peptides. Score 0.439 Round 2: 563 peptides, 78 chains. Longest chain 23 peptides. Score 0.529 Round 3: 565 peptides, 78 chains. Longest chain 24 peptides. Score 0.531 Round 4: 582 peptides, 83 chains. Longest chain 22 peptides. Score 0.525 Round 5: 563 peptides, 69 chains. Longest chain 28 peptides. Score 0.575 Taking the results from Round 5 Chains 72, Residues 494, Estimated correctness of the model 20.3 % 5 chains (40 residues) have been docked in sequence ------------------------------------------------------ 16710 reflections ( 99.63 % complete ) and 16364 restraints for refining 7529 atoms. 14328 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2088 (Rfree = 0.000) for 7529 atoms. Found 40 (56 requested) and removed 30 (28 requested) atoms. Cycle 32: After refmac, R = 0.1983 (Rfree = 0.000) for 7516 atoms. Found 17 (56 requested) and removed 29 (28 requested) atoms. Cycle 33: After refmac, R = 0.1898 (Rfree = 0.000) for 7494 atoms. Found 9 (56 requested) and removed 28 (28 requested) atoms. Cycle 34: After refmac, R = 0.1876 (Rfree = 0.000) for 7468 atoms. Found 11 (56 requested) and removed 28 (28 requested) atoms. Cycle 35: After refmac, R = 0.1830 (Rfree = 0.000) for 7446 atoms. Found 14 (56 requested) and removed 28 (28 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.36 3.27 Search for helices and strands: 0 residues in 0 chains, 7676 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 7693 seeds are put forward Round 1: 509 peptides, 86 chains. Longest chain 17 peptides. Score 0.417 Round 2: 526 peptides, 69 chains. Longest chain 25 peptides. Score 0.533 Round 3: 535 peptides, 74 chains. Longest chain 24 peptides. Score 0.517 Round 4: 520 peptides, 69 chains. Longest chain 23 peptides. Score 0.526 Round 5: 561 peptides, 76 chains. Longest chain 30 peptides. Score 0.537 Taking the results from Round 5 Chains 80, Residues 485, Estimated correctness of the model 6.8 % 3 chains (37 residues) have been docked in sequence ------------------------------------------------------ 16710 reflections ( 99.63 % complete ) and 16583 restraints for refining 7529 atoms. 14577 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2045 (Rfree = 0.000) for 7529 atoms. Found 48 (56 requested) and removed 30 (28 requested) atoms. Cycle 37: After refmac, R = 0.1937 (Rfree = 0.000) for 7517 atoms. Found 23 (56 requested) and removed 30 (28 requested) atoms. Cycle 38: After refmac, R = 0.1868 (Rfree = 0.000) for 7501 atoms. Found 10 (56 requested) and removed 29 (28 requested) atoms. Failed to save intermediate PDB Cycle 39: After refmac, R = 0.1832 (Rfree = 0.000) for 7469 atoms. Found 16 (56 requested) and removed 29 (28 requested) atoms. Cycle 40: After refmac, R = 0.1785 (Rfree = 0.000) for 7448 atoms. Found 12 (56 requested) and removed 28 (28 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.37 3.28 Search for helices and strands: 0 residues in 0 chains, 7639 seeds are put forward NCS extension: 20 residues added (3 deleted due to clashes), 7659 seeds are put forward Round 1: 447 peptides, 74 chains. Longest chain 13 peptides. Score 0.404 Round 2: 501 peptides, 72 chains. Longest chain 27 peptides. Score 0.486 Round 3: 502 peptides, 74 chains. Longest chain 29 peptides. Score 0.477 Round 4: 504 peptides, 70 chains. Longest chain 21 peptides. Score 0.501 Round 5: 518 peptides, 70 chains. Longest chain 21 peptides. Score 0.518 Taking the results from Round 5 Chains 70, Residues 448, Estimated correctness of the model 0.0 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 16710 reflections ( 99.63 % complete ) and 16976 restraints for refining 7528 atoms. 15205 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2011 (Rfree = 0.000) for 7528 atoms. Found 34 (56 requested) and removed 33 (28 requested) atoms. Cycle 42: After refmac, R = 0.1868 (Rfree = 0.000) for 7513 atoms. Found 14 (56 requested) and removed 29 (28 requested) atoms. Cycle 43: After refmac, R = 0.1831 (Rfree = 0.000) for 7491 atoms. Found 19 (56 requested) and removed 30 (28 requested) atoms. Cycle 44: After refmac, R = 0.1787 (Rfree = 0.000) for 7475 atoms. Found 18 (56 requested) and removed 30 (28 requested) atoms. Cycle 45: After refmac, R = 0.1765 (Rfree = 0.000) for 7458 atoms. Found 14 (56 requested) and removed 30 (28 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.38 3.29 Search for helices and strands: 0 residues in 0 chains, 7640 seeds are put forward NCS extension: 31 residues added (1 deleted due to clashes), 7671 seeds are put forward Round 1: 460 peptides, 83 chains. Longest chain 13 peptides. Score 0.367 Round 2: 493 peptides, 78 chains. Longest chain 15 peptides. Score 0.442 Round 3: 501 peptides, 79 chains. Longest chain 29 peptides. Score 0.447 Round 4: 514 peptides, 75 chains. Longest chain 29 peptides. Score 0.486 Round 5: 525 peptides, 75 chains. Longest chain 19 peptides. Score 0.500 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 77, Residues 450, Estimated correctness of the model 0.0 % 3 chains (20 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 77 chains (450 residues) following loop building 3 chains (20 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 16710 reflections ( 99.63 % complete ) and 17140 restraints for refining 7526 atoms. 15353 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2094 (Rfree = 0.000) for 7526 atoms. Found 0 (56 requested) and removed 28 (28 requested) atoms. Cycle 47: After refmac, R = 0.2021 (Rfree = 0.000) for 7472 atoms. Found 0 (56 requested) and removed 28 (28 requested) atoms. Cycle 48: After refmac, R = 0.2032 (Rfree = 0.000) for 7429 atoms. Found 0 (56 requested) and removed 28 (28 requested) atoms. Cycle 49: After refmac, R = 0.1981 (Rfree = 0.000) for 7393 atoms. TimeTaking 80.6