Sun 23 Dec 22:22:44 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 2ouw-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ouw-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ouw-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ouw-3.8-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/2ouw-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ouw-3.8-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 22:22:53 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/2ouw-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ouw-3.8-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 153 and 0 Target number of residues in the AU: 153 Target solvent content: 0.6631 Checking the provided sequence file Detected sequence length: 138 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 276 Adjusted target solvent content: 0.39 Input MTZ file: 2ouw-3.8-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: 182 Cell parameters: 62.683 62.683 216.710 90.000 90.000 120.000 Input sequence file: 2ouw-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 2208 target number of atoms Had to go as low as 0.70 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: 108.355 3.800 Wilson plot Bfac: 87.14 2882 reflections ( 99.76 % complete ) and 0 restraints for refining 2432 atoms. Observations/parameters ratio is 0.30 ------------------------------------------------------ Starting model: R = 0.3846 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3533 (Rfree = 0.000) for 2432 atoms. Found 13 (13 requested) and removed 16 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.71 4.31 Search for helices and strands: 0 residues in 0 chains, 2487 seeds are put forward NCS extension: 0 residues added, 2487 seeds are put forward Round 1: 72 peptides, 15 chains. Longest chain 8 peptides. Score 0.264 Round 2: 97 peptides, 18 chains. Longest chain 8 peptides. Score 0.353 Round 3: 105 peptides, 15 chains. Longest chain 23 peptides. Score 0.487 Round 4: 106 peptides, 15 chains. Longest chain 16 peptides. Score 0.493 Round 5: 118 peptides, 13 chains. Longest chain 26 peptides. Score 0.607 Taking the results from Round 5 Chains 15, Residues 105, Estimated correctness of the model 2.1 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 2882 reflections ( 99.76 % complete ) and 4566 restraints for refining 1996 atoms. 4130 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3159 (Rfree = 0.000) for 1996 atoms. Found 10 (10 requested) and removed 43 (5 requested) atoms. Cycle 2: After refmac, R = 0.3249 (Rfree = 0.000) for 1924 atoms. Found 7 (10 requested) and removed 39 (5 requested) atoms. Cycle 3: After refmac, R = 0.3202 (Rfree = 0.000) for 1868 atoms. Found 10 (10 requested) and removed 53 (5 requested) atoms. Cycle 4: After refmac, R = 0.3297 (Rfree = 0.000) for 1810 atoms. Found 10 (10 requested) and removed 43 (5 requested) atoms. Cycle 5: After refmac, R = 0.3252 (Rfree = 0.000) for 1766 atoms. Found 9 (9 requested) and removed 14 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.87 3.33 Search for helices and strands: 0 residues in 0 chains, 1835 seeds are put forward NCS extension: 53 residues added (1 deleted due to clashes), 1888 seeds are put forward Round 1: 75 peptides, 17 chains. Longest chain 6 peptides. Score 0.223 Round 2: 102 peptides, 20 chains. Longest chain 10 peptides. Score 0.329 Round 3: 105 peptides, 20 chains. Longest chain 10 peptides. Score 0.350 Round 4: 109 peptides, 19 chains. Longest chain 14 peptides. Score 0.404 Round 5: 95 peptides, 16 chains. Longest chain 14 peptides. Score 0.397 Taking the results from Round 4 Chains 19, Residues 90, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 2882 reflections ( 99.76 % complete ) and 4056 restraints for refining 1780 atoms. 3701 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3288 (Rfree = 0.000) for 1780 atoms. Found 9 (9 requested) and removed 39 (4 requested) atoms. Cycle 7: After refmac, R = 0.3084 (Rfree = 0.000) for 1732 atoms. Found 9 (9 requested) and removed 27 (4 requested) atoms. Cycle 8: After refmac, R = 0.3325 (Rfree = 0.000) for 1704 atoms. Found 9 (9 requested) and removed 23 (4 requested) atoms. Cycle 9: After refmac, R = 0.3114 (Rfree = 0.000) for 1681 atoms. Found 9 (9 requested) and removed 14 (4 requested) atoms. Cycle 10: After refmac, R = 0.3218 (Rfree = 0.000) for 1667 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.23 3.75 Search for helices and strands: 0 residues in 0 chains, 1757 seeds are put forward NCS extension: 0 residues added, 1757 seeds are put forward Round 1: 93 peptides, 21 chains. Longest chain 6 peptides. Score 0.235 Round 2: 101 peptides, 21 chains. Longest chain 7 peptides. Score 0.293 Round 3: 107 peptides, 21 chains. Longest chain 9 peptides. Score 0.335 Round 4: 113 peptides, 20 chains. Longest chain 12 peptides. Score 0.402 Round 5: 110 peptides, 19 chains. Longest chain 12 peptides. Score 0.411 Taking the results from Round 5 Chains 20, Residues 91, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 2882 reflections ( 99.76 % complete ) and 3861 restraints for refining 1742 atoms. 3490 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3541 (Rfree = 0.000) for 1742 atoms. Found 9 (9 requested) and removed 23 (4 requested) atoms. Cycle 12: After refmac, R = 0.3276 (Rfree = 0.000) for 1709 atoms. Found 9 (9 requested) and removed 23 (4 requested) atoms. Cycle 13: After refmac, R = 0.2698 (Rfree = 0.000) for 1686 atoms. Found 6 (9 requested) and removed 11 (4 requested) atoms. Cycle 14: After refmac, R = 0.3038 (Rfree = 0.000) for 1670 atoms. Found 9 (9 requested) and removed 14 (4 requested) atoms. Cycle 15: After refmac, R = 0.2652 (Rfree = 0.000) for 1655 atoms. Found 3 (9 requested) and removed 13 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.22 3.74 Search for helices and strands: 0 residues in 0 chains, 1721 seeds are put forward NCS extension: 0 residues added, 1721 seeds are put forward Round 1: 84 peptides, 20 chains. Longest chain 5 peptides. Score 0.198 Round 2: 100 peptides, 20 chains. Longest chain 7 peptides. Score 0.315 Round 3: 110 peptides, 22 chains. Longest chain 8 peptides. Score 0.327 Round 4: 109 peptides, 21 chains. Longest chain 9 peptides. Score 0.348 Round 5: 107 peptides, 20 chains. Longest chain 10 peptides. Score 0.363 Taking the results from Round 5 Chains 20, Residues 87, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2882 reflections ( 99.76 % complete ) and 3827 restraints for refining 1708 atoms. 3499 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3402 (Rfree = 0.000) for 1708 atoms. Found 9 (9 requested) and removed 30 (4 requested) atoms. Cycle 17: After refmac, R = 0.3286 (Rfree = 0.000) for 1677 atoms. Found 9 (9 requested) and removed 20 (4 requested) atoms. Cycle 18: After refmac, R = 0.3579 (Rfree = 0.000) for 1660 atoms. Found 9 (9 requested) and removed 14 (4 requested) atoms. Cycle 19: After refmac, R = 0.3311 (Rfree = 0.000) for 1648 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 20: After refmac, R = 0.3328 (Rfree = 0.000) for 1645 atoms. Found 9 (9 requested) and removed 16 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.08 3.57 Search for helices and strands: 0 residues in 0 chains, 1740 seeds are put forward NCS extension: 0 residues added, 1740 seeds are put forward Round 1: 81 peptides, 17 chains. Longest chain 7 peptides. Score 0.269 Round 2: 79 peptides, 17 chains. Longest chain 7 peptides. Score 0.254 Round 3: 76 peptides, 14 chains. Longest chain 10 peptides. Score 0.326 Round 4: 80 peptides, 15 chains. Longest chain 7 peptides. Score 0.324 Round 5: 84 peptides, 15 chains. Longest chain 8 peptides. Score 0.352 Taking the results from Round 5 Chains 15, Residues 69, Estimated correctness of the model 0.0 % 3 chains (15 residues) have been docked in sequence ------------------------------------------------------ 2882 reflections ( 99.76 % complete ) and 3755 restraints for refining 1722 atoms. 3455 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3389 (Rfree = 0.000) for 1722 atoms. Found 9 (9 requested) and removed 22 (4 requested) atoms. Cycle 22: After refmac, R = 0.3589 (Rfree = 0.000) for 1699 atoms. Found 9 (9 requested) and removed 27 (4 requested) atoms. Cycle 23: After refmac, R = 0.3523 (Rfree = 0.000) for 1676 atoms. Found 9 (9 requested) and removed 15 (4 requested) atoms. Cycle 24: After refmac, R = 0.3421 (Rfree = 0.000) for 1666 atoms. Found 9 (9 requested) and removed 14 (4 requested) atoms. Cycle 25: After refmac, R = 0.3615 (Rfree = 0.000) for 1658 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.04 3.53 Search for helices and strands: 0 residues in 0 chains, 1745 seeds are put forward NCS extension: 0 residues added, 1745 seeds are put forward Round 1: 68 peptides, 16 chains. Longest chain 5 peptides. Score 0.200 Round 2: 91 peptides, 16 chains. Longest chain 11 peptides. Score 0.370 Round 3: 92 peptides, 17 chains. Longest chain 8 peptides. Score 0.348 Round 4: 101 peptides, 17 chains. Longest chain 12 peptides. Score 0.408 Round 5: 89 peptides, 17 chains. Longest chain 9 peptides. Score 0.327 Taking the results from Round 4 Chains 17, Residues 84, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2882 reflections ( 99.76 % complete ) and 3707 restraints for refining 1695 atoms. 3388 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3666 (Rfree = 0.000) for 1695 atoms. Found 9 (9 requested) and removed 22 (4 requested) atoms. Cycle 27: After refmac, R = 0.3470 (Rfree = 0.000) for 1674 atoms. Found 9 (9 requested) and removed 18 (4 requested) atoms. Cycle 28: After refmac, R = 0.3481 (Rfree = 0.000) for 1661 atoms. Found 9 (9 requested) and removed 16 (4 requested) atoms. Cycle 29: After refmac, R = 0.3487 (Rfree = 0.000) for 1652 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. Cycle 30: After refmac, R = 0.3322 (Rfree = 0.000) for 1644 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.24 3.76 Search for helices and strands: 0 residues in 0 chains, 1716 seeds are put forward NCS extension: 0 residues added, 1716 seeds are put forward Round 1: 71 peptides, 15 chains. Longest chain 11 peptides. Score 0.256 Round 2: 82 peptides, 17 chains. Longest chain 8 peptides. Score 0.276 Round 3: 90 peptides, 15 chains. Longest chain 11 peptides. Score 0.393 Round 4: 85 peptides, 15 chains. Longest chain 12 peptides. Score 0.359 Round 5: 91 peptides, 16 chains. Longest chain 13 peptides. Score 0.370 Taking the results from Round 3 Chains 15, Residues 75, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 2882 reflections ( 99.76 % complete ) and 3408 restraints for refining 1651 atoms. 3108 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3632 (Rfree = 0.000) for 1651 atoms. Found 9 (9 requested) and removed 22 (4 requested) atoms. Cycle 32: After refmac, R = 0.3447 (Rfree = 0.000) for 1634 atoms. Found 9 (9 requested) and removed 14 (4 requested) atoms. Cycle 33: After refmac, R = 0.3486 (Rfree = 0.000) for 1625 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. Cycle 34: After refmac, R = 0.3433 (Rfree = 0.000) for 1619 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. Cycle 35: After refmac, R = 0.3658 (Rfree = 0.000) for 1612 atoms. Found 8 (8 requested) and removed 15 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.04 3.53 Search for helices and strands: 0 residues in 0 chains, 1670 seeds are put forward NCS extension: 0 residues added, 1670 seeds are put forward Round 1: 76 peptides, 18 chains. Longest chain 6 peptides. Score 0.199 Round 2: 82 peptides, 16 chains. Longest chain 8 peptides. Score 0.307 Round 3: 93 peptides, 17 chains. Longest chain 9 peptides. Score 0.355 Round 4: 91 peptides, 17 chains. Longest chain 8 peptides. Score 0.341 Round 5: 93 peptides, 16 chains. Longest chain 11 peptides. Score 0.384 Taking the results from Round 5 Chains 16, Residues 77, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 2882 reflections ( 99.76 % complete ) and 3526 restraints for refining 1647 atoms. 3221 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3678 (Rfree = 0.000) for 1647 atoms. Found 9 (9 requested) and removed 25 (4 requested) atoms. Cycle 37: After refmac, R = 0.3668 (Rfree = 0.000) for 1624 atoms. Found 8 (8 requested) and removed 15 (4 requested) atoms. Cycle 38: After refmac, R = 0.3488 (Rfree = 0.000) for 1615 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. Cycle 39: After refmac, R = 0.3625 (Rfree = 0.000) for 1607 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. Cycle 40: After refmac, R = 0.3744 (Rfree = 0.000) for 1607 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.05 3.54 Search for helices and strands: 0 residues in 0 chains, 1672 seeds are put forward NCS extension: 0 residues added, 1672 seeds are put forward Round 1: 61 peptides, 13 chains. Longest chain 7 peptides. Score 0.244 Round 2: 74 peptides, 13 chains. Longest chain 9 peptides. Score 0.343 Round 3: 73 peptides, 13 chains. Longest chain 13 peptides. Score 0.336 Round 4: 65 peptides, 9 chains. Longest chain 12 peptides. Score 0.406 Round 5: 69 peptides, 9 chains. Longest chain 14 peptides. Score 0.433 Taking the results from Round 5 Chains 9, Residues 60, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 2882 reflections ( 99.76 % complete ) and 3257 restraints for refining 1587 atoms. 3002 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3716 (Rfree = 0.000) for 1587 atoms. Found 8 (8 requested) and removed 17 (4 requested) atoms. Cycle 42: After refmac, R = 0.3561 (Rfree = 0.000) for 1569 atoms. Found 8 (8 requested) and removed 18 (4 requested) atoms. Cycle 43: After refmac, R = 0.3516 (Rfree = 0.000) for 1551 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 44: After refmac, R = 0.3601 (Rfree = 0.000) for 1545 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. Cycle 45: After refmac, R = 0.3702 (Rfree = 0.000) for 1537 atoms. Found 8 (8 requested) and removed 15 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.03 3.52 Search for helices and strands: 0 residues in 0 chains, 1570 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 1584 seeds are put forward Round 1: 43 peptides, 10 chains. Longest chain 5 peptides. Score 0.196 Round 2: 59 peptides, 13 chains. Longest chain 7 peptides. Score 0.227 Round 3: 62 peptides, 11 chains. Longest chain 9 peptides. Score 0.319 Round 4: 61 peptides, 12 chains. Longest chain 9 peptides. Score 0.278 Round 5: 62 peptides, 12 chains. Longest chain 7 peptides. Score 0.285 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 11, Residues 51, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2ouw-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2882 reflections ( 99.76 % complete ) and 3240 restraints for refining 1518 atoms. 3047 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3569 (Rfree = 0.000) for 1518 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.3492 (Rfree = 0.000) for 1509 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.3535 (Rfree = 0.000) for 1499 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.3497 (Rfree = 0.000) for 1494 atoms. TimeTaking 44.32