null Sun 23 Dec 22:22:59 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-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ouw-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ouw-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ouw-4.0-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-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ouw-4.0-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 22:23:09 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-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ouw-4.0-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 148 and 0 Target number of residues in the AU: 148 Target solvent content: 0.6741 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-4.0-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-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 2208 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: 108.355 4.000 Wilson plot Bfac: 94.17 2488 reflections ( 99.72 % complete ) and 0 restraints for refining 2433 atoms. Observations/parameters ratio is 0.26 ------------------------------------------------------ Starting model: R = 0.3950 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3627 (Rfree = 0.000) for 2433 atoms. Found 11 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.90 4.53 Search for helices and strands: 0 residues in 0 chains, 2499 seeds are put forward NCS extension: 0 residues added, 2499 seeds are put forward Round 1: 60 peptides, 12 chains. Longest chain 7 peptides. Score 0.270 Round 2: 92 peptides, 18 chains. Longest chain 8 peptides. Score 0.318 Round 3: 105 peptides, 17 chains. Longest chain 11 peptides. Score 0.434 Round 4: 112 peptides, 17 chains. Longest chain 14 peptides. Score 0.476 Round 5: 115 peptides, 18 chains. Longest chain 11 peptides. Score 0.468 Taking the results from Round 4 Chains 17, Residues 95, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 2488 reflections ( 99.72 % complete ) and 4616 restraints for refining 1914 atoms. 4232 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3374 (Rfree = 0.000) for 1914 atoms. Found 9 (9 requested) and removed 28 (4 requested) atoms. Cycle 2: After refmac, R = 0.3267 (Rfree = 0.000) for 1853 atoms. Found 9 (9 requested) and removed 35 (4 requested) atoms. Cycle 3: After refmac, R = 0.3300 (Rfree = 0.000) for 1802 atoms. Found 8 (8 requested) and removed 53 (4 requested) atoms. Cycle 4: After refmac, R = 0.3403 (Rfree = 0.000) for 1733 atoms. Found 8 (8 requested) and removed 27 (4 requested) atoms. Cycle 5: After refmac, R = 0.3384 (Rfree = 0.000) for 1698 atoms. Found 8 (8 requested) and removed 18 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.30 3.83 Search for helices and strands: 0 residues in 0 chains, 1774 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 1788 seeds are put forward Round 1: 64 peptides, 14 chains. Longest chain 8 peptides. Score 0.234 Round 2: 87 peptides, 18 chains. Longest chain 8 peptides. Score 0.282 Round 3: 93 peptides, 18 chains. Longest chain 7 peptides. Score 0.325 Round 4: 96 peptides, 18 chains. Longest chain 8 peptides. Score 0.346 Round 5: 109 peptides, 20 chains. Longest chain 12 peptides. Score 0.376 Taking the results from Round 5 Chains 20, Residues 89, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 2488 reflections ( 99.72 % complete ) and 3821 restraints for refining 1709 atoms. 3465 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3464 (Rfree = 0.000) for 1709 atoms. Found 8 (8 requested) and removed 29 (4 requested) atoms. Cycle 7: After refmac, R = 0.3352 (Rfree = 0.000) for 1672 atoms. Found 8 (8 requested) and removed 21 (4 requested) atoms. Cycle 8: After refmac, R = 0.3354 (Rfree = 0.000) for 1649 atoms. Found 7 (7 requested) and removed 13 (3 requested) atoms. Cycle 9: After refmac, R = 0.3401 (Rfree = 0.000) for 1635 atoms. Found 7 (7 requested) and removed 13 (3 requested) atoms. Cycle 10: After refmac, R = 0.3241 (Rfree = 0.000) for 1618 atoms. Found 7 (7 requested) and removed 17 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.43 3.98 Search for helices and strands: 0 residues in 0 chains, 1710 seeds are put forward NCS extension: 0 residues added, 1710 seeds are put forward Round 1: 73 peptides, 17 chains. Longest chain 6 peptides. Score 0.207 Round 2: 102 peptides, 22 chains. Longest chain 7 peptides. Score 0.271 Round 3: 97 peptides, 18 chains. Longest chain 9 peptides. Score 0.353 Round 4: 109 peptides, 19 chains. Longest chain 11 peptides. Score 0.404 Round 5: 112 peptides, 16 chains. Longest chain 15 peptides. Score 0.502 Taking the results from Round 5 Chains 16, Residues 96, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2488 reflections ( 99.72 % complete ) and 3983 restraints for refining 1773 atoms. 3615 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3607 (Rfree = 0.000) for 1773 atoms. Found 8 (8 requested) and removed 32 (4 requested) atoms. Cycle 12: After refmac, R = 0.3626 (Rfree = 0.000) for 1731 atoms. Found 8 (8 requested) and removed 17 (4 requested) atoms. Cycle 13: After refmac, R = 0.3519 (Rfree = 0.000) for 1713 atoms. Found 8 (8 requested) and removed 20 (4 requested) atoms. Cycle 14: After refmac, R = 0.3467 (Rfree = 0.000) for 1694 atoms. Found 8 (8 requested) and removed 15 (4 requested) atoms. Cycle 15: After refmac, R = 0.3151 (Rfree = 0.000) for 1678 atoms. Found 8 (8 requested) and removed 14 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.32 3.85 Search for helices and strands: 0 residues in 0 chains, 1737 seeds are put forward NCS extension: 0 residues added, 1737 seeds are put forward Round 1: 70 peptides, 15 chains. Longest chain 8 peptides. Score 0.249 Round 2: 76 peptides, 16 chains. Longest chain 8 peptides. Score 0.263 Round 3: 73 peptides, 15 chains. Longest chain 8 peptides. Score 0.272 Round 4: 82 peptides, 15 chains. Longest chain 9 peptides. Score 0.338 Round 5: 76 peptides, 15 chains. Longest chain 9 peptides. Score 0.294 Taking the results from Round 4 Chains 15, Residues 67, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2488 reflections ( 99.72 % complete ) and 3685 restraints for refining 1649 atoms. 3432 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3610 (Rfree = 0.000) for 1649 atoms. Found 7 (7 requested) and removed 14 (3 requested) atoms. Cycle 17: After refmac, R = 0.3728 (Rfree = 0.000) for 1636 atoms. Found 7 (7 requested) and removed 9 (3 requested) atoms. Cycle 18: After refmac, R = 0.3663 (Rfree = 0.000) for 1628 atoms. Found 7 (7 requested) and removed 12 (3 requested) atoms. Cycle 19: After refmac, R = 0.3635 (Rfree = 0.000) for 1617 atoms. Found 7 (7 requested) and removed 10 (3 requested) atoms. Cycle 20: After refmac, R = 0.3847 (Rfree = 0.000) for 1605 atoms. Found 7 (7 requested) and removed 13 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.35 3.89 Search for helices and strands: 0 residues in 0 chains, 1668 seeds are put forward NCS extension: 0 residues added, 1668 seeds are put forward Round 1: 55 peptides, 13 chains. Longest chain 6 peptides. Score 0.193 Round 2: 68 peptides, 14 chains. Longest chain 8 peptides. Score 0.266 Round 3: 84 peptides, 18 chains. Longest chain 8 peptides. Score 0.260 Round 4: 73 peptides, 15 chains. Longest chain 11 peptides. Score 0.272 Round 5: 73 peptides, 16 chains. Longest chain 6 peptides. Score 0.239 Taking the results from Round 4 Chains 15, Residues 58, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2488 reflections ( 99.72 % complete ) and 3625 restraints for refining 1650 atoms. 3408 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3979 (Rfree = 0.000) for 1650 atoms. Found 7 (7 requested) and removed 17 (3 requested) atoms. Cycle 22: After refmac, R = 0.4006 (Rfree = 0.000) for 1635 atoms. Found 7 (7 requested) and removed 12 (3 requested) atoms. Cycle 23: After refmac, R = 0.3933 (Rfree = 0.000) for 1622 atoms. Found 7 (7 requested) and removed 15 (3 requested) atoms. Cycle 24: After refmac, R = 0.3880 (Rfree = 0.000) for 1610 atoms. Found 7 (7 requested) and removed 12 (3 requested) atoms. Cycle 25: After refmac, R = 0.3430 (Rfree = 0.000) for 1603 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.16 3.67 Search for helices and strands: 0 residues in 0 chains, 1664 seeds are put forward NCS extension: 0 residues added, 1664 seeds are put forward Round 1: 50 peptides, 11 chains. Longest chain 7 peptides. Score 0.222 Round 2: 64 peptides, 14 chains. Longest chain 6 peptides. Score 0.234 Round 3: 64 peptides, 13 chains. Longest chain 8 peptides. Score 0.268 Round 4: 69 peptides, 14 chains. Longest chain 8 peptides. Score 0.273 Round 5: 79 peptides, 14 chains. Longest chain 9 peptides. Score 0.347 Taking the results from Round 5 Chains 14, Residues 65, Estimated correctness of the model 0.0 % 2 chains (11 residues) have been docked in sequence ------------------------------------------------------ 2488 reflections ( 99.72 % complete ) and 2976 restraints for refining 1538 atoms. 2699 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3899 (Rfree = 0.000) for 1538 atoms. Found 7 (7 requested) and removed 13 (3 requested) atoms. Cycle 27: After refmac, R = 0.3959 (Rfree = 0.000) for 1527 atoms. Found 7 (7 requested) and removed 12 (3 requested) atoms. Cycle 28: After refmac, R = 0.3742 (Rfree = 0.000) for 1516 atoms. Found 7 (7 requested) and removed 13 (3 requested) atoms. Cycle 29: After refmac, R = 0.3889 (Rfree = 0.000) for 1507 atoms. Found 7 (7 requested) and removed 9 (3 requested) atoms. Cycle 30: After refmac, R = 0.3819 (Rfree = 0.000) for 1503 atoms. Found 7 (7 requested) and removed 11 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.84 3.30 Search for helices and strands: 0 residues in 0 chains, 1548 seeds are put forward NCS extension: 0 residues added, 1548 seeds are put forward Round 1: 77 peptides, 17 chains. Longest chain 8 peptides. Score 0.238 Round 2: 93 peptides, 18 chains. Longest chain 10 peptides. Score 0.325 Round 3: 74 peptides, 14 chains. Longest chain 8 peptides. Score 0.311 Round 4: 79 peptides, 14 chains. Longest chain 11 peptides. Score 0.347 Round 5: 85 peptides, 15 chains. Longest chain 12 peptides. Score 0.359 Taking the results from Round 5 Chains 15, Residues 70, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 2488 reflections ( 99.72 % complete ) and 3150 restraints for refining 1565 atoms. 2861 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3725 (Rfree = 0.000) for 1565 atoms. Found 7 (7 requested) and removed 19 (3 requested) atoms. Cycle 32: After refmac, R = 0.3648 (Rfree = 0.000) for 1548 atoms. Found 7 (7 requested) and removed 10 (3 requested) atoms. Cycle 33: After refmac, R = 0.3240 (Rfree = 0.000) for 1536 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 34: After refmac, R = 0.3153 (Rfree = 0.000) for 1535 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 35: After refmac, R = 0.3752 (Rfree = 0.000) for 1534 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.27 3.80 Search for helices and strands: 0 residues in 0 chains, 1583 seeds are put forward NCS extension: 0 residues added, 1583 seeds are put forward Round 1: 69 peptides, 15 chains. Longest chain 9 peptides. Score 0.241 Round 2: 81 peptides, 16 chains. Longest chain 8 peptides. Score 0.300 Round 3: 92 peptides, 18 chains. Longest chain 9 peptides. Score 0.318 Round 4: 88 peptides, 16 chains. Longest chain 9 peptides. Score 0.350 Round 5: 84 peptides, 16 chains. Longest chain 8 peptides. Score 0.322 Taking the results from Round 4 Chains 16, Residues 72, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2488 reflections ( 99.72 % complete ) and 3160 restraints for refining 1517 atoms. 2888 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3782 (Rfree = 0.000) for 1517 atoms. Found 7 (7 requested) and removed 23 (3 requested) atoms. Cycle 37: After refmac, R = 0.4053 (Rfree = 0.000) for 1492 atoms. Found 7 (7 requested) and removed 26 (3 requested) atoms. Cycle 38: After refmac, R = 0.3907 (Rfree = 0.000) for 1469 atoms. Found 6 (6 requested) and removed 21 (3 requested) atoms. Cycle 39: After refmac, R = 0.3692 (Rfree = 0.000) for 1446 atoms. Found 6 (6 requested) and removed 13 (3 requested) atoms. Cycle 40: After refmac, R = 0.3837 (Rfree = 0.000) for 1437 atoms. Found 6 (6 requested) and removed 17 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.84 3.30 Search for helices and strands: 0 residues in 0 chains, 1486 seeds are put forward NCS extension: 0 residues added, 1486 seeds are put forward Round 1: 66 peptides, 15 chains. Longest chain 6 peptides. Score 0.217 Round 2: 90 peptides, 19 chains. Longest chain 8 peptides. Score 0.274 Round 3: 75 peptides, 15 chains. Longest chain 7 peptides. Score 0.287 Round 4: 83 peptides, 15 chains. Longest chain 8 peptides. Score 0.345 Round 5: 84 peptides, 14 chains. Longest chain 8 peptides. Score 0.382 Taking the results from Round 5 Chains 14, Residues 70, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2488 reflections ( 99.72 % complete ) and 3179 restraints for refining 1533 atoms. 2913 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3770 (Rfree = 0.000) for 1533 atoms. Found 7 (7 requested) and removed 30 (3 requested) atoms. Cycle 42: After refmac, R = 0.3798 (Rfree = 0.000) for 1504 atoms. Found 7 (7 requested) and removed 15 (3 requested) atoms. Cycle 43: After refmac, R = 0.3640 (Rfree = 0.000) for 1490 atoms. Found 7 (7 requested) and removed 15 (3 requested) atoms. Cycle 44: After refmac, R = 0.3642 (Rfree = 0.000) for 1478 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. Cycle 45: After refmac, R = 0.3591 (Rfree = 0.000) for 1470 atoms. Found 7 (7 requested) and removed 9 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.19 3.70 Search for helices and strands: 0 residues in 0 chains, 1526 seeds are put forward NCS extension: 0 residues added, 1526 seeds are put forward Round 1: 55 peptides, 12 chains. Longest chain 7 peptides. Score 0.229 Round 2: 65 peptides, 14 chains. Longest chain 6 peptides. Score 0.242 Round 3: 66 peptides, 13 chains. Longest chain 7 peptides. Score 0.283 Round 4: 67 peptides, 13 chains. Longest chain 8 peptides. Score 0.291 Round 5: 63 peptides, 11 chains. Longest chain 8 peptides. Score 0.327 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 11, Residues 52, Estimated correctness of the model 0.0 % 3 chains (12 residues) have been docked in sequence Sequence coverage is 22 % Consider running further cycles of model building using 2ouw-4_warpNtrace.pdb as input Building loops using Loopy2018 11 chains (52 residues) following loop building 3 chains (12 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2488 reflections ( 99.72 % complete ) and 226 restraints for refining 1506 atoms. 0 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3800 (Rfree = 0.000) for 1506 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.3835 (Rfree = 0.000) for 1497 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.3734 (Rfree = 0.000) for 1486 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.3652 (Rfree = 0.000) for 1479 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:06:41 GMT 2018 Job finished. TimeTaking 43.7 Used memory is bytes: 3644784