Mon 24 Dec 00:19:57 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 2obn-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2obn-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2obn-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2obn-3.6-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/2obn-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2obn-3.6-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 ============================================================ Mon 24 Dec 00:20:02 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/2obn-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2obn-3.6-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 879 and 0 Target number of residues in the AU: 879 Target solvent content: 0.6480 Checking the provided sequence file Detected sequence length: 349 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1396 Adjusted target solvent content: 0.44 Input MTZ file: 2obn-3.6-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: 4 Cell parameters: 75.040 122.990 75.170 90.000 103.099 90.000 Input sequence file: 2obn-3.6-parrot-mrncs.fasta_lf Building free atoms model in initial map for 11168 target number of atoms Had to go as low as 0.65 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: 73.214 3.600 Wilson plot Bfac: 76.69 15421 reflections ( 99.62 % complete ) and 0 restraints for refining 12403 atoms. Observations/parameters ratio is 0.31 ------------------------------------------------------ Starting model: R = 0.3041 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2858 (Rfree = 0.000) for 12403 atoms. Found 79 (79 requested) and removed 89 (39 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.52 3.81 Search for helices and strands: 0 residues in 0 chains, 12646 seeds are put forward NCS extension: 0 residues added, 12646 seeds are put forward Round 1: 541 peptides, 104 chains. Longest chain 17 peptides. Score 0.336 Round 2: 694 peptides, 111 chains. Longest chain 22 peptides. Score 0.479 Round 3: 751 peptides, 116 chains. Longest chain 24 peptides. Score 0.515 Round 4: 811 peptides, 112 chains. Longest chain 29 peptides. Score 0.589 Round 5: 828 peptides, 116 chains. Longest chain 24 peptides. Score 0.588 Taking the results from Round 4 Chains 122, Residues 699, Estimated correctness of the model 10.3 % 13 chains (97 residues) have been docked in sequence ------------------------------------------------------ 15421 reflections ( 99.62 % complete ) and 22200 restraints for refining 10121 atoms. 19240 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2347 (Rfree = 0.000) for 10121 atoms. Found 31 (64 requested) and removed 69 (32 requested) atoms. Cycle 2: After refmac, R = 0.2170 (Rfree = 0.000) for 9942 atoms. Found 16 (64 requested) and removed 58 (32 requested) atoms. Cycle 3: After refmac, R = 0.2052 (Rfree = 0.000) for 9857 atoms. Found 17 (63 requested) and removed 41 (31 requested) atoms. Cycle 4: After refmac, R = 0.1973 (Rfree = 0.000) for 9799 atoms. Found 18 (63 requested) and removed 41 (31 requested) atoms. Cycle 5: After refmac, R = 0.1910 (Rfree = 0.000) for 9749 atoms. Found 19 (62 requested) and removed 41 (31 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.46 3.75 Search for helices and strands: 0 residues in 0 chains, 10049 seeds are put forward NCS extension: 20 residues added (7 deleted due to clashes), 10069 seeds are put forward Round 1: 689 peptides, 122 chains. Longest chain 14 peptides. Score 0.421 Round 2: 789 peptides, 115 chains. Longest chain 23 peptides. Score 0.556 Round 3: 800 peptides, 107 chains. Longest chain 34 peptides. Score 0.598 Round 4: 781 peptides, 99 chains. Longest chain 24 peptides. Score 0.613 Round 5: 794 peptides, 103 chains. Longest chain 26 peptides. Score 0.609 Taking the results from Round 4 Chains 105, Residues 682, Estimated correctness of the model 19.7 % 13 chains (109 residues) have been docked in sequence ------------------------------------------------------ 15421 reflections ( 99.62 % complete ) and 22624 restraints for refining 10120 atoms. 19672 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2148 (Rfree = 0.000) for 10120 atoms. Found 49 (64 requested) and removed 73 (32 requested) atoms. Cycle 7: After refmac, R = 0.1941 (Rfree = 0.000) for 10030 atoms. Found 31 (64 requested) and removed 62 (32 requested) atoms. Cycle 8: After refmac, R = 0.1815 (Rfree = 0.000) for 9970 atoms. Found 18 (64 requested) and removed 47 (32 requested) atoms. Cycle 9: After refmac, R = 0.1774 (Rfree = 0.000) for 9924 atoms. Found 18 (63 requested) and removed 41 (31 requested) atoms. Cycle 10: After refmac, R = 0.1722 (Rfree = 0.000) for 9883 atoms. Found 14 (63 requested) and removed 39 (31 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.47 3.76 Search for helices and strands: 0 residues in 0 chains, 10180 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 10197 seeds are put forward Round 1: 631 peptides, 112 chains. Longest chain 16 peptides. Score 0.404 Round 2: 734 peptides, 99 chains. Longest chain 25 peptides. Score 0.571 Round 3: 760 peptides, 101 chains. Longest chain 23 peptides. Score 0.587 Round 4: 759 peptides, 105 chains. Longest chain 22 peptides. Score 0.569 Round 5: 738 peptides, 99 chains. Longest chain 21 peptides. Score 0.575 Taking the results from Round 3 Chains 104, Residues 659, Estimated correctness of the model 9.5 % 10 chains (70 residues) have been docked in sequence ------------------------------------------------------ 15421 reflections ( 99.62 % complete ) and 22917 restraints for refining 10124 atoms. 20195 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2108 (Rfree = 0.000) for 10124 atoms. Found 49 (64 requested) and removed 82 (32 requested) atoms. Cycle 12: After refmac, R = 0.1897 (Rfree = 0.000) for 10048 atoms. Found 28 (64 requested) and removed 48 (32 requested) atoms. Cycle 13: After refmac, R = 0.1835 (Rfree = 0.000) for 10011 atoms. Found 29 (64 requested) and removed 50 (32 requested) atoms. Cycle 14: After refmac, R = 0.1754 (Rfree = 0.000) for 9969 atoms. Found 24 (64 requested) and removed 53 (32 requested) atoms. Cycle 15: After refmac, R = 0.1724 (Rfree = 0.000) for 9928 atoms. Found 28 (63 requested) and removed 44 (31 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.47 3.76 Search for helices and strands: 0 residues in 0 chains, 10252 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 10269 seeds are put forward Round 1: 627 peptides, 112 chains. Longest chain 14 peptides. Score 0.399 Round 2: 723 peptides, 105 chains. Longest chain 22 peptides. Score 0.535 Round 3: 726 peptides, 103 chains. Longest chain 17 peptides. Score 0.547 Round 4: 704 peptides, 93 chains. Longest chain 25 peptides. Score 0.568 Round 5: 738 peptides, 101 chains. Longest chain 26 peptides. Score 0.566 Taking the results from Round 4 Chains 98, Residues 611, Estimated correctness of the model 1.7 % 12 chains (96 residues) have been docked in sequence ------------------------------------------------------ 15421 reflections ( 99.62 % complete ) and 22710 restraints for refining 10122 atoms. 20065 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2043 (Rfree = 0.000) for 10122 atoms. Found 46 (64 requested) and removed 60 (32 requested) atoms. Cycle 17: After refmac, R = 0.1920 (Rfree = 0.000) for 10049 atoms. Found 23 (64 requested) and removed 44 (32 requested) atoms. Cycle 18: After refmac, R = 0.1782 (Rfree = 0.000) for 9998 atoms. Found 19 (64 requested) and removed 48 (32 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.1708 (Rfree = 0.000) for 9946 atoms. Found 19 (63 requested) and removed 43 (31 requested) atoms. Cycle 20: After refmac, R = 0.1621 (Rfree = 0.000) for 9909 atoms. Found 19 (63 requested) and removed 43 (31 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.48 3.77 Search for helices and strands: 0 residues in 0 chains, 10183 seeds are put forward NCS extension: 33 residues added (1 deleted due to clashes), 10216 seeds are put forward Round 1: 591 peptides, 105 chains. Longest chain 17 peptides. Score 0.392 Round 2: 678 peptides, 97 chains. Longest chain 21 peptides. Score 0.525 Round 3: 678 peptides, 98 chains. Longest chain 19 peptides. Score 0.521 Round 4: 702 peptides, 100 chains. Longest chain 21 peptides. Score 0.536 Round 5: 691 peptides, 100 chains. Longest chain 27 peptides. Score 0.525 Taking the results from Round 4 Chains 105, Residues 602, Estimated correctness of the model 0.0 % 7 chains (59 residues) have been docked in sequence ------------------------------------------------------ 15421 reflections ( 99.62 % complete ) and 23206 restraints for refining 10123 atoms. 20737 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1903 (Rfree = 0.000) for 10123 atoms. Found 43 (64 requested) and removed 46 (32 requested) atoms. Cycle 22: After refmac, R = 0.1727 (Rfree = 0.000) for 10092 atoms. Found 24 (64 requested) and removed 36 (32 requested) atoms. Cycle 23: After refmac, R = 0.1644 (Rfree = 0.000) for 10068 atoms. Found 17 (64 requested) and removed 46 (32 requested) atoms. Cycle 24: After refmac, R = 0.1577 (Rfree = 0.000) for 10033 atoms. Found 17 (64 requested) and removed 40 (32 requested) atoms. Cycle 25: After refmac, R = 0.1547 (Rfree = 0.000) for 10000 atoms. Found 24 (64 requested) and removed 36 (32 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.44 3.73 Search for helices and strands: 0 residues in 0 chains, 10311 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 10330 seeds are put forward Round 1: 575 peptides, 111 chains. Longest chain 15 peptides. Score 0.342 Round 2: 644 peptides, 102 chains. Longest chain 16 peptides. Score 0.467 Round 3: 650 peptides, 106 chains. Longest chain 19 peptides. Score 0.454 Round 4: 626 peptides, 95 chains. Longest chain 19 peptides. Score 0.481 Round 5: 627 peptides, 98 chains. Longest chain 18 peptides. Score 0.467 Taking the results from Round 4 Chains 95, Residues 531, Estimated correctness of the model 0.0 % 6 chains (33 residues) have been docked in sequence ------------------------------------------------------ 15421 reflections ( 99.62 % complete ) and 24045 restraints for refining 10124 atoms. 21943 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1782 (Rfree = 0.000) for 10124 atoms. Found 43 (64 requested) and removed 42 (32 requested) atoms. Failed to save intermediate PDB Cycle 27: After refmac, R = 0.1664 (Rfree = 0.000) for 10098 atoms. Found 37 (64 requested) and removed 45 (32 requested) atoms. Cycle 28: After refmac, R = 0.1600 (Rfree = 0.000) for 10072 atoms. Found 29 (64 requested) and removed 37 (32 requested) atoms. Cycle 29: After refmac, R = 0.1523 (Rfree = 0.000) for 10054 atoms. Found 32 (64 requested) and removed 38 (32 requested) atoms. Cycle 30: After refmac, R = 0.1467 (Rfree = 0.000) for 10035 atoms. Found 24 (64 requested) and removed 38 (32 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.49 3.78 Search for helices and strands: 0 residues in 0 chains, 10340 seeds are put forward NCS extension: 29 residues added (2 deleted due to clashes), 10369 seeds are put forward Round 1: 499 peptides, 104 chains. Longest chain 10 peptides. Score 0.282 Round 2: 578 peptides, 102 chains. Longest chain 20 peptides. Score 0.392 Round 3: 599 peptides, 106 chains. Longest chain 20 peptides. Score 0.396 Round 4: 607 peptides, 98 chains. Longest chain 25 peptides. Score 0.445 Round 5: 580 peptides, 97 chains. Longest chain 13 peptides. Score 0.419 Taking the results from Round 4 Chains 100, Residues 509, Estimated correctness of the model 0.0 % 7 chains (45 residues) have been docked in sequence ------------------------------------------------------ 15421 reflections ( 99.62 % complete ) and 23820 restraints for refining 10121 atoms. 21771 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1850 (Rfree = 0.000) for 10121 atoms. Found 43 (64 requested) and removed 38 (32 requested) atoms. Cycle 32: After refmac, R = 0.1726 (Rfree = 0.000) for 10076 atoms. Found 42 (64 requested) and removed 36 (32 requested) atoms. Cycle 33: After refmac, R = 0.1680 (Rfree = 0.000) for 10058 atoms. Found 46 (64 requested) and removed 37 (32 requested) atoms. Cycle 34: After refmac, R = 0.1628 (Rfree = 0.000) for 10050 atoms. Found 50 (64 requested) and removed 35 (32 requested) atoms. Cycle 35: After refmac, R = 0.1586 (Rfree = 0.000) for 10050 atoms. Found 33 (64 requested) and removed 36 (32 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.48 3.77 Search for helices and strands: 0 residues in 0 chains, 10316 seeds are put forward NCS extension: 21 residues added (3 deleted due to clashes), 10337 seeds are put forward Round 1: 464 peptides, 91 chains. Longest chain 13 peptides. Score 0.308 Round 2: 545 peptides, 103 chains. Longest chain 13 peptides. Score 0.346 Round 3: 567 peptides, 103 chains. Longest chain 12 peptides. Score 0.373 Round 4: 564 peptides, 94 chains. Longest chain 16 peptides. Score 0.416 Round 5: 569 peptides, 96 chains. Longest chain 16 peptides. Score 0.412 Taking the results from Round 4 Chains 94, Residues 470, Estimated correctness of the model 0.0 % 7 chains (40 residues) have been docked in sequence ------------------------------------------------------ 15421 reflections ( 99.62 % complete ) and 23909 restraints for refining 10123 atoms. 22034 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1796 (Rfree = 0.000) for 10123 atoms. Found 60 (64 requested) and removed 43 (32 requested) atoms. Cycle 37: After refmac, R = 0.1715 (Rfree = 0.000) for 10105 atoms. Found 54 (65 requested) and removed 37 (32 requested) atoms. Cycle 38: After refmac, R = 0.1587 (Rfree = 0.000) for 10096 atoms. Found 32 (64 requested) and removed 35 (32 requested) atoms. Cycle 39: After refmac, R = 0.1615 (Rfree = 0.000) for 10073 atoms. Found 44 (64 requested) and removed 38 (32 requested) atoms. Cycle 40: After refmac, R = 0.1526 (Rfree = 0.000) for 10062 atoms. Found 31 (64 requested) and removed 35 (32 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.46 3.75 Search for helices and strands: 0 residues in 0 chains, 10355 seeds are put forward NCS extension: 14 residues added (3 deleted due to clashes), 10369 seeds are put forward Round 1: 406 peptides, 85 chains. Longest chain 12 peptides. Score 0.264 Round 2: 500 peptides, 93 chains. Longest chain 12 peptides. Score 0.343 Round 3: 494 peptides, 85 chains. Longest chain 13 peptides. Score 0.379 Round 4: 497 peptides, 87 chains. Longest chain 12 peptides. Score 0.372 Round 5: 485 peptides, 85 chains. Longest chain 12 peptides. Score 0.368 Taking the results from Round 3 Chains 87, Residues 409, Estimated correctness of the model 0.0 % 6 chains (31 residues) have been docked in sequence ------------------------------------------------------ 15421 reflections ( 99.62 % complete ) and 24391 restraints for refining 10123 atoms. 22756 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1660 (Rfree = 0.000) for 10123 atoms. Found 50 (64 requested) and removed 37 (32 requested) atoms. Cycle 42: After refmac, R = 0.1549 (Rfree = 0.000) for 10116 atoms. Found 47 (65 requested) and removed 34 (32 requested) atoms. Cycle 43: After refmac, R = 0.1532 (Rfree = 0.000) for 10114 atoms. Found 48 (64 requested) and removed 44 (32 requested) atoms. Cycle 44: After refmac, R = 0.1451 (Rfree = 0.000) for 10106 atoms. Found 28 (64 requested) and removed 33 (32 requested) atoms. Cycle 45: After refmac, R = 0.1435 (Rfree = 0.000) for 10091 atoms. Found 49 (64 requested) and removed 35 (32 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.48 3.77 Search for helices and strands: 0 residues in 0 chains, 10421 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 10435 seeds are put forward Round 1: 422 peptides, 92 chains. Longest chain 9 peptides. Score 0.245 Round 2: 486 peptides, 94 chains. Longest chain 11 peptides. Score 0.320 Round 3: 491 peptides, 88 chains. Longest chain 11 peptides. Score 0.359 Round 4: 502 peptides, 90 chains. Longest chain 14 peptides. Score 0.362 Round 5: 502 peptides, 91 chains. Longest chain 12 peptides. Score 0.357 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 90, Residues 412, Estimated correctness of the model 0.0 % 4 chains (21 residues) have been docked in sequence Sequence coverage is 5 % Consider running further cycles of model building using 2obn-3_warpNtrace.pdb as input Building loops using Loopy2018 90 chains (412 residues) following loop building 4 chains (21 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 15421 reflections ( 99.62 % complete ) and 24298 restraints for refining 10122 atoms. 22659 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1608 (Rfree = 0.000) for 10122 atoms. Found 0 (64 requested) and removed 32 (32 requested) atoms. Cycle 47: After refmac, R = 0.1570 (Rfree = 0.000) for 10052 atoms. Found 0 (64 requested) and removed 32 (32 requested) atoms. Cycle 48: After refmac, R = 0.1516 (Rfree = 0.000) for 10002 atoms. Found 0 (64 requested) and removed 32 (32 requested) atoms. Cycle 49: After refmac, R = 0.1493 (Rfree = 0.000) for 9962 atoms. TimeTaking 115.3