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 2awa-2.7-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2awa-2.7-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2awa-2.7-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2awa-2.7-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/2awa-2.7-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2awa-2.7-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 22:23:08 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/2awa-2.7-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2awa-2.7-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 1347 and 0 Target number of residues in the AU: 1347 Target solvent content: 0.5978 Checking the provided sequence file Detected sequence length: 390 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1560 Adjusted target solvent content: 0.53 Input MTZ file: 2awa-2.7-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: 4 Cell parameters: 94.281 70.854 135.686 90.000 91.232 90.000 Input sequence file: 2awa-2.7-parrot-hancs.fasta_lf Building free atoms model in initial map for 12480 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: 135.654 2.690 Wilson plot Bfac: 51.62 48746 reflections ( 97.20 % complete ) and 0 restraints for refining 13758 atoms. Observations/parameters ratio is 0.89 ------------------------------------------------------ Starting model: R = 0.3726 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2830 (Rfree = 0.000) for 13758 atoms. Found 86 (202 requested) and removed 181 (101 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.81 2.70 NCS extension: 0 residues added, 13663 seeds are put forward Round 1: 618 peptides, 131 chains. Longest chain 10 peptides. Score 0.266 Round 2: 706 peptides, 135 chains. Longest chain 13 peptides. Score 0.335 Round 3: 734 peptides, 131 chains. Longest chain 13 peptides. Score 0.377 Round 4: 744 peptides, 134 chains. Longest chain 12 peptides. Score 0.374 Round 5: 741 peptides, 131 chains. Longest chain 13 peptides. Score 0.383 Taking the results from Round 5 Chains 131, Residues 610, Estimated correctness of the model 24.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 48746 reflections ( 97.20 % complete ) and 25789 restraints for refining 11585 atoms. 23480 conditional restraints added. Observations/parameters ratio is 1.05 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2899 (Rfree = 0.000) for 11585 atoms. Found 113 (170 requested) and removed 99 (85 requested) atoms. Cycle 2: After refmac, R = 0.2945 (Rfree = 0.000) for 11538 atoms. Found 123 (170 requested) and removed 94 (85 requested) atoms. Cycle 3: After refmac, R = 0.2931 (Rfree = 0.000) for 11528 atoms. Found 170 (170 requested) and removed 93 (85 requested) atoms. Cycle 4: After refmac, R = 0.2884 (Rfree = 0.000) for 11562 atoms. Found 168 (170 requested) and removed 99 (85 requested) atoms. Cycle 5: After refmac, R = 0.2864 (Rfree = 0.000) for 11595 atoms. Found 161 (171 requested) and removed 97 (85 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.80 2.69 NCS extension: 8 residues added (1 deleted due to clashes), 11889 seeds are put forward Round 1: 711 peptides, 140 chains. Longest chain 11 peptides. Score 0.320 Round 2: 797 peptides, 140 chains. Longest chain 18 peptides. Score 0.399 Round 3: 813 peptides, 134 chains. Longest chain 12 peptides. Score 0.435 Round 4: 797 peptides, 132 chains. Longest chain 17 peptides. Score 0.429 Round 5: 844 peptides, 136 chains. Longest chain 18 peptides. Score 0.454 Taking the results from Round 5 Chains 136, Residues 708, Estimated correctness of the model 39.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 48746 reflections ( 97.20 % complete ) and 24965 restraints for refining 11586 atoms. 22269 conditional restraints added. Observations/parameters ratio is 1.05 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2917 (Rfree = 0.000) for 11586 atoms. Found 142 (170 requested) and removed 104 (85 requested) atoms. Cycle 7: After refmac, R = 0.2813 (Rfree = 0.000) for 11563 atoms. Found 160 (171 requested) and removed 90 (85 requested) atoms. Cycle 8: After refmac, R = 0.2731 (Rfree = 0.000) for 11607 atoms. Found 155 (171 requested) and removed 94 (85 requested) atoms. Cycle 9: After refmac, R = 0.2709 (Rfree = 0.000) for 11644 atoms. Found 163 (171 requested) and removed 95 (85 requested) atoms. Cycle 10: After refmac, R = 0.2655 (Rfree = 0.000) for 11692 atoms. Found 172 (172 requested) and removed 104 (86 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.80 2.69 NCS extension: 49 residues added (4 deleted due to clashes), 12003 seeds are put forward Round 1: 701 peptides, 136 chains. Longest chain 11 peptides. Score 0.327 Round 2: 800 peptides, 135 chains. Longest chain 19 peptides. Score 0.420 Round 3: 776 peptides, 128 chains. Longest chain 19 peptides. Score 0.426 Round 4: 783 peptides, 124 chains. Longest chain 18 peptides. Score 0.446 Round 5: 785 peptides, 126 chains. Longest chain 20 peptides. Score 0.441 Taking the results from Round 4 Chains 124, Residues 659, Estimated correctness of the model 38.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 48746 reflections ( 97.20 % complete ) and 24987 restraints for refining 11585 atoms. 22475 conditional restraints added. Observations/parameters ratio is 1.05 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2782 (Rfree = 0.000) for 11585 atoms. Found 137 (170 requested) and removed 101 (85 requested) atoms. Cycle 12: After refmac, R = 0.2709 (Rfree = 0.000) for 11594 atoms. Found 150 (171 requested) and removed 88 (85 requested) atoms. Cycle 13: After refmac, R = 0.2690 (Rfree = 0.000) for 11630 atoms. Found 142 (171 requested) and removed 91 (85 requested) atoms. Cycle 14: After refmac, R = 0.2633 (Rfree = 0.000) for 11664 atoms. Found 151 (171 requested) and removed 94 (85 requested) atoms. Cycle 15: After refmac, R = 0.2228 (Rfree = 0.000) for 11703 atoms. Found 73 (172 requested) and removed 89 (86 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.80 2.69 NCS extension: 14 residues added (1 deleted due to clashes), 11846 seeds are put forward Round 1: 727 peptides, 137 chains. Longest chain 13 peptides. Score 0.347 Round 2: 781 peptides, 134 chains. Longest chain 21 peptides. Score 0.407 Round 3: 767 peptides, 124 chains. Longest chain 21 peptides. Score 0.433 Round 4: 780 peptides, 126 chains. Longest chain 17 peptides. Score 0.436 Round 5: 785 peptides, 125 chains. Longest chain 23 peptides. Score 0.444 Taking the results from Round 5 Chains 125, Residues 660, Estimated correctness of the model 37.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 48746 reflections ( 97.20 % complete ) and 24472 restraints for refining 11586 atoms. 21957 conditional restraints added. Observations/parameters ratio is 1.05 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2662 (Rfree = 0.000) for 11586 atoms. Found 144 (170 requested) and removed 92 (85 requested) atoms. Cycle 17: After refmac, R = 0.2584 (Rfree = 0.000) for 11613 atoms. Found 137 (171 requested) and removed 90 (85 requested) atoms. Cycle 18: After refmac, R = 0.2550 (Rfree = 0.000) for 11633 atoms. Found 151 (171 requested) and removed 86 (85 requested) atoms. Cycle 19: After refmac, R = 0.2499 (Rfree = 0.000) for 11679 atoms. Found 156 (172 requested) and removed 91 (86 requested) atoms. Cycle 20: After refmac, R = 0.2136 (Rfree = 0.000) for 11728 atoms. Found 60 (172 requested) and removed 89 (86 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.80 2.69 NCS extension: 41 residues added (1 deleted due to clashes), 11870 seeds are put forward Round 1: 704 peptides, 131 chains. Longest chain 16 peptides. Score 0.349 Round 2: 752 peptides, 126 chains. Longest chain 17 peptides. Score 0.412 Round 3: 777 peptides, 123 chains. Longest chain 18 peptides. Score 0.445 Round 4: 759 peptides, 133 chains. Longest chain 16 peptides. Score 0.392 Round 5: 759 peptides, 121 chains. Longest chain 16 peptides. Score 0.437 Taking the results from Round 3 Chains 124, Residues 654, Estimated correctness of the model 38.0 % 3 chains (20 residues) have been docked in sequence ------------------------------------------------------ 48746 reflections ( 97.20 % complete ) and 24270 restraints for refining 11582 atoms. 21723 conditional restraints added. Observations/parameters ratio is 1.05 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2554 (Rfree = 0.000) for 11582 atoms. Found 140 (170 requested) and removed 89 (85 requested) atoms. Cycle 22: After refmac, R = 0.2557 (Rfree = 0.000) for 11620 atoms. Found 171 (171 requested) and removed 92 (85 requested) atoms. Cycle 23: After refmac, R = 0.2542 (Rfree = 0.000) for 11679 atoms. Found 149 (172 requested) and removed 92 (86 requested) atoms. Cycle 24: After refmac, R = 0.2147 (Rfree = 0.000) for 11717 atoms. Found 65 (172 requested) and removed 87 (86 requested) atoms. Cycle 25: After refmac, R = 0.2039 (Rfree = 0.000) for 11684 atoms. Found 30 (172 requested) and removed 88 (86 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.79 2.68 NCS extension: 55 residues added (5 deleted due to clashes), 11789 seeds are put forward Round 1: 719 peptides, 134 chains. Longest chain 15 peptides. Score 0.352 Round 2: 767 peptides, 128 chains. Longest chain 15 peptides. Score 0.418 Round 3: 763 peptides, 121 chains. Longest chain 19 peptides. Score 0.441 Round 4: 799 peptides, 127 chains. Longest chain 16 peptides. Score 0.449 Round 5: 774 peptides, 123 chains. Longest chain 16 peptides. Score 0.442 Taking the results from Round 4 Chains 127, Residues 672, Estimated correctness of the model 38.8 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 48746 reflections ( 97.20 % complete ) and 24259 restraints for refining 11585 atoms. 21677 conditional restraints added. Observations/parameters ratio is 1.05 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2531 (Rfree = 0.000) for 11585 atoms. Found 151 (170 requested) and removed 91 (85 requested) atoms. Cycle 27: After refmac, R = 0.2543 (Rfree = 0.000) for 11626 atoms. Found 154 (171 requested) and removed 94 (85 requested) atoms. Cycle 28: After refmac, R = 0.2476 (Rfree = 0.000) for 11669 atoms. Found 146 (172 requested) and removed 87 (86 requested) atoms. Cycle 29: After refmac, R = 0.2476 (Rfree = 0.000) for 11713 atoms. Found 145 (172 requested) and removed 88 (86 requested) atoms. Cycle 30: After refmac, R = 0.2474 (Rfree = 0.000) for 11757 atoms. Found 157 (173 requested) and removed 91 (86 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.80 2.69 NCS extension: 24 residues added (0 deleted due to clashes), 11940 seeds are put forward Round 1: 675 peptides, 130 chains. Longest chain 10 peptides. Score 0.326 Round 2: 745 peptides, 125 chains. Longest chain 19 peptides. Score 0.410 Round 3: 745 peptides, 127 chains. Longest chain 18 peptides. Score 0.402 Round 4: 739 peptides, 121 chains. Longest chain 15 peptides. Score 0.420 Round 5: 722 peptides, 117 chains. Longest chain 17 peptides. Score 0.420 Taking the results from Round 5 Chains 117, Residues 605, Estimated correctness of the model 32.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 48746 reflections ( 97.20 % complete ) and 24187 restraints for refining 11586 atoms. 21884 conditional restraints added. Observations/parameters ratio is 1.05 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2512 (Rfree = 0.000) for 11586 atoms. Found 141 (170 requested) and removed 88 (85 requested) atoms. Cycle 32: After refmac, R = 0.2143 (Rfree = 0.000) for 11607 atoms. Found 74 (171 requested) and removed 87 (85 requested) atoms. Cycle 33: After refmac, R = 0.1987 (Rfree = 0.000) for 11582 atoms. Found 49 (170 requested) and removed 86 (85 requested) atoms. Cycle 34: After refmac, R = 0.1933 (Rfree = 0.000) for 11541 atoms. Found 43 (169 requested) and removed 86 (84 requested) atoms. Cycle 35: After refmac, R = 0.1903 (Rfree = 0.000) for 11493 atoms. Found 32 (169 requested) and removed 84 (84 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.81 2.70 NCS extension: 55 residues added (5 deleted due to clashes), 11568 seeds are put forward Round 1: 716 peptides, 136 chains. Longest chain 15 peptides. Score 0.341 Round 2: 749 peptides, 125 chains. Longest chain 15 peptides. Score 0.413 Round 3: 728 peptides, 115 chains. Longest chain 21 peptides. Score 0.433 Round 4: 719 peptides, 118 chains. Longest chain 17 peptides. Score 0.414 Round 5: 757 peptides, 120 chains. Longest chain 15 peptides. Score 0.439 Taking the results from Round 5 Chains 120, Residues 637, Estimated correctness of the model 36.7 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 48746 reflections ( 97.20 % complete ) and 23932 restraints for refining 11586 atoms. 21479 conditional restraints added. Observations/parameters ratio is 1.05 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2303 (Rfree = 0.000) for 11586 atoms. Found 107 (170 requested) and removed 85 (85 requested) atoms. Cycle 37: After refmac, R = 0.2096 (Rfree = 0.000) for 11600 atoms. Found 58 (170 requested) and removed 85 (85 requested) atoms. Cycle 38: After refmac, R = 0.2008 (Rfree = 0.000) for 11563 atoms. Found 42 (170 requested) and removed 85 (85 requested) atoms. Cycle 39: After refmac, R = 0.1980 (Rfree = 0.000) for 11517 atoms. Found 36 (169 requested) and removed 84 (84 requested) atoms. Cycle 40: After refmac, R = 0.1936 (Rfree = 0.000) for 11465 atoms. Found 30 (168 requested) and removed 84 (84 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.81 2.70 NCS extension: 0 residues added, 11460 seeds are put forward Round 1: 638 peptides, 116 chains. Longest chain 14 peptides. Score 0.348 Round 2: 687 peptides, 113 chains. Longest chain 14 peptides. Score 0.405 Round 3: 700 peptides, 114 chains. Longest chain 24 peptides. Score 0.413 Round 4: 715 peptides, 117 chains. Longest chain 16 peptides. Score 0.414 Round 5: 681 peptides, 106 chains. Longest chain 16 peptides. Score 0.427 Taking the results from Round 5 Chains 106, Residues 575, Estimated correctness of the model 34.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 48746 reflections ( 97.20 % complete ) and 24332 restraints for refining 11585 atoms. 22138 conditional restraints added. Observations/parameters ratio is 1.05 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2393 (Rfree = 0.000) for 11585 atoms. Found 150 (170 requested) and removed 87 (85 requested) atoms. Cycle 42: After refmac, R = 0.2416 (Rfree = 0.000) for 11634 atoms. Found 171 (171 requested) and removed 87 (85 requested) atoms. Cycle 43: After refmac, R = 0.1976 (Rfree = 0.000) for 11696 atoms. Found 60 (172 requested) and removed 89 (86 requested) atoms. Cycle 44: After refmac, R = 0.2199 (Rfree = 0.000) for 11658 atoms. Found 161 (171 requested) and removed 86 (85 requested) atoms. Cycle 45: After refmac, R = 0.1887 (Rfree = 0.000) for 11726 atoms. Found 47 (172 requested) and removed 87 (86 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.82 2.71 NCS extension: 0 residues added, 11749 seeds are put forward Round 1: 628 peptides, 115 chains. Longest chain 13 peptides. Score 0.342 Round 2: 634 peptides, 106 chains. Longest chain 18 peptides. Score 0.385 Round 3: 683 peptides, 116 chains. Longest chain 11 peptides. Score 0.389 Round 4: 674 peptides, 110 chains. Longest chain 17 peptides. Score 0.405 Round 5: 689 peptides, 113 chains. Longest chain 15 peptides. Score 0.407 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 113, Residues 576, Estimated correctness of the model 30.0 % 1 chains (9 residues) have been docked in sequence Sequence coverage is 1 % Consider running further cycles of model building using 2awa-2_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 48746 reflections ( 97.20 % complete ) and 24159 restraints for refining 11586 atoms. 21936 conditional restraints added. Observations/parameters ratio is 1.05 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2356 (Rfree = 0.000) for 11586 atoms. Found 0 (170 requested) and removed 85 (85 requested) atoms. Cycle 47: After refmac, R = 0.2417 (Rfree = 0.000) for 11482 atoms. Found 0 (169 requested) and removed 84 (84 requested) atoms. Cycle 48: After refmac, R = 0.2407 (Rfree = 0.000) for 11389 atoms. Found 0 (167 requested) and removed 83 (83 requested) atoms. Cycle 49: After refmac, R = 0.2321 (Rfree = 0.000) for 11291 atoms. Found 0 (166 requested) and removed 83 (83 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 00:36:07 GMT 2018 Job finished. TimeTaking 133.14 Used memory is bytes: 20579496