null Tue 25 Dec 19:27:57 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 1vkm-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vkm-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vkm-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkm-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/1vkm-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkm-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 ============================================================ Tue 25 Dec 19:28:06 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/1vkm-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkm-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 1136 and 0 Target number of residues in the AU: 1136 Target solvent content: 0.6344 Checking the provided sequence file Detected sequence length: 297 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 6 Adjusted target number of residues: 1782 Adjusted target solvent content: 0.43 Input MTZ file: 1vkm-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: 19 Cell parameters: 91.732 131.100 139.844 90.000 90.000 90.000 Input sequence file: 1vkm-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 14256 target number of atoms Had to go as low as 0.60 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: 75.160 3.800 Wilson plot Bfac: 68.83 17186 reflections ( 99.97 % complete ) and 0 restraints for refining 15846 atoms. Observations/parameters ratio is 0.27 ------------------------------------------------------ Starting model: R = 0.3153 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3176 (Rfree = 0.000) for 15846 atoms. Found 87 (87 requested) and removed 137 (43 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.54 3.89 Search for helices and strands: 0 residues in 0 chains, 16142 seeds are put forward NCS extension: 0 residues added, 16142 seeds are put forward Round 1: 573 peptides, 118 chains. Longest chain 11 peptides. Score 0.282 Round 2: 782 peptides, 141 chains. Longest chain 21 peptides. Score 0.394 Round 3: 872 peptides, 132 chains. Longest chain 22 peptides. Score 0.508 Round 4: 887 peptides, 127 chains. Longest chain 26 peptides. Score 0.538 Round 5: 922 peptides, 131 chains. Longest chain 36 peptides. Score 0.551 Taking the results from Round 5 Chains 136, Residues 791, Estimated correctness of the model 0.0 % 7 chains (67 residues) have been docked in sequence ------------------------------------------------------ 17186 reflections ( 99.97 % complete ) and 30107 restraints for refining 12891 atoms. 26881 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2755 (Rfree = 0.000) for 12891 atoms. Found 63 (70 requested) and removed 130 (35 requested) atoms. Cycle 2: After refmac, R = 0.2526 (Rfree = 0.000) for 12609 atoms. Found 56 (70 requested) and removed 125 (35 requested) atoms. Cycle 3: After refmac, R = 0.2470 (Rfree = 0.000) for 12376 atoms. Found 60 (68 requested) and removed 93 (34 requested) atoms. Cycle 4: After refmac, R = 0.2360 (Rfree = 0.000) for 12235 atoms. Found 48 (67 requested) and removed 79 (33 requested) atoms. Cycle 5: After refmac, R = 0.2246 (Rfree = 0.000) for 12117 atoms. Found 42 (67 requested) and removed 70 (33 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.44 3.78 Search for helices and strands: 0 residues in 0 chains, 12539 seeds are put forward NCS extension: 39 residues added (1 deleted due to clashes), 12578 seeds are put forward Round 1: 753 peptides, 141 chains. Longest chain 16 peptides. Score 0.367 Round 2: 839 peptides, 132 chains. Longest chain 18 peptides. Score 0.480 Round 3: 915 peptides, 130 chains. Longest chain 25 peptides. Score 0.549 Round 4: 905 peptides, 125 chains. Longest chain 29 peptides. Score 0.559 Round 5: 957 peptides, 127 chains. Longest chain 21 peptides. Score 0.590 Taking the results from Round 5 Chains 131, Residues 830, Estimated correctness of the model 0.0 % 5 chains (34 residues) have been docked in sequence ------------------------------------------------------ 17186 reflections ( 99.97 % complete ) and 27505 restraints for refining 12185 atoms. 24242 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2369 (Rfree = 0.000) for 12185 atoms. Found 45 (67 requested) and removed 120 (33 requested) atoms. Cycle 7: After refmac, R = 0.2067 (Rfree = 0.000) for 12006 atoms. Found 42 (66 requested) and removed 79 (33 requested) atoms. Cycle 8: After refmac, R = 0.1950 (Rfree = 0.000) for 11911 atoms. Found 40 (65 requested) and removed 57 (32 requested) atoms. Cycle 9: After refmac, R = 0.1870 (Rfree = 0.000) for 11849 atoms. Found 46 (65 requested) and removed 58 (32 requested) atoms. Cycle 10: After refmac, R = 0.1922 (Rfree = 0.000) for 11797 atoms. Found 56 (65 requested) and removed 44 (32 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.43 3.77 Search for helices and strands: 0 residues in 0 chains, 12253 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 12274 seeds are put forward Round 1: 714 peptides, 131 chains. Longest chain 12 peptides. Score 0.370 Round 2: 851 peptides, 136 chains. Longest chain 19 peptides. Score 0.476 Round 3: 806 peptides, 123 chains. Longest chain 19 peptides. Score 0.486 Round 4: 850 peptides, 126 chains. Longest chain 16 peptides. Score 0.512 Round 5: 842 peptides, 120 chains. Longest chain 23 peptides. Score 0.527 Taking the results from Round 5 Chains 124, Residues 722, Estimated correctness of the model 0.0 % 8 chains (63 residues) have been docked in sequence ------------------------------------------------------ 17186 reflections ( 99.97 % complete ) and 27825 restraints for refining 12290 atoms. 24882 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2196 (Rfree = 0.000) for 12290 atoms. Found 58 (67 requested) and removed 137 (33 requested) atoms. Cycle 12: After refmac, R = 0.1976 (Rfree = 0.000) for 12120 atoms. Found 49 (67 requested) and removed 90 (33 requested) atoms. Cycle 13: After refmac, R = 0.1876 (Rfree = 0.000) for 12039 atoms. Found 38 (66 requested) and removed 71 (33 requested) atoms. Cycle 14: After refmac, R = 0.1660 (Rfree = 0.000) for 11983 atoms. Found 19 (66 requested) and removed 49 (33 requested) atoms. Cycle 15: After refmac, R = 0.1673 (Rfree = 0.000) for 11946 atoms. Found 9 (65 requested) and removed 46 (32 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.49 3.83 Search for helices and strands: 0 residues in 0 chains, 12343 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 12362 seeds are put forward Round 1: 754 peptides, 137 chains. Longest chain 21 peptides. Score 0.384 Round 2: 798 peptides, 127 chains. Longest chain 16 peptides. Score 0.464 Round 3: 816 peptides, 121 chains. Longest chain 21 peptides. Score 0.502 Round 4: 828 peptides, 124 chains. Longest chain 21 peptides. Score 0.501 Round 5: 848 peptides, 127 chains. Longest chain 19 peptides. Score 0.506 Taking the results from Round 5 Chains 127, Residues 721, Estimated correctness of the model 0.0 % 8 chains (33 residues) have been docked in sequence ------------------------------------------------------ 17186 reflections ( 99.97 % complete ) and 29439 restraints for refining 12737 atoms. 26620 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2159 (Rfree = 0.000) for 12737 atoms. Found 60 (70 requested) and removed 116 (35 requested) atoms. Cycle 17: After refmac, R = 0.2070 (Rfree = 0.000) for 12605 atoms. Found 69 (69 requested) and removed 92 (34 requested) atoms. Cycle 18: After refmac, R = 0.1917 (Rfree = 0.000) for 12532 atoms. Found 61 (69 requested) and removed 73 (34 requested) atoms. Cycle 19: After refmac, R = 0.1855 (Rfree = 0.000) for 12482 atoms. Found 61 (68 requested) and removed 63 (34 requested) atoms. Cycle 20: After refmac, R = 0.1829 (Rfree = 0.000) for 12459 atoms. Found 66 (68 requested) and removed 63 (34 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.48 3.82 Search for helices and strands: 0 residues in 0 chains, 12880 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 12899 seeds are put forward Round 1: 616 peptides, 129 chains. Longest chain 11 peptides. Score 0.279 Round 2: 764 peptides, 131 chains. Longest chain 15 peptides. Score 0.417 Round 3: 795 peptides, 127 chains. Longest chain 15 peptides. Score 0.461 Round 4: 785 peptides, 130 chains. Longest chain 20 peptides. Score 0.441 Round 5: 792 peptides, 126 chains. Longest chain 21 peptides. Score 0.462 Taking the results from Round 5 Chains 126, Residues 666, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 17186 reflections ( 99.97 % complete ) and 30439 restraints for refining 12843 atoms. 27879 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2101 (Rfree = 0.000) for 12843 atoms. Found 57 (70 requested) and removed 107 (35 requested) atoms. Cycle 22: After refmac, R = 0.1921 (Rfree = 0.000) for 12718 atoms. Found 50 (70 requested) and removed 71 (35 requested) atoms. Cycle 23: After refmac, R = 0.1884 (Rfree = 0.000) for 12646 atoms. Found 57 (69 requested) and removed 75 (34 requested) atoms. Cycle 24: After refmac, R = 0.1537 (Rfree = 0.000) for 12591 atoms. Found 8 (69 requested) and removed 45 (34 requested) atoms. Cycle 25: After refmac, R = 0.1464 (Rfree = 0.000) for 12543 atoms. Found 8 (69 requested) and removed 40 (34 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.45 3.79 Search for helices and strands: 0 residues in 0 chains, 12901 seeds are put forward NCS extension: 17 residues added (3 deleted due to clashes), 12918 seeds are put forward Round 1: 632 peptides, 129 chains. Longest chain 12 peptides. Score 0.295 Round 2: 719 peptides, 125 chains. Longest chain 22 peptides. Score 0.399 Round 3: 728 peptides, 125 chains. Longest chain 14 peptides. Score 0.408 Round 4: 743 peptides, 125 chains. Longest chain 15 peptides. Score 0.422 Round 5: 756 peptides, 125 chains. Longest chain 16 peptides. Score 0.434 Taking the results from Round 5 Chains 125, Residues 631, Estimated correctness of the model 0.0 % 5 chains (21 residues) have been docked in sequence ------------------------------------------------------ 17186 reflections ( 99.97 % complete ) and 30356 restraints for refining 12895 atoms. 27911 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1946 (Rfree = 0.000) for 12895 atoms. Found 45 (70 requested) and removed 97 (35 requested) atoms. Cycle 27: After refmac, R = 0.1854 (Rfree = 0.000) for 12787 atoms. Found 46 (70 requested) and removed 74 (35 requested) atoms. Cycle 28: After refmac, R = 0.1914 (Rfree = 0.000) for 12731 atoms. Found 67 (70 requested) and removed 61 (35 requested) atoms. Cycle 29: After refmac, R = 0.1791 (Rfree = 0.000) for 12714 atoms. Found 56 (70 requested) and removed 51 (35 requested) atoms. Cycle 30: After refmac, R = 0.1585 (Rfree = 0.000) for 12703 atoms. Found 14 (69 requested) and removed 46 (34 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.50 3.84 Search for helices and strands: 0 residues in 0 chains, 13068 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 13083 seeds are put forward Round 1: 623 peptides, 131 chains. Longest chain 10 peptides. Score 0.277 Round 2: 680 peptides, 122 chains. Longest chain 13 peptides. Score 0.374 Round 3: 703 peptides, 121 chains. Longest chain 19 peptides. Score 0.401 Round 4: 724 peptides, 120 chains. Longest chain 18 peptides. Score 0.424 Round 5: 707 peptides, 118 chains. Longest chain 13 peptides. Score 0.417 Taking the results from Round 4 Chains 120, Residues 604, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 17186 reflections ( 99.97 % complete ) and 30306 restraints for refining 12893 atoms. 28010 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2010 (Rfree = 0.000) for 12893 atoms. Found 53 (70 requested) and removed 87 (35 requested) atoms. Cycle 32: After refmac, R = 0.1916 (Rfree = 0.000) for 12820 atoms. Found 70 (70 requested) and removed 76 (35 requested) atoms. Cycle 33: After refmac, R = 0.1892 (Rfree = 0.000) for 12797 atoms. Found 70 (70 requested) and removed 61 (35 requested) atoms. Cycle 34: After refmac, R = 0.1538 (Rfree = 0.000) for 12787 atoms. Found 16 (70 requested) and removed 49 (35 requested) atoms. Cycle 35: After refmac, R = 0.1489 (Rfree = 0.000) for 12744 atoms. Found 10 (70 requested) and removed 48 (35 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.48 3.82 Search for helices and strands: 0 residues in 0 chains, 13070 seeds are put forward NCS extension: 11 residues added (2 deleted due to clashes), 13081 seeds are put forward Round 1: 574 peptides, 120 chains. Longest chain 11 peptides. Score 0.274 Round 2: 662 peptides, 122 chains. Longest chain 16 peptides. Score 0.356 Round 3: 663 peptides, 119 chains. Longest chain 14 peptides. Score 0.370 Round 4: 677 peptides, 113 chains. Longest chain 16 peptides. Score 0.409 Round 5: 687 peptides, 111 chains. Longest chain 20 peptides. Score 0.426 Taking the results from Round 5 Chains 112, Residues 576, Estimated correctness of the model 0.0 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 17186 reflections ( 99.97 % complete ) and 30481 restraints for refining 12895 atoms. 28227 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2000 (Rfree = 0.000) for 12895 atoms. Found 57 (70 requested) and removed 82 (35 requested) atoms. Cycle 37: After refmac, R = 0.1927 (Rfree = 0.000) for 12832 atoms. Found 65 (70 requested) and removed 53 (35 requested) atoms. Cycle 38: After refmac, R = 0.1891 (Rfree = 0.000) for 12819 atoms. Found 63 (70 requested) and removed 50 (35 requested) atoms. Cycle 39: After refmac, R = 0.1803 (Rfree = 0.000) for 12817 atoms. Found 56 (70 requested) and removed 52 (35 requested) atoms. Cycle 40: After refmac, R = 0.1830 (Rfree = 0.000) for 12808 atoms. Found 64 (70 requested) and removed 59 (35 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.45 3.79 Search for helices and strands: 0 residues in 0 chains, 13166 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 13184 seeds are put forward Round 1: 556 peptides, 116 chains. Longest chain 12 peptides. Score 0.272 Round 2: 635 peptides, 119 chains. Longest chain 13 peptides. Score 0.342 Round 3: 636 peptides, 114 chains. Longest chain 16 peptides. Score 0.365 Round 4: 645 peptides, 112 chains. Longest chain 15 peptides. Score 0.382 Round 5: 647 peptides, 112 chains. Longest chain 16 peptides. Score 0.384 Taking the results from Round 5 Chains 112, Residues 535, Estimated correctness of the model 0.0 % 8 chains (33 residues) have been docked in sequence ------------------------------------------------------ 17186 reflections ( 99.97 % complete ) and 30294 restraints for refining 12893 atoms. 28187 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2064 (Rfree = 0.000) for 12893 atoms. Found 58 (70 requested) and removed 73 (35 requested) atoms. Cycle 42: After refmac, R = 0.1978 (Rfree = 0.000) for 12846 atoms. Found 66 (70 requested) and removed 59 (35 requested) atoms. Cycle 43: After refmac, R = 0.1620 (Rfree = 0.000) for 12829 atoms. Found 16 (70 requested) and removed 45 (35 requested) atoms. Cycle 44: After refmac, R = 0.1764 (Rfree = 0.000) for 12787 atoms. Found 45 (70 requested) and removed 56 (35 requested) atoms. Cycle 45: After refmac, R = 0.1855 (Rfree = 0.000) for 12767 atoms. Found 55 (70 requested) and removed 50 (35 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.45 3.79 Search for helices and strands: 0 residues in 0 chains, 13055 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 13071 seeds are put forward Round 1: 508 peptides, 108 chains. Longest chain 11 peptides. Score 0.256 Round 2: 585 peptides, 107 chains. Longest chain 11 peptides. Score 0.343 Round 3: 576 peptides, 103 chains. Longest chain 15 peptides. Score 0.352 Round 4: 572 peptides, 102 chains. Longest chain 13 peptides. Score 0.352 Round 5: 563 peptides, 98 chains. Longest chain 16 peptides. Score 0.361 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 98, Residues 465, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence Sequence coverage is 1 % Consider running further cycles of model building using 1vkm-3_warpNtrace.pdb as input Building loops using Loopy2018 98 chains (465 residues) following loop building 2 chains (6 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 17186 reflections ( 99.97 % complete ) and 31010 restraints for refining 12894 atoms. 29239 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2031 (Rfree = 0.000) for 12894 atoms. Found 0 (70 requested) and removed 35 (35 requested) atoms. Cycle 47: After refmac, R = 0.2034 (Rfree = 0.000) for 12819 atoms. Found 0 (70 requested) and removed 35 (35 requested) atoms. Cycle 48: After refmac, R = 0.1521 (Rfree = 0.000) for 12768 atoms. Found 0 (70 requested) and removed 35 (35 requested) atoms. Cycle 49: After refmac, R = 0.1449 (Rfree = 0.000) for 12723 atoms. Found 0 (70 requested) and removed 35 (35 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 22:08:25 GMT 2018 Job finished. TimeTaking 160.48 Used memory is bytes: 9823192