Mon 24 Dec 07:39:54 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vkd-4.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vkd-4.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vkd-4.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkd-4.0-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/1vkd-4.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkd-4.0-parrot-noncs ############### 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 07:39:59 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/noncs/ArpWArp/wArpResults/WorkingDir/1vkd-4.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkd-4.0-parrot-noncs/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 1592 and 0 Target number of residues in the AU: 1592 Target solvent content: 0.6169 Checking the provided sequence file Detected sequence length: 338 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 6 Adjusted target number of residues: 2028 Adjusted target solvent content: 0.51 Input MTZ file: 1vkd-4.0-parrot-noncs.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: 86.922 101.512 254.880 90.000 90.000 90.000 Input sequence file: 1vkd-4.0-parrot-noncs.fasta_lf Building free atoms model in initial map for 16224 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: 127.440 4.000 Wilson plot Bfac: 59.94 19706 reflections ( 99.63 % complete ) and 0 restraints for refining 17916 atoms. Observations/parameters ratio is 0.27 ------------------------------------------------------ Starting model: R = 0.3275 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3011 (Rfree = 0.000) for 17916 atoms. Found 85 (85 requested) and removed 109 (42 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.44 3.39 Search for helices and strands: 0 residues in 0 chains, 18062 seeds are put forward NCS extension: 0 residues added, 18062 seeds are put forward Round 1: 674 peptides, 141 chains. Longest chain 10 peptides. Score 0.264 Round 2: 929 peptides, 163 chains. Longest chain 19 peptides. Score 0.389 Round 3: 1020 peptides, 169 chains. Longest chain 18 peptides. Score 0.435 Round 4: 1058 peptides, 166 chains. Longest chain 18 peptides. Score 0.469 Round 5: 1061 peptides, 160 chains. Longest chain 17 peptides. Score 0.488 Taking the results from Round 5 Chains 162, Residues 901, Estimated correctness of the model 0.0 % 11 chains (70 residues) have been docked in sequence ------------------------------------------------------ 19706 reflections ( 99.63 % complete ) and 33838 restraints for refining 14650 atoms. 30193 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2383 (Rfree = 0.000) for 14650 atoms. Found 53 (69 requested) and removed 100 (34 requested) atoms. Cycle 2: After refmac, R = 0.2361 (Rfree = 0.000) for 14354 atoms. Found 62 (69 requested) and removed 88 (34 requested) atoms. Failed to save intermediate PDB Cycle 3: After refmac, R = 0.2222 (Rfree = 0.000) for 14184 atoms. Found 68 (68 requested) and removed 102 (34 requested) atoms. Cycle 4: After refmac, R = 0.1822 (Rfree = 0.000) for 14057 atoms. Found 22 (67 requested) and removed 59 (33 requested) atoms. Failed to save intermediate PDB Cycle 5: After refmac, R = 0.1701 (Rfree = 0.000) for 13962 atoms. Found 20 (66 requested) and removed 51 (33 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.46 3.41 Search for helices and strands: 0 residues in 0 chains, 14215 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 14232 seeds are put forward Round 1: 904 peptides, 171 chains. Longest chain 14 peptides. Score 0.345 Round 2: 1042 peptides, 167 chains. Longest chain 17 peptides. Score 0.455 Round 3: 1060 peptides, 162 chains. Longest chain 23 peptides. Score 0.481 Round 4: 1050 peptides, 148 chains. Longest chain 25 peptides. Score 0.514 Round 5: 1083 peptides, 150 chains. Longest chain 20 peptides. Score 0.529 Taking the results from Round 5 Chains 155, Residues 933, Estimated correctness of the model 0.0 % 7 chains (56 residues) have been docked in sequence ------------------------------------------------------ 19706 reflections ( 99.63 % complete ) and 33825 restraints for refining 14652 atoms. 30061 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2127 (Rfree = 0.000) for 14652 atoms. Found 69 (69 requested) and removed 117 (34 requested) atoms. Cycle 7: After refmac, R = 0.2031 (Rfree = 0.000) for 14458 atoms. Found 69 (69 requested) and removed 98 (34 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.1668 (Rfree = 0.000) for 14344 atoms. Found 27 (68 requested) and removed 70 (34 requested) atoms. Cycle 9: After refmac, R = 0.1568 (Rfree = 0.000) for 14249 atoms. Found 19 (67 requested) and removed 70 (33 requested) atoms. Cycle 10: After refmac, R = 0.1700 (Rfree = 0.000) for 14165 atoms. Found 31 (67 requested) and removed 55 (33 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.46 3.41 Search for helices and strands: 0 residues in 0 chains, 14403 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 14423 seeds are put forward Round 1: 886 peptides, 163 chains. Longest chain 13 peptides. Score 0.357 Round 2: 980 peptides, 155 chains. Longest chain 21 peptides. Score 0.449 Round 3: 1044 peptides, 158 chains. Longest chain 18 peptides. Score 0.482 Round 4: 1065 peptides, 159 chains. Longest chain 23 peptides. Score 0.493 Round 5: 1060 peptides, 149 chains. Longest chain 21 peptides. Score 0.517 Taking the results from Round 5 Chains 152, Residues 911, Estimated correctness of the model 0.0 % 10 chains (84 residues) have been docked in sequence ------------------------------------------------------ 19706 reflections ( 99.63 % complete ) and 33017 restraints for refining 14652 atoms. 29215 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2097 (Rfree = 0.000) for 14652 atoms. Found 58 (69 requested) and removed 88 (34 requested) atoms. Cycle 12: After refmac, R = 0.2020 (Rfree = 0.000) for 14474 atoms. Found 69 (69 requested) and removed 85 (34 requested) atoms. Cycle 13: After refmac, R = 0.1914 (Rfree = 0.000) for 14370 atoms. Found 57 (68 requested) and removed 76 (34 requested) atoms. Cycle 14: After refmac, R = 0.1543 (Rfree = 0.000) for 14294 atoms. Found 14 (68 requested) and removed 58 (34 requested) atoms. Cycle 15: After refmac, R = 0.1484 (Rfree = 0.000) for 14223 atoms. Found 8 (67 requested) and removed 45 (33 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.46 3.41 Search for helices and strands: 0 residues in 0 chains, 14507 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 14524 seeds are put forward Round 1: 927 peptides, 178 chains. Longest chain 14 peptides. Score 0.340 Round 2: 991 peptides, 159 chains. Longest chain 14 peptides. Score 0.444 Round 3: 1063 peptides, 172 chains. Longest chain 17 peptides. Score 0.455 Round 4: 1049 peptides, 160 chains. Longest chain 14 peptides. Score 0.480 Round 5: 1064 peptides, 163 chains. Longest chain 16 peptides. Score 0.481 Taking the results from Round 5 Chains 165, Residues 901, Estimated correctness of the model 0.0 % 6 chains (31 residues) have been docked in sequence ------------------------------------------------------ 19706 reflections ( 99.63 % complete ) and 33937 restraints for refining 14651 atoms. 30412 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1989 (Rfree = 0.000) for 14651 atoms. Found 42 (69 requested) and removed 84 (34 requested) atoms. Cycle 17: After refmac, R = 0.1927 (Rfree = 0.000) for 14491 atoms. Found 69 (69 requested) and removed 85 (34 requested) atoms. Cycle 18: After refmac, R = 0.1963 (Rfree = 0.000) for 14413 atoms. Found 68 (68 requested) and removed 77 (34 requested) atoms. Cycle 19: After refmac, R = 0.1900 (Rfree = 0.000) for 14363 atoms. Found 68 (68 requested) and removed 62 (34 requested) atoms. Cycle 20: After refmac, R = 0.1844 (Rfree = 0.000) for 14326 atoms. Found 68 (68 requested) and removed 62 (34 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.43 3.38 Search for helices and strands: 0 residues in 0 chains, 14609 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 14625 seeds are put forward Round 1: 854 peptides, 164 chains. Longest chain 16 peptides. Score 0.330 Round 2: 937 peptides, 153 chains. Longest chain 16 peptides. Score 0.425 Round 3: 964 peptides, 156 chains. Longest chain 18 peptides. Score 0.435 Round 4: 994 peptides, 148 chains. Longest chain 18 peptides. Score 0.478 Round 5: 980 peptides, 142 chains. Longest chain 22 peptides. Score 0.487 Taking the results from Round 5 Chains 145, Residues 838, Estimated correctness of the model 0.0 % 14 chains (80 residues) have been docked in sequence ------------------------------------------------------ 19706 reflections ( 99.63 % complete ) and 33813 restraints for refining 14648 atoms. 30378 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2113 (Rfree = 0.000) for 14648 atoms. Found 69 (69 requested) and removed 90 (34 requested) atoms. Cycle 22: After refmac, R = 0.2013 (Rfree = 0.000) for 14512 atoms. Found 62 (69 requested) and removed 79 (34 requested) atoms. Cycle 23: After refmac, R = 0.1962 (Rfree = 0.000) for 14418 atoms. Found 68 (68 requested) and removed 76 (34 requested) atoms. Cycle 24: After refmac, R = 0.1892 (Rfree = 0.000) for 14357 atoms. Found 68 (68 requested) and removed 68 (34 requested) atoms. Cycle 25: After refmac, R = 0.1887 (Rfree = 0.000) for 14337 atoms. Found 68 (68 requested) and removed 68 (34 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.45 3.40 Search for helices and strands: 0 residues in 0 chains, 14538 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 14555 seeds are put forward Round 1: 784 peptides, 154 chains. Longest chain 13 peptides. Score 0.308 Round 2: 897 peptides, 149 chains. Longest chain 13 peptides. Score 0.409 Round 3: 904 peptides, 135 chains. Longest chain 21 peptides. Score 0.457 Round 4: 935 peptides, 138 chains. Longest chain 19 peptides. Score 0.469 Round 5: 946 peptides, 145 chains. Longest chain 15 peptides. Score 0.455 Taking the results from Round 4 Chains 141, Residues 797, Estimated correctness of the model 0.0 % 8 chains (47 residues) have been docked in sequence ------------------------------------------------------ 19706 reflections ( 99.63 % complete ) and 34454 restraints for refining 14652 atoms. 31248 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2011 (Rfree = 0.000) for 14652 atoms. Found 62 (69 requested) and removed 101 (34 requested) atoms. Cycle 27: After refmac, R = 0.2030 (Rfree = 0.000) for 14548 atoms. Found 69 (69 requested) and removed 83 (34 requested) atoms. Cycle 28: After refmac, R = 0.1907 (Rfree = 0.000) for 14495 atoms. Found 67 (69 requested) and removed 72 (34 requested) atoms. Cycle 29: After refmac, R = 0.1479 (Rfree = 0.000) for 14450 atoms. Found 12 (68 requested) and removed 47 (34 requested) atoms. Cycle 30: After refmac, R = 0.1409 (Rfree = 0.000) for 14390 atoms. Found 11 (68 requested) and removed 49 (34 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.44 3.39 Search for helices and strands: 0 residues in 0 chains, 14612 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 14624 seeds are put forward Round 1: 845 peptides, 163 chains. Longest chain 13 peptides. Score 0.326 Round 2: 937 peptides, 159 chains. Longest chain 20 peptides. Score 0.407 Round 3: 908 peptides, 146 chains. Longest chain 16 peptides. Score 0.426 Round 4: 896 peptides, 145 chains. Longest chain 18 peptides. Score 0.421 Round 5: 889 peptides, 144 chains. Longest chain 20 peptides. Score 0.419 Taking the results from Round 3 Chains 147, Residues 762, Estimated correctness of the model 0.0 % 3 chains (22 residues) have been docked in sequence ------------------------------------------------------ 19706 reflections ( 99.63 % complete ) and 34436 restraints for refining 14649 atoms. 31448 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1924 (Rfree = 0.000) for 14649 atoms. Found 61 (69 requested) and removed 80 (34 requested) atoms. Cycle 32: After refmac, R = 0.1951 (Rfree = 0.000) for 14541 atoms. Found 69 (69 requested) and removed 68 (34 requested) atoms. Cycle 33: After refmac, R = 0.1926 (Rfree = 0.000) for 14492 atoms. Found 69 (69 requested) and removed 62 (34 requested) atoms. Cycle 34: After refmac, R = 0.1852 (Rfree = 0.000) for 14451 atoms. Found 68 (68 requested) and removed 51 (34 requested) atoms. Cycle 35: After refmac, R = 0.1817 (Rfree = 0.000) for 14427 atoms. Found 68 (68 requested) and removed 60 (34 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.45 3.40 Search for helices and strands: 0 residues in 0 chains, 14637 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 14652 seeds are put forward Round 1: 746 peptides, 151 chains. Longest chain 11 peptides. Score 0.288 Round 2: 847 peptides, 147 chains. Longest chain 15 peptides. Score 0.379 Round 3: 863 peptides, 149 chains. Longest chain 12 peptides. Score 0.385 Round 4: 869 peptides, 137 chains. Longest chain 21 peptides. Score 0.427 Round 5: 886 peptides, 147 chains. Longest chain 22 peptides. Score 0.408 Taking the results from Round 4 Chains 138, Residues 732, Estimated correctness of the model 0.0 % 5 chains (39 residues) have been docked in sequence ------------------------------------------------------ 19706 reflections ( 99.63 % complete ) and 34466 restraints for refining 14652 atoms. 31540 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2092 (Rfree = 0.000) for 14652 atoms. Found 69 (69 requested) and removed 91 (34 requested) atoms. Failed to save intermediate PDB Cycle 37: After refmac, R = 0.1888 (Rfree = 0.000) for 14552 atoms. Found 68 (69 requested) and removed 83 (34 requested) atoms. Cycle 38: After refmac, R = 0.1810 (Rfree = 0.000) for 14492 atoms. Found 69 (69 requested) and removed 59 (34 requested) atoms. Cycle 39: After refmac, R = 0.1902 (Rfree = 0.000) for 14463 atoms. Found 68 (68 requested) and removed 68 (34 requested) atoms. Cycle 40: After refmac, R = 0.1406 (Rfree = 0.000) for 14438 atoms. Found 26 (68 requested) and removed 46 (34 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.42 3.37 Search for helices and strands: 0 residues in 0 chains, 14647 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 14664 seeds are put forward Round 1: 688 peptides, 143 chains. Longest chain 11 peptides. Score 0.268 Round 2: 782 peptides, 140 chains. Longest chain 21 peptides. Score 0.353 Round 3: 825 peptides, 141 chains. Longest chain 15 peptides. Score 0.382 Round 4: 823 peptides, 141 chains. Longest chain 15 peptides. Score 0.381 Round 5: 858 peptides, 141 chains. Longest chain 14 peptides. Score 0.406 Taking the results from Round 5 Chains 141, Residues 717, Estimated correctness of the model 0.0 % 5 chains (35 residues) have been docked in sequence ------------------------------------------------------ 19706 reflections ( 99.63 % complete ) and 34466 restraints for refining 14652 atoms. 31634 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1882 (Rfree = 0.000) for 14652 atoms. Found 48 (69 requested) and removed 72 (34 requested) atoms. Cycle 42: After refmac, R = 0.2002 (Rfree = 0.000) for 14549 atoms. Found 69 (69 requested) and removed 75 (34 requested) atoms. Cycle 43: After refmac, R = 0.1991 (Rfree = 0.000) for 14495 atoms. Found 69 (69 requested) and removed 71 (34 requested) atoms. Failed to save intermediate PDB Cycle 44: After refmac, R = 0.1996 (Rfree = 0.000) for 14456 atoms. Found 68 (68 requested) and removed 71 (34 requested) atoms. Failed to save intermediate PDB Cycle 45: After refmac, R = 0.1924 (Rfree = 0.000) for 14412 atoms. Found 68 (68 requested) and removed 68 (34 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.38 3.34 Search for helices and strands: 0 residues in 0 chains, 14641 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 14659 seeds are put forward Round 1: 627 peptides, 134 chains. Longest chain 11 peptides. Score 0.249 Round 2: 712 peptides, 132 chains. Longest chain 12 peptides. Score 0.326 Round 3: 763 peptides, 136 chains. Longest chain 16 peptides. Score 0.352 Round 4: 744 peptides, 126 chains. Longest chain 15 peptides. Score 0.371 Round 5: 743 peptides, 126 chains. Longest chain 14 peptides. Score 0.370 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 126, Residues 618, Estimated correctness of the model 0.0 % 8 chains (50 residues) have been docked in sequence Sequence coverage is 8 % Consider running further cycles of model building using 1vkd-4_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 302 B and 316 B 126 chains (629 residues) following loop building 7 chains (63 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 19706 reflections ( 99.63 % complete ) and 34119 restraints for refining 14542 atoms. 31551 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1971 (Rfree = 0.000) for 14542 atoms. Found 0 (69 requested) and removed 34 (34 requested) atoms. Cycle 47: After refmac, R = 0.2001 (Rfree = 0.000) for 14445 atoms. Found 0 (68 requested) and removed 34 (34 requested) atoms. Cycle 48: After refmac, R = 0.1929 (Rfree = 0.000) for 14364 atoms. Found 0 (68 requested) and removed 34 (34 requested) atoms. Cycle 49: After refmac, R = 0.1785 (Rfree = 0.000) for 14288 atoms. TimeTaking 138.43