null Mon 24 Dec 07:34:25 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 1vkm-4.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vkm-4.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vkm-4.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkm-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/1vkm-4.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkm-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 07:34:29 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/1vkm-4.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkm-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 1100 and 0 Target number of residues in the AU: 1100 Target solvent content: 0.6460 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-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: 91.732 131.100 139.844 90.000 90.000 90.000 Input sequence file: 1vkm-4.0-parrot-noncs.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 4.000 Wilson plot Bfac: 75.51 14774 reflections ( 99.96 % complete ) and 0 restraints for refining 15834 atoms. Observations/parameters ratio is 0.23 ------------------------------------------------------ Starting model: R = 0.3297 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3127 (Rfree = 0.000) for 15834 atoms. Found 75 (75 requested) and removed 154 (37 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.69 4.05 Search for helices and strands: 0 residues in 0 chains, 16080 seeds are put forward NCS extension: 0 residues added, 16080 seeds are put forward Round 1: 478 peptides, 104 chains. Longest chain 9 peptides. Score 0.241 Round 2: 656 peptides, 124 chains. Longest chain 18 peptides. Score 0.342 Round 3: 709 peptides, 126 chains. Longest chain 12 peptides. Score 0.386 Round 4: 764 peptides, 125 chains. Longest chain 15 peptides. Score 0.441 Round 5: 804 peptides, 123 chains. Longest chain 18 peptides. Score 0.484 Taking the results from Round 5 Chains 125, Residues 681, Estimated correctness of the model 0.0 % 11 chains (57 residues) have been docked in sequence ------------------------------------------------------ 14774 reflections ( 99.96 % complete ) and 30920 restraints for refining 12864 atoms. 28189 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2731 (Rfree = 0.000) for 12864 atoms. Found 32 (61 requested) and removed 110 (30 requested) atoms. Cycle 2: After refmac, R = 0.2307 (Rfree = 0.000) for 12551 atoms. Found 26 (60 requested) and removed 97 (30 requested) atoms. Cycle 3: After refmac, R = 0.2180 (Rfree = 0.000) for 12367 atoms. Found 18 (59 requested) and removed 61 (29 requested) atoms. Cycle 4: After refmac, R = 0.2101 (Rfree = 0.000) for 12249 atoms. Found 18 (58 requested) and removed 58 (29 requested) atoms. Cycle 5: After refmac, R = 0.2041 (Rfree = 0.000) for 12171 atoms. Found 9 (58 requested) and removed 54 (29 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.63 3.99 Search for helices and strands: 0 residues in 0 chains, 12575 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 12589 seeds are put forward Round 1: 642 peptides, 128 chains. Longest chain 10 peptides. Score 0.310 Round 2: 758 peptides, 128 chains. Longest chain 19 peptides. Score 0.424 Round 3: 763 peptides, 128 chains. Longest chain 16 peptides. Score 0.428 Round 4: 798 peptides, 124 chains. Longest chain 16 peptides. Score 0.475 Round 5: 781 peptides, 118 chains. Longest chain 20 peptides. Score 0.483 Taking the results from Round 5 Chains 119, Residues 663, Estimated correctness of the model 0.0 % 5 chains (35 residues) have been docked in sequence ------------------------------------------------------ 14774 reflections ( 99.96 % complete ) and 28769 restraints for refining 12136 atoms. 26155 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2221 (Rfree = 0.000) for 12136 atoms. Found 35 (57 requested) and removed 100 (28 requested) atoms. Cycle 7: After refmac, R = 0.1982 (Rfree = 0.000) for 11990 atoms. Found 20 (57 requested) and removed 74 (28 requested) atoms. Cycle 8: After refmac, R = 0.1887 (Rfree = 0.000) for 11894 atoms. Found 4 (56 requested) and removed 57 (28 requested) atoms. Cycle 9: After refmac, R = 0.1853 (Rfree = 0.000) for 11828 atoms. Found 6 (56 requested) and removed 45 (28 requested) atoms. Cycle 10: After refmac, R = 0.1838 (Rfree = 0.000) for 11780 atoms. Found 5 (56 requested) and removed 45 (28 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.67 4.03 Search for helices and strands: 0 residues in 0 chains, 12187 seeds are put forward NCS extension: 28 residues added (2 deleted due to clashes), 12215 seeds are put forward Round 1: 683 peptides, 133 chains. Longest chain 11 peptides. Score 0.331 Round 2: 748 peptides, 121 chains. Longest chain 25 peptides. Score 0.442 Round 3: 775 peptides, 125 chains. Longest chain 14 peptides. Score 0.451 Round 4: 789 peptides, 119 chains. Longest chain 15 peptides. Score 0.486 Round 5: 772 peptides, 120 chains. Longest chain 17 peptides. Score 0.468 Taking the results from Round 4 Chains 119, Residues 670, Estimated correctness of the model 0.0 % 2 chains (14 residues) have been docked in sequence ------------------------------------------------------ 14774 reflections ( 99.96 % complete ) and 28990 restraints for refining 12323 atoms. 26393 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2138 (Rfree = 0.000) for 12323 atoms. Found 19 (58 requested) and removed 117 (29 requested) atoms. Cycle 12: After refmac, R = 0.2027 (Rfree = 0.000) for 12153 atoms. Found 18 (58 requested) and removed 74 (29 requested) atoms. Cycle 13: After refmac, R = 0.1982 (Rfree = 0.000) for 12072 atoms. Found 6 (57 requested) and removed 64 (28 requested) atoms. Cycle 14: After refmac, R = 0.1967 (Rfree = 0.000) for 12004 atoms. Found 5 (57 requested) and removed 50 (28 requested) atoms. Cycle 15: After refmac, R = 0.1986 (Rfree = 0.000) for 11954 atoms. Found 5 (56 requested) and removed 41 (28 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.68 4.04 Search for helices and strands: 0 residues in 0 chains, 12331 seeds are put forward NCS extension: 12 residues added (2 deleted due to clashes), 12343 seeds are put forward Round 1: 674 peptides, 134 chains. Longest chain 13 peptides. Score 0.317 Round 2: 757 peptides, 127 chains. Longest chain 13 peptides. Score 0.427 Round 3: 810 peptides, 127 chains. Longest chain 18 peptides. Score 0.474 Round 4: 783 peptides, 117 chains. Longest chain 20 peptides. Score 0.489 Round 5: 778 peptides, 122 chains. Longest chain 14 peptides. Score 0.465 Taking the results from Round 4 Chains 121, Residues 666, Estimated correctness of the model 0.0 % 4 chains (33 residues) have been docked in sequence ------------------------------------------------------ 14774 reflections ( 99.96 % complete ) and 29997 restraints for refining 12654 atoms. 27368 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2568 (Rfree = 0.000) for 12654 atoms. Found 54 (60 requested) and removed 152 (30 requested) atoms. Cycle 17: After refmac, R = 0.2241 (Rfree = 0.000) for 12473 atoms. Found 40 (59 requested) and removed 91 (29 requested) atoms. Cycle 18: After refmac, R = 0.2027 (Rfree = 0.000) for 12318 atoms. Found 36 (59 requested) and removed 81 (29 requested) atoms. Cycle 19: After refmac, R = 0.1991 (Rfree = 0.000) for 12212 atoms. Found 32 (58 requested) and removed 59 (29 requested) atoms. Cycle 20: After refmac, R = 0.1992 (Rfree = 0.000) for 12126 atoms. Found 25 (57 requested) and removed 49 (28 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.64 4.00 Search for helices and strands: 0 residues in 0 chains, 12534 seeds are put forward NCS extension: 17 residues added (4 deleted due to clashes), 12551 seeds are put forward Round 1: 587 peptides, 121 chains. Longest chain 10 peptides. Score 0.283 Round 2: 661 peptides, 129 chains. Longest chain 12 peptides. Score 0.325 Round 3: 684 peptides, 125 chains. Longest chain 15 peptides. Score 0.365 Round 4: 687 peptides, 125 chains. Longest chain 20 peptides. Score 0.368 Round 5: 716 peptides, 124 chains. Longest chain 17 peptides. Score 0.401 Taking the results from Round 5 Chains 124, Residues 592, Estimated correctness of the model 0.0 % 7 chains (27 residues) have been docked in sequence ------------------------------------------------------ 14774 reflections ( 99.96 % complete ) and 28714 restraints for refining 12244 atoms. 26425 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2094 (Rfree = 0.000) for 12244 atoms. Found 40 (58 requested) and removed 136 (29 requested) atoms. Cycle 22: After refmac, R = 0.2046 (Rfree = 0.000) for 12096 atoms. Found 51 (57 requested) and removed 91 (28 requested) atoms. Cycle 23: After refmac, R = 0.2038 (Rfree = 0.000) for 12017 atoms. Found 57 (57 requested) and removed 68 (28 requested) atoms. Cycle 24: After refmac, R = 0.2000 (Rfree = 0.000) for 11957 atoms. Found 57 (57 requested) and removed 84 (28 requested) atoms. Cycle 25: After refmac, R = 0.1960 (Rfree = 0.000) for 11903 atoms. Found 47 (56 requested) and removed 59 (28 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.56 3.91 Search for helices and strands: 0 residues in 0 chains, 12326 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 12343 seeds are put forward Round 1: 542 peptides, 120 chains. Longest chain 10 peptides. Score 0.238 Round 2: 657 peptides, 126 chains. Longest chain 11 peptides. Score 0.334 Round 3: 663 peptides, 121 chains. Longest chain 15 peptides. Score 0.362 Round 4: 664 peptides, 117 chains. Longest chain 14 peptides. Score 0.380 Round 5: 669 peptides, 118 chains. Longest chain 16 peptides. Score 0.380 Taking the results from Round 5 Chains 118, Residues 551, Estimated correctness of the model 0.0 % 3 chains (17 residues) have been docked in sequence ------------------------------------------------------ 14774 reflections ( 99.96 % complete ) and 28058 restraints for refining 12177 atoms. 25928 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2076 (Rfree = 0.000) for 12177 atoms. Found 38 (57 requested) and removed 125 (28 requested) atoms. Cycle 27: After refmac, R = 0.1872 (Rfree = 0.000) for 12000 atoms. Found 32 (57 requested) and removed 64 (28 requested) atoms. Cycle 28: After refmac, R = 0.1957 (Rfree = 0.000) for 11926 atoms. Found 46 (56 requested) and removed 66 (28 requested) atoms. Cycle 29: After refmac, R = 0.1856 (Rfree = 0.000) for 11875 atoms. Found 56 (56 requested) and removed 63 (28 requested) atoms. Cycle 30: After refmac, R = 0.1436 (Rfree = 0.000) for 11843 atoms. Found 8 (56 requested) and removed 51 (28 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.57 3.92 Search for helices and strands: 0 residues in 0 chains, 12137 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 12163 seeds are put forward Round 1: 556 peptides, 119 chains. Longest chain 12 peptides. Score 0.259 Round 2: 643 peptides, 121 chains. Longest chain 13 peptides. Score 0.342 Round 3: 691 peptides, 129 chains. Longest chain 11 peptides. Score 0.356 Round 4: 695 peptides, 123 chains. Longest chain 17 peptides. Score 0.385 Round 5: 686 peptides, 119 chains. Longest chain 13 peptides. Score 0.393 Taking the results from Round 5 Chains 119, Residues 567, Estimated correctness of the model 0.0 % 7 chains (35 residues) have been docked in sequence ------------------------------------------------------ 14774 reflections ( 99.96 % complete ) and 28441 restraints for refining 12358 atoms. 26213 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2158 (Rfree = 0.000) for 12358 atoms. Found 58 (58 requested) and removed 150 (29 requested) atoms. Cycle 32: After refmac, R = 0.1881 (Rfree = 0.000) for 12211 atoms. Found 55 (58 requested) and removed 84 (29 requested) atoms. Cycle 33: After refmac, R = 0.2090 (Rfree = 0.000) for 12138 atoms. Found 57 (57 requested) and removed 95 (28 requested) atoms. Cycle 34: After refmac, R = 0.1991 (Rfree = 0.000) for 12062 atoms. Found 57 (57 requested) and removed 73 (28 requested) atoms. Cycle 35: After refmac, R = 0.1839 (Rfree = 0.000) for 12005 atoms. Found 57 (57 requested) and removed 54 (28 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.58 3.93 Search for helices and strands: 0 residues in 0 chains, 12328 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 12343 seeds are put forward Round 1: 456 peptides, 104 chains. Longest chain 7 peptides. Score 0.215 Round 2: 544 peptides, 104 chains. Longest chain 14 peptides. Score 0.314 Round 3: 533 peptides, 95 chains. Longest chain 16 peptides. Score 0.343 Round 4: 545 peptides, 101 chains. Longest chain 14 peptides. Score 0.329 Round 5: 549 peptides, 103 chains. Longest chain 16 peptides. Score 0.324 Taking the results from Round 3 Chains 98, Residues 438, Estimated correctness of the model 0.0 % 4 chains (29 residues) have been docked in sequence ------------------------------------------------------ 14774 reflections ( 99.96 % complete ) and 27458 restraints for refining 12041 atoms. 25693 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2011 (Rfree = 0.000) for 12041 atoms. Found 57 (57 requested) and removed 109 (28 requested) atoms. Cycle 37: After refmac, R = 0.1905 (Rfree = 0.000) for 11947 atoms. Found 56 (56 requested) and removed 67 (28 requested) atoms. Cycle 38: After refmac, R = 0.1437 (Rfree = 0.000) for 11897 atoms. Found 20 (56 requested) and removed 40 (28 requested) atoms. Cycle 39: After refmac, R = 0.1351 (Rfree = 0.000) for 11847 atoms. Found 16 (56 requested) and removed 47 (28 requested) atoms. Cycle 40: After refmac, R = 0.1357 (Rfree = 0.000) for 11808 atoms. Found 15 (56 requested) and removed 35 (28 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.60 3.95 Search for helices and strands: 0 residues in 0 chains, 12082 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 12101 seeds are put forward Round 1: 478 peptides, 106 chains. Longest chain 8 peptides. Score 0.231 Round 2: 531 peptides, 102 chains. Longest chain 10 peptides. Score 0.309 Round 3: 537 peptides, 105 chains. Longest chain 11 peptides. Score 0.302 Round 4: 533 peptides, 97 chains. Longest chain 14 peptides. Score 0.334 Round 5: 526 peptides, 101 chains. Longest chain 11 peptides. Score 0.309 Taking the results from Round 4 Chains 97, Residues 436, Estimated correctness of the model 0.0 % 5 chains (29 residues) have been docked in sequence ------------------------------------------------------ 14774 reflections ( 99.96 % complete ) and 27964 restraints for refining 12078 atoms. 26258 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2046 (Rfree = 0.000) for 12078 atoms. Found 57 (57 requested) and removed 100 (28 requested) atoms. Cycle 42: After refmac, R = 0.1954 (Rfree = 0.000) for 12000 atoms. Found 57 (57 requested) and removed 78 (28 requested) atoms. Cycle 43: After refmac, R = 0.1446 (Rfree = 0.000) for 11951 atoms. Found 23 (56 requested) and removed 50 (28 requested) atoms. Cycle 44: After refmac, R = 0.1321 (Rfree = 0.000) for 11905 atoms. Found 14 (56 requested) and removed 42 (28 requested) atoms. Cycle 45: After refmac, R = 0.1273 (Rfree = 0.000) for 11867 atoms. Found 4 (56 requested) and removed 35 (28 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.60 3.95 Search for helices and strands: 0 residues in 0 chains, 12102 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 12121 seeds are put forward Round 1: 450 peptides, 98 chains. Longest chain 10 peptides. Score 0.237 Round 2: 505 peptides, 97 chains. Longest chain 14 peptides. Score 0.304 Round 3: 503 peptides, 96 chains. Longest chain 11 peptides. Score 0.307 Round 4: 521 peptides, 98 chains. Longest chain 11 peptides. Score 0.317 Round 5: 504 peptides, 91 chains. Longest chain 12 peptides. Score 0.331 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 91, Residues 413, Estimated correctness of the model 0.0 % 5 chains (15 residues) have been docked in sequence Sequence coverage is 3 % Consider running further cycles of model building using 1vkm-4_warpNtrace.pdb as input Building loops using Loopy2018 91 chains (413 residues) following loop building 5 chains (15 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 14774 reflections ( 99.96 % complete ) and 27749 restraints for refining 12036 atoms. 26163 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2016 (Rfree = 0.000) for 12036 atoms. Found 0 (57 requested) and removed 28 (28 requested) atoms. Cycle 47: After refmac, R = 0.1882 (Rfree = 0.000) for 11966 atoms. Found 0 (57 requested) and removed 28 (28 requested) atoms. Cycle 48: After refmac, R = 0.2018 (Rfree = 0.000) for 11905 atoms. Found 0 (56 requested) and removed 28 (28 requested) atoms. Cycle 49: After refmac, R = 0.1778 (Rfree = 0.000) for 11859 atoms. Found 0 (56 requested) and removed 28 (28 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 09:25:45 GMT 2018 Job finished. TimeTaking 111.34 Used memory is bytes: 9559696