null Sun 23 Dec 23:48:10 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 1vkn-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vkn-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vkn-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vkn-3.8-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/1vkn-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vkn-3.8-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 ============================================================ Sun 23 Dec 23:48:15 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/1vkn-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vkn-3.8-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 943 and 0 Target number of residues in the AU: 943 Target solvent content: 0.6523 Checking the provided sequence file Detected sequence length: 351 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1404 Adjusted target solvent content: 0.48 Input MTZ file: 1vkn-3.8-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: 85.135 92.128 101.299 90.000 112.538 90.000 Input sequence file: 1vkn-3.8-parrot-mrncs.fasta_lf Building free atoms model in initial map for 11232 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: 93.562 3.800 Wilson plot Bfac: 79.66 14292 reflections ( 98.94 % complete ) and 0 restraints for refining 12427 atoms. Observations/parameters ratio is 0.29 ------------------------------------------------------ Starting model: R = 0.3140 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2937 (Rfree = 0.000) for 12427 atoms. Found 68 (68 requested) and removed 102 (34 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.63 3.73 Search for helices and strands: 0 residues in 0 chains, 12627 seeds are put forward NCS extension: 0 residues added, 12627 seeds are put forward Round 1: 558 peptides, 112 chains. Longest chain 14 peptides. Score 0.306 Round 2: 726 peptides, 111 chains. Longest chain 24 peptides. Score 0.492 Round 3: 742 peptides, 106 chains. Longest chain 28 peptides. Score 0.528 Round 4: 781 peptides, 107 chains. Longest chain 26 peptides. Score 0.559 Round 5: 784 peptides, 98 chains. Longest chain 29 peptides. Score 0.596 Taking the results from Round 5 Chains 104, Residues 686, Estimated correctness of the model 0.0 % 12 chains (88 residues) have been docked in sequence ------------------------------------------------------ 14292 reflections ( 98.94 % complete ) and 22620 restraints for refining 10155 atoms. 19727 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2299 (Rfree = 0.000) for 10155 atoms. Found 44 (55 requested) and removed 95 (27 requested) atoms. Cycle 2: After refmac, R = 0.2088 (Rfree = 0.000) for 9949 atoms. Found 49 (55 requested) and removed 60 (27 requested) atoms. Cycle 3: After refmac, R = 0.1941 (Rfree = 0.000) for 9866 atoms. Found 48 (54 requested) and removed 49 (27 requested) atoms. Cycle 4: After refmac, R = 0.1860 (Rfree = 0.000) for 9820 atoms. Found 41 (54 requested) and removed 44 (27 requested) atoms. Cycle 5: After refmac, R = 0.1806 (Rfree = 0.000) for 9778 atoms. Found 43 (53 requested) and removed 38 (26 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.59 3.69 Search for helices and strands: 0 residues in 0 chains, 10061 seeds are put forward NCS extension: 25 residues added (4 deleted due to clashes), 10086 seeds are put forward Round 1: 694 peptides, 125 chains. Longest chain 18 peptides. Score 0.398 Round 2: 767 peptides, 117 chains. Longest chain 21 peptides. Score 0.506 Round 3: 760 peptides, 109 chains. Longest chain 18 peptides. Score 0.532 Round 4: 771 peptides, 107 chains. Longest chain 18 peptides. Score 0.550 Round 5: 790 peptides, 103 chains. Longest chain 21 peptides. Score 0.582 Taking the results from Round 5 Chains 105, Residues 687, Estimated correctness of the model 0.0 % 7 chains (52 residues) have been docked in sequence ------------------------------------------------------ 14292 reflections ( 98.94 % complete ) and 22982 restraints for refining 10160 atoms. 20202 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2020 (Rfree = 0.000) for 10160 atoms. Found 55 (55 requested) and removed 68 (27 requested) atoms. Cycle 7: After refmac, R = 0.1883 (Rfree = 0.000) for 10041 atoms. Found 45 (55 requested) and removed 53 (27 requested) atoms. Cycle 8: After refmac, R = 0.1802 (Rfree = 0.000) for 9977 atoms. Found 38 (55 requested) and removed 51 (27 requested) atoms. Cycle 9: After refmac, R = 0.1708 (Rfree = 0.000) for 9918 atoms. Found 40 (54 requested) and removed 36 (27 requested) atoms. Cycle 10: After refmac, R = 0.1368 (Rfree = 0.000) for 9895 atoms. Found 12 (54 requested) and removed 38 (27 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.60 3.70 Search for helices and strands: 0 residues in 0 chains, 10239 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 10254 seeds are put forward Round 1: 680 peptides, 126 chains. Longest chain 15 peptides. Score 0.378 Round 2: 763 peptides, 124 chains. Longest chain 22 peptides. Score 0.473 Round 3: 776 peptides, 121 chains. Longest chain 21 peptides. Score 0.498 Round 4: 775 peptides, 118 chains. Longest chain 17 peptides. Score 0.510 Round 5: 754 peptides, 110 chains. Longest chain 25 peptides. Score 0.523 Taking the results from Round 5 Chains 111, Residues 644, Estimated correctness of the model 0.0 % 9 chains (61 residues) have been docked in sequence ------------------------------------------------------ 14292 reflections ( 98.94 % complete ) and 23084 restraints for refining 10158 atoms. 20447 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2001 (Rfree = 0.000) for 10158 atoms. Found 55 (55 requested) and removed 60 (27 requested) atoms. Cycle 12: After refmac, R = 0.1733 (Rfree = 0.000) for 10079 atoms. Found 36 (55 requested) and removed 48 (27 requested) atoms. Cycle 13: After refmac, R = 0.1674 (Rfree = 0.000) for 10041 atoms. Found 39 (55 requested) and removed 43 (27 requested) atoms. Cycle 14: After refmac, R = 0.1641 (Rfree = 0.000) for 10012 atoms. Found 38 (55 requested) and removed 43 (27 requested) atoms. Cycle 15: After refmac, R = 0.1643 (Rfree = 0.000) for 9981 atoms. Found 44 (55 requested) and removed 36 (27 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.61 3.71 Search for helices and strands: 0 residues in 0 chains, 10296 seeds are put forward NCS extension: 19 residues added (3 deleted due to clashes), 10315 seeds are put forward Round 1: 646 peptides, 126 chains. Longest chain 14 peptides. Score 0.340 Round 2: 689 peptides, 111 chains. Longest chain 17 peptides. Score 0.455 Round 3: 727 peptides, 119 chains. Longest chain 15 peptides. Score 0.459 Round 4: 747 peptides, 116 chains. Longest chain 16 peptides. Score 0.491 Round 5: 751 peptides, 114 chains. Longest chain 20 peptides. Score 0.504 Taking the results from Round 5 Chains 118, Residues 637, Estimated correctness of the model 0.0 % 5 chains (42 residues) have been docked in sequence ------------------------------------------------------ 14292 reflections ( 98.94 % complete ) and 23556 restraints for refining 10158 atoms. 20974 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2022 (Rfree = 0.000) for 10158 atoms. Found 55 (55 requested) and removed 55 (27 requested) atoms. Cycle 17: After refmac, R = 0.1816 (Rfree = 0.000) for 10062 atoms. Found 48 (55 requested) and removed 48 (27 requested) atoms. Cycle 18: After refmac, R = 0.1724 (Rfree = 0.000) for 10024 atoms. Found 41 (55 requested) and removed 42 (27 requested) atoms. Cycle 19: After refmac, R = 0.1614 (Rfree = 0.000) for 10004 atoms. Found 45 (55 requested) and removed 49 (27 requested) atoms. Cycle 20: After refmac, R = 0.1615 (Rfree = 0.000) for 9983 atoms. Found 42 (54 requested) and removed 45 (27 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.63 3.73 Search for helices and strands: 0 residues in 0 chains, 10272 seeds are put forward NCS extension: 14 residues added (3 deleted due to clashes), 10286 seeds are put forward Round 1: 619 peptides, 116 chains. Longest chain 19 peptides. Score 0.357 Round 2: 664 peptides, 104 chains. Longest chain 20 peptides. Score 0.461 Round 3: 685 peptides, 106 chains. Longest chain 18 peptides. Score 0.473 Round 4: 662 peptides, 98 chains. Longest chain 21 peptides. Score 0.485 Round 5: 669 peptides, 102 chains. Longest chain 20 peptides. Score 0.475 Taking the results from Round 4 Chains 99, Residues 564, Estimated correctness of the model 0.0 % 4 chains (31 residues) have been docked in sequence ------------------------------------------------------ 14292 reflections ( 98.94 % complete ) and 23957 restraints for refining 10159 atoms. 21715 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1957 (Rfree = 0.000) for 10159 atoms. Found 49 (55 requested) and removed 48 (27 requested) atoms. Cycle 22: After refmac, R = 0.1860 (Rfree = 0.000) for 10112 atoms. Found 55 (55 requested) and removed 42 (27 requested) atoms. Cycle 23: After refmac, R = 0.1823 (Rfree = 0.000) for 10085 atoms. Found 55 (55 requested) and removed 51 (27 requested) atoms. Cycle 24: After refmac, R = 0.1731 (Rfree = 0.000) for 10064 atoms. Found 55 (55 requested) and removed 40 (27 requested) atoms. Cycle 25: After refmac, R = 0.1773 (Rfree = 0.000) for 10067 atoms. Found 55 (55 requested) and removed 38 (27 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.63 3.73 Search for helices and strands: 0 residues in 0 chains, 10422 seeds are put forward NCS extension: 31 residues added (3 deleted due to clashes), 10453 seeds are put forward Round 1: 529 peptides, 110 chains. Longest chain 10 peptides. Score 0.281 Round 2: 624 peptides, 100 chains. Longest chain 24 peptides. Score 0.438 Round 3: 620 peptides, 100 chains. Longest chain 26 peptides. Score 0.434 Round 4: 637 peptides, 92 chains. Longest chain 27 peptides. Score 0.487 Round 5: 632 peptides, 95 chains. Longest chain 21 peptides. Score 0.469 Taking the results from Round 4 Chains 97, Residues 545, Estimated correctness of the model 0.0 % 7 chains (55 residues) have been docked in sequence ------------------------------------------------------ 14292 reflections ( 98.94 % complete ) and 23619 restraints for refining 10159 atoms. 21370 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1891 (Rfree = 0.000) for 10159 atoms. Found 55 (55 requested) and removed 55 (27 requested) atoms. Cycle 27: After refmac, R = 0.1800 (Rfree = 0.000) for 10115 atoms. Found 55 (55 requested) and removed 53 (27 requested) atoms. Cycle 28: After refmac, R = 0.1829 (Rfree = 0.000) for 10101 atoms. Found 55 (55 requested) and removed 44 (27 requested) atoms. Cycle 29: After refmac, R = 0.1704 (Rfree = 0.000) for 10091 atoms. Found 55 (55 requested) and removed 41 (27 requested) atoms. Cycle 30: After refmac, R = 0.1365 (Rfree = 0.000) for 10094 atoms. Found 13 (55 requested) and removed 35 (27 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.63 3.73 Search for helices and strands: 0 residues in 0 chains, 10378 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 10398 seeds are put forward Round 1: 506 peptides, 103 chains. Longest chain 11 peptides. Score 0.289 Round 2: 597 peptides, 112 chains. Longest chain 13 peptides. Score 0.352 Round 3: 611 peptides, 107 chains. Longest chain 14 peptides. Score 0.391 Round 4: 630 peptides, 101 chains. Longest chain 22 peptides. Score 0.439 Round 5: 619 peptides, 104 chains. Longest chain 12 peptides. Score 0.414 Taking the results from Round 4 Chains 101, Residues 529, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 14292 reflections ( 98.94 % complete ) and 24295 restraints for refining 10158 atoms. 22280 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1724 (Rfree = 0.000) for 10158 atoms. Found 41 (55 requested) and removed 43 (27 requested) atoms. Cycle 32: After refmac, R = 0.1722 (Rfree = 0.000) for 10106 atoms. Found 55 (55 requested) and removed 50 (27 requested) atoms. Cycle 33: After refmac, R = 0.1730 (Rfree = 0.000) for 10084 atoms. Found 55 (55 requested) and removed 36 (27 requested) atoms. Cycle 34: After refmac, R = 0.1318 (Rfree = 0.000) for 10084 atoms. Found 17 (55 requested) and removed 40 (27 requested) atoms. Cycle 35: After refmac, R = 0.1250 (Rfree = 0.000) for 10048 atoms. Found 19 (55 requested) and removed 35 (27 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.60 3.70 Search for helices and strands: 0 residues in 0 chains, 10307 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 10327 seeds are put forward Round 1: 478 peptides, 99 chains. Longest chain 15 peptides. Score 0.275 Round 2: 526 peptides, 96 chains. Longest chain 11 peptides. Score 0.348 Round 3: 573 peptides, 98 chains. Longest chain 14 peptides. Score 0.392 Round 4: 601 peptides, 103 chains. Longest chain 16 peptides. Score 0.399 Round 5: 588 peptides, 100 chains. Longest chain 19 peptides. Score 0.399 Taking the results from Round 5 Chains 100, Residues 488, Estimated correctness of the model 0.0 % 10 chains (44 residues) have been docked in sequence ------------------------------------------------------ 14292 reflections ( 98.94 % complete ) and 24057 restraints for refining 10158 atoms. 22091 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1821 (Rfree = 0.000) for 10158 atoms. Found 55 (55 requested) and removed 42 (27 requested) atoms. Cycle 37: After refmac, R = 0.1704 (Rfree = 0.000) for 10125 atoms. Found 55 (55 requested) and removed 40 (27 requested) atoms. Cycle 38: After refmac, R = 0.1328 (Rfree = 0.000) for 10112 atoms. Found 21 (55 requested) and removed 29 (27 requested) atoms. Cycle 39: After refmac, R = 0.1238 (Rfree = 0.000) for 10080 atoms. Found 16 (55 requested) and removed 28 (27 requested) atoms. Cycle 40: After refmac, R = 0.1227 (Rfree = 0.000) for 10056 atoms. Found 19 (55 requested) and removed 33 (27 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.59 3.69 Search for helices and strands: 0 residues in 0 chains, 10312 seeds are put forward NCS extension: 31 residues added (3 deleted due to clashes), 10343 seeds are put forward Round 1: 474 peptides, 98 chains. Longest chain 12 peptides. Score 0.275 Round 2: 534 peptides, 98 chains. Longest chain 10 peptides. Score 0.348 Round 3: 560 peptides, 98 chains. Longest chain 16 peptides. Score 0.378 Round 4: 555 peptides, 92 chains. Longest chain 17 peptides. Score 0.401 Round 5: 556 peptides, 95 chains. Longest chain 16 peptides. Score 0.388 Taking the results from Round 4 Chains 93, Residues 463, Estimated correctness of the model 0.0 % 4 chains (25 residues) have been docked in sequence ------------------------------------------------------ 14292 reflections ( 98.94 % complete ) and 24345 restraints for refining 10160 atoms. 22510 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1743 (Rfree = 0.000) for 10160 atoms. Found 55 (55 requested) and removed 38 (27 requested) atoms. Cycle 42: After refmac, R = 0.1707 (Rfree = 0.000) for 10142 atoms. Found 55 (55 requested) and removed 40 (27 requested) atoms. Cycle 43: After refmac, R = 0.1641 (Rfree = 0.000) for 10133 atoms. Found 55 (55 requested) and removed 35 (27 requested) atoms. Cycle 44: After refmac, R = 0.1642 (Rfree = 0.000) for 10132 atoms. Found 55 (55 requested) and removed 38 (27 requested) atoms. Cycle 45: After refmac, R = 0.1242 (Rfree = 0.000) for 10136 atoms. Found 14 (55 requested) and removed 30 (27 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.58 3.68 Search for helices and strands: 0 residues in 0 chains, 10372 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 10387 seeds are put forward Round 1: 395 peptides, 84 chains. Longest chain 9 peptides. Score 0.249 Round 2: 467 peptides, 84 chains. Longest chain 14 peptides. Score 0.340 Round 3: 476 peptides, 79 chains. Longest chain 16 peptides. Score 0.376 Round 4: 463 peptides, 80 chains. Longest chain 15 peptides. Score 0.356 Round 5: 480 peptides, 80 chains. Longest chain 12 peptides. Score 0.376 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 80, Residues 400, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence Sequence coverage is 1 % Consider running further cycles of model building using 1vkn-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 14292 reflections ( 98.94 % complete ) and 25009 restraints for refining 10158 atoms. 23468 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1752 (Rfree = 0.000) for 10158 atoms. Found 0 (55 requested) and removed 27 (27 requested) atoms. Cycle 47: After refmac, R = 0.1786 (Rfree = 0.000) for 10100 atoms. Found 0 (55 requested) and removed 27 (27 requested) atoms. Cycle 48: After refmac, R = 0.1641 (Rfree = 0.000) for 10050 atoms. Found 0 (55 requested) and removed 27 (27 requested) atoms. Cycle 49: After refmac, R = 0.1650 (Rfree = 0.000) for 10003 atoms. Found 0 (55 requested) and removed 27 (27 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:47:06 GMT 2018 Job finished. TimeTaking 118.93 Used memory is bytes: 8951472