null Mon 24 Dec 08:07:30 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 1vkn-4.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vkn-4.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vkn-4.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkn-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/1vkn-4.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkn-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 08:07:35 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/1vkn-4.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkn-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 918 and 0 Target number of residues in the AU: 918 Target solvent content: 0.6615 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-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: 4 Cell parameters: 85.135 92.128 101.299 90.000 112.538 90.000 Input sequence file: 1vkn-4.0-parrot-noncs.fasta_lf Building free atoms model in initial map for 11232 target number of atoms Had to go as low as 0.75 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 4.000 Wilson plot Bfac: 85.81 12267 reflections ( 98.92 % complete ) and 0 restraints for refining 12361 atoms. Observations/parameters ratio is 0.25 ------------------------------------------------------ Starting model: R = 0.3208 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2980 (Rfree = 0.000) for 12361 atoms. Found 58 (58 requested) and removed 60 (29 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.74 3.84 Search for helices and strands: 0 residues in 0 chains, 12533 seeds are put forward NCS extension: 0 residues added, 12533 seeds are put forward Round 1: 482 peptides, 98 chains. Longest chain 12 peptides. Score 0.285 Round 2: 614 peptides, 99 chains. Longest chain 18 peptides. Score 0.432 Round 3: 663 peptides, 104 chains. Longest chain 23 peptides. Score 0.460 Round 4: 716 peptides, 103 chains. Longest chain 16 peptides. Score 0.516 Round 5: 726 peptides, 105 chains. Longest chain 23 peptides. Score 0.517 Taking the results from Round 5 Chains 109, Residues 621, Estimated correctness of the model 0.0 % 7 chains (42 residues) have been docked in sequence ------------------------------------------------------ 12267 reflections ( 98.92 % complete ) and 23665 restraints for refining 10137 atoms. 21192 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2258 (Rfree = 0.000) for 10137 atoms. Found 48 (48 requested) and removed 75 (24 requested) atoms. Cycle 2: After refmac, R = 0.2092 (Rfree = 0.000) for 9929 atoms. Found 45 (48 requested) and removed 58 (24 requested) atoms. Cycle 3: After refmac, R = 0.1997 (Rfree = 0.000) for 9797 atoms. Found 47 (47 requested) and removed 55 (23 requested) atoms. Cycle 4: After refmac, R = 0.1899 (Rfree = 0.000) for 9708 atoms. Found 46 (46 requested) and removed 44 (23 requested) atoms. Cycle 5: After refmac, R = 0.1824 (Rfree = 0.000) for 9653 atoms. Found 46 (46 requested) and removed 37 (23 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.71 3.81 Search for helices and strands: 0 residues in 0 chains, 9965 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 9987 seeds are put forward Round 1: 582 peptides, 104 chains. Longest chain 21 peptides. Score 0.373 Round 2: 651 peptides, 93 chains. Longest chain 20 peptides. Score 0.496 Round 3: 678 peptides, 95 chains. Longest chain 19 peptides. Score 0.514 Round 4: 675 peptides, 95 chains. Longest chain 20 peptides. Score 0.511 Round 5: 705 peptides, 93 chains. Longest chain 28 peptides. Score 0.547 Taking the results from Round 5 Chains 94, Residues 612, Estimated correctness of the model 0.0 % 4 chains (40 residues) have been docked in sequence ------------------------------------------------------ 12267 reflections ( 98.92 % complete ) and 23412 restraints for refining 10142 atoms. 20928 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1988 (Rfree = 0.000) for 10142 atoms. Found 48 (48 requested) and removed 84 (24 requested) atoms. Cycle 7: After refmac, R = 0.1874 (Rfree = 0.000) for 10019 atoms. Found 48 (48 requested) and removed 55 (24 requested) atoms. Cycle 8: After refmac, R = 0.1881 (Rfree = 0.000) for 9966 atoms. Found 47 (47 requested) and removed 59 (23 requested) atoms. Cycle 9: After refmac, R = 0.1751 (Rfree = 0.000) for 9906 atoms. Found 47 (47 requested) and removed 60 (23 requested) atoms. Cycle 10: After refmac, R = 0.1701 (Rfree = 0.000) for 9864 atoms. Found 47 (47 requested) and removed 54 (23 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.74 3.84 Search for helices and strands: 0 residues in 0 chains, 10158 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 10181 seeds are put forward Round 1: 579 peptides, 108 chains. Longest chain 13 peptides. Score 0.350 Round 2: 666 peptides, 106 chains. Longest chain 15 peptides. Score 0.454 Round 3: 681 peptides, 100 chains. Longest chain 18 peptides. Score 0.495 Round 4: 660 peptides, 95 chains. Longest chain 20 peptides. Score 0.496 Round 5: 658 peptides, 95 chains. Longest chain 20 peptides. Score 0.495 Taking the results from Round 4 Chains 95, Residues 565, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 12267 reflections ( 98.92 % complete ) and 23890 restraints for refining 10142 atoms. 21704 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1920 (Rfree = 0.000) for 10142 atoms. Found 48 (48 requested) and removed 78 (24 requested) atoms. Cycle 12: After refmac, R = 0.1897 (Rfree = 0.000) for 10026 atoms. Found 48 (48 requested) and removed 63 (24 requested) atoms. Cycle 13: After refmac, R = 0.1745 (Rfree = 0.000) for 9963 atoms. Found 47 (47 requested) and removed 50 (23 requested) atoms. Cycle 14: After refmac, R = 0.1793 (Rfree = 0.000) for 9917 atoms. Found 47 (47 requested) and removed 39 (23 requested) atoms. Cycle 15: After refmac, R = 0.1727 (Rfree = 0.000) for 9887 atoms. Found 47 (47 requested) and removed 44 (23 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.77 3.87 Search for helices and strands: 0 residues in 0 chains, 10195 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 10208 seeds are put forward Round 1: 549 peptides, 110 chains. Longest chain 11 peptides. Score 0.305 Round 2: 639 peptides, 108 chains. Longest chain 13 peptides. Score 0.417 Round 3: 658 peptides, 98 chains. Longest chain 17 peptides. Score 0.481 Round 4: 636 peptides, 95 chains. Longest chain 16 peptides. Score 0.473 Round 5: 651 peptides, 91 chains. Longest chain 20 peptides. Score 0.505 Taking the results from Round 5 Chains 91, Residues 560, Estimated correctness of the model 0.0 % 4 chains (21 residues) have been docked in sequence ------------------------------------------------------ 12267 reflections ( 98.92 % complete ) and 23743 restraints for refining 10142 atoms. 21549 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2022 (Rfree = 0.000) for 10142 atoms. Found 48 (48 requested) and removed 71 (24 requested) atoms. Cycle 17: After refmac, R = 0.1905 (Rfree = 0.000) for 10040 atoms. Found 48 (48 requested) and removed 59 (24 requested) atoms. Cycle 18: After refmac, R = 0.1776 (Rfree = 0.000) for 9971 atoms. Found 47 (47 requested) and removed 43 (23 requested) atoms. Cycle 19: After refmac, R = 0.1678 (Rfree = 0.000) for 9945 atoms. Found 47 (47 requested) and removed 45 (23 requested) atoms. Cycle 20: After refmac, R = 0.1715 (Rfree = 0.000) for 9927 atoms. Found 47 (47 requested) and removed 43 (23 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.73 3.83 Search for helices and strands: 0 residues in 0 chains, 10214 seeds are put forward NCS extension: 28 residues added (1 deleted due to clashes), 10242 seeds are put forward Round 1: 542 peptides, 108 chains. Longest chain 11 peptides. Score 0.307 Round 2: 593 peptides, 94 chains. Longest chain 22 peptides. Score 0.433 Round 3: 598 peptides, 92 chains. Longest chain 15 peptides. Score 0.447 Round 4: 626 peptides, 94 chains. Longest chain 23 peptides. Score 0.467 Round 5: 607 peptides, 92 chains. Longest chain 19 peptides. Score 0.457 Taking the results from Round 4 Chains 94, Residues 532, Estimated correctness of the model 0.0 % 3 chains (38 residues) have been docked in sequence ------------------------------------------------------ 12267 reflections ( 98.92 % complete ) and 23430 restraints for refining 10142 atoms. 21245 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1775 (Rfree = 0.000) for 10142 atoms. Found 48 (48 requested) and removed 74 (24 requested) atoms. Cycle 22: After refmac, R = 0.1688 (Rfree = 0.000) for 10052 atoms. Found 48 (48 requested) and removed 53 (24 requested) atoms. Cycle 23: After refmac, R = 0.1689 (Rfree = 0.000) for 10009 atoms. Found 47 (47 requested) and removed 48 (23 requested) atoms. Cycle 24: After refmac, R = 0.1592 (Rfree = 0.000) for 9981 atoms. Found 47 (47 requested) and removed 43 (23 requested) atoms. Cycle 25: After refmac, R = 0.1680 (Rfree = 0.000) for 9959 atoms. Found 47 (47 requested) and removed 43 (23 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.75 3.85 Search for helices and strands: 0 residues in 0 chains, 10238 seeds are put forward NCS extension: 32 residues added (1 deleted due to clashes), 10270 seeds are put forward Round 1: 490 peptides, 102 chains. Longest chain 9 peptides. Score 0.274 Round 2: 548 peptides, 95 chains. Longest chain 13 peptides. Score 0.379 Round 3: 572 peptides, 99 chains. Longest chain 16 peptides. Score 0.386 Round 4: 560 peptides, 94 chains. Longest chain 17 peptides. Score 0.397 Round 5: 580 peptides, 95 chains. Longest chain 20 peptides. Score 0.414 Taking the results from Round 5 Chains 95, Residues 485, Estimated correctness of the model 0.0 % 5 chains (39 residues) have been docked in sequence ------------------------------------------------------ 12267 reflections ( 98.92 % complete ) and 23612 restraints for refining 10140 atoms. 21634 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1904 (Rfree = 0.000) for 10140 atoms. Found 48 (48 requested) and removed 60 (24 requested) atoms. Cycle 27: After refmac, R = 0.1847 (Rfree = 0.000) for 10050 atoms. Found 48 (48 requested) and removed 51 (24 requested) atoms. Cycle 28: After refmac, R = 0.1786 (Rfree = 0.000) for 10013 atoms. Found 47 (47 requested) and removed 51 (23 requested) atoms. Cycle 29: After refmac, R = 0.1717 (Rfree = 0.000) for 9967 atoms. Found 47 (47 requested) and removed 43 (23 requested) atoms. Cycle 30: After refmac, R = 0.1290 (Rfree = 0.000) for 9939 atoms. Found 16 (47 requested) and removed 30 (23 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.76 3.86 Search for helices and strands: 0 residues in 0 chains, 10188 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 10211 seeds are put forward Round 1: 406 peptides, 87 chains. Longest chain 9 peptides. Score 0.247 Round 2: 490 peptides, 91 chains. Longest chain 19 peptides. Score 0.331 Round 3: 495 peptides, 89 chains. Longest chain 15 peptides. Score 0.347 Round 4: 513 peptides, 91 chains. Longest chain 19 peptides. Score 0.358 Round 5: 512 peptides, 90 chains. Longest chain 14 peptides. Score 0.362 Taking the results from Round 5 Chains 90, Residues 422, Estimated correctness of the model 0.0 % 3 chains (16 residues) have been docked in sequence ------------------------------------------------------ 12267 reflections ( 98.92 % complete ) and 23641 restraints for refining 9905 atoms. 22008 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1753 (Rfree = 0.000) for 9905 atoms. Found 47 (47 requested) and removed 62 (23 requested) atoms. Cycle 32: After refmac, R = 0.1751 (Rfree = 0.000) for 9841 atoms. Found 46 (46 requested) and removed 51 (23 requested) atoms. Cycle 33: After refmac, R = 0.1310 (Rfree = 0.000) for 9806 atoms. Found 17 (46 requested) and removed 32 (23 requested) atoms. Cycle 34: After refmac, R = 0.1239 (Rfree = 0.000) for 9769 atoms. Found 12 (46 requested) and removed 30 (23 requested) atoms. Cycle 35: After refmac, R = 0.1224 (Rfree = 0.000) for 9744 atoms. Found 9 (46 requested) and removed 37 (23 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.76 3.86 Search for helices and strands: 0 residues in 0 chains, 9948 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 9966 seeds are put forward Round 1: 408 peptides, 88 chains. Longest chain 9 peptides. Score 0.244 Round 2: 488 peptides, 92 chains. Longest chain 14 peptides. Score 0.324 Round 3: 498 peptides, 89 chains. Longest chain 13 peptides. Score 0.351 Round 4: 513 peptides, 88 chains. Longest chain 13 peptides. Score 0.373 Round 5: 487 peptides, 83 chains. Longest chain 12 peptides. Score 0.369 Taking the results from Round 4 Chains 90, Residues 425, Estimated correctness of the model 0.0 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 12267 reflections ( 98.92 % complete ) and 23766 restraints for refining 10055 atoms. 22080 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1800 (Rfree = 0.000) for 10055 atoms. Found 47 (47 requested) and removed 72 (23 requested) atoms. Cycle 37: After refmac, R = 0.1688 (Rfree = 0.000) for 9994 atoms. Found 47 (47 requested) and removed 48 (23 requested) atoms. Cycle 38: After refmac, R = 0.1807 (Rfree = 0.000) for 9964 atoms. Found 47 (47 requested) and removed 48 (23 requested) atoms. Cycle 39: After refmac, R = 0.1677 (Rfree = 0.000) for 9943 atoms. Found 47 (47 requested) and removed 36 (23 requested) atoms. Cycle 40: After refmac, R = 0.1722 (Rfree = 0.000) for 9919 atoms. Found 47 (47 requested) and removed 45 (23 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.77 3.87 Search for helices and strands: 0 residues in 0 chains, 10245 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 10262 seeds are put forward Round 1: 373 peptides, 79 chains. Longest chain 9 peptides. Score 0.248 Round 2: 448 peptides, 83 chains. Longest chain 17 peptides. Score 0.322 Round 3: 468 peptides, 84 chains. Longest chain 11 peptides. Score 0.341 Round 4: 459 peptides, 75 chains. Longest chain 16 peptides. Score 0.377 Round 5: 435 peptides, 75 chains. Longest chain 11 peptides. Score 0.349 Taking the results from Round 4 Chains 75, Residues 384, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 12267 reflections ( 98.92 % complete ) and 24113 restraints for refining 10060 atoms. 22652 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1800 (Rfree = 0.000) for 10060 atoms. Found 47 (47 requested) and removed 69 (23 requested) atoms. Cycle 42: After refmac, R = 0.1870 (Rfree = 0.000) for 10005 atoms. Found 47 (47 requested) and removed 56 (23 requested) atoms. Cycle 43: After refmac, R = 0.1735 (Rfree = 0.000) for 9975 atoms. Found 47 (47 requested) and removed 48 (23 requested) atoms. Cycle 44: After refmac, R = 0.1307 (Rfree = 0.000) for 9952 atoms. Found 27 (47 requested) and removed 35 (23 requested) atoms. Cycle 45: After refmac, R = 0.1192 (Rfree = 0.000) for 9935 atoms. Found 17 (47 requested) and removed 33 (23 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.79 3.89 Search for helices and strands: 0 residues in 0 chains, 10206 seeds are put forward NCS extension: 21 residues added (4 deleted due to clashes), 10227 seeds are put forward Round 1: 370 peptides, 80 chains. Longest chain 8 peptides. Score 0.238 Round 2: 432 peptides, 83 chains. Longest chain 10 peptides. Score 0.302 Round 3: 439 peptides, 79 chains. Longest chain 12 peptides. Score 0.332 Round 4: 455 peptides, 86 chains. Longest chain 10 peptides. Score 0.315 Round 5: 444 peptides, 80 chains. Longest chain 15 peptides. Score 0.333 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 80, Residues 364, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 1vkn-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 12267 reflections ( 98.92 % complete ) and 24532 restraints for refining 10141 atoms. 23156 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1733 (Rfree = 0.000) for 10141 atoms. Found 0 (48 requested) and removed 24 (24 requested) atoms. Cycle 47: After refmac, R = 0.1799 (Rfree = 0.000) for 10078 atoms. Found 0 (48 requested) and removed 24 (24 requested) atoms. Cycle 48: After refmac, R = 0.1762 (Rfree = 0.000) for 10039 atoms. Found 0 (47 requested) and removed 23 (23 requested) atoms. Cycle 49: After refmac, R = 0.1243 (Rfree = 0.000) for 9995 atoms. Found 0 (47 requested) and removed 23 (23 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 10:02:05 GMT 2018 Job finished. TimeTaking 114.58 Used memory is bytes: 8790328