Mon 24 Dec 00:30:55 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 1vrb-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vrb-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vrb-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vrb-3.4-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/1vrb-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vrb-3.4-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 ============================================================ Mon 24 Dec 00:31:00 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/1vrb-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vrb-3.4-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 927 and 0 Target number of residues in the AU: 927 Target solvent content: 0.6462 Checking the provided sequence file Detected sequence length: 342 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1368 Adjusted target solvent content: 0.48 Input MTZ file: 1vrb-3.4-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: 19 Cell parameters: 47.576 104.273 285.843 90.000 90.000 90.000 Input sequence file: 1vrb-3.4-parrot-mrncs.fasta_lf Building free atoms model in initial map for 10944 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: 48.979 3.400 Wilson plot Bfac: 75.79 20098 reflections ( 98.18 % complete ) and 0 restraints for refining 12131 atoms. Observations/parameters ratio is 0.41 ------------------------------------------------------ Starting model: R = 0.3337 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2770 (Rfree = 0.000) for 12131 atoms. Found 66 (91 requested) and removed 166 (45 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.29 3.38 Search for helices and strands: 0 residues in 0 chains, 12279 seeds are put forward NCS extension: 0 residues added, 12279 seeds are put forward Round 1: 544 peptides, 106 chains. Longest chain 12 peptides. Score 0.323 Round 2: 653 peptides, 103 chains. Longest chain 22 peptides. Score 0.462 Round 3: 700 peptides, 102 chains. Longest chain 22 peptides. Score 0.513 Round 4: 705 peptides, 103 chains. Longest chain 23 peptides. Score 0.514 Round 5: 729 peptides, 103 chains. Longest chain 29 peptides. Score 0.537 Taking the results from Round 5 Chains 105, Residues 626, Estimated correctness of the model 6.8 % 4 chains (51 residues) have been docked in sequence ------------------------------------------------------ 20098 reflections ( 98.18 % complete ) and 22858 restraints for refining 9951 atoms. 20280 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2534 (Rfree = 0.000) for 9951 atoms. Found 56 (75 requested) and removed 83 (37 requested) atoms. Cycle 2: After refmac, R = 0.2384 (Rfree = 0.000) for 9792 atoms. Found 41 (74 requested) and removed 60 (37 requested) atoms. Cycle 3: After refmac, R = 0.2295 (Rfree = 0.000) for 9717 atoms. Found 21 (73 requested) and removed 53 (36 requested) atoms. Cycle 4: After refmac, R = 0.2336 (Rfree = 0.000) for 9648 atoms. Found 24 (73 requested) and removed 48 (36 requested) atoms. Cycle 5: After refmac, R = 0.2230 (Rfree = 0.000) for 9589 atoms. Found 19 (72 requested) and removed 45 (36 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.32 3.41 Search for helices and strands: 0 residues in 0 chains, 9896 seeds are put forward NCS extension: 21 residues added (2 deleted due to clashes), 9917 seeds are put forward Round 1: 624 peptides, 114 chains. Longest chain 13 peptides. Score 0.378 Round 2: 701 peptides, 104 chains. Longest chain 23 peptides. Score 0.506 Round 3: 706 peptides, 98 chains. Longest chain 31 peptides. Score 0.536 Round 4: 706 peptides, 99 chains. Longest chain 22 peptides. Score 0.532 Round 5: 725 peptides, 100 chains. Longest chain 28 peptides. Score 0.546 Taking the results from Round 5 Chains 104, Residues 625, Estimated correctness of the model 10.1 % 6 chains (57 residues) have been docked in sequence ------------------------------------------------------ 20098 reflections ( 98.18 % complete ) and 22113 restraints for refining 9849 atoms. 19503 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2491 (Rfree = 0.000) for 9849 atoms. Found 53 (74 requested) and removed 102 (37 requested) atoms. Cycle 7: After refmac, R = 0.2298 (Rfree = 0.000) for 9755 atoms. Found 30 (73 requested) and removed 64 (36 requested) atoms. Cycle 8: After refmac, R = 0.2302 (Rfree = 0.000) for 9694 atoms. Found 21 (73 requested) and removed 55 (36 requested) atoms. Cycle 9: After refmac, R = 0.2211 (Rfree = 0.000) for 9643 atoms. Found 23 (72 requested) and removed 41 (36 requested) atoms. Cycle 10: After refmac, R = 0.2114 (Rfree = 0.000) for 9612 atoms. Found 13 (72 requested) and removed 39 (36 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.34 3.43 Search for helices and strands: 0 residues in 0 chains, 9959 seeds are put forward NCS extension: 19 residues added (3 deleted due to clashes), 9978 seeds are put forward Round 1: 645 peptides, 115 chains. Longest chain 19 peptides. Score 0.397 Round 2: 713 peptides, 104 chains. Longest chain 19 peptides. Score 0.518 Round 3: 727 peptides, 103 chains. Longest chain 27 peptides. Score 0.535 Round 4: 728 peptides, 108 chains. Longest chain 18 peptides. Score 0.515 Round 5: 717 peptides, 106 chains. Longest chain 27 peptides. Score 0.513 Taking the results from Round 3 Chains 107, Residues 624, Estimated correctness of the model 6.0 % 9 chains (79 residues) have been docked in sequence ------------------------------------------------------ 20098 reflections ( 98.18 % complete ) and 22203 restraints for refining 9951 atoms. 19492 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2440 (Rfree = 0.000) for 9951 atoms. Found 66 (75 requested) and removed 75 (37 requested) atoms. Cycle 12: After refmac, R = 0.2265 (Rfree = 0.000) for 9919 atoms. Found 31 (75 requested) and removed 49 (37 requested) atoms. Failed to save intermediate PDB Cycle 13: After refmac, R = 0.2191 (Rfree = 0.000) for 9864 atoms. Found 26 (74 requested) and removed 47 (37 requested) atoms. Cycle 14: After refmac, R = 0.2105 (Rfree = 0.000) for 9823 atoms. Found 15 (74 requested) and removed 44 (37 requested) atoms. Cycle 15: After refmac, R = 0.2111 (Rfree = 0.000) for 9780 atoms. Found 16 (73 requested) and removed 40 (36 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.35 3.44 Search for helices and strands: 0 residues in 0 chains, 10119 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 10133 seeds are put forward Round 1: 613 peptides, 113 chains. Longest chain 13 peptides. Score 0.370 Round 2: 664 peptides, 102 chains. Longest chain 20 peptides. Score 0.477 Round 3: 671 peptides, 107 chains. Longest chain 17 peptides. Score 0.462 Round 4: 666 peptides, 100 chains. Longest chain 24 peptides. Score 0.488 Round 5: 663 peptides, 101 chains. Longest chain 22 peptides. Score 0.481 Taking the results from Round 4 Chains 102, Residues 566, Estimated correctness of the model 0.0 % 4 chains (30 residues) have been docked in sequence ------------------------------------------------------ 20098 reflections ( 98.18 % complete ) and 22965 restraints for refining 9951 atoms. 20712 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2721 (Rfree = 0.000) for 9951 atoms. Found 75 (75 requested) and removed 52 (37 requested) atoms. Cycle 17: After refmac, R = 0.2334 (Rfree = 0.000) for 9967 atoms. Found 30 (75 requested) and removed 42 (37 requested) atoms. Cycle 18: After refmac, R = 0.2261 (Rfree = 0.000) for 9931 atoms. Found 22 (75 requested) and removed 41 (37 requested) atoms. Cycle 19: After refmac, R = 0.2211 (Rfree = 0.000) for 9905 atoms. Found 15 (74 requested) and removed 39 (37 requested) atoms. Cycle 20: After refmac, R = 0.2204 (Rfree = 0.000) for 9872 atoms. Found 16 (74 requested) and removed 38 (37 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.42 3.51 Search for helices and strands: 0 residues in 0 chains, 10161 seeds are put forward NCS extension: 30 residues added (0 deleted due to clashes), 10191 seeds are put forward Round 1: 598 peptides, 103 chains. Longest chain 19 peptides. Score 0.402 Round 2: 652 peptides, 96 chains. Longest chain 19 peptides. Score 0.492 Round 3: 647 peptides, 96 chains. Longest chain 24 peptides. Score 0.487 Round 4: 676 peptides, 100 chains. Longest chain 21 peptides. Score 0.498 Round 5: 678 peptides, 99 chains. Longest chain 22 peptides. Score 0.505 Taking the results from Round 5 Chains 102, Residues 579, Estimated correctness of the model 0.0 % 5 chains (51 residues) have been docked in sequence ------------------------------------------------------ 20098 reflections ( 98.18 % complete ) and 22756 restraints for refining 9951 atoms. 20336 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2611 (Rfree = 0.000) for 9951 atoms. Found 75 (75 requested) and removed 65 (37 requested) atoms. Cycle 22: After refmac, R = 0.2259 (Rfree = 0.000) for 9951 atoms. Found 33 (75 requested) and removed 37 (37 requested) atoms. Cycle 23: After refmac, R = 0.2146 (Rfree = 0.000) for 9933 atoms. Found 18 (75 requested) and removed 37 (37 requested) atoms. Cycle 24: After refmac, R = 0.2097 (Rfree = 0.000) for 9906 atoms. Found 10 (74 requested) and removed 39 (37 requested) atoms. Cycle 25: After refmac, R = 0.2076 (Rfree = 0.000) for 9872 atoms. Found 14 (74 requested) and removed 38 (37 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.39 3.48 Search for helices and strands: 0 residues in 0 chains, 10170 seeds are put forward NCS extension: 26 residues added (4 deleted due to clashes), 10196 seeds are put forward Round 1: 546 peptides, 105 chains. Longest chain 12 peptides. Score 0.331 Round 2: 598 peptides, 92 chains. Longest chain 13 peptides. Score 0.454 Round 3: 631 peptides, 95 chains. Longest chain 22 peptides. Score 0.475 Round 4: 644 peptides, 95 chains. Longest chain 23 peptides. Score 0.488 Round 5: 619 peptides, 85 chains. Longest chain 25 peptides. Score 0.508 Taking the results from Round 5 Chains 88, Residues 534, Estimated correctness of the model 0.0 % 4 chains (34 residues) have been docked in sequence ------------------------------------------------------ 20098 reflections ( 98.18 % complete ) and 22792 restraints for refining 9951 atoms. 20598 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2240 (Rfree = 0.000) for 9951 atoms. Found 60 (75 requested) and removed 56 (37 requested) atoms. Cycle 27: After refmac, R = 0.2018 (Rfree = 0.000) for 9921 atoms. Found 18 (75 requested) and removed 39 (37 requested) atoms. Cycle 28: After refmac, R = 0.2029 (Rfree = 0.000) for 9882 atoms. Found 17 (74 requested) and removed 38 (37 requested) atoms. Cycle 29: After refmac, R = 0.1946 (Rfree = 0.000) for 9856 atoms. Found 17 (74 requested) and removed 39 (37 requested) atoms. Cycle 30: After refmac, R = 0.1957 (Rfree = 0.000) for 9826 atoms. Found 8 (74 requested) and removed 39 (37 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.39 3.48 Search for helices and strands: 0 residues in 0 chains, 10124 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 10146 seeds are put forward Round 1: 500 peptides, 95 chains. Longest chain 18 peptides. Score 0.327 Round 2: 558 peptides, 88 chains. Longest chain 19 peptides. Score 0.430 Round 3: 561 peptides, 91 chains. Longest chain 18 peptides. Score 0.419 Round 4: 557 peptides, 80 chains. Longest chain 19 peptides. Score 0.467 Round 5: 550 peptides, 88 chains. Longest chain 18 peptides. Score 0.421 Taking the results from Round 4 Chains 80, Residues 477, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 20098 reflections ( 98.18 % complete ) and 23805 restraints for refining 9951 atoms. 21977 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2269 (Rfree = 0.000) for 9951 atoms. Found 55 (75 requested) and removed 51 (37 requested) atoms. Cycle 32: After refmac, R = 0.2078 (Rfree = 0.000) for 9935 atoms. Found 26 (75 requested) and removed 40 (37 requested) atoms. Cycle 33: After refmac, R = 0.2059 (Rfree = 0.000) for 9914 atoms. Found 12 (74 requested) and removed 37 (37 requested) atoms. Cycle 34: After refmac, R = 0.2070 (Rfree = 0.000) for 9879 atoms. Found 14 (74 requested) and removed 37 (37 requested) atoms. Cycle 35: After refmac, R = 0.2078 (Rfree = 0.000) for 9852 atoms. Found 13 (74 requested) and removed 37 (37 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.36 3.45 Search for helices and strands: 0 residues in 0 chains, 10107 seeds are put forward NCS extension: 34 residues added (1 deleted due to clashes), 10141 seeds are put forward Round 1: 517 peptides, 100 chains. Longest chain 15 peptides. Score 0.321 Round 2: 618 peptides, 93 chains. Longest chain 19 peptides. Score 0.471 Round 3: 624 peptides, 95 chains. Longest chain 19 peptides. Score 0.468 Round 4: 633 peptides, 100 chains. Longest chain 19 peptides. Score 0.454 Round 5: 621 peptides, 90 chains. Longest chain 18 peptides. Score 0.488 Taking the results from Round 5 Chains 90, Residues 531, Estimated correctness of the model 0.0 % 5 chains (22 residues) have been docked in sequence ------------------------------------------------------ 20098 reflections ( 98.18 % complete ) and 23082 restraints for refining 9951 atoms. 21003 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2259 (Rfree = 0.000) for 9951 atoms. Found 52 (75 requested) and removed 49 (37 requested) atoms. Cycle 37: After refmac, R = 0.2108 (Rfree = 0.000) for 9931 atoms. Found 22 (75 requested) and removed 45 (37 requested) atoms. Cycle 38: After refmac, R = 0.2059 (Rfree = 0.000) for 9897 atoms. Found 11 (74 requested) and removed 40 (37 requested) atoms. Cycle 39: After refmac, R = 0.2027 (Rfree = 0.000) for 9857 atoms. Found 17 (74 requested) and removed 37 (37 requested) atoms. Cycle 40: After refmac, R = 0.1990 (Rfree = 0.000) for 9833 atoms. Found 10 (74 requested) and removed 37 (37 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.34 3.43 Search for helices and strands: 0 residues in 0 chains, 10096 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 10116 seeds are put forward Round 1: 451 peptides, 89 chains. Longest chain 11 peptides. Score 0.297 Round 2: 520 peptides, 90 chains. Longest chain 14 peptides. Score 0.377 Round 3: 539 peptides, 87 chains. Longest chain 17 peptides. Score 0.414 Round 4: 540 peptides, 83 chains. Longest chain 15 peptides. Score 0.434 Round 5: 535 peptides, 82 chains. Longest chain 17 peptides. Score 0.434 Taking the results from Round 5 Chains 82, Residues 453, Estimated correctness of the model 0.0 % 3 chains (13 residues) have been docked in sequence ------------------------------------------------------ 20098 reflections ( 98.18 % complete ) and 23606 restraints for refining 9951 atoms. 21847 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2170 (Rfree = 0.000) for 9951 atoms. Found 60 (75 requested) and removed 46 (37 requested) atoms. Cycle 42: After refmac, R = 0.2057 (Rfree = 0.000) for 9942 atoms. Found 20 (75 requested) and removed 39 (37 requested) atoms. Cycle 43: After refmac, R = 0.2007 (Rfree = 0.000) for 9917 atoms. Found 21 (74 requested) and removed 38 (37 requested) atoms. Cycle 44: After refmac, R = 0.1975 (Rfree = 0.000) for 9893 atoms. Found 11 (74 requested) and removed 37 (37 requested) atoms. Cycle 45: After refmac, R = 0.1968 (Rfree = 0.000) for 9857 atoms. Found 16 (74 requested) and removed 39 (37 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.36 3.45 Search for helices and strands: 0 residues in 0 chains, 10133 seeds are put forward NCS extension: 35 residues added (1 deleted due to clashes), 10168 seeds are put forward Round 1: 449 peptides, 88 chains. Longest chain 14 peptides. Score 0.300 Round 2: 489 peptides, 81 chains. Longest chain 17 peptides. Score 0.386 Round 3: 487 peptides, 81 chains. Longest chain 14 peptides. Score 0.384 Round 4: 507 peptides, 81 chains. Longest chain 18 peptides. Score 0.407 Round 5: 478 peptides, 80 chains. Longest chain 19 peptides. Score 0.379 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 82, Residues 426, Estimated correctness of the model 0.0 % 3 chains (17 residues) have been docked in sequence Sequence coverage is 3 % Consider running further cycles of model building using 1vrb-3_warpNtrace.pdb as input Building loops using Loopy2018 82 chains (426 residues) following loop building 3 chains (17 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 20098 reflections ( 98.18 % complete ) and 23660 restraints for refining 9950 atoms. 21988 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2134 (Rfree = 0.000) for 9950 atoms. Found 0 (75 requested) and removed 37 (37 requested) atoms. Cycle 47: After refmac, R = 0.2077 (Rfree = 0.000) for 9890 atoms. Found 0 (74 requested) and removed 34 (37 requested) atoms. Cycle 48: After refmac, R = 0.2055 (Rfree = 0.000) for 9849 atoms. Found 0 (74 requested) and removed 17 (37 requested) atoms. Cycle 49: After refmac, R = 0.2056 (Rfree = 0.000) for 9832 atoms. Found 0 (74 requested) and removed 17 (37 requested) atoms. Writing output files ... TimeTaking 113.95