null Mon 24 Dec 07:42:42 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 1vrb-3.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vrb-3.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vrb-3.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vrb-3.2-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/1vrb-3.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vrb-3.2-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 07:42:47 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/1vrb-3.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vrb-3.2-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 972 and 0 Target number of residues in the AU: 972 Target solvent content: 0.6290 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-3.2-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: 47.576 104.273 285.843 90.000 90.000 90.000 Input sequence file: 1vrb-3.2-parrot-noncs.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 3.200 Wilson plot Bfac: 66.01 23615 reflections ( 96.55 % complete ) and 0 restraints for refining 12114 atoms. Observations/parameters ratio is 0.49 ------------------------------------------------------ Starting model: R = 0.3463 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2956 (Rfree = 0.000) for 12114 atoms. Found 71 (108 requested) and removed 194 (54 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.08 3.16 Search for helices and strands: 0 residues in 0 chains, 12212 seeds are put forward NCS extension: 0 residues added, 12212 seeds are put forward Round 1: 467 peptides, 97 chains. Longest chain 8 peptides. Score 0.274 Round 2: 562 peptides, 104 chains. Longest chain 13 peptides. Score 0.355 Round 3: 577 peptides, 100 chains. Longest chain 16 peptides. Score 0.393 Round 4: 603 peptides, 105 chains. Longest chain 18 peptides. Score 0.398 Round 5: 627 peptides, 105 chains. Longest chain 22 peptides. Score 0.424 Taking the results from Round 5 Chains 105, Residues 522, Estimated correctness of the model 0.0 % 5 chains (28 residues) have been docked in sequence ------------------------------------------------------ 23615 reflections ( 96.55 % complete ) and 23553 restraints for refining 9991 atoms. 21492 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2795 (Rfree = 0.000) for 9991 atoms. Found 62 (89 requested) and removed 81 (44 requested) atoms. Cycle 2: After refmac, R = 0.2761 (Rfree = 0.000) for 9877 atoms. Found 51 (89 requested) and removed 67 (44 requested) atoms. Cycle 3: After refmac, R = 0.2666 (Rfree = 0.000) for 9804 atoms. Found 49 (88 requested) and removed 66 (44 requested) atoms. Cycle 4: After refmac, R = 0.2643 (Rfree = 0.000) for 9738 atoms. Found 37 (87 requested) and removed 57 (43 requested) atoms. Cycle 5: After refmac, R = 0.2744 (Rfree = 0.000) for 9669 atoms. Found 58 (87 requested) and removed 59 (43 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.00 3.08 Search for helices and strands: 0 residues in 0 chains, 10012 seeds are put forward NCS extension: 26 residues added (0 deleted due to clashes), 10038 seeds are put forward Round 1: 495 peptides, 102 chains. Longest chain 9 peptides. Score 0.283 Round 2: 531 peptides, 93 chains. Longest chain 12 peptides. Score 0.374 Round 3: 552 peptides, 92 chains. Longest chain 20 peptides. Score 0.404 Round 4: 558 peptides, 92 chains. Longest chain 14 peptides. Score 0.410 Round 5: 553 peptides, 84 chains. Longest chain 19 peptides. Score 0.444 Taking the results from Round 5 Chains 86, Residues 469, Estimated correctness of the model 0.0 % 9 chains (47 residues) have been docked in sequence ------------------------------------------------------ 23615 reflections ( 96.55 % complete ) and 22825 restraints for refining 9858 atoms. 20887 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2692 (Rfree = 0.000) for 9858 atoms. Found 60 (88 requested) and removed 79 (44 requested) atoms. Cycle 7: After refmac, R = 0.2576 (Rfree = 0.000) for 9775 atoms. Found 34 (88 requested) and removed 68 (44 requested) atoms. Cycle 8: After refmac, R = 0.2550 (Rfree = 0.000) for 9708 atoms. Found 40 (87 requested) and removed 58 (43 requested) atoms. Cycle 9: After refmac, R = 0.2528 (Rfree = 0.000) for 9650 atoms. Found 30 (86 requested) and removed 56 (43 requested) atoms. Cycle 10: After refmac, R = 0.2475 (Rfree = 0.000) for 9595 atoms. Found 26 (86 requested) and removed 55 (43 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.96 3.04 Search for helices and strands: 0 residues in 0 chains, 9822 seeds are put forward NCS extension: 29 residues added (0 deleted due to clashes), 9851 seeds are put forward Round 1: 494 peptides, 100 chains. Longest chain 16 peptides. Score 0.293 Round 2: 561 peptides, 97 chains. Longest chain 19 peptides. Score 0.389 Round 3: 609 peptides, 107 chains. Longest chain 16 peptides. Score 0.395 Round 4: 598 peptides, 106 chains. Longest chain 16 peptides. Score 0.387 Round 5: 583 peptides, 98 chains. Longest chain 16 peptides. Score 0.409 Taking the results from Round 5 Chains 99, Residues 485, Estimated correctness of the model 0.0 % 6 chains (31 residues) have been docked in sequence ------------------------------------------------------ 23615 reflections ( 96.55 % complete ) and 22269 restraints for refining 9806 atoms. 20359 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2651 (Rfree = 0.000) for 9806 atoms. Found 57 (88 requested) and removed 89 (44 requested) atoms. Cycle 12: After refmac, R = 0.2494 (Rfree = 0.000) for 9748 atoms. Found 28 (87 requested) and removed 57 (43 requested) atoms. Cycle 13: After refmac, R = 0.2476 (Rfree = 0.000) for 9698 atoms. Found 36 (87 requested) and removed 59 (43 requested) atoms. Cycle 14: After refmac, R = 0.2414 (Rfree = 0.000) for 9650 atoms. Found 34 (86 requested) and removed 52 (43 requested) atoms. Cycle 15: After refmac, R = 0.2398 (Rfree = 0.000) for 9620 atoms. Found 17 (86 requested) and removed 53 (43 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.02 3.10 Search for helices and strands: 0 residues in 0 chains, 9835 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 9852 seeds are put forward Round 1: 504 peptides, 99 chains. Longest chain 12 peptides. Score 0.311 Round 2: 565 peptides, 101 chains. Longest chain 12 peptides. Score 0.374 Round 3: 582 peptides, 98 chains. Longest chain 16 peptides. Score 0.408 Round 4: 593 peptides, 92 chains. Longest chain 19 peptides. Score 0.449 Round 5: 608 peptides, 98 chains. Longest chain 20 peptides. Score 0.437 Taking the results from Round 4 Chains 96, Residues 501, Estimated correctness of the model 0.0 % 9 chains (56 residues) have been docked in sequence ------------------------------------------------------ 23615 reflections ( 96.55 % complete ) and 22310 restraints for refining 9991 atoms. 20225 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2532 (Rfree = 0.000) for 9991 atoms. Found 59 (89 requested) and removed 70 (44 requested) atoms. Cycle 17: After refmac, R = 0.2414 (Rfree = 0.000) for 9950 atoms. Found 30 (89 requested) and removed 63 (44 requested) atoms. Cycle 18: After refmac, R = 0.2331 (Rfree = 0.000) for 9890 atoms. Found 14 (89 requested) and removed 54 (44 requested) atoms. Cycle 19: After refmac, R = 0.2303 (Rfree = 0.000) for 9832 atoms. Found 21 (88 requested) and removed 49 (44 requested) atoms. Cycle 20: After refmac, R = 0.2262 (Rfree = 0.000) for 9799 atoms. Found 8 (87 requested) and removed 45 (43 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.07 3.15 Search for helices and strands: 0 residues in 0 chains, 9979 seeds are put forward NCS extension: 21 residues added (2 deleted due to clashes), 10000 seeds are put forward Round 1: 529 peptides, 109 chains. Longest chain 11 peptides. Score 0.289 Round 2: 571 peptides, 101 chains. Longest chain 17 peptides. Score 0.381 Round 3: 580 peptides, 100 chains. Longest chain 17 peptides. Score 0.396 Round 4: 583 peptides, 93 chains. Longest chain 18 peptides. Score 0.433 Round 5: 570 peptides, 93 chains. Longest chain 20 peptides. Score 0.419 Taking the results from Round 4 Chains 93, Residues 490, Estimated correctness of the model 0.0 % 8 chains (38 residues) have been docked in sequence ------------------------------------------------------ 23615 reflections ( 96.55 % complete ) and 22663 restraints for refining 9991 atoms. 20699 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2437 (Rfree = 0.000) for 9991 atoms. Found 58 (89 requested) and removed 62 (44 requested) atoms. Cycle 22: After refmac, R = 0.2375 (Rfree = 0.000) for 9964 atoms. Found 22 (89 requested) and removed 54 (44 requested) atoms. Cycle 23: After refmac, R = 0.2328 (Rfree = 0.000) for 9912 atoms. Found 25 (89 requested) and removed 49 (44 requested) atoms. Cycle 24: After refmac, R = 0.2303 (Rfree = 0.000) for 9880 atoms. Found 15 (88 requested) and removed 44 (44 requested) atoms. Cycle 25: After refmac, R = 0.2467 (Rfree = 0.000) for 9845 atoms. Found 53 (88 requested) and removed 45 (44 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.07 3.15 Search for helices and strands: 0 residues in 0 chains, 10064 seeds are put forward NCS extension: 22 residues added (3 deleted due to clashes), 10086 seeds are put forward Round 1: 497 peptides, 102 chains. Longest chain 15 peptides. Score 0.286 Round 2: 565 peptides, 102 chains. Longest chain 16 peptides. Score 0.369 Round 3: 609 peptides, 109 chains. Longest chain 17 peptides. Score 0.385 Round 4: 584 peptides, 97 chains. Longest chain 15 peptides. Score 0.415 Round 5: 581 peptides, 100 chains. Longest chain 16 peptides. Score 0.397 Taking the results from Round 4 Chains 97, Residues 487, Estimated correctness of the model 0.0 % 7 chains (42 residues) have been docked in sequence ------------------------------------------------------ 23615 reflections ( 96.55 % complete ) and 22752 restraints for refining 9991 atoms. 20797 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2516 (Rfree = 0.000) for 9991 atoms. Found 39 (89 requested) and removed 56 (44 requested) atoms. Cycle 27: After refmac, R = 0.2503 (Rfree = 0.000) for 9940 atoms. Found 64 (89 requested) and removed 52 (44 requested) atoms. Cycle 28: After refmac, R = 0.2584 (Rfree = 0.000) for 9937 atoms. Found 70 (89 requested) and removed 65 (44 requested) atoms. Cycle 29: After refmac, R = 0.2435 (Rfree = 0.000) for 9924 atoms. Found 49 (89 requested) and removed 52 (44 requested) atoms. Cycle 30: After refmac, R = 0.2459 (Rfree = 0.000) for 9901 atoms. Found 49 (89 requested) and removed 53 (44 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.03 3.11 Search for helices and strands: 0 residues in 0 chains, 10162 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 10181 seeds are put forward Round 1: 417 peptides, 88 chains. Longest chain 10 peptides. Score 0.258 Round 2: 500 peptides, 92 chains. Longest chain 16 peptides. Score 0.342 Round 3: 516 peptides, 93 chains. Longest chain 19 peptides. Score 0.356 Round 4: 510 peptides, 88 chains. Longest chain 19 peptides. Score 0.375 Round 5: 518 peptides, 85 chains. Longest chain 19 peptides. Score 0.400 Taking the results from Round 5 Chains 85, Residues 433, Estimated correctness of the model 0.0 % 7 chains (35 residues) have been docked in sequence ------------------------------------------------------ 23615 reflections ( 96.55 % complete ) and 22945 restraints for refining 9991 atoms. 21217 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2517 (Rfree = 0.000) for 9991 atoms. Found 54 (89 requested) and removed 56 (44 requested) atoms. Cycle 32: After refmac, R = 0.2378 (Rfree = 0.000) for 9955 atoms. Found 47 (89 requested) and removed 46 (44 requested) atoms. Cycle 33: After refmac, R = 0.2354 (Rfree = 0.000) for 9931 atoms. Found 44 (89 requested) and removed 47 (44 requested) atoms. Cycle 34: After refmac, R = 0.2382 (Rfree = 0.000) for 9917 atoms. Found 50 (89 requested) and removed 54 (44 requested) atoms. Cycle 35: After refmac, R = 0.2380 (Rfree = 0.000) for 9901 atoms. Found 49 (88 requested) and removed 49 (44 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.02 3.10 Search for helices and strands: 0 residues in 0 chains, 10073 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 10093 seeds are put forward Round 1: 425 peptides, 91 chains. Longest chain 10 peptides. Score 0.252 Round 2: 484 peptides, 89 chains. Longest chain 12 peptides. Score 0.339 Round 3: 495 peptides, 91 chains. Longest chain 13 peptides. Score 0.341 Round 4: 486 peptides, 89 chains. Longest chain 12 peptides. Score 0.341 Round 5: 502 peptides, 90 chains. Longest chain 12 peptides. Score 0.355 Taking the results from Round 5 Chains 91, Residues 412, Estimated correctness of the model 0.0 % 6 chains (39 residues) have been docked in sequence ------------------------------------------------------ 23615 reflections ( 96.55 % complete ) and 22855 restraints for refining 9991 atoms. 21174 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2442 (Rfree = 0.000) for 9991 atoms. Found 56 (89 requested) and removed 50 (44 requested) atoms. Cycle 37: After refmac, R = 0.2425 (Rfree = 0.000) for 9980 atoms. Found 64 (89 requested) and removed 58 (44 requested) atoms. Cycle 38: After refmac, R = 0.2290 (Rfree = 0.000) for 9973 atoms. Found 39 (89 requested) and removed 50 (44 requested) atoms. Cycle 39: After refmac, R = 0.2285 (Rfree = 0.000) for 9944 atoms. Found 35 (89 requested) and removed 50 (44 requested) atoms. Cycle 40: After refmac, R = 0.2244 (Rfree = 0.000) for 9918 atoms. Found 48 (89 requested) and removed 47 (44 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.01 3.09 Search for helices and strands: 0 residues in 0 chains, 10145 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 10158 seeds are put forward Round 1: 379 peptides, 83 chains. Longest chain 8 peptides. Score 0.235 Round 2: 421 peptides, 82 chains. Longest chain 10 peptides. Score 0.297 Round 3: 437 peptides, 80 chains. Longest chain 12 peptides. Score 0.328 Round 4: 424 peptides, 82 chains. Longest chain 12 peptides. Score 0.301 Round 5: 421 peptides, 74 chains. Longest chain 13 peptides. Score 0.341 Taking the results from Round 5 Chains 74, Residues 347, Estimated correctness of the model 0.0 % 5 chains (26 residues) have been docked in sequence ------------------------------------------------------ 23615 reflections ( 96.55 % complete ) and 23460 restraints for refining 9991 atoms. 22072 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2340 (Rfree = 0.000) for 9991 atoms. Found 53 (89 requested) and removed 57 (44 requested) atoms. Cycle 42: After refmac, R = 0.2252 (Rfree = 0.000) for 9969 atoms. Found 15 (89 requested) and removed 49 (44 requested) atoms. Cycle 43: After refmac, R = 0.2244 (Rfree = 0.000) for 9928 atoms. Found 27 (89 requested) and removed 48 (44 requested) atoms. Cycle 44: After refmac, R = 0.2271 (Rfree = 0.000) for 9900 atoms. Found 31 (88 requested) and removed 45 (44 requested) atoms. Cycle 45: After refmac, R = 0.2245 (Rfree = 0.000) for 9881 atoms. Found 19 (88 requested) and removed 46 (44 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.00 3.08 Search for helices and strands: 0 residues in 0 chains, 10023 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 10039 seeds are put forward Round 1: 381 peptides, 82 chains. Longest chain 10 peptides. Score 0.243 Round 2: 412 peptides, 75 chains. Longest chain 15 peptides. Score 0.324 Round 3: 401 peptides, 77 chains. Longest chain 10 peptides. Score 0.299 Round 4: 404 peptides, 75 chains. Longest chain 16 peptides. Score 0.314 Round 5: 422 peptides, 81 chains. Longest chain 10 peptides. Score 0.304 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 75, Residues 337, Estimated correctness of the model 0.0 % 6 chains (23 residues) have been docked in sequence Sequence coverage is 6 % Consider running further cycles of model building using 1vrb-3_warpNtrace.pdb as input Building loops using Loopy2018 75 chains (337 residues) following loop building 6 chains (23 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 23615 reflections ( 96.55 % complete ) and 23120 restraints for refining 9976 atoms. 21809 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2323 (Rfree = 0.000) for 9976 atoms. Found 0 (89 requested) and removed 44 (44 requested) atoms. Cycle 47: After refmac, R = 0.2365 (Rfree = 0.000) for 9920 atoms. Found 0 (89 requested) and removed 44 (44 requested) atoms. Cycle 48: After refmac, R = 0.2330 (Rfree = 0.000) for 9862 atoms. Found 0 (88 requested) and removed 44 (44 requested) atoms. Cycle 49: After refmac, R = 0.2276 (Rfree = 0.000) for 9809 atoms. Found 0 (88 requested) and removed 44 (44 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 09:27:28 GMT 2018 Job finished. TimeTaking 104.77 Used memory is bytes: 12771752