Mon 24 Dec 00:24:31 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 1vl4-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vl4-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vl4-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vl4-3.4-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/1vl4-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vl4-3.4-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 00:24:36 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/1vl4-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vl4-3.4-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 734 and 0 Target number of residues in the AU: 734 Target solvent content: 0.6140 Checking the provided sequence file Detected sequence length: 447 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 894 Adjusted target solvent content: 0.53 Input MTZ file: 1vl4-3.4-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: 80.171 107.117 119.834 90.000 90.000 90.000 Input sequence file: 1vl4-3.4-parrot-mrncs.fasta_lf Building free atoms model in initial map for 7152 target number of atoms Had to go as low as 0.65 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: 79.862 3.400 Wilson plot Bfac: 58.63 14660 reflections ( 99.46 % complete ) and 0 restraints for refining 7914 atoms. Observations/parameters ratio is 0.46 ------------------------------------------------------ Starting model: R = 0.3028 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3069 (Rfree = 0.000) for 7914 atoms. Found 59 (59 requested) and removed 56 (29 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.20 3.07 Search for helices and strands: 0 residues in 0 chains, 8025 seeds are put forward NCS extension: 0 residues added, 8025 seeds are put forward Round 1: 422 peptides, 72 chains. Longest chain 14 peptides. Score 0.402 Round 2: 542 peptides, 75 chains. Longest chain 21 peptides. Score 0.552 Round 3: 586 peptides, 68 chains. Longest chain 28 peptides. Score 0.640 Round 4: 596 peptides, 71 chains. Longest chain 33 peptides. Score 0.636 Round 5: 606 peptides, 64 chains. Longest chain 33 peptides. Score 0.679 Taking the results from Round 5 Chains 70, Residues 542, Estimated correctness of the model 52.3 % 9 chains (131 residues) have been docked in sequence ------------------------------------------------------ 14660 reflections ( 99.46 % complete ) and 12674 restraints for refining 6500 atoms. 10091 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2750 (Rfree = 0.000) for 6500 atoms. Found 42 (49 requested) and removed 73 (24 requested) atoms. Cycle 2: After refmac, R = 0.2719 (Rfree = 0.000) for 6383 atoms. Found 37 (48 requested) and removed 48 (24 requested) atoms. Cycle 3: After refmac, R = 0.2513 (Rfree = 0.000) for 6330 atoms. Found 24 (48 requested) and removed 34 (24 requested) atoms. Cycle 4: After refmac, R = 0.2595 (Rfree = 0.000) for 6290 atoms. Found 17 (47 requested) and removed 38 (23 requested) atoms. Cycle 5: After refmac, R = 0.2347 (Rfree = 0.000) for 6244 atoms. Found 15 (47 requested) and removed 34 (23 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.17 3.05 Search for helices and strands: 0 residues in 0 chains, 6402 seeds are put forward NCS extension: 13 residues added (6 deleted due to clashes), 6415 seeds are put forward Round 1: 543 peptides, 73 chains. Longest chain 21 peptides. Score 0.565 Round 2: 589 peptides, 65 chains. Longest chain 28 peptides. Score 0.657 Round 3: 605 peptides, 68 chains. Longest chain 27 peptides. Score 0.660 Round 4: 625 peptides, 66 chains. Longest chain 44 peptides. Score 0.688 Round 5: 620 peptides, 63 chains. Longest chain 41 peptides. Score 0.697 Taking the results from Round 5 Chains 70, Residues 557, Estimated correctness of the model 57.1 % 9 chains (140 residues) have been docked in sequence ------------------------------------------------------ 14660 reflections ( 99.46 % complete ) and 12674 restraints for refining 6503 atoms. 9969 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2740 (Rfree = 0.000) for 6503 atoms. Found 35 (49 requested) and removed 73 (24 requested) atoms. Cycle 7: After refmac, R = 0.2527 (Rfree = 0.000) for 6415 atoms. Found 24 (48 requested) and removed 46 (24 requested) atoms. Cycle 8: After refmac, R = 0.2454 (Rfree = 0.000) for 6366 atoms. Found 28 (48 requested) and removed 46 (24 requested) atoms. Cycle 9: After refmac, R = 0.2411 (Rfree = 0.000) for 6336 atoms. Found 28 (47 requested) and removed 38 (23 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.2320 (Rfree = 0.000) for 6313 atoms. Found 17 (47 requested) and removed 50 (23 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.11 2.99 Search for helices and strands: 0 residues in 0 chains, 6443 seeds are put forward NCS extension: 18 residues added (16 deleted due to clashes), 6461 seeds are put forward Round 1: 562 peptides, 75 chains. Longest chain 27 peptides. Score 0.577 Round 2: 607 peptides, 70 chains. Longest chain 36 peptides. Score 0.652 Round 3: 597 peptides, 71 chains. Longest chain 32 peptides. Score 0.637 Round 4: 565 peptides, 61 chains. Longest chain 45 peptides. Score 0.652 Round 5: 575 peptides, 61 chains. Longest chain 31 peptides. Score 0.662 Taking the results from Round 5 Chains 66, Residues 514, Estimated correctness of the model 47.6 % 8 chains (98 residues) have been docked in sequence ------------------------------------------------------ 14660 reflections ( 99.46 % complete ) and 13228 restraints for refining 6503 atoms. 10844 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2620 (Rfree = 0.000) for 6503 atoms. Found 37 (49 requested) and removed 57 (24 requested) atoms. Cycle 12: After refmac, R = 0.2365 (Rfree = 0.000) for 6451 atoms. Found 32 (48 requested) and removed 44 (24 requested) atoms. Cycle 13: After refmac, R = 0.2273 (Rfree = 0.000) for 6422 atoms. Found 26 (48 requested) and removed 41 (24 requested) atoms. Cycle 14: After refmac, R = 0.2280 (Rfree = 0.000) for 6389 atoms. Found 30 (48 requested) and removed 34 (24 requested) atoms. Cycle 15: After refmac, R = 0.2132 (Rfree = 0.000) for 6372 atoms. Found 15 (48 requested) and removed 31 (24 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.12 3.00 Search for helices and strands: 0 residues in 0 chains, 6524 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 6537 seeds are put forward Round 1: 534 peptides, 82 chains. Longest chain 28 peptides. Score 0.501 Round 2: 577 peptides, 74 chains. Longest chain 27 peptides. Score 0.600 Round 3: 571 peptides, 66 chains. Longest chain 36 peptides. Score 0.634 Round 4: 574 peptides, 72 chains. Longest chain 39 peptides. Score 0.607 Round 5: 584 peptides, 68 chains. Longest chain 36 peptides. Score 0.638 Taking the results from Round 5 Chains 79, Residues 516, Estimated correctness of the model 40.6 % 12 chains (149 residues) have been docked in sequence ------------------------------------------------------ 14660 reflections ( 99.46 % complete ) and 12607 restraints for refining 6501 atoms. 10016 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2559 (Rfree = 0.000) for 6501 atoms. Found 40 (49 requested) and removed 45 (24 requested) atoms. Cycle 17: After refmac, R = 0.2352 (Rfree = 0.000) for 6446 atoms. Found 30 (49 requested) and removed 36 (24 requested) atoms. Cycle 18: After refmac, R = 0.2239 (Rfree = 0.000) for 6419 atoms. Found 18 (48 requested) and removed 34 (24 requested) atoms. Cycle 19: After refmac, R = 0.2483 (Rfree = 0.000) for 6384 atoms. Found 43 (48 requested) and removed 36 (24 requested) atoms. Cycle 20: After refmac, R = 0.2152 (Rfree = 0.000) for 6355 atoms. Found 21 (48 requested) and removed 27 (24 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.12 3.00 Search for helices and strands: 0 residues in 0 chains, 6496 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 6514 seeds are put forward Round 1: 510 peptides, 82 chains. Longest chain 18 peptides. Score 0.468 Round 2: 553 peptides, 71 chains. Longest chain 30 peptides. Score 0.587 Round 3: 543 peptides, 70 chains. Longest chain 26 peptides. Score 0.581 Round 4: 545 peptides, 68 chains. Longest chain 35 peptides. Score 0.594 Round 5: 531 peptides, 69 chains. Longest chain 22 peptides. Score 0.572 Taking the results from Round 4 Chains 70, Residues 477, Estimated correctness of the model 26.7 % 9 chains (90 residues) have been docked in sequence ------------------------------------------------------ 14660 reflections ( 99.46 % complete ) and 13528 restraints for refining 6503 atoms. 11308 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2445 (Rfree = 0.000) for 6503 atoms. Found 46 (49 requested) and removed 35 (24 requested) atoms. Cycle 22: After refmac, R = 0.2355 (Rfree = 0.000) for 6485 atoms. Found 24 (49 requested) and removed 34 (24 requested) atoms. Cycle 23: After refmac, R = 0.2211 (Rfree = 0.000) for 6455 atoms. Found 15 (48 requested) and removed 28 (24 requested) atoms. Cycle 24: After refmac, R = 0.2165 (Rfree = 0.000) for 6430 atoms. Found 10 (48 requested) and removed 29 (24 requested) atoms. Cycle 25: After refmac, R = 0.2077 (Rfree = 0.000) for 6395 atoms. Found 12 (48 requested) and removed 26 (24 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.14 3.02 Search for helices and strands: 0 residues in 0 chains, 6540 seeds are put forward NCS extension: 58 residues added (5 deleted due to clashes), 6598 seeds are put forward Round 1: 499 peptides, 83 chains. Longest chain 19 peptides. Score 0.446 Round 2: 527 peptides, 69 chains. Longest chain 25 peptides. Score 0.567 Round 3: 542 peptides, 71 chains. Longest chain 23 peptides. Score 0.574 Round 4: 538 peptides, 74 chains. Longest chain 26 peptides. Score 0.553 Round 5: 553 peptides, 68 chains. Longest chain 29 peptides. Score 0.603 Taking the results from Round 5 Chains 68, Residues 485, Estimated correctness of the model 29.7 % 4 chains (32 residues) have been docked in sequence ------------------------------------------------------ 14660 reflections ( 99.46 % complete ) and 14237 restraints for refining 6503 atoms. 12262 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2420 (Rfree = 0.000) for 6503 atoms. Found 42 (49 requested) and removed 32 (24 requested) atoms. Cycle 27: After refmac, R = 0.2247 (Rfree = 0.000) for 6495 atoms. Found 21 (49 requested) and removed 27 (24 requested) atoms. Cycle 28: After refmac, R = 0.2162 (Rfree = 0.000) for 6473 atoms. Found 10 (48 requested) and removed 28 (24 requested) atoms. Cycle 29: After refmac, R = 0.2102 (Rfree = 0.000) for 6447 atoms. Found 9 (48 requested) and removed 29 (24 requested) atoms. Cycle 30: After refmac, R = 0.2121 (Rfree = 0.000) for 6420 atoms. Found 12 (48 requested) and removed 25 (24 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.14 3.02 Search for helices and strands: 0 residues in 0 chains, 6549 seeds are put forward NCS extension: 14 residues added (5 deleted due to clashes), 6563 seeds are put forward Round 1: 469 peptides, 76 chains. Longest chain 21 peptides. Score 0.446 Round 2: 538 peptides, 70 chains. Longest chain 27 peptides. Score 0.575 Round 3: 533 peptides, 69 chains. Longest chain 22 peptides. Score 0.574 Round 4: 537 peptides, 68 chains. Longest chain 23 peptides. Score 0.584 Round 5: 562 peptides, 70 chains. Longest chain 22 peptides. Score 0.603 Taking the results from Round 5 Chains 71, Residues 492, Estimated correctness of the model 29.7 % 4 chains (44 residues) have been docked in sequence ------------------------------------------------------ 14660 reflections ( 99.46 % complete ) and 13751 restraints for refining 6503 atoms. 11673 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2437 (Rfree = 0.000) for 6503 atoms. Found 31 (49 requested) and removed 36 (24 requested) atoms. Cycle 32: After refmac, R = 0.2278 (Rfree = 0.000) for 6474 atoms. Found 24 (49 requested) and removed 30 (24 requested) atoms. Cycle 33: After refmac, R = 0.2222 (Rfree = 0.000) for 6453 atoms. Found 13 (48 requested) and removed 29 (24 requested) atoms. Cycle 34: After refmac, R = 0.2176 (Rfree = 0.000) for 6428 atoms. Found 13 (48 requested) and removed 31 (24 requested) atoms. Cycle 35: After refmac, R = 0.2143 (Rfree = 0.000) for 6402 atoms. Found 6 (48 requested) and removed 30 (24 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.16 3.04 Search for helices and strands: 0 residues in 0 chains, 6549 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 6564 seeds are put forward Round 1: 466 peptides, 76 chains. Longest chain 16 peptides. Score 0.442 Round 2: 497 peptides, 69 chains. Longest chain 23 peptides. Score 0.529 Round 3: 522 peptides, 66 chains. Longest chain 23 peptides. Score 0.577 Round 4: 517 peptides, 71 chains. Longest chain 24 peptides. Score 0.543 Round 5: 525 peptides, 63 chains. Longest chain 23 peptides. Score 0.597 Taking the results from Round 5 Chains 66, Residues 462, Estimated correctness of the model 27.7 % 7 chains (88 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 14660 reflections ( 99.46 % complete ) and 13541 restraints for refining 6502 atoms. 11394 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2482 (Rfree = 0.000) for 6502 atoms. Found 26 (49 requested) and removed 52 (24 requested) atoms. Cycle 37: After refmac, R = 0.2333 (Rfree = 0.000) for 6455 atoms. Found 25 (48 requested) and removed 35 (24 requested) atoms. Cycle 38: After refmac, R = 0.2231 (Rfree = 0.000) for 6436 atoms. Found 28 (48 requested) and removed 31 (24 requested) atoms. Cycle 39: After refmac, R = 0.2191 (Rfree = 0.000) for 6426 atoms. Found 15 (48 requested) and removed 32 (24 requested) atoms. Cycle 40: After refmac, R = 0.2137 (Rfree = 0.000) for 6406 atoms. Found 13 (48 requested) and removed 28 (24 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.12 3.00 Search for helices and strands: 0 residues in 0 chains, 6553 seeds are put forward NCS extension: 19 residues added (4 deleted due to clashes), 6572 seeds are put forward Round 1: 425 peptides, 67 chains. Longest chain 23 peptides. Score 0.439 Round 2: 487 peptides, 62 chains. Longest chain 27 peptides. Score 0.556 Round 3: 478 peptides, 57 chains. Longest chain 24 peptides. Score 0.574 Round 4: 497 peptides, 64 chains. Longest chain 25 peptides. Score 0.557 Round 5: 467 peptides, 59 chains. Longest chain 29 peptides. Score 0.548 Taking the results from Round 3 Chains 58, Residues 421, Estimated correctness of the model 20.0 % 2 chains (26 residues) have been docked in sequence ------------------------------------------------------ 14660 reflections ( 99.46 % complete ) and 14384 restraints for refining 6502 atoms. 12640 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2410 (Rfree = 0.000) for 6502 atoms. Found 34 (49 requested) and removed 58 (24 requested) atoms. Cycle 42: After refmac, R = 0.2220 (Rfree = 0.000) for 6460 atoms. Found 40 (48 requested) and removed 32 (24 requested) atoms. Failed to save intermediate PDB Cycle 43: After refmac, R = 0.2048 (Rfree = 0.000) for 6456 atoms. Found 30 (48 requested) and removed 28 (24 requested) atoms. Cycle 44: After refmac, R = 0.1999 (Rfree = 0.000) for 6447 atoms. Found 22 (48 requested) and removed 25 (24 requested) atoms. Cycle 45: After refmac, R = 0.2047 (Rfree = 0.000) for 6434 atoms. Found 33 (48 requested) and removed 26 (24 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.10 2.98 Search for helices and strands: 0 residues in 0 chains, 6550 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 6571 seeds are put forward Round 1: 391 peptides, 69 chains. Longest chain 15 peptides. Score 0.373 Round 2: 458 peptides, 64 chains. Longest chain 21 peptides. Score 0.506 Round 3: 472 peptides, 65 chains. Longest chain 25 peptides. Score 0.519 Round 4: 454 peptides, 60 chains. Longest chain 23 peptides. Score 0.525 Round 5: 474 peptides, 63 chains. Longest chain 23 peptides. Score 0.534 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 71, Residues 411, Estimated correctness of the model 5.7 % 9 chains (92 residues) have been docked in sequence Sequence coverage is 22 % Consider running further cycles of model building using 1vl4-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 376 A and 384 A 70 chains (413 residues) following loop building 8 chains (99 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 14660 reflections ( 99.46 % complete ) and 13688 restraints for refining 6501 atoms. 11728 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2305 (Rfree = 0.000) for 6501 atoms. Found 0 (49 requested) and removed 24 (24 requested) atoms. Cycle 47: After refmac, R = 0.2265 (Rfree = 0.000) for 6452 atoms. Found 0 (48 requested) and removed 24 (24 requested) atoms. Cycle 48: After refmac, R = 0.2136 (Rfree = 0.000) for 6412 atoms. Found 0 (48 requested) and removed 24 (24 requested) atoms. Cycle 49: After refmac, R = 0.2123 (Rfree = 0.000) for 6376 atoms. TimeTaking 68.05