Mon 24 Dec 07:26:18 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 1ztc-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1ztc-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1ztc-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1ztc-3.6-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/1ztc-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1ztc-3.6-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 07:26:22 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/1ztc-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1ztc-3.6-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 1117 and 0 Target number of residues in the AU: 1117 Target solvent content: 0.6527 Checking the provided sequence file Detected sequence length: 221 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 884 Adjusted target solvent content: 0.73 Input MTZ file: 1ztc-3.6-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: 89.783 127.343 152.224 90.000 90.000 90.000 Input sequence file: 1ztc-3.6-parrot-noncs.fasta_lf Building free atoms model in initial map for 7072 target number of atoms Had to go as low as 1.10 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: 97.673 3.600 Wilson plot Bfac: 79.77 20576 reflections ( 98.68 % complete ) and 0 restraints for refining 7907 atoms. Observations/parameters ratio is 0.65 ------------------------------------------------------ Starting model: R = 0.3532 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3342 (Rfree = 0.000) for 7907 atoms. Found 50 (50 requested) and removed 38 (25 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.58 2.57 Search for helices and strands: 0 residues in 0 chains, 8075 seeds are put forward NCS extension: 0 residues added, 8075 seeds are put forward Round 1: 559 peptides, 76 chains. Longest chain 29 peptides. Score 0.446 Round 2: 620 peptides, 64 chains. Longest chain 31 peptides. Score 0.546 Round 3: 635 peptides, 58 chains. Longest chain 40 peptides. Score 0.579 Round 4: 631 peptides, 58 chains. Longest chain 44 peptides. Score 0.576 Round 5: 638 peptides, 52 chains. Longest chain 48 peptides. Score 0.603 Taking the results from Round 5 Chains 53, Residues 586, Estimated correctness of the model 15.8 % 2 chains (49 residues) have been docked in sequence ------------------------------------------------------ 20576 reflections ( 98.68 % complete ) and 13143 restraints for refining 6408 atoms. 10644 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2797 (Rfree = 0.000) for 6408 atoms. Found 41 (41 requested) and removed 54 (20 requested) atoms. Cycle 2: After refmac, R = 0.2561 (Rfree = 0.000) for 6285 atoms. Found 41 (41 requested) and removed 28 (20 requested) atoms. Cycle 3: After refmac, R = 0.2433 (Rfree = 0.000) for 6253 atoms. Found 35 (40 requested) and removed 37 (20 requested) atoms. Cycle 4: After refmac, R = 0.2312 (Rfree = 0.000) for 6212 atoms. Found 27 (40 requested) and removed 29 (20 requested) atoms. Cycle 5: After refmac, R = 0.2271 (Rfree = 0.000) for 6189 atoms. Found 34 (39 requested) and removed 28 (19 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.53 2.53 Search for helices and strands: 0 residues in 0 chains, 6390 seeds are put forward NCS extension: 29 residues added (17 deleted due to clashes), 6419 seeds are put forward Round 1: 625 peptides, 63 chains. Longest chain 39 peptides. Score 0.553 Round 2: 623 peptides, 59 chains. Longest chain 28 peptides. Score 0.567 Round 3: 669 peptides, 64 chains. Longest chain 46 peptides. Score 0.583 Round 4: 646 peptides, 51 chains. Longest chain 36 peptides. Score 0.612 Round 5: 637 peptides, 58 chains. Longest chain 32 peptides. Score 0.581 Taking the results from Round 4 Chains 53, Residues 595, Estimated correctness of the model 19.3 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 20576 reflections ( 98.68 % complete ) and 13344 restraints for refining 6409 atoms. 10953 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2645 (Rfree = 0.000) for 6409 atoms. Found 41 (41 requested) and removed 40 (20 requested) atoms. Cycle 7: After refmac, R = 0.2395 (Rfree = 0.000) for 6365 atoms. Found 41 (41 requested) and removed 33 (20 requested) atoms. Cycle 8: After refmac, R = 0.2269 (Rfree = 0.000) for 6338 atoms. Found 26 (40 requested) and removed 22 (20 requested) atoms. Cycle 9: After refmac, R = 0.2205 (Rfree = 0.000) for 6317 atoms. Found 22 (40 requested) and removed 28 (20 requested) atoms. Cycle 10: After refmac, R = 0.2154 (Rfree = 0.000) for 6302 atoms. Found 11 (40 requested) and removed 24 (20 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.53 2.53 Search for helices and strands: 0 residues in 0 chains, 6566 seeds are put forward NCS extension: 34 residues added (18 deleted due to clashes), 6600 seeds are put forward Round 1: 635 peptides, 68 chains. Longest chain 28 peptides. Score 0.542 Round 2: 643 peptides, 55 chains. Longest chain 51 peptides. Score 0.596 Round 3: 657 peptides, 55 chains. Longest chain 44 peptides. Score 0.606 Round 4: 644 peptides, 52 chains. Longest chain 49 peptides. Score 0.607 Round 5: 655 peptides, 56 chains. Longest chain 41 peptides. Score 0.601 Taking the results from Round 4 Chains 57, Residues 592, Estimated correctness of the model 17.4 % 3 chains (59 residues) have been docked in sequence ------------------------------------------------------ 20576 reflections ( 98.68 % complete ) and 12886 restraints for refining 6409 atoms. 10325 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2560 (Rfree = 0.000) for 6409 atoms. Found 41 (41 requested) and removed 31 (20 requested) atoms. Cycle 12: After refmac, R = 0.2390 (Rfree = 0.000) for 6354 atoms. Found 36 (41 requested) and removed 46 (20 requested) atoms. Cycle 13: After refmac, R = 0.2335 (Rfree = 0.000) for 6308 atoms. Found 17 (40 requested) and removed 29 (20 requested) atoms. Cycle 14: After refmac, R = 0.2324 (Rfree = 0.000) for 6281 atoms. Found 20 (40 requested) and removed 26 (20 requested) atoms. Cycle 15: After refmac, R = 0.2267 (Rfree = 0.000) for 6258 atoms. Found 23 (40 requested) and removed 27 (20 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.53 2.53 Search for helices and strands: 0 residues in 0 chains, 6458 seeds are put forward NCS extension: 21 residues added (20 deleted due to clashes), 6479 seeds are put forward Round 1: 610 peptides, 67 chains. Longest chain 30 peptides. Score 0.526 Round 2: 643 peptides, 49 chains. Longest chain 47 peptides. Score 0.617 Round 3: 666 peptides, 58 chains. Longest chain 37 peptides. Score 0.602 Round 4: 653 peptides, 54 chains. Longest chain 45 peptides. Score 0.607 Round 5: 644 peptides, 53 chains. Longest chain 42 peptides. Score 0.604 Taking the results from Round 2 Chains 58, Residues 594, Estimated correctness of the model 21.2 % 6 chains (115 residues) have been docked in sequence ------------------------------------------------------ 20576 reflections ( 98.68 % complete ) and 12278 restraints for refining 6410 atoms. 9458 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2548 (Rfree = 0.000) for 6410 atoms. Found 41 (41 requested) and removed 40 (20 requested) atoms. Cycle 17: After refmac, R = 0.2429 (Rfree = 0.000) for 6370 atoms. Found 41 (41 requested) and removed 30 (20 requested) atoms. Cycle 18: After refmac, R = 0.2348 (Rfree = 0.000) for 6357 atoms. Found 32 (40 requested) and removed 34 (20 requested) atoms. Cycle 19: After refmac, R = 0.2327 (Rfree = 0.000) for 6339 atoms. Found 31 (40 requested) and removed 38 (20 requested) atoms. Cycle 20: After refmac, R = 0.2273 (Rfree = 0.000) for 6322 atoms. Found 22 (40 requested) and removed 22 (20 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.51 2.52 Search for helices and strands: 0 residues in 0 chains, 6527 seeds are put forward NCS extension: 37 residues added (25 deleted due to clashes), 6564 seeds are put forward Round 1: 621 peptides, 57 chains. Longest chain 38 peptides. Score 0.573 Round 2: 635 peptides, 48 chains. Longest chain 51 peptides. Score 0.615 Round 3: 628 peptides, 54 chains. Longest chain 51 peptides. Score 0.589 Round 4: 647 peptides, 56 chains. Longest chain 39 peptides. Score 0.595 Round 5: 643 peptides, 49 chains. Longest chain 34 peptides. Score 0.617 Taking the results from Round 5 Chains 56, Residues 594, Estimated correctness of the model 21.2 % 6 chains (96 residues) have been docked in sequence ------------------------------------------------------ 20576 reflections ( 98.68 % complete ) and 12553 restraints for refining 6410 atoms. 9807 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2719 (Rfree = 0.000) for 6410 atoms. Found 41 (41 requested) and removed 36 (20 requested) atoms. Cycle 22: After refmac, R = 0.2560 (Rfree = 0.000) for 6369 atoms. Found 41 (41 requested) and removed 28 (20 requested) atoms. Cycle 23: After refmac, R = 0.2456 (Rfree = 0.000) for 6366 atoms. Found 40 (40 requested) and removed 22 (20 requested) atoms. Cycle 24: After refmac, R = 0.2476 (Rfree = 0.000) for 6365 atoms. Found 40 (40 requested) and removed 29 (20 requested) atoms. Cycle 25: After refmac, R = 0.2477 (Rfree = 0.000) for 6368 atoms. Found 40 (40 requested) and removed 21 (20 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.54 2.54 Search for helices and strands: 0 residues in 0 chains, 6551 seeds are put forward NCS extension: 19 residues added (8 deleted due to clashes), 6570 seeds are put forward Round 1: 619 peptides, 66 chains. Longest chain 29 peptides. Score 0.537 Round 2: 624 peptides, 52 chains. Longest chain 43 peptides. Score 0.593 Round 3: 619 peptides, 53 chains. Longest chain 31 peptides. Score 0.586 Round 4: 640 peptides, 58 chains. Longest chain 36 peptides. Score 0.583 Round 5: 633 peptides, 62 chains. Longest chain 44 peptides. Score 0.563 Taking the results from Round 2 Chains 55, Residues 572, Estimated correctness of the model 11.9 % 4 chains (83 residues) have been docked in sequence ------------------------------------------------------ 20576 reflections ( 98.68 % complete ) and 12792 restraints for refining 6411 atoms. 10175 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2586 (Rfree = 0.000) for 6411 atoms. Found 41 (41 requested) and removed 27 (20 requested) atoms. Cycle 27: After refmac, R = 0.2452 (Rfree = 0.000) for 6387 atoms. Found 41 (41 requested) and removed 26 (20 requested) atoms. Cycle 28: After refmac, R = 0.2335 (Rfree = 0.000) for 6390 atoms. Found 34 (41 requested) and removed 22 (20 requested) atoms. Cycle 29: After refmac, R = 0.2303 (Rfree = 0.000) for 6390 atoms. Found 23 (41 requested) and removed 22 (20 requested) atoms. Cycle 30: After refmac, R = 0.2243 (Rfree = 0.000) for 6377 atoms. Found 29 (41 requested) and removed 23 (20 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.53 2.53 Search for helices and strands: 0 residues in 0 chains, 6552 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 6572 seeds are put forward Round 1: 612 peptides, 67 chains. Longest chain 36 peptides. Score 0.528 Round 2: 650 peptides, 57 chains. Longest chain 39 peptides. Score 0.594 Round 3: 631 peptides, 57 chains. Longest chain 34 peptides. Score 0.580 Round 4: 623 peptides, 57 chains. Longest chain 38 peptides. Score 0.574 Round 5: 626 peptides, 53 chains. Longest chain 42 peptides. Score 0.591 Taking the results from Round 2 Chains 60, Residues 593, Estimated correctness of the model 12.3 % 5 chains (98 residues) have been docked in sequence ------------------------------------------------------ 20576 reflections ( 98.68 % complete ) and 12657 restraints for refining 6408 atoms. 9885 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2562 (Rfree = 0.000) for 6408 atoms. Found 41 (41 requested) and removed 30 (20 requested) atoms. Cycle 32: After refmac, R = 0.2435 (Rfree = 0.000) for 6356 atoms. Found 41 (41 requested) and removed 23 (20 requested) atoms. Cycle 33: After refmac, R = 0.2345 (Rfree = 0.000) for 6351 atoms. Found 33 (40 requested) and removed 23 (20 requested) atoms. Cycle 34: After refmac, R = 0.2292 (Rfree = 0.000) for 6339 atoms. Found 29 (40 requested) and removed 24 (20 requested) atoms. Cycle 35: After refmac, R = 0.2248 (Rfree = 0.000) for 6329 atoms. Found 23 (40 requested) and removed 23 (20 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.54 2.54 Search for helices and strands: 0 residues in 0 chains, 6506 seeds are put forward NCS extension: 15 residues added (13 deleted due to clashes), 6521 seeds are put forward Round 1: 581 peptides, 65 chains. Longest chain 24 peptides. Score 0.510 Round 2: 631 peptides, 59 chains. Longest chain 51 peptides. Score 0.573 Round 3: 648 peptides, 60 chains. Longest chain 36 peptides. Score 0.582 Round 4: 640 peptides, 62 chains. Longest chain 33 peptides. Score 0.568 Round 5: 636 peptides, 57 chains. Longest chain 52 peptides. Score 0.584 Taking the results from Round 5 Chains 58, Residues 579, Estimated correctness of the model 8.3 % 3 chains (123 residues) have been docked in sequence ------------------------------------------------------ 20576 reflections ( 98.68 % complete ) and 12651 restraints for refining 6411 atoms. 9846 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2592 (Rfree = 0.000) for 6411 atoms. Found 41 (41 requested) and removed 36 (20 requested) atoms. Cycle 37: After refmac, R = 0.2382 (Rfree = 0.000) for 6370 atoms. Found 35 (41 requested) and removed 25 (20 requested) atoms. Cycle 38: After refmac, R = 0.2342 (Rfree = 0.000) for 6355 atoms. Found 28 (40 requested) and removed 23 (20 requested) atoms. Cycle 39: After refmac, R = 0.2204 (Rfree = 0.000) for 6351 atoms. Found 12 (40 requested) and removed 20 (20 requested) atoms. Cycle 40: After refmac, R = 0.2178 (Rfree = 0.000) for 6328 atoms. Found 16 (40 requested) and removed 20 (20 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.52 2.53 Search for helices and strands: 0 residues in 0 chains, 6532 seeds are put forward NCS extension: 16 residues added (15 deleted due to clashes), 6548 seeds are put forward Round 1: 575 peptides, 66 chains. Longest chain 23 peptides. Score 0.501 Round 2: 623 peptides, 59 chains. Longest chain 37 peptides. Score 0.567 Round 3: 628 peptides, 61 chains. Longest chain 26 peptides. Score 0.563 Round 4: 627 peptides, 60 chains. Longest chain 33 peptides. Score 0.566 Round 5: 634 peptides, 65 chains. Longest chain 41 peptides. Score 0.553 Taking the results from Round 2 Chains 60, Residues 564, Estimated correctness of the model 1.3 % 2 chains (48 residues) have been docked in sequence ------------------------------------------------------ 20576 reflections ( 98.68 % complete ) and 13464 restraints for refining 6410 atoms. 11052 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2565 (Rfree = 0.000) for 6410 atoms. Found 41 (41 requested) and removed 28 (20 requested) atoms. Cycle 42: After refmac, R = 0.2388 (Rfree = 0.000) for 6387 atoms. Found 41 (41 requested) and removed 30 (20 requested) atoms. Cycle 43: After refmac, R = 0.2325 (Rfree = 0.000) for 6379 atoms. Found 38 (41 requested) and removed 25 (20 requested) atoms. Cycle 44: After refmac, R = 0.2273 (Rfree = 0.000) for 6379 atoms. Found 32 (41 requested) and removed 27 (20 requested) atoms. Cycle 45: After refmac, R = 0.2255 (Rfree = 0.000) for 6374 atoms. Found 28 (40 requested) and removed 20 (20 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.54 2.54 Search for helices and strands: 0 residues in 0 chains, 6565 seeds are put forward NCS extension: 29 residues added (8 deleted due to clashes), 6594 seeds are put forward Round 1: 611 peptides, 69 chains. Longest chain 35 peptides. Score 0.519 Round 2: 636 peptides, 64 chains. Longest chain 37 peptides. Score 0.558 Round 3: 635 peptides, 62 chains. Longest chain 39 peptides. Score 0.565 Round 4: 654 peptides, 58 chains. Longest chain 42 peptides. Score 0.593 Round 5: 643 peptides, 57 chains. Longest chain 42 peptides. Score 0.589 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 61, Residues 596, Estimated correctness of the model 11.9 % 4 chains (89 residues) have been docked in sequence Sequence coverage is 14 % Consider running further cycles of model building using 1ztc-3_warpNtrace.pdb as input Building loops using Loopy2018 61 chains (596 residues) following loop building 4 chains (89 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. Failed to save intermediate PDB 20576 reflections ( 98.68 % complete ) and 12854 restraints for refining 6410 atoms. 10133 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2592 (Rfree = 0.000) for 6410 atoms. Found 0 (41 requested) and removed 20 (20 requested) atoms. Cycle 47: After refmac, R = 0.2471 (Rfree = 0.000) for 6343 atoms. Found 0 (40 requested) and removed 20 (20 requested) atoms. Cycle 48: After refmac, R = 0.2413 (Rfree = 0.000) for 6307 atoms. Found 0 (40 requested) and removed 17 (20 requested) atoms. Cycle 49: After refmac, R = 0.2383 (Rfree = 0.000) for 6274 atoms. TimeTaking 76.43