Mon 24 Dec 08:01:30 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 1ztc-4.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1ztc-4.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1ztc-4.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1ztc-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/1ztc-4.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1ztc-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 08:01:35 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/1ztc-4.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1ztc-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 1067 and 0 Target number of residues in the AU: 1067 Target solvent content: 0.6682 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-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: 19 Cell parameters: 89.783 127.343 152.224 90.000 90.000 90.000 Input sequence file: 1ztc-4.0-parrot-noncs.fasta_lf Building free atoms model in initial map for 7072 target number of atoms Had to go as low as 1.15 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 4.000 Wilson plot Bfac: 91.02 15050 reflections ( 98.31 % complete ) and 0 restraints for refining 7791 atoms. Observations/parameters ratio is 0.48 ------------------------------------------------------ Starting model: R = 0.3626 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3533 (Rfree = 0.000) for 7791 atoms. Found 37 (37 requested) and removed 38 (18 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.78 2.71 Search for helices and strands: 0 residues in 0 chains, 7941 seeds are put forward NCS extension: 0 residues added, 7941 seeds are put forward Round 1: 474 peptides, 72 chains. Longest chain 16 peptides. Score 0.383 Round 2: 533 peptides, 66 chains. Longest chain 37 peptides. Score 0.464 Round 3: 551 peptides, 56 chains. Longest chain 28 peptides. Score 0.521 Round 4: 580 peptides, 61 chains. Longest chain 27 peptides. Score 0.525 Round 5: 589 peptides, 56 chains. Longest chain 36 peptides. Score 0.552 Taking the results from Round 5 Chains 56, Residues 533, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 15050 reflections ( 98.31 % complete ) and 14387 restraints for refining 6383 atoms. 12311 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2997 (Rfree = 0.000) for 6383 atoms. Found 30 (30 requested) and removed 24 (15 requested) atoms. Cycle 2: After refmac, R = 0.2629 (Rfree = 0.000) for 6267 atoms. Found 30 (30 requested) and removed 28 (15 requested) atoms. Cycle 3: After refmac, R = 0.2599 (Rfree = 0.000) for 6202 atoms. Found 29 (29 requested) and removed 29 (14 requested) atoms. Cycle 4: After refmac, R = 0.2470 (Rfree = 0.000) for 6170 atoms. Found 29 (29 requested) and removed 26 (14 requested) atoms. Cycle 5: After refmac, R = 0.2412 (Rfree = 0.000) for 6141 atoms. Found 29 (29 requested) and removed 27 (14 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.82 2.74 Search for helices and strands: 0 residues in 0 chains, 6365 seeds are put forward NCS extension: 22 residues added (10 deleted due to clashes), 6387 seeds are put forward Round 1: 576 peptides, 68 chains. Longest chain 32 peptides. Score 0.494 Round 2: 569 peptides, 58 chains. Longest chain 31 peptides. Score 0.528 Round 3: 568 peptides, 59 chains. Longest chain 25 peptides. Score 0.523 Round 4: 573 peptides, 57 chains. Longest chain 45 peptides. Score 0.535 Round 5: 586 peptides, 56 chains. Longest chain 34 peptides. Score 0.549 Taking the results from Round 5 Chains 57, Residues 530, Estimated correctness of the model 0.0 % 1 chains (19 residues) have been docked in sequence ------------------------------------------------------ 15050 reflections ( 98.31 % complete ) and 13858 restraints for refining 6385 atoms. 11696 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2886 (Rfree = 0.000) for 6385 atoms. Found 30 (30 requested) and removed 26 (15 requested) atoms. Cycle 7: After refmac, R = 0.2763 (Rfree = 0.000) for 6329 atoms. Found 30 (30 requested) and removed 24 (15 requested) atoms. Cycle 8: After refmac, R = 0.2386 (Rfree = 0.000) for 6284 atoms. Found 25 (30 requested) and removed 27 (15 requested) atoms. Cycle 9: After refmac, R = 0.2504 (Rfree = 0.000) for 6244 atoms. Found 29 (29 requested) and removed 26 (14 requested) atoms. Cycle 10: After refmac, R = 0.2526 (Rfree = 0.000) for 6223 atoms. Found 29 (29 requested) and removed 26 (14 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.78 2.71 Search for helices and strands: 0 residues in 0 chains, 6451 seeds are put forward NCS extension: 30 residues added (8 deleted due to clashes), 6481 seeds are put forward Round 1: 545 peptides, 67 chains. Longest chain 23 peptides. Score 0.471 Round 2: 584 peptides, 59 chains. Longest chain 34 peptides. Score 0.536 Round 3: 573 peptides, 60 chains. Longest chain 26 peptides. Score 0.523 Round 4: 582 peptides, 58 chains. Longest chain 37 peptides. Score 0.538 Round 5: 605 peptides, 58 chains. Longest chain 37 peptides. Score 0.557 Taking the results from Round 5 Chains 59, Residues 547, Estimated correctness of the model 0.0 % 1 chains (30 residues) have been docked in sequence ------------------------------------------------------ 15050 reflections ( 98.31 % complete ) and 13635 restraints for refining 6381 atoms. 11373 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2726 (Rfree = 0.000) for 6381 atoms. Found 30 (30 requested) and removed 22 (15 requested) atoms. Cycle 12: After refmac, R = 0.2542 (Rfree = 0.000) for 6318 atoms. Found 30 (30 requested) and removed 22 (15 requested) atoms. Cycle 13: After refmac, R = 0.2532 (Rfree = 0.000) for 6279 atoms. Found 30 (30 requested) and removed 30 (15 requested) atoms. Cycle 14: After refmac, R = 0.2253 (Rfree = 0.000) for 6249 atoms. Found 11 (29 requested) and removed 17 (14 requested) atoms. Cycle 15: After refmac, R = 0.2232 (Rfree = 0.000) for 6224 atoms. Found 12 (29 requested) and removed 23 (14 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.80 2.73 Search for helices and strands: 0 residues in 0 chains, 6451 seeds are put forward NCS extension: 29 residues added (2 deleted due to clashes), 6480 seeds are put forward Round 1: 562 peptides, 68 chains. Longest chain 29 peptides. Score 0.482 Round 2: 572 peptides, 61 chains. Longest chain 37 peptides. Score 0.518 Round 3: 589 peptides, 61 chains. Longest chain 26 peptides. Score 0.532 Round 4: 595 peptides, 64 chains. Longest chain 30 peptides. Score 0.526 Round 5: 591 peptides, 58 chains. Longest chain 26 peptides. Score 0.546 Taking the results from Round 5 Chains 58, Residues 533, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 15050 reflections ( 98.31 % complete ) and 14072 restraints for refining 6387 atoms. 11998 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2590 (Rfree = 0.000) for 6387 atoms. Found 30 (30 requested) and removed 18 (15 requested) atoms. Cycle 17: After refmac, R = 0.2381 (Rfree = 0.000) for 6316 atoms. Found 21 (30 requested) and removed 19 (15 requested) atoms. Cycle 18: After refmac, R = 0.2300 (Rfree = 0.000) for 6296 atoms. Found 7 (30 requested) and removed 21 (15 requested) atoms. Cycle 19: After refmac, R = 0.2274 (Rfree = 0.000) for 6272 atoms. Found 10 (29 requested) and removed 24 (14 requested) atoms. Cycle 20: After refmac, R = 0.2243 (Rfree = 0.000) for 6248 atoms. Found 4 (29 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.84 2.76 Search for helices and strands: 0 residues in 0 chains, 6467 seeds are put forward NCS extension: 35 residues added (3 deleted due to clashes), 6502 seeds are put forward Round 1: 531 peptides, 68 chains. Longest chain 29 peptides. Score 0.454 Round 2: 584 peptides, 63 chains. Longest chain 28 peptides. Score 0.520 Round 3: 563 peptides, 53 chains. Longest chain 30 peptides. Score 0.543 Round 4: 570 peptides, 54 chains. Longest chain 38 peptides. Score 0.544 Round 5: 573 peptides, 57 chains. Longest chain 35 peptides. Score 0.535 Taking the results from Round 4 Chains 56, Residues 516, Estimated correctness of the model 0.0 % 2 chains (19 residues) have been docked in sequence ------------------------------------------------------ 15050 reflections ( 98.31 % complete ) and 13914 restraints for refining 6387 atoms. 11829 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2707 (Rfree = 0.000) for 6387 atoms. Found 29 (30 requested) and removed 16 (15 requested) atoms. Cycle 22: After refmac, R = 0.2503 (Rfree = 0.000) for 6336 atoms. Found 30 (30 requested) and removed 20 (15 requested) atoms. Failed to save intermediate PDB Cycle 23: After refmac, R = 0.2460 (Rfree = 0.000) for 6323 atoms. Found 26 (30 requested) and removed 19 (15 requested) atoms. Cycle 24: After refmac, R = 0.2368 (Rfree = 0.000) for 6317 atoms. Found 14 (30 requested) and removed 17 (15 requested) atoms. Cycle 25: After refmac, R = 0.2408 (Rfree = 0.000) for 6301 atoms. Found 21 (30 requested) and removed 20 (15 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.80 2.73 Search for helices and strands: 0 residues in 0 chains, 6527 seeds are put forward NCS extension: 19 residues added (7 deleted due to clashes), 6546 seeds are put forward Round 1: 524 peptides, 67 chains. Longest chain 21 peptides. Score 0.452 Round 2: 556 peptides, 67 chains. Longest chain 38 peptides. Score 0.481 Round 3: 559 peptides, 61 chains. Longest chain 26 peptides. Score 0.508 Round 4: 537 peptides, 59 chains. Longest chain 32 peptides. Score 0.497 Round 5: 560 peptides, 65 chains. Longest chain 26 peptides. Score 0.492 Taking the results from Round 3 Chains 61, Residues 498, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 15050 reflections ( 98.31 % complete ) and 14388 restraints for refining 6386 atoms. 12457 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2707 (Rfree = 0.000) for 6386 atoms. Found 30 (30 requested) and removed 20 (15 requested) atoms. Cycle 27: After refmac, R = 0.2635 (Rfree = 0.000) for 6272 atoms. Found 30 (30 requested) and removed 18 (15 requested) atoms. Cycle 28: After refmac, R = 0.2487 (Rfree = 0.000) for 6213 atoms. Found 29 (29 requested) and removed 23 (14 requested) atoms. Cycle 29: After refmac, R = 0.2446 (Rfree = 0.000) for 6168 atoms. Found 29 (29 requested) and removed 19 (14 requested) atoms. Cycle 30: After refmac, R = 0.2363 (Rfree = 0.000) for 6132 atoms. Found 29 (29 requested) and removed 32 (14 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.77 2.71 Search for helices and strands: 0 residues in 0 chains, 6378 seeds are put forward NCS extension: 27 residues added (6 deleted due to clashes), 6405 seeds are put forward Round 1: 529 peptides, 74 chains. Longest chain 19 peptides. Score 0.427 Round 2: 566 peptides, 69 chains. Longest chain 26 peptides. Score 0.481 Round 3: 577 peptides, 62 chains. Longest chain 26 peptides. Score 0.519 Round 4: 569 peptides, 60 chains. Longest chain 28 peptides. Score 0.520 Round 5: 577 peptides, 66 chains. Longest chain 27 peptides. Score 0.503 Taking the results from Round 4 Chains 62, Residues 509, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 15050 reflections ( 98.31 % complete ) and 14192 restraints for refining 6387 atoms. 12178 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2767 (Rfree = 0.000) for 6387 atoms. Found 30 (30 requested) and removed 18 (15 requested) atoms. Failed to save intermediate PDB Cycle 32: After refmac, R = 0.2569 (Rfree = 0.000) for 6278 atoms. Found 30 (30 requested) and removed 21 (15 requested) atoms. Cycle 33: After refmac, R = 0.2495 (Rfree = 0.000) for 6226 atoms. Found 29 (29 requested) and removed 21 (14 requested) atoms. Cycle 34: After refmac, R = 0.2447 (Rfree = 0.000) for 6201 atoms. Found 29 (29 requested) and removed 18 (14 requested) atoms. Cycle 35: After refmac, R = 0.2360 (Rfree = 0.000) for 6189 atoms. Found 29 (29 requested) and removed 25 (14 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.80 2.73 Search for helices and strands: 0 residues in 0 chains, 6465 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 6480 seeds are put forward Round 1: 502 peptides, 68 chains. Longest chain 18 peptides. Score 0.427 Round 2: 553 peptides, 63 chains. Longest chain 24 peptides. Score 0.494 Round 3: 541 peptides, 57 chains. Longest chain 29 peptides. Score 0.509 Round 4: 547 peptides, 64 chains. Longest chain 29 peptides. Score 0.485 Round 5: 569 peptides, 61 chains. Longest chain 33 peptides. Score 0.516 Taking the results from Round 5 Chains 61, Residues 508, Estimated correctness of the model 0.0 % 1 chains (16 residues) have been docked in sequence ------------------------------------------------------ 15050 reflections ( 98.31 % complete ) and 14021 restraints for refining 6386 atoms. 11985 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2590 (Rfree = 0.000) for 6386 atoms. Found 30 (30 requested) and removed 17 (15 requested) atoms. Cycle 37: After refmac, R = 0.2520 (Rfree = 0.000) for 6285 atoms. Found 30 (30 requested) and removed 27 (15 requested) atoms. Cycle 38: After refmac, R = 0.2540 (Rfree = 0.000) for 6252 atoms. Found 29 (29 requested) and removed 33 (14 requested) atoms. Cycle 39: After refmac, R = 0.2494 (Rfree = 0.000) for 6218 atoms. Found 29 (29 requested) and removed 31 (14 requested) atoms. Cycle 40: After refmac, R = 0.2362 (Rfree = 0.000) for 6199 atoms. Found 29 (29 requested) and removed 20 (14 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.81 2.74 Search for helices and strands: 0 residues in 0 chains, 6462 seeds are put forward NCS extension: 37 residues added (9 deleted due to clashes), 6499 seeds are put forward Round 1: 486 peptides, 75 chains. Longest chain 15 peptides. Score 0.381 Round 2: 548 peptides, 67 chains. Longest chain 23 peptides. Score 0.474 Round 3: 543 peptides, 66 chains. Longest chain 31 peptides. Score 0.473 Round 4: 557 peptides, 57 chains. Longest chain 37 peptides. Score 0.522 Round 5: 542 peptides, 57 chains. Longest chain 33 peptides. Score 0.510 Taking the results from Round 4 Chains 60, Residues 500, Estimated correctness of the model 0.0 % 2 chains (53 residues) have been docked in sequence ------------------------------------------------------ 15050 reflections ( 98.31 % complete ) and 13430 restraints for refining 6387 atoms. 11227 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2677 (Rfree = 0.000) for 6387 atoms. Found 30 (30 requested) and removed 21 (15 requested) atoms. Cycle 42: After refmac, R = 0.2381 (Rfree = 0.000) for 6328 atoms. Found 22 (30 requested) and removed 20 (15 requested) atoms. Cycle 43: After refmac, R = 0.2375 (Rfree = 0.000) for 6308 atoms. Found 23 (30 requested) and removed 21 (15 requested) atoms. Cycle 44: After refmac, R = 0.2342 (Rfree = 0.000) for 6296 atoms. Found 27 (29 requested) and removed 19 (14 requested) atoms. Cycle 45: After refmac, R = 0.2295 (Rfree = 0.000) for 6285 atoms. Found 29 (29 requested) and removed 18 (14 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.88 2.79 Search for helices and strands: 0 residues in 0 chains, 6536 seeds are put forward NCS extension: 16 residues added (6 deleted due to clashes), 6552 seeds are put forward Round 1: 487 peptides, 72 chains. Longest chain 20 peptides. Score 0.395 Round 2: 514 peptides, 62 chains. Longest chain 28 peptides. Score 0.464 Round 3: 514 peptides, 59 chains. Longest chain 22 peptides. Score 0.477 Round 4: 516 peptides, 61 chains. Longest chain 22 peptides. Score 0.470 Round 5: 523 peptides, 61 chains. Longest chain 23 peptides. Score 0.477 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 61, Residues 462, 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 1ztc-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 15050 reflections ( 98.31 % complete ) and 14711 restraints for refining 6387 atoms. 12924 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2774 (Rfree = 0.000) for 6387 atoms. Found 0 (30 requested) and removed 15 (15 requested) atoms. Cycle 47: After refmac, R = 0.2556 (Rfree = 0.000) for 6322 atoms. Found 0 (30 requested) and removed 15 (15 requested) atoms. Cycle 48: After refmac, R = 0.2546 (Rfree = 0.000) for 6286 atoms. Found 0 (29 requested) and removed 14 (14 requested) atoms. Cycle 49: After refmac, R = 0.2445 (Rfree = 0.000) for 6249 atoms. TimeTaking 75.17