Mon 24 Dec 00:24:14 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 1ztc-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1ztc-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1ztc-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1ztc-3.6-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/1ztc-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1ztc-3.6-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 00:24:19 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/1ztc-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1ztc-3.6-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 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-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: 89.783 127.343 152.224 90.000 90.000 90.000 Input sequence file: 1ztc-3.6-parrot-mrncs.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 7829 atoms. Observations/parameters ratio is 0.66 ------------------------------------------------------ Starting model: R = 0.3276 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2978 (Rfree = 0.000) for 7829 atoms. Found 50 (50 requested) and removed 28 (25 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.52 2.53 Search for helices and strands: 0 residues in 0 chains, 7995 seeds are put forward NCS extension: 0 residues added, 7995 seeds are put forward Round 1: 616 peptides, 68 chains. Longest chain 25 peptides. Score 0.527 Round 2: 671 peptides, 58 chains. Longest chain 48 peptides. Score 0.606 Round 3: 663 peptides, 59 chains. Longest chain 32 peptides. Score 0.596 Round 4: 661 peptides, 57 chains. Longest chain 42 peptides. Score 0.602 Round 5: 638 peptides, 53 chains. Longest chain 37 peptides. Score 0.600 Taking the results from Round 2 Chains 59, Residues 613, Estimated correctness of the model 17.0 % 2 chains (62 residues) have been docked in sequence ------------------------------------------------------ 20576 reflections ( 98.68 % complete ) and 13160 restraints for refining 6600 atoms. 10498 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2695 (Rfree = 0.000) for 6600 atoms. Found 42 (42 requested) and removed 34 (21 requested) atoms. Cycle 2: After refmac, R = 0.2517 (Rfree = 0.000) for 6478 atoms. Found 42 (42 requested) and removed 33 (21 requested) atoms. Cycle 3: After refmac, R = 0.2421 (Rfree = 0.000) for 6442 atoms. Found 41 (41 requested) and removed 30 (20 requested) atoms. Cycle 4: After refmac, R = 0.2307 (Rfree = 0.000) for 6418 atoms. Found 30 (41 requested) and removed 28 (20 requested) atoms. Cycle 5: After refmac, R = 0.2258 (Rfree = 0.000) for 6393 atoms. Found 41 (41 requested) and removed 22 (20 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.54 2.54 Search for helices and strands: 0 residues in 0 chains, 6639 seeds are put forward NCS extension: 25 residues added (12 deleted due to clashes), 6664 seeds are put forward Round 1: 643 peptides, 67 chains. Longest chain 27 peptides. Score 0.552 Round 2: 657 peptides, 59 chains. Longest chain 34 peptides. Score 0.592 Round 3: 636 peptides, 49 chains. Longest chain 54 peptides. Score 0.612 Round 4: 636 peptides, 55 chains. Longest chain 47 peptides. Score 0.591 Round 5: 658 peptides, 53 chains. Longest chain 41 peptides. Score 0.614 Taking the results from Round 5 Chains 57, Residues 605, Estimated correctness of the model 20.0 % 3 chains (51 residues) have been docked in sequence ------------------------------------------------------ 20576 reflections ( 98.68 % complete ) and 13097 restraints for refining 6411 atoms. 10485 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2594 (Rfree = 0.000) for 6411 atoms. Found 41 (41 requested) and removed 28 (20 requested) atoms. Cycle 7: After refmac, R = 0.2363 (Rfree = 0.000) for 6362 atoms. Found 41 (41 requested) and removed 27 (20 requested) atoms. Cycle 8: After refmac, R = 0.2263 (Rfree = 0.000) for 6338 atoms. Found 32 (40 requested) and removed 23 (20 requested) atoms. Cycle 9: After refmac, R = 0.2196 (Rfree = 0.000) for 6321 atoms. Found 20 (40 requested) and removed 24 (20 requested) atoms. Cycle 10: After refmac, R = 0.2142 (Rfree = 0.000) for 6301 atoms. Found 17 (40 requested) and removed 25 (20 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.54 2.54 Search for helices and strands: 0 residues in 0 chains, 6485 seeds are put forward NCS extension: 22 residues added (22 deleted due to clashes), 6507 seeds are put forward Round 1: 628 peptides, 61 chains. Longest chain 30 peptides. Score 0.563 Round 2: 649 peptides, 55 chains. Longest chain 42 peptides. Score 0.600 Round 3: 649 peptides, 53 chains. Longest chain 41 peptides. Score 0.608 Round 4: 653 peptides, 55 chains. Longest chain 50 peptides. Score 0.603 Round 5: 639 peptides, 55 chains. Longest chain 45 peptides. Score 0.593 Taking the results from Round 3 Chains 61, Residues 596, Estimated correctness of the model 17.8 % 4 chains (96 residues) have been docked in sequence ------------------------------------------------------ 20576 reflections ( 98.68 % complete ) and 12585 restraints for refining 6411 atoms. 9824 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2542 (Rfree = 0.000) for 6411 atoms. Found 41 (41 requested) and removed 27 (20 requested) atoms. Cycle 12: After refmac, R = 0.2362 (Rfree = 0.000) for 6378 atoms. Found 29 (41 requested) and removed 29 (20 requested) atoms. Cycle 13: After refmac, R = 0.2276 (Rfree = 0.000) for 6357 atoms. Found 22 (40 requested) and removed 25 (20 requested) atoms. Cycle 14: After refmac, R = 0.2203 (Rfree = 0.000) for 6338 atoms. Found 16 (40 requested) and removed 20 (20 requested) atoms. Cycle 15: After refmac, R = 0.2174 (Rfree = 0.000) for 6322 atoms. Found 11 (40 requested) and removed 21 (20 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.52 2.53 Search for helices and strands: 0 residues in 0 chains, 6502 seeds are put forward NCS extension: 14 residues added (10 deleted due to clashes), 6516 seeds are put forward Round 1: 632 peptides, 58 chains. Longest chain 32 peptides. Score 0.577 Round 2: 666 peptides, 55 chains. Longest chain 48 peptides. Score 0.612 Round 3: 641 peptides, 57 chains. Longest chain 34 peptides. Score 0.587 Round 4: 656 peptides, 52 chains. Longest chain 31 peptides. Score 0.616 Round 5: 653 peptides, 58 chains. Longest chain 39 peptides. Score 0.593 Taking the results from Round 4 Chains 59, Residues 604, Estimated correctness of the model 20.8 % 6 chains (123 residues) have been docked in sequence ------------------------------------------------------ 20576 reflections ( 98.68 % complete ) and 12149 restraints for refining 6411 atoms. 9227 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2597 (Rfree = 0.000) for 6411 atoms. Found 41 (41 requested) and removed 38 (20 requested) atoms. Cycle 17: After refmac, R = 0.2361 (Rfree = 0.000) for 6353 atoms. Found 30 (41 requested) and removed 30 (20 requested) atoms. Cycle 18: After refmac, R = 0.2281 (Rfree = 0.000) for 6332 atoms. Found 15 (40 requested) and removed 27 (20 requested) atoms. Cycle 19: After refmac, R = 0.2240 (Rfree = 0.000) for 6304 atoms. Found 17 (40 requested) and removed 23 (20 requested) atoms. Cycle 20: After refmac, R = 0.2190 (Rfree = 0.000) for 6289 atoms. Found 8 (40 requested) and removed 22 (20 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.52 2.53 Search for helices and strands: 0 residues in 0 chains, 6487 seeds are put forward NCS extension: 15 residues added (9 deleted due to clashes), 6502 seeds are put forward Round 1: 637 peptides, 61 chains. Longest chain 54 peptides. Score 0.570 Round 2: 646 peptides, 52 chains. Longest chain 47 peptides. Score 0.609 Round 3: 630 peptides, 61 chains. Longest chain 54 peptides. Score 0.565 Round 4: 631 peptides, 56 chains. Longest chain 39 peptides. Score 0.584 Round 5: 637 peptides, 55 chains. Longest chain 42 peptides. Score 0.592 Taking the results from Round 2 Chains 57, Residues 594, Estimated correctness of the model 18.1 % 7 chains (200 residues) have been docked in sequence ------------------------------------------------------ 20576 reflections ( 98.68 % complete ) and 11428 restraints for refining 6410 atoms. 8200 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2513 (Rfree = 0.000) for 6410 atoms. Found 41 (41 requested) and removed 37 (20 requested) atoms. Cycle 22: After refmac, R = 0.2334 (Rfree = 0.000) for 6378 atoms. Found 30 (41 requested) and removed 24 (20 requested) atoms. Cycle 23: After refmac, R = 0.2205 (Rfree = 0.000) for 6370 atoms. Found 16 (40 requested) and removed 21 (20 requested) atoms. Cycle 24: After refmac, R = 0.2182 (Rfree = 0.000) for 6353 atoms. Found 20 (40 requested) and removed 21 (20 requested) atoms. Cycle 25: After refmac, R = 0.2146 (Rfree = 0.000) for 6341 atoms. Found 21 (40 requested) and removed 20 (20 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.54 2.54 Search for helices and strands: 0 residues in 0 chains, 6521 seeds are put forward NCS extension: 20 residues added (9 deleted due to clashes), 6541 seeds are put forward Round 1: 628 peptides, 65 chains. Longest chain 29 peptides. Score 0.548 Round 2: 635 peptides, 59 chains. Longest chain 29 peptides. Score 0.576 Round 3: 652 peptides, 59 chains. Longest chain 42 peptides. Score 0.588 Round 4: 654 peptides, 58 chains. Longest chain 38 peptides. Score 0.593 Round 5: 642 peptides, 55 chains. Longest chain 38 peptides. Score 0.595 Taking the results from Round 5 Chains 61, Residues 587, Estimated correctness of the model 12.7 % 7 chains (119 residues) have been docked in sequence ------------------------------------------------------ 20576 reflections ( 98.68 % complete ) and 13350 restraints for refining 6661 atoms. 10537 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2636 (Rfree = 0.000) for 6661 atoms. Found 42 (42 requested) and removed 50 (21 requested) atoms. Failed to save intermediate PDB Cycle 27: After refmac, R = 0.2578 (Rfree = 0.000) for 6583 atoms. Found 42 (42 requested) and removed 38 (21 requested) atoms. Cycle 28: After refmac, R = 0.2430 (Rfree = 0.000) for 6559 atoms. Found 42 (42 requested) and removed 37 (21 requested) atoms. Cycle 29: After refmac, R = 0.2364 (Rfree = 0.000) for 6543 atoms. Found 42 (42 requested) and removed 40 (21 requested) atoms. Cycle 30: After refmac, R = 0.2312 (Rfree = 0.000) for 6531 atoms. Found 37 (41 requested) and removed 30 (20 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.54 2.54 Search for helices and strands: 0 residues in 0 chains, 6736 seeds are put forward NCS extension: 24 residues added (9 deleted due to clashes), 6760 seeds are put forward Round 1: 614 peptides, 70 chains. Longest chain 23 peptides. Score 0.518 Round 2: 635 peptides, 56 chains. Longest chain 35 peptides. Score 0.587 Round 3: 662 peptides, 60 chains. Longest chain 38 peptides. Score 0.592 Round 4: 667 peptides, 52 chains. Longest chain 30 peptides. Score 0.623 Round 5: 684 peptides, 55 chains. Longest chain 51 peptides. Score 0.625 Taking the results from Round 5 Chains 61, Residues 629, Estimated correctness of the model 24.2 % 4 chains (82 residues) have been docked in sequence ------------------------------------------------------ 20576 reflections ( 98.68 % complete ) and 12721 restraints for refining 6411 atoms. 9904 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2665 (Rfree = 0.000) for 6411 atoms. Found 41 (41 requested) and removed 36 (20 requested) atoms. Cycle 32: After refmac, R = 0.2448 (Rfree = 0.000) for 6351 atoms. Found 41 (41 requested) and removed 24 (20 requested) atoms. Cycle 33: After refmac, R = 0.2377 (Rfree = 0.000) for 6349 atoms. Found 20 (40 requested) and removed 25 (20 requested) atoms. Cycle 34: After refmac, R = 0.2317 (Rfree = 0.000) for 6329 atoms. Found 11 (40 requested) and removed 23 (20 requested) atoms. Cycle 35: After refmac, R = 0.2282 (Rfree = 0.000) for 6304 atoms. Found 22 (40 requested) and removed 21 (20 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.54 2.54 Search for helices and strands: 0 residues in 0 chains, 6456 seeds are put forward NCS extension: 21 residues added (11 deleted due to clashes), 6477 seeds are put forward Round 1: 608 peptides, 70 chains. Longest chain 24 peptides. Score 0.513 Round 2: 635 peptides, 53 chains. Longest chain 35 peptides. Score 0.598 Round 3: 666 peptides, 58 chains. Longest chain 48 peptides. Score 0.602 Round 4: 652 peptides, 54 chains. Longest chain 43 peptides. Score 0.606 Round 5: 664 peptides, 59 chains. Longest chain 30 peptides. Score 0.597 Taking the results from Round 4 Chains 57, Residues 598, Estimated correctness of the model 17.0 % 3 chains (67 residues) have been docked in sequence ------------------------------------------------------ 20576 reflections ( 98.68 % complete ) and 12858 restraints for refining 6411 atoms. 10195 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2716 (Rfree = 0.000) for 6411 atoms. Found 41 (41 requested) and removed 37 (20 requested) atoms. Failed to save intermediate PDB Cycle 37: After refmac, R = 0.2571 (Rfree = 0.000) for 6384 atoms. Found 30 (41 requested) and removed 36 (20 requested) atoms. Cycle 38: After refmac, R = 0.2434 (Rfree = 0.000) for 6362 atoms. Found 35 (40 requested) and removed 28 (20 requested) atoms. Cycle 39: After refmac, R = 0.2424 (Rfree = 0.000) for 6365 atoms. Found 26 (40 requested) and removed 29 (20 requested) atoms. Cycle 40: After refmac, R = 0.2419 (Rfree = 0.000) for 6353 atoms. Found 24 (40 requested) and removed 26 (20 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.53 2.53 Search for helices and strands: 0 residues in 0 chains, 6560 seeds are put forward NCS extension: 32 residues added (8 deleted due to clashes), 6592 seeds are put forward Round 1: 589 peptides, 71 chains. Longest chain 30 peptides. Score 0.493 Round 2: 626 peptides, 56 chains. Longest chain 39 peptides. Score 0.580 Round 3: 615 peptides, 58 chains. Longest chain 34 peptides. Score 0.564 Round 4: 642 peptides, 57 chains. Longest chain 33 peptides. Score 0.588 Round 5: 639 peptides, 55 chains. Longest chain 40 peptides. Score 0.593 Taking the results from Round 5 Chains 61, Residues 584, Estimated correctness of the model 11.9 % 6 chains (145 residues) have been docked in sequence ------------------------------------------------------ 20576 reflections ( 98.68 % complete ) and 12132 restraints for refining 6410 atoms. 9207 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2669 (Rfree = 0.000) for 6410 atoms. Found 41 (41 requested) and removed 44 (20 requested) atoms. Cycle 42: After refmac, R = 0.2468 (Rfree = 0.000) for 6370 atoms. Found 41 (41 requested) and removed 32 (20 requested) atoms. Cycle 43: After refmac, R = 0.2440 (Rfree = 0.000) for 6357 atoms. Found 37 (40 requested) and removed 27 (20 requested) atoms. Cycle 44: After refmac, R = 0.2447 (Rfree = 0.000) for 6352 atoms. Found 40 (40 requested) and removed 27 (20 requested) atoms. Cycle 45: After refmac, R = 0.2514 (Rfree = 0.000) for 6341 atoms. Found 40 (40 requested) and removed 24 (20 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.53 2.53 Search for helices and strands: 0 residues in 0 chains, 6533 seeds are put forward NCS extension: 26 residues added (15 deleted due to clashes), 6559 seeds are put forward Round 1: 579 peptides, 67 chains. Longest chain 22 peptides. Score 0.500 Round 2: 629 peptides, 62 chains. Longest chain 36 peptides. Score 0.560 Round 3: 623 peptides, 59 chains. Longest chain 37 peptides. Score 0.567 Round 4: 629 peptides, 57 chains. Longest chain 33 peptides. Score 0.579 Round 5: 626 peptides, 59 chains. Longest chain 49 peptides. Score 0.569 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 59, Residues 572, Estimated correctness of the model 6.3 % 3 chains (57 residues) have been docked in sequence Sequence coverage is 9 % Consider running further cycles of model building using 1ztc-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 66 A and 79 A 56 chains (575 residues) following loop building 2 chains (69 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 20576 reflections ( 98.68 % complete ) and 13198 restraints for refining 6409 atoms. 10779 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2829 (Rfree = 0.000) for 6409 atoms. Found 0 (41 requested) and removed 20 (20 requested) atoms. Cycle 47: After refmac, R = 0.2691 (Rfree = 0.000) for 6342 atoms. Found 0 (40 requested) and removed 20 (20 requested) atoms. Cycle 48: After refmac, R = 0.2566 (Rfree = 0.000) for 6300 atoms. Found 0 (40 requested) and removed 20 (20 requested) atoms. Cycle 49: After refmac, R = 0.2533 (Rfree = 0.000) for 6267 atoms. TimeTaking 80.45