null Mon 24 Dec 08:00:23 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 2ash-4.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2ash-4.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2ash-4.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ash-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/2ash-4.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ash-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 08:00:28 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/2ash-4.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ash-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 1052 and 0 Target number of residues in the AU: 1052 Target solvent content: 0.6761 Checking the provided sequence file Detected sequence length: 381 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1524 Adjusted target solvent content: 0.53 Input MTZ file: 2ash-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: 5 Cell parameters: 170.109 99.745 124.866 90.000 123.929 90.000 Input sequence file: 2ash-4.0-parrot-noncs.fasta_lf Building free atoms model in initial map for 12192 target number of atoms Had to go as low as 0.85 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: 103.605 4.000 Wilson plot Bfac: 97.66 14751 reflections ( 99.68 % complete ) and 0 restraints for refining 13434 atoms. Observations/parameters ratio is 0.27 ------------------------------------------------------ Starting model: R = 0.3471 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3218 (Rfree = 0.000) for 13434 atoms. Found 63 (63 requested) and removed 66 (31 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.91 3.76 Search for helices and strands: 0 residues in 0 chains, 13623 seeds are put forward NCS extension: 0 residues added, 13623 seeds are put forward Round 1: 463 peptides, 97 chains. Longest chain 9 peptides. Score 0.255 Round 2: 571 peptides, 100 chains. Longest chain 13 peptides. Score 0.354 Round 3: 616 peptides, 95 chains. Longest chain 19 peptides. Score 0.418 Round 4: 638 peptides, 96 chains. Longest chain 19 peptides. Score 0.434 Round 5: 676 peptides, 101 chains. Longest chain 28 peptides. Score 0.448 Taking the results from Round 5 Chains 101, Residues 575, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 14751 reflections ( 99.68 % complete ) and 26702 restraints for refining 11003 atoms. 24488 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2677 (Rfree = 0.000) for 11003 atoms. Found 52 (52 requested) and removed 51 (26 requested) atoms. Cycle 2: After refmac, R = 0.2533 (Rfree = 0.000) for 10776 atoms. Found 52 (52 requested) and removed 57 (26 requested) atoms. Cycle 3: After refmac, R = 0.2515 (Rfree = 0.000) for 10664 atoms. Found 51 (51 requested) and removed 49 (25 requested) atoms. Cycle 4: After refmac, R = 0.2467 (Rfree = 0.000) for 10565 atoms. Found 50 (50 requested) and removed 49 (25 requested) atoms. Cycle 5: After refmac, R = 0.2494 (Rfree = 0.000) for 10475 atoms. Found 50 (50 requested) and removed 41 (25 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.85 3.70 Search for helices and strands: 0 residues in 0 chains, 10822 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 10836 seeds are put forward Round 1: 568 peptides, 112 chains. Longest chain 10 peptides. Score 0.299 Round 2: 666 peptides, 108 chains. Longest chain 20 peptides. Score 0.411 Round 3: 682 peptides, 104 chains. Longest chain 20 peptides. Score 0.441 Round 4: 679 peptides, 105 chains. Longest chain 18 peptides. Score 0.435 Round 5: 686 peptides, 99 chains. Longest chain 20 peptides. Score 0.464 Taking the results from Round 5 Chains 99, Residues 587, Estimated correctness of the model 0.0 % 1 chains (19 residues) have been docked in sequence ------------------------------------------------------ 14751 reflections ( 99.68 % complete ) and 24475 restraints for refining 10536 atoms. 22133 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2429 (Rfree = 0.000) for 10536 atoms. Found 50 (50 requested) and removed 65 (25 requested) atoms. Cycle 7: After refmac, R = 0.2305 (Rfree = 0.000) for 10413 atoms. Found 49 (49 requested) and removed 50 (24 requested) atoms. Cycle 8: After refmac, R = 0.2243 (Rfree = 0.000) for 10330 atoms. Found 49 (49 requested) and removed 42 (24 requested) atoms. Cycle 9: After refmac, R = 0.1843 (Rfree = 0.000) for 10250 atoms. Found 27 (49 requested) and removed 35 (24 requested) atoms. Cycle 10: After refmac, R = 0.2121 (Rfree = 0.000) for 10202 atoms. Found 48 (48 requested) and removed 42 (24 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.88 3.73 Search for helices and strands: 0 residues in 0 chains, 10541 seeds are put forward NCS extension: 33 residues added (2 deleted due to clashes), 10574 seeds are put forward Round 1: 567 peptides, 105 chains. Longest chain 18 peptides. Score 0.328 Round 2: 648 peptides, 108 chains. Longest chain 19 peptides. Score 0.394 Round 3: 673 peptides, 107 chains. Longest chain 28 peptides. Score 0.421 Round 4: 693 peptides, 105 chains. Longest chain 18 peptides. Score 0.447 Round 5: 636 peptides, 103 chains. Longest chain 26 peptides. Score 0.404 Taking the results from Round 4 Chains 105, Residues 588, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 14751 reflections ( 99.68 % complete ) and 24788 restraints for refining 10613 atoms. 22531 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2198 (Rfree = 0.000) for 10613 atoms. Found 50 (50 requested) and removed 62 (25 requested) atoms. Cycle 12: After refmac, R = 0.2202 (Rfree = 0.000) for 10506 atoms. Found 50 (50 requested) and removed 50 (25 requested) atoms. Cycle 13: After refmac, R = 0.2082 (Rfree = 0.000) for 10425 atoms. Found 49 (49 requested) and removed 40 (24 requested) atoms. Cycle 14: After refmac, R = 0.2136 (Rfree = 0.000) for 10370 atoms. Found 49 (49 requested) and removed 45 (24 requested) atoms. Cycle 15: After refmac, R = 0.2006 (Rfree = 0.000) for 10315 atoms. Found 49 (49 requested) and removed 40 (24 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.86 3.71 Search for helices and strands: 0 residues in 0 chains, 10711 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 10727 seeds are put forward Round 1: 518 peptides, 99 chains. Longest chain 10 peptides. Score 0.305 Round 2: 601 peptides, 95 chains. Longest chain 13 peptides. Score 0.404 Round 3: 659 peptides, 104 chains. Longest chain 16 peptides. Score 0.421 Round 4: 668 peptides, 96 chains. Longest chain 21 peptides. Score 0.460 Round 5: 662 peptides, 103 chains. Longest chain 15 peptides. Score 0.427 Taking the results from Round 4 Chains 97, Residues 572, Estimated correctness of the model 0.0 % 3 chains (19 residues) have been docked in sequence ------------------------------------------------------ 14751 reflections ( 99.68 % complete ) and 24623 restraints for refining 10641 atoms. 22378 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2130 (Rfree = 0.000) for 10641 atoms. Found 50 (50 requested) and removed 71 (25 requested) atoms. Cycle 17: After refmac, R = 0.2104 (Rfree = 0.000) for 10519 atoms. Found 50 (50 requested) and removed 53 (25 requested) atoms. Cycle 18: After refmac, R = 0.2115 (Rfree = 0.000) for 10457 atoms. Found 49 (49 requested) and removed 45 (24 requested) atoms. Cycle 19: After refmac, R = 0.2056 (Rfree = 0.000) for 10417 atoms. Found 49 (49 requested) and removed 49 (24 requested) atoms. Cycle 20: After refmac, R = 0.1706 (Rfree = 0.000) for 10371 atoms. Found 19 (49 requested) and removed 31 (24 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.87 3.72 Search for helices and strands: 0 residues in 0 chains, 10674 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 10694 seeds are put forward Round 1: 565 peptides, 112 chains. Longest chain 13 peptides. Score 0.296 Round 2: 618 peptides, 99 chains. Longest chain 19 peptides. Score 0.403 Round 3: 641 peptides, 104 chains. Longest chain 17 peptides. Score 0.404 Round 4: 663 peptides, 102 chains. Longest chain 16 peptides. Score 0.432 Round 5: 657 peptides, 98 chains. Longest chain 17 peptides. Score 0.443 Taking the results from Round 5 Chains 98, Residues 559, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 14751 reflections ( 99.68 % complete ) and 24966 restraints for refining 10668 atoms. 22828 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2266 (Rfree = 0.000) for 10668 atoms. Found 50 (50 requested) and removed 93 (25 requested) atoms. Cycle 22: After refmac, R = 0.2338 (Rfree = 0.000) for 10549 atoms. Found 50 (50 requested) and removed 98 (25 requested) atoms. Cycle 23: After refmac, R = 0.2155 (Rfree = 0.000) for 10440 atoms. Found 49 (49 requested) and removed 62 (24 requested) atoms. Cycle 24: After refmac, R = 0.2251 (Rfree = 0.000) for 10360 atoms. Found 49 (49 requested) and removed 69 (24 requested) atoms. Cycle 25: After refmac, R = 0.2100 (Rfree = 0.000) for 10294 atoms. Found 49 (49 requested) and removed 45 (24 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.85 3.70 Search for helices and strands: 0 residues in 0 chains, 10680 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 10696 seeds are put forward Round 1: 513 peptides, 104 chains. Longest chain 10 peptides. Score 0.277 Round 2: 576 peptides, 103 chains. Longest chain 14 peptides. Score 0.346 Round 3: 582 peptides, 93 chains. Longest chain 17 peptides. Score 0.394 Round 4: 589 peptides, 88 chains. Longest chain 17 peptides. Score 0.422 Round 5: 587 peptides, 92 chains. Longest chain 20 peptides. Score 0.403 Taking the results from Round 4 Chains 90, Residues 501, Estimated correctness of the model 0.0 % 3 chains (22 residues) have been docked in sequence ------------------------------------------------------ 14751 reflections ( 99.68 % complete ) and 24318 restraints for refining 10484 atoms. 22329 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2208 (Rfree = 0.000) for 10484 atoms. Found 49 (49 requested) and removed 51 (24 requested) atoms. Cycle 27: After refmac, R = 0.2339 (Rfree = 0.000) for 10403 atoms. Found 49 (49 requested) and removed 53 (24 requested) atoms. Cycle 28: After refmac, R = 0.2210 (Rfree = 0.000) for 10344 atoms. Found 49 (49 requested) and removed 40 (24 requested) atoms. Cycle 29: After refmac, R = 0.2170 (Rfree = 0.000) for 10317 atoms. Found 49 (49 requested) and removed 35 (24 requested) atoms. Cycle 30: After refmac, R = 0.2195 (Rfree = 0.000) for 10290 atoms. Found 49 (49 requested) and removed 37 (24 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.89 3.74 Search for helices and strands: 0 residues in 0 chains, 10678 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 10695 seeds are put forward Round 1: 462 peptides, 95 chains. Longest chain 9 peptides. Score 0.263 Round 2: 559 peptides, 99 chains. Longest chain 13 peptides. Score 0.346 Round 3: 555 peptides, 99 chains. Longest chain 14 peptides. Score 0.342 Round 4: 583 peptides, 95 chains. Longest chain 16 peptides. Score 0.387 Round 5: 571 peptides, 100 chains. Longest chain 13 peptides. Score 0.354 Taking the results from Round 4 Chains 95, Residues 488, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 14751 reflections ( 99.68 % complete ) and 23764 restraints for refining 10184 atoms. 21907 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2401 (Rfree = 0.000) for 10184 atoms. Found 48 (48 requested) and removed 66 (24 requested) atoms. Cycle 32: After refmac, R = 0.2144 (Rfree = 0.000) for 10102 atoms. Found 48 (48 requested) and removed 56 (24 requested) atoms. Cycle 33: After refmac, R = 0.2138 (Rfree = 0.000) for 10040 atoms. Found 47 (47 requested) and removed 43 (23 requested) atoms. Cycle 34: After refmac, R = 0.2079 (Rfree = 0.000) for 10002 atoms. Found 47 (47 requested) and removed 34 (23 requested) atoms. Cycle 35: After refmac, R = 0.1670 (Rfree = 0.000) for 9980 atoms. Found 18 (47 requested) and removed 39 (23 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.88 3.73 Search for helices and strands: 0 residues in 0 chains, 10266 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 10285 seeds are put forward Round 1: 449 peptides, 99 chains. Longest chain 8 peptides. Score 0.229 Round 2: 553 peptides, 99 chains. Longest chain 19 peptides. Score 0.340 Round 3: 551 peptides, 93 chains. Longest chain 17 peptides. Score 0.364 Round 4: 570 peptides, 96 chains. Longest chain 17 peptides. Score 0.370 Round 5: 584 peptides, 98 chains. Longest chain 17 peptides. Score 0.375 Taking the results from Round 5 Chains 98, Residues 486, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 14751 reflections ( 99.68 % complete ) and 23813 restraints for refining 10199 atoms. 21967 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2288 (Rfree = 0.000) for 10199 atoms. Found 48 (48 requested) and removed 284 (24 requested) atoms. Cycle 37: After refmac, R = 0.2185 (Rfree = 0.000) for 9897 atoms. Found 47 (47 requested) and removed 39 (23 requested) atoms. Cycle 38: After refmac, R = 0.2202 (Rfree = 0.000) for 9865 atoms. Found 47 (47 requested) and removed 39 (23 requested) atoms. Cycle 39: After refmac, R = 0.2047 (Rfree = 0.000) for 9816 atoms. Found 46 (46 requested) and removed 29 (23 requested) atoms. Cycle 40: After refmac, R = 0.2054 (Rfree = 0.000) for 9808 atoms. Found 46 (46 requested) and removed 30 (23 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.87 3.72 Search for helices and strands: 0 residues in 0 chains, 10171 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 10195 seeds are put forward Round 1: 434 peptides, 96 chains. Longest chain 9 peptides. Score 0.227 Round 2: 511 peptides, 100 chains. Longest chain 11 peptides. Score 0.293 Round 3: 543 peptides, 96 chains. Longest chain 14 peptides. Score 0.344 Round 4: 537 peptides, 95 chains. Longest chain 11 peptides. Score 0.342 Round 5: 532 peptides, 89 chains. Longest chain 13 peptides. Score 0.363 Taking the results from Round 5 Chains 90, Residues 443, Estimated correctness of the model 0.0 % 3 chains (20 residues) have been docked in sequence ------------------------------------------------------ 14751 reflections ( 99.68 % complete ) and 23389 restraints for refining 10099 atoms. 21649 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2213 (Rfree = 0.000) for 10099 atoms. Found 47 (47 requested) and removed 51 (23 requested) atoms. Cycle 42: After refmac, R = 0.2029 (Rfree = 0.000) for 10047 atoms. Found 47 (47 requested) and removed 35 (23 requested) atoms. Cycle 43: After refmac, R = 0.1990 (Rfree = 0.000) for 10043 atoms. Found 47 (47 requested) and removed 43 (23 requested) atoms. Cycle 44: After refmac, R = 0.1999 (Rfree = 0.000) for 10021 atoms. Found 47 (47 requested) and removed 39 (23 requested) atoms. Cycle 45: After refmac, R = 0.1522 (Rfree = 0.000) for 10005 atoms. Found 24 (47 requested) and removed 28 (23 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.88 3.73 Search for helices and strands: 0 residues in 0 chains, 10278 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 10293 seeds are put forward Round 1: 430 peptides, 92 chains. Longest chain 10 peptides. Score 0.241 Round 2: 508 peptides, 89 chains. Longest chain 18 peptides. Score 0.339 Round 3: 514 peptides, 89 chains. Longest chain 12 peptides. Score 0.345 Round 4: 512 peptides, 88 chains. Longest chain 13 peptides. Score 0.348 Round 5: 528 peptides, 87 chains. Longest chain 14 peptides. Score 0.368 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 87, Residues 441, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence Sequence coverage is 2 % Consider running further cycles of model building using 2ash-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 14751 reflections ( 99.68 % complete ) and 24012 restraints for refining 10285 atoms. 22301 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2035 (Rfree = 0.000) for 10285 atoms. Found 0 (48 requested) and removed 24 (24 requested) atoms. Cycle 47: After refmac, R = 0.2130 (Rfree = 0.000) for 10214 atoms. Found 0 (48 requested) and removed 24 (24 requested) atoms. Cycle 48: After refmac, R = 0.1955 (Rfree = 0.000) for 10143 atoms. Found 0 (48 requested) and removed 24 (24 requested) atoms. Cycle 49: After refmac, R = 0.1990 (Rfree = 0.000) for 10081 atoms. Found 0 (48 requested) and removed 24 (24 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 09:48:44 GMT 2018 Job finished. TimeTaking 108.35 Used memory is bytes: 23180392