null Mon 24 Dec 07:53:17 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 2fqp-3.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2fqp-3.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2fqp-3.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2fqp-3.8-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/2fqp-3.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2fqp-3.8-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 07:53:22 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/2fqp-3.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2fqp-3.8-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 225 and 0 Target number of residues in the AU: 225 Target solvent content: 0.6404 Checking the provided sequence file Detected sequence length: 97 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 388 Adjusted target solvent content: 0.38 Input MTZ file: 2fqp-3.8-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: 4 Cell parameters: 35.909 92.640 53.056 90.000 106.409 90.000 Input sequence file: 2fqp-3.8-parrot-noncs.fasta_lf Building free atoms model in initial map for 3104 target number of atoms Had to go as low as 0.60 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: 50.895 3.801 Wilson plot Bfac: 71.89 2715 reflections ( 81.65 % complete ) and 0 restraints for refining 3451 atoms. Observations/parameters ratio is 0.20 ------------------------------------------------------ Starting model: R = 0.3248 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2851 (Rfree = 0.000) for 3451 atoms. Found 18 (18 requested) and removed 68 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.48 4.10 Search for helices and strands: 0 residues in 0 chains, 3425 seeds are put forward NCS extension: 0 residues added, 3425 seeds are put forward Round 1: 67 peptides, 15 chains. Longest chain 7 peptides. Score 0.214 Round 2: 83 peptides, 16 chains. Longest chain 12 peptides. Score 0.285 Round 3: 107 peptides, 22 chains. Longest chain 11 peptides. Score 0.276 Round 4: 113 peptides, 23 chains. Longest chain 11 peptides. Score 0.286 Round 5: 129 peptides, 25 chains. Longest chain 11 peptides. Score 0.326 Taking the results from Round 5 Chains 25, Residues 104, Estimated correctness of the model 0.0 % 2 chains (10 residues) have been docked in sequence ------------------------------------------------------ 2715 reflections ( 81.65 % complete ) and 6827 restraints for refining 2808 atoms. 6407 conditional restraints added. Observations/parameters ratio is 0.24 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2201 (Rfree = 0.000) for 2808 atoms. Found 6 (15 requested) and removed 20 (7 requested) atoms. Cycle 2: After refmac, R = 0.1893 (Rfree = 0.000) for 2751 atoms. Found 12 (15 requested) and removed 15 (7 requested) atoms. Cycle 3: After refmac, R = 0.1752 (Rfree = 0.000) for 2732 atoms. Found 12 (15 requested) and removed 10 (7 requested) atoms. Cycle 4: After refmac, R = 0.1971 (Rfree = 0.000) for 2724 atoms. Found 15 (15 requested) and removed 13 (7 requested) atoms. Cycle 5: After refmac, R = 0.1126 (Rfree = 0.000) for 2720 atoms. Found 6 (14 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.44 4.05 Search for helices and strands: 0 residues in 0 chains, 2765 seeds are put forward NCS extension: 0 residues added, 2765 seeds are put forward Round 1: 102 peptides, 21 chains. Longest chain 9 peptides. Score 0.272 Round 2: 138 peptides, 26 chains. Longest chain 10 peptides. Score 0.349 Round 3: 142 peptides, 25 chains. Longest chain 12 peptides. Score 0.390 Round 4: 144 peptides, 26 chains. Longest chain 13 peptides. Score 0.379 Round 5: 138 peptides, 27 chains. Longest chain 11 peptides. Score 0.328 Taking the results from Round 3 Chains 25, Residues 117, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2715 reflections ( 81.65 % complete ) and 6169 restraints for refining 2577 atoms. 5726 conditional restraints added. Observations/parameters ratio is 0.26 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1574 (Rfree = 0.000) for 2577 atoms. Found 14 (14 requested) and removed 15 (7 requested) atoms. Cycle 7: After refmac, R = 0.1611 (Rfree = 0.000) for 2562 atoms. Found 14 (14 requested) and removed 9 (7 requested) atoms. Cycle 8: After refmac, R = 0.1742 (Rfree = 0.000) for 2559 atoms. Found 14 (14 requested) and removed 9 (7 requested) atoms. Cycle 9: After refmac, R = 0.1761 (Rfree = 0.000) for 2554 atoms. Found 14 (14 requested) and removed 14 (7 requested) atoms. Cycle 10: After refmac, R = 0.1414 (Rfree = 0.000) for 2544 atoms. Found 14 (14 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.42 4.03 Search for helices and strands: 0 residues in 0 chains, 2609 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 2627 seeds are put forward Round 1: 116 peptides, 25 chains. Longest chain 7 peptides. Score 0.257 Round 2: 133 peptides, 26 chains. Longest chain 9 peptides. Score 0.324 Round 3: 144 peptides, 26 chains. Longest chain 10 peptides. Score 0.379 Round 4: 145 peptides, 26 chains. Longest chain 11 peptides. Score 0.384 Round 5: 130 peptides, 24 chains. Longest chain 8 peptides. Score 0.352 Taking the results from Round 4 Chains 26, Residues 119, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2715 reflections ( 81.65 % complete ) and 6010 restraints for refining 2542 atoms. 5560 conditional restraints added. Observations/parameters ratio is 0.27 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1897 (Rfree = 0.000) for 2542 atoms. Found 13 (13 requested) and removed 16 (6 requested) atoms. Cycle 12: After refmac, R = 0.1599 (Rfree = 0.000) for 2518 atoms. Found 12 (13 requested) and removed 15 (6 requested) atoms. Cycle 13: After refmac, R = 0.1675 (Rfree = 0.000) for 2505 atoms. Found 13 (13 requested) and removed 13 (6 requested) atoms. Cycle 14: After refmac, R = 0.1486 (Rfree = 0.000) for 2496 atoms. Found 13 (13 requested) and removed 11 (6 requested) atoms. Cycle 15: After refmac, R = 0.1357 (Rfree = 0.000) for 2496 atoms. Found 13 (13 requested) and removed 11 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.31 3.90 Search for helices and strands: 0 residues in 0 chains, 2548 seeds are put forward NCS extension: 0 residues added, 2548 seeds are put forward Round 1: 126 peptides, 27 chains. Longest chain 7 peptides. Score 0.266 Round 2: 150 peptides, 28 chains. Longest chain 8 peptides. Score 0.367 Round 3: 138 peptides, 27 chains. Longest chain 9 peptides. Score 0.328 Round 4: 139 peptides, 28 chains. Longest chain 8 peptides. Score 0.312 Round 5: 144 peptides, 25 chains. Longest chain 10 peptides. Score 0.399 Taking the results from Round 5 Chains 25, Residues 119, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2715 reflections ( 81.65 % complete ) and 6331 restraints for refining 2645 atoms. 5880 conditional restraints added. Observations/parameters ratio is 0.26 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1426 (Rfree = 0.000) for 2645 atoms. Found 7 (14 requested) and removed 15 (7 requested) atoms. Cycle 17: After refmac, R = 0.1562 (Rfree = 0.000) for 2625 atoms. Found 14 (14 requested) and removed 12 (7 requested) atoms. Cycle 18: After refmac, R = 0.1017 (Rfree = 0.000) for 2617 atoms. Found 2 (14 requested) and removed 13 (7 requested) atoms. Cycle 19: After refmac, R = 0.1004 (Rfree = 0.000) for 2599 atoms. Found 1 (14 requested) and removed 7 (7 requested) atoms. Cycle 20: After refmac, R = 0.1015 (Rfree = 0.000) for 2590 atoms. Found 5 (14 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.35 3.94 Search for helices and strands: 0 residues in 0 chains, 2627 seeds are put forward NCS extension: 0 residues added, 2627 seeds are put forward Round 1: 119 peptides, 26 chains. Longest chain 10 peptides. Score 0.251 Round 2: 132 peptides, 27 chains. Longest chain 8 peptides. Score 0.298 Round 3: 142 peptides, 26 chains. Longest chain 11 peptides. Score 0.369 Round 4: 134 peptides, 26 chains. Longest chain 8 peptides. Score 0.329 Round 5: 130 peptides, 25 chains. Longest chain 8 peptides. Score 0.331 Taking the results from Round 3 Chains 26, Residues 116, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2715 reflections ( 81.65 % complete ) and 6081 restraints for refining 2619 atoms. 5643 conditional restraints added. Observations/parameters ratio is 0.26 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1351 (Rfree = 0.000) for 2619 atoms. Found 9 (14 requested) and removed 11 (7 requested) atoms. Cycle 22: After refmac, R = 0.1574 (Rfree = 0.000) for 2607 atoms. Found 14 (14 requested) and removed 16 (7 requested) atoms. Cycle 23: After refmac, R = 0.1222 (Rfree = 0.000) for 2601 atoms. Found 14 (14 requested) and removed 16 (7 requested) atoms. Cycle 24: After refmac, R = 0.1362 (Rfree = 0.000) for 2594 atoms. Found 14 (14 requested) and removed 14 (7 requested) atoms. Cycle 25: After refmac, R = 0.1129 (Rfree = 0.000) for 2592 atoms. Found 14 (14 requested) and removed 15 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.29 3.87 Search for helices and strands: 0 residues in 0 chains, 2645 seeds are put forward NCS extension: 0 residues added, 2645 seeds are put forward Round 1: 109 peptides, 25 chains. Longest chain 8 peptides. Score 0.218 Round 2: 129 peptides, 25 chains. Longest chain 9 peptides. Score 0.326 Round 3: 124 peptides, 26 chains. Longest chain 7 peptides. Score 0.278 Round 4: 120 peptides, 24 chains. Longest chain 7 peptides. Score 0.301 Round 5: 111 peptides, 21 chains. Longest chain 8 peptides. Score 0.320 Taking the results from Round 2 Chains 25, Residues 104, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2715 reflections ( 81.65 % complete ) and 6030 restraints for refining 2597 atoms. 5639 conditional restraints added. Observations/parameters ratio is 0.26 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1260 (Rfree = 0.000) for 2597 atoms. Found 13 (14 requested) and removed 20 (7 requested) atoms. Cycle 27: After refmac, R = 0.0894 (Rfree = 0.000) for 2585 atoms. Found 7 (14 requested) and removed 10 (7 requested) atoms. Cycle 28: After refmac, R = 0.0798 (Rfree = 0.000) for 2576 atoms. Found 4 (14 requested) and removed 9 (7 requested) atoms. Cycle 29: After refmac, R = 0.0833 (Rfree = 0.000) for 2569 atoms. Found 2 (14 requested) and removed 8 (7 requested) atoms. Cycle 30: After refmac, R = 0.0826 (Rfree = 0.000) for 2563 atoms. Found 8 (14 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.38 3.98 Search for helices and strands: 0 residues in 0 chains, 2611 seeds are put forward NCS extension: 0 residues added, 2611 seeds are put forward Round 1: 129 peptides, 28 chains. Longest chain 7 peptides. Score 0.260 Round 2: 144 peptides, 29 chains. Longest chain 8 peptides. Score 0.316 Round 3: 149 peptides, 28 chains. Longest chain 9 peptides. Score 0.362 Round 4: 160 peptides, 28 chains. Longest chain 15 peptides. Score 0.414 Round 5: 145 peptides, 28 chains. Longest chain 9 peptides. Score 0.342 Taking the results from Round 4 Chains 28, Residues 132, Estimated correctness of the model 0.0 % 2 chains (11 residues) have been docked in sequence ------------------------------------------------------ 2715 reflections ( 81.65 % complete ) and 5985 restraints for refining 2664 atoms. 5440 conditional restraints added. Observations/parameters ratio is 0.25 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1205 (Rfree = 0.000) for 2664 atoms. Found 14 (14 requested) and removed 17 (7 requested) atoms. Cycle 32: After refmac, R = 0.0980 (Rfree = 0.000) for 2654 atoms. Found 9 (14 requested) and removed 14 (7 requested) atoms. Cycle 33: After refmac, R = 0.2119 (Rfree = 0.000) for 2643 atoms. Found 14 (14 requested) and removed 22 (7 requested) atoms. Cycle 34: After refmac, R = 0.1072 (Rfree = 0.000) for 2628 atoms. Found 14 (14 requested) and removed 10 (7 requested) atoms. Cycle 35: After refmac, R = 0.0785 (Rfree = 0.000) for 2623 atoms. Found 12 (14 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.31 3.90 Search for helices and strands: 0 residues in 0 chains, 2692 seeds are put forward NCS extension: 21 residues added (2 deleted due to clashes), 2713 seeds are put forward Round 1: 97 peptides, 22 chains. Longest chain 6 peptides. Score 0.220 Round 2: 110 peptides, 20 chains. Longest chain 12 peptides. Score 0.338 Round 3: 119 peptides, 23 chains. Longest chain 13 peptides. Score 0.318 Round 4: 122 peptides, 22 chains. Longest chain 13 peptides. Score 0.355 Round 5: 118 peptides, 21 chains. Longest chain 13 peptides. Score 0.356 Taking the results from Round 5 Chains 21, Residues 97, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2715 reflections ( 81.65 % complete ) and 6293 restraints for refining 2679 atoms. 5926 conditional restraints added. Observations/parameters ratio is 0.25 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1597 (Rfree = 0.000) for 2679 atoms. Found 14 (14 requested) and removed 17 (7 requested) atoms. Cycle 37: After refmac, R = 0.1334 (Rfree = 0.000) for 2668 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. Cycle 38: After refmac, R = 0.1470 (Rfree = 0.000) for 2661 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. Cycle 39: After refmac, R = 0.1368 (Rfree = 0.000) for 2657 atoms. Found 14 (14 requested) and removed 10 (7 requested) atoms. Cycle 40: After refmac, R = 0.1207 (Rfree = 0.000) for 2656 atoms. Found 14 (14 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.37 3.97 Search for helices and strands: 0 residues in 0 chains, 2722 seeds are put forward NCS extension: 0 residues added, 2722 seeds are put forward Round 1: 83 peptides, 19 chains. Longest chain 5 peptides. Score 0.210 Round 2: 90 peptides, 17 chains. Longest chain 8 peptides. Score 0.300 Round 3: 94 peptides, 17 chains. Longest chain 8 peptides. Score 0.322 Round 4: 103 peptides, 20 chains. Longest chain 10 peptides. Score 0.301 Round 5: 97 peptides, 18 chains. Longest chain 8 peptides. Score 0.315 Taking the results from Round 3 Chains 17, Residues 77, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2715 reflections ( 81.65 % complete ) and 6247 restraints for refining 2616 atoms. 5956 conditional restraints added. Observations/parameters ratio is 0.26 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1157 (Rfree = 0.000) for 2616 atoms. Found 14 (14 requested) and removed 16 (7 requested) atoms. Cycle 42: After refmac, R = 0.1319 (Rfree = 0.000) for 2610 atoms. Found 14 (14 requested) and removed 10 (7 requested) atoms. Cycle 43: After refmac, R = 0.1283 (Rfree = 0.000) for 2607 atoms. Found 14 (14 requested) and removed 14 (7 requested) atoms. Cycle 44: After refmac, R = 0.1361 (Rfree = 0.000) for 2603 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. Cycle 45: After refmac, R = 0.1216 (Rfree = 0.000) for 2602 atoms. Found 14 (14 requested) and removed 15 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.26 3.84 Search for helices and strands: 0 residues in 0 chains, 2657 seeds are put forward NCS extension: 0 residues added, 2657 seeds are put forward Round 1: 76 peptides, 18 chains. Longest chain 5 peptides. Score 0.192 Round 2: 93 peptides, 18 chains. Longest chain 9 peptides. Score 0.293 Round 3: 104 peptides, 19 chains. Longest chain 9 peptides. Score 0.329 Round 4: 92 peptides, 16 chains. Longest chain 9 peptides. Score 0.335 Round 5: 92 peptides, 17 chains. Longest chain 9 peptides. Score 0.311 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 16, Residues 76, 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 2fqp-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2715 reflections ( 81.65 % complete ) and 6075 restraints for refining 2586 atoms. 5787 conditional restraints added. Observations/parameters ratio is 0.26 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1263 (Rfree = 0.000) for 2586 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.1450 (Rfree = 0.000) for 2574 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.1002 (Rfree = 0.000) for 2564 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.0837 (Rfree = 0.000) for 2555 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:25:38 GMT 2018 Job finished. TimeTaking 32.36 Used memory is bytes: 9747472