Sun 23 Dec 23:54:14 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 2ooj-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2ooj-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2ooj-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ooj-4.0-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/2ooj-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ooj-4.0-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 ============================================================ Sun 23 Dec 23:54:18 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/2ooj-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ooj-4.0-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 185 and 0 Target number of residues in the AU: 185 Target solvent content: 0.6382 Checking the provided sequence file Detected sequence length: 141 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 282 Adjusted target solvent content: 0.45 Input MTZ file: 2ooj-4.0-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: 47.211 55.254 106.086 90.000 90.000 90.000 Input sequence file: 2ooj-4.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 2256 target number of atoms Had to go as low as 0.65 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: 53.043 4.000 Wilson plot Bfac: 70.85 2539 reflections ( 98.68 % complete ) and 0 restraints for refining 2491 atoms. Observations/parameters ratio is 0.25 ------------------------------------------------------ Starting model: R = 0.3644 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2602 (Rfree = 0.000) for 2491 atoms. Found 2 (11 requested) and removed 20 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.55 3.80 Search for helices and strands: 0 residues in 0 chains, 2490 seeds are put forward NCS extension: 0 residues added, 2490 seeds are put forward Round 1: 65 peptides, 15 chains. Longest chain 6 peptides. Score 0.205 Round 2: 76 peptides, 15 chains. Longest chain 8 peptides. Score 0.284 Round 3: 83 peptides, 18 chains. Longest chain 7 peptides. Score 0.246 Round 4: 93 peptides, 19 chains. Longest chain 8 peptides. Score 0.285 Round 5: 93 peptides, 19 chains. Longest chain 8 peptides. Score 0.285 Taking the results from Round 5 Chains 19, Residues 74, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 2539 reflections ( 98.68 % complete ) and 4972 restraints for refining 2035 atoms. 4670 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2969 (Rfree = 0.000) for 2035 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Failed to save intermediate PDB Cycle 2: After refmac, R = 0.2788 (Rfree = 0.000) for 2027 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 3: After refmac, R = 0.2703 (Rfree = 0.000) for 2017 atoms. Found 2 (9 requested) and removed 5 (4 requested) atoms. Cycle 4: After refmac, R = 0.2931 (Rfree = 0.000) for 2011 atoms. Found 7 (9 requested) and removed 7 (4 requested) atoms. Cycle 5: After refmac, R = 0.2764 (Rfree = 0.000) for 2003 atoms. Found 3 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.59 3.84 Search for helices and strands: 0 residues in 0 chains, 2034 seeds are put forward NCS extension: 0 residues added, 2034 seeds are put forward Round 1: 81 peptides, 18 chains. Longest chain 7 peptides. Score 0.232 Round 2: 90 peptides, 17 chains. Longest chain 14 peptides. Score 0.320 Round 3: 92 peptides, 18 chains. Longest chain 8 peptides. Score 0.306 Round 4: 97 peptides, 18 chains. Longest chain 11 peptides. Score 0.338 Round 5: 95 peptides, 16 chains. Longest chain 15 peptides. Score 0.379 Taking the results from Round 5 Chains 16, Residues 79, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 2539 reflections ( 98.68 % complete ) and 4976 restraints for refining 2035 atoms. 4665 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2776 (Rfree = 0.000) for 2035 atoms. Found 8 (9 requested) and removed 12 (4 requested) atoms. Cycle 7: After refmac, R = 0.2669 (Rfree = 0.000) for 2026 atoms. Found 3 (9 requested) and removed 6 (4 requested) atoms. Cycle 8: After refmac, R = 0.2906 (Rfree = 0.000) for 2019 atoms. Found 7 (9 requested) and removed 11 (4 requested) atoms. Cycle 9: After refmac, R = 0.2747 (Rfree = 0.000) for 2004 atoms. Found 3 (9 requested) and removed 4 (4 requested) atoms. Cycle 10: After refmac, R = 0.2629 (Rfree = 0.000) for 2003 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.57 3.82 Search for helices and strands: 0 residues in 0 chains, 2023 seeds are put forward NCS extension: 0 residues added, 2023 seeds are put forward Round 1: 92 peptides, 18 chains. Longest chain 12 peptides. Score 0.306 Round 2: 109 peptides, 19 chains. Longest chain 14 peptides. Score 0.385 Round 3: 103 peptides, 18 chains. Longest chain 12 peptides. Score 0.375 Round 4: 111 peptides, 18 chains. Longest chain 14 peptides. Score 0.422 Round 5: 115 peptides, 17 chains. Longest chain 15 peptides. Score 0.468 Taking the results from Round 5 Chains 17, Residues 98, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2539 reflections ( 98.68 % complete ) and 4974 restraints for refining 2032 atoms. 4599 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2865 (Rfree = 0.000) for 2032 atoms. Found 6 (9 requested) and removed 10 (4 requested) atoms. Cycle 12: After refmac, R = 0.2794 (Rfree = 0.000) for 2028 atoms. Found 2 (9 requested) and removed 5 (4 requested) atoms. Cycle 13: After refmac, R = 0.2758 (Rfree = 0.000) for 2023 atoms. Found 2 (9 requested) and removed 4 (4 requested) atoms. Cycle 14: After refmac, R = 0.2713 (Rfree = 0.000) for 2019 atoms. Found 2 (9 requested) and removed 4 (4 requested) atoms. Cycle 15: After refmac, R = 0.2662 (Rfree = 0.000) for 2017 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.58 3.83 Search for helices and strands: 0 residues in 0 chains, 2041 seeds are put forward NCS extension: 0 residues added, 2041 seeds are put forward Round 1: 89 peptides, 16 chains. Longest chain 9 peptides. Score 0.342 Round 2: 97 peptides, 17 chains. Longest chain 9 peptides. Score 0.364 Round 3: 104 peptides, 18 chains. Longest chain 12 peptides. Score 0.381 Round 4: 109 peptides, 17 chains. Longest chain 13 peptides. Score 0.435 Round 5: 108 peptides, 17 chains. Longest chain 14 peptides. Score 0.429 Taking the results from Round 4 Chains 17, Residues 92, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2539 reflections ( 98.68 % complete ) and 5068 restraints for refining 2037 atoms. 4717 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2849 (Rfree = 0.000) for 2037 atoms. Found 8 (9 requested) and removed 5 (4 requested) atoms. Cycle 17: After refmac, R = 0.2672 (Rfree = 0.000) for 2039 atoms. Found 4 (9 requested) and removed 5 (4 requested) atoms. Cycle 18: After refmac, R = 0.2576 (Rfree = 0.000) for 2038 atoms. Found 1 (9 requested) and removed 5 (4 requested) atoms. Cycle 19: After refmac, R = 0.2866 (Rfree = 0.000) for 2033 atoms. Found 1 (9 requested) and removed 4 (4 requested) atoms. Cycle 20: After refmac, R = 0.2622 (Rfree = 0.000) for 2028 atoms. Found 1 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.65 3.90 Search for helices and strands: 0 residues in 0 chains, 2054 seeds are put forward NCS extension: 0 residues added, 2054 seeds are put forward Round 1: 87 peptides, 17 chains. Longest chain 15 peptides. Score 0.301 Round 2: 91 peptides, 17 chains. Longest chain 9 peptides. Score 0.327 Round 3: 80 peptides, 15 chains. Longest chain 7 peptides. Score 0.311 Round 4: 80 peptides, 13 chains. Longest chain 14 peptides. Score 0.368 Round 5: 78 peptides, 14 chains. Longest chain 13 peptides. Score 0.327 Taking the results from Round 4 Chains 13, Residues 67, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2539 reflections ( 98.68 % complete ) and 5194 restraints for refining 2037 atoms. 4939 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2705 (Rfree = 0.000) for 2037 atoms. Found 7 (9 requested) and removed 4 (4 requested) atoms. Cycle 22: After refmac, R = 0.2567 (Rfree = 0.000) for 2036 atoms. Found 1 (9 requested) and removed 5 (4 requested) atoms. Cycle 23: After refmac, R = 0.2938 (Rfree = 0.000) for 2031 atoms. Found 1 (9 requested) and removed 6 (4 requested) atoms. Cycle 24: After refmac, R = 0.2916 (Rfree = 0.000) for 2026 atoms. Found 1 (9 requested) and removed 6 (4 requested) atoms. Cycle 25: After refmac, R = 0.2509 (Rfree = 0.000) for 2021 atoms. Found 2 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.52 3.76 Search for helices and strands: 0 residues in 0 chains, 2040 seeds are put forward NCS extension: 0 residues added, 2040 seeds are put forward Round 1: 76 peptides, 16 chains. Longest chain 8 peptides. Score 0.255 Round 2: 80 peptides, 16 chains. Longest chain 10 peptides. Score 0.283 Round 3: 89 peptides, 17 chains. Longest chain 9 peptides. Score 0.314 Round 4: 97 peptides, 17 chains. Longest chain 11 peptides. Score 0.364 Round 5: 100 peptides, 18 chains. Longest chain 11 peptides. Score 0.356 Taking the results from Round 4 Chains 17, Residues 80, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2539 reflections ( 98.68 % complete ) and 5122 restraints for refining 2037 atoms. 4819 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2658 (Rfree = 0.000) for 2037 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. Cycle 27: After refmac, R = 0.2596 (Rfree = 0.000) for 2034 atoms. Found 3 (9 requested) and removed 6 (4 requested) atoms. Cycle 28: After refmac, R = 0.2413 (Rfree = 0.000) for 2030 atoms. Found 2 (9 requested) and removed 6 (4 requested) atoms. Cycle 29: After refmac, R = 0.2474 (Rfree = 0.000) for 2023 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 30: After refmac, R = 0.2420 (Rfree = 0.000) for 2018 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.56 3.81 Search for helices and strands: 0 residues in 0 chains, 2049 seeds are put forward NCS extension: 0 residues added, 2049 seeds are put forward Round 1: 78 peptides, 18 chains. Longest chain 7 peptides. Score 0.211 Round 2: 69 peptides, 14 chains. Longest chain 9 peptides. Score 0.265 Round 3: 71 peptides, 14 chains. Longest chain 8 peptides. Score 0.279 Round 4: 67 peptides, 12 chains. Longest chain 10 peptides. Score 0.312 Round 5: 76 peptides, 15 chains. Longest chain 8 peptides. Score 0.284 Taking the results from Round 4 Chains 12, Residues 55, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2539 reflections ( 98.68 % complete ) and 5376 restraints for refining 2037 atoms. 5168 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2646 (Rfree = 0.000) for 2037 atoms. Found 4 (9 requested) and removed 5 (4 requested) atoms. Cycle 32: After refmac, R = 0.2984 (Rfree = 0.000) for 2034 atoms. Found 8 (9 requested) and removed 14 (4 requested) atoms. Cycle 33: After refmac, R = 0.2376 (Rfree = 0.000) for 2028 atoms. Found 2 (9 requested) and removed 6 (4 requested) atoms. Cycle 34: After refmac, R = 0.2354 (Rfree = 0.000) for 2024 atoms. Found 2 (9 requested) and removed 4 (4 requested) atoms. Cycle 35: After refmac, R = 0.2339 (Rfree = 0.000) for 2021 atoms. Found 1 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.60 3.85 Search for helices and strands: 0 residues in 0 chains, 2059 seeds are put forward NCS extension: 0 residues added, 2059 seeds are put forward Round 1: 81 peptides, 18 chains. Longest chain 7 peptides. Score 0.232 Round 2: 84 peptides, 19 chains. Longest chain 7 peptides. Score 0.224 Round 3: 85 peptides, 18 chains. Longest chain 8 peptides. Score 0.259 Round 4: 82 peptides, 16 chains. Longest chain 9 peptides. Score 0.296 Round 5: 92 peptides, 18 chains. Longest chain 8 peptides. Score 0.306 Taking the results from Round 5 Chains 18, Residues 74, Estimated correctness of the model 0.0 % 2 chains (10 residues) have been docked in sequence ------------------------------------------------------ 2539 reflections ( 98.68 % complete ) and 5247 restraints for refining 2037 atoms. 4944 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2865 (Rfree = 0.000) for 2037 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. Cycle 37: After refmac, R = 0.2651 (Rfree = 0.000) for 2039 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. Cycle 38: After refmac, R = 0.3104 (Rfree = 0.000) for 2041 atoms. Found 6 (9 requested) and removed 5 (4 requested) atoms. Cycle 39: After refmac, R = 0.3087 (Rfree = 0.000) for 2041 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 40: After refmac, R = 0.2425 (Rfree = 0.000) for 2036 atoms. Found 2 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.57 3.82 Search for helices and strands: 0 residues in 0 chains, 2071 seeds are put forward NCS extension: 0 residues added, 2071 seeds are put forward Round 1: 63 peptides, 14 chains. Longest chain 7 peptides. Score 0.221 Round 2: 65 peptides, 13 chains. Longest chain 7 peptides. Score 0.267 Round 3: 64 peptides, 13 chains. Longest chain 7 peptides. Score 0.260 Round 4: 80 peptides, 17 chains. Longest chain 8 peptides. Score 0.254 Round 5: 72 peptides, 14 chains. Longest chain 8 peptides. Score 0.286 Taking the results from Round 5 Chains 14, Residues 58, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2539 reflections ( 98.68 % complete ) and 5380 restraints for refining 2037 atoms. 5162 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2866 (Rfree = 0.000) for 2037 atoms. Found 8 (9 requested) and removed 6 (4 requested) atoms. Cycle 42: After refmac, R = 0.2733 (Rfree = 0.000) for 2037 atoms. Found 4 (9 requested) and removed 22 (4 requested) atoms. Cycle 43: After refmac, R = 0.2684 (Rfree = 0.000) for 2019 atoms. Found 2 (9 requested) and removed 8 (4 requested) atoms. Cycle 44: After refmac, R = 0.2647 (Rfree = 0.000) for 2013 atoms. Found 3 (9 requested) and removed 5 (4 requested) atoms. Cycle 45: After refmac, R = 0.2625 (Rfree = 0.000) for 2010 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.54 3.78 Search for helices and strands: 0 residues in 0 chains, 2031 seeds are put forward NCS extension: 0 residues added, 2031 seeds are put forward Round 1: 48 peptides, 11 chains. Longest chain 7 peptides. Score 0.201 Round 2: 51 peptides, 11 chains. Longest chain 7 peptides. Score 0.226 Round 3: 56 peptides, 11 chains. Longest chain 10 peptides. Score 0.264 Round 4: 58 peptides, 10 chains. Longest chain 10 peptides. Score 0.311 Round 5: 58 peptides, 9 chains. Longest chain 11 peptides. Score 0.343 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 9, Residues 49, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence Sequence coverage is 24 % Consider running further cycles of model building using 2ooj-4_warpNtrace.pdb as input Building loops using Loopy2018 9 chains (49 residues) following loop building 2 chains (12 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2539 reflections ( 98.68 % complete ) and 5182 restraints for refining 2037 atoms. 4966 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2705 (Rfree = 0.000) for 2037 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.2589 (Rfree = 0.000) for 2029 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.2584 (Rfree = 0.000) for 2023 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.2543 (Rfree = 0.000) for 2018 atoms. Found 0 (9 requested) and removed 2 (4 requested) atoms. Writing output files ... TimeTaking 26.28