Mon 24 Dec 00:27:15 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-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2ooj-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2ooj-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ooj-3.2-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-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ooj-3.2-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 00:27:20 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-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ooj-3.2-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 196 and 0 Target number of residues in the AU: 196 Target solvent content: 0.6167 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-3.2-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-3.2-parrot-mrncs.fasta_lf Building free atoms model in initial map for 2256 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: 53.043 3.200 Wilson plot Bfac: 59.19 4889 reflections ( 99.31 % complete ) and 0 restraints for refining 2506 atoms. Observations/parameters ratio is 0.49 ------------------------------------------------------ Starting model: R = 0.3457 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2933 (Rfree = 0.000) for 2506 atoms. Found 16 (22 requested) and removed 28 (11 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.15 3.37 Search for helices and strands: 0 residues in 0 chains, 2509 seeds are put forward NCS extension: 0 residues added, 2509 seeds are put forward Round 1: 140 peptides, 25 chains. Longest chain 9 peptides. Score 0.415 Round 2: 162 peptides, 22 chains. Longest chain 25 peptides. Score 0.589 Round 3: 171 peptides, 20 chains. Longest chain 21 peptides. Score 0.662 Round 4: 157 peptides, 21 chains. Longest chain 14 peptides. Score 0.587 Round 5: 182 peptides, 24 chains. Longest chain 15 peptides. Score 0.635 Taking the results from Round 3 Chains 22, Residues 151, Estimated correctness of the model 56.7 % 4 chains (28 residues) have been docked in sequence ------------------------------------------------------ 4889 reflections ( 99.31 % complete ) and 4230 restraints for refining 2060 atoms. 3589 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2732 (Rfree = 0.000) for 2060 atoms. Found 10 (18 requested) and removed 19 (9 requested) atoms. Cycle 2: After refmac, R = 0.2577 (Rfree = 0.000) for 2037 atoms. Found 7 (18 requested) and removed 9 (9 requested) atoms. Cycle 3: After refmac, R = 0.2548 (Rfree = 0.000) for 2027 atoms. Found 3 (18 requested) and removed 9 (9 requested) atoms. Cycle 4: After refmac, R = 0.2517 (Rfree = 0.000) for 2015 atoms. Found 1 (18 requested) and removed 9 (9 requested) atoms. Cycle 5: After refmac, R = 0.2500 (Rfree = 0.000) for 2004 atoms. Found 3 (18 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.13 3.35 Search for helices and strands: 0 residues in 0 chains, 2050 seeds are put forward NCS extension: 37 residues added (4 deleted due to clashes), 2087 seeds are put forward Round 1: 140 peptides, 25 chains. Longest chain 11 peptides. Score 0.415 Round 2: 175 peptides, 26 chains. Longest chain 15 peptides. Score 0.569 Round 3: 167 peptides, 21 chains. Longest chain 16 peptides. Score 0.629 Round 4: 160 peptides, 19 chains. Longest chain 18 peptides. Score 0.637 Round 5: 166 peptides, 21 chains. Longest chain 17 peptides. Score 0.625 Taking the results from Round 4 Chains 19, Residues 141, Estimated correctness of the model 50.7 % 2 chains (19 residues) have been docked in sequence ------------------------------------------------------ 4889 reflections ( 99.31 % complete ) and 4409 restraints for refining 2020 atoms. 3815 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2850 (Rfree = 0.000) for 2020 atoms. Found 12 (18 requested) and removed 15 (9 requested) atoms. Cycle 7: After refmac, R = 0.2590 (Rfree = 0.000) for 2013 atoms. Found 2 (18 requested) and removed 14 (9 requested) atoms. Cycle 8: After refmac, R = 0.2535 (Rfree = 0.000) for 1993 atoms. Found 4 (17 requested) and removed 10 (8 requested) atoms. Cycle 9: After refmac, R = 0.2476 (Rfree = 0.000) for 1984 atoms. Found 2 (17 requested) and removed 9 (8 requested) atoms. Cycle 10: After refmac, R = 0.2438 (Rfree = 0.000) for 1972 atoms. Found 1 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.12 3.34 Search for helices and strands: 0 residues in 0 chains, 2012 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 2027 seeds are put forward Round 1: 151 peptides, 21 chains. Longest chain 18 peptides. Score 0.560 Round 2: 159 peptides, 18 chains. Longest chain 19 peptides. Score 0.651 Round 3: 156 peptides, 19 chains. Longest chain 18 peptides. Score 0.621 Round 4: 162 peptides, 19 chains. Longest chain 21 peptides. Score 0.645 Round 5: 168 peptides, 19 chains. Longest chain 19 peptides. Score 0.668 Taking the results from Round 5 Chains 19, Residues 149, Estimated correctness of the model 58.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4889 reflections ( 99.31 % complete ) and 4492 restraints for refining 2018 atoms. 3915 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2732 (Rfree = 0.000) for 2018 atoms. Found 8 (18 requested) and removed 11 (9 requested) atoms. Cycle 12: After refmac, R = 0.2621 (Rfree = 0.000) for 2013 atoms. Found 1 (18 requested) and removed 11 (9 requested) atoms. Cycle 13: After refmac, R = 0.2597 (Rfree = 0.000) for 2001 atoms. Found 1 (17 requested) and removed 8 (8 requested) atoms. Cycle 14: After refmac, R = 0.2584 (Rfree = 0.000) for 1993 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 15: After refmac, R = 0.2572 (Rfree = 0.000) for 1984 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.13 3.35 Search for helices and strands: 0 residues in 0 chains, 2014 seeds are put forward NCS extension: 27 residues added (0 deleted due to clashes), 2041 seeds are put forward Round 1: 148 peptides, 23 chains. Longest chain 14 peptides. Score 0.503 Round 2: 164 peptides, 20 chains. Longest chain 20 peptides. Score 0.635 Round 3: 180 peptides, 22 chains. Longest chain 16 peptides. Score 0.661 Round 4: 180 peptides, 23 chains. Longest chain 15 peptides. Score 0.645 Round 5: 173 peptides, 20 chains. Longest chain 17 peptides. Score 0.669 Taking the results from Round 5 Chains 21, Residues 153, Estimated correctness of the model 58.3 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 4889 reflections ( 99.31 % complete ) and 4597 restraints for refining 2060 atoms. 3974 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2881 (Rfree = 0.000) for 2060 atoms. Found 13 (18 requested) and removed 15 (9 requested) atoms. Cycle 17: After refmac, R = 0.2778 (Rfree = 0.000) for 2052 atoms. Found 3 (18 requested) and removed 9 (9 requested) atoms. Cycle 18: After refmac, R = 0.2754 (Rfree = 0.000) for 2045 atoms. Found 4 (18 requested) and removed 9 (9 requested) atoms. Cycle 19: After refmac, R = 0.2751 (Rfree = 0.000) for 2037 atoms. Found 2 (18 requested) and removed 9 (9 requested) atoms. Cycle 20: After refmac, R = 0.2723 (Rfree = 0.000) for 2030 atoms. Found 1 (18 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.15 3.37 Search for helices and strands: 0 residues in 0 chains, 2052 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 2070 seeds are put forward Round 1: 149 peptides, 24 chains. Longest chain 12 peptides. Score 0.486 Round 2: 177 peptides, 26 chains. Longest chain 15 peptides. Score 0.578 Round 3: 162 peptides, 21 chains. Longest chain 13 peptides. Score 0.608 Round 4: 163 peptides, 21 chains. Longest chain 17 peptides. Score 0.612 Round 5: 160 peptides, 21 chains. Longest chain 17 peptides. Score 0.600 Taking the results from Round 4 Chains 21, Residues 142, Estimated correctness of the model 44.3 % 3 chains (11 residues) have been docked in sequence ------------------------------------------------------ 4889 reflections ( 99.31 % complete ) and 4690 restraints for refining 2060 atoms. 4122 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2746 (Rfree = 0.000) for 2060 atoms. Found 7 (18 requested) and removed 11 (9 requested) atoms. Cycle 22: After refmac, R = 0.2671 (Rfree = 0.000) for 2049 atoms. Found 1 (18 requested) and removed 12 (9 requested) atoms. Cycle 23: After refmac, R = 0.2700 (Rfree = 0.000) for 2034 atoms. Found 6 (18 requested) and removed 9 (9 requested) atoms. Cycle 24: After refmac, R = 0.2679 (Rfree = 0.000) for 2029 atoms. Found 6 (18 requested) and removed 9 (9 requested) atoms. Cycle 25: After refmac, R = 0.2502 (Rfree = 0.000) for 2021 atoms. Found 1 (18 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.11 3.32 Search for helices and strands: 0 residues in 0 chains, 2048 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 2071 seeds are put forward Round 1: 123 peptides, 21 chains. Longest chain 13 peptides. Score 0.416 Round 2: 157 peptides, 21 chains. Longest chain 20 peptides. Score 0.587 Round 3: 152 peptides, 20 chains. Longest chain 18 peptides. Score 0.584 Round 4: 150 peptides, 19 chains. Longest chain 22 peptides. Score 0.595 Round 5: 148 peptides, 19 chains. Longest chain 20 peptides. Score 0.587 Taking the results from Round 4 Chains 21, Residues 131, Estimated correctness of the model 39.7 % 2 chains (21 residues) have been docked in sequence ------------------------------------------------------ 4889 reflections ( 99.31 % complete ) and 4666 restraints for refining 2060 atoms. 4086 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2858 (Rfree = 0.000) for 2060 atoms. Found 5 (18 requested) and removed 48 (9 requested) atoms. Cycle 27: After refmac, R = 0.2723 (Rfree = 0.000) for 2010 atoms. Found 7 (18 requested) and removed 17 (9 requested) atoms. Cycle 28: After refmac, R = 0.2631 (Rfree = 0.000) for 1998 atoms. Found 2 (17 requested) and removed 10 (8 requested) atoms. Cycle 29: After refmac, R = 0.2607 (Rfree = 0.000) for 1984 atoms. Found 6 (17 requested) and removed 8 (8 requested) atoms. Cycle 30: After refmac, R = 0.2494 (Rfree = 0.000) for 1978 atoms. Found 3 (17 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.08 3.29 Search for helices and strands: 0 residues in 0 chains, 2020 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 2034 seeds are put forward Round 1: 129 peptides, 21 chains. Longest chain 11 peptides. Score 0.449 Round 2: 144 peptides, 18 chains. Longest chain 21 peptides. Score 0.589 Round 3: 148 peptides, 20 chains. Longest chain 18 peptides. Score 0.566 Round 4: 157 peptides, 19 chains. Longest chain 24 peptides. Score 0.625 Round 5: 161 peptides, 21 chains. Longest chain 24 peptides. Score 0.604 Taking the results from Round 4 Chains 20, Residues 138, Estimated correctness of the model 47.6 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 4889 reflections ( 99.31 % complete ) and 4678 restraints for refining 2060 atoms. 4113 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2657 (Rfree = 0.000) for 2060 atoms. Found 11 (18 requested) and removed 11 (9 requested) atoms. Cycle 32: After refmac, R = 0.2526 (Rfree = 0.000) for 2057 atoms. Found 5 (18 requested) and removed 11 (9 requested) atoms. Cycle 33: After refmac, R = 0.2570 (Rfree = 0.000) for 2050 atoms. Found 2 (18 requested) and removed 10 (9 requested) atoms. Cycle 34: After refmac, R = 0.2498 (Rfree = 0.000) for 2039 atoms. Found 6 (18 requested) and removed 10 (9 requested) atoms. Cycle 35: After refmac, R = 0.2509 (Rfree = 0.000) for 2033 atoms. Found 2 (18 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.09 3.30 Search for helices and strands: 0 residues in 0 chains, 2054 seeds are put forward NCS extension: 36 residues added (1 deleted due to clashes), 2090 seeds are put forward Round 1: 117 peptides, 19 chains. Longest chain 16 peptides. Score 0.431 Round 2: 137 peptides, 21 chains. Longest chain 16 peptides. Score 0.492 Round 3: 129 peptides, 17 chains. Longest chain 15 peptides. Score 0.540 Round 4: 126 peptides, 16 chains. Longest chain 16 peptides. Score 0.547 Round 5: 131 peptides, 18 chains. Longest chain 16 peptides. Score 0.528 Taking the results from Round 4 Chains 16, Residues 110, Estimated correctness of the model 26.0 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 4889 reflections ( 99.31 % complete ) and 4771 restraints for refining 2060 atoms. 4301 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2629 (Rfree = 0.000) for 2060 atoms. Found 10 (18 requested) and removed 10 (9 requested) atoms. Cycle 37: After refmac, R = 0.2483 (Rfree = 0.000) for 2059 atoms. Found 7 (18 requested) and removed 9 (9 requested) atoms. Cycle 38: After refmac, R = 0.2378 (Rfree = 0.000) for 2053 atoms. Found 2 (18 requested) and removed 10 (9 requested) atoms. Cycle 39: After refmac, R = 0.2397 (Rfree = 0.000) for 2040 atoms. Found 4 (18 requested) and removed 9 (9 requested) atoms. Cycle 40: After refmac, R = 0.2305 (Rfree = 0.000) for 2029 atoms. Found 2 (18 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.10 3.31 Search for helices and strands: 0 residues in 0 chains, 2054 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 2073 seeds are put forward Round 1: 122 peptides, 21 chains. Longest chain 13 peptides. Score 0.410 Round 2: 148 peptides, 22 chains. Longest chain 15 peptides. Score 0.525 Round 3: 137 peptides, 20 chains. Longest chain 15 peptides. Score 0.514 Round 4: 141 peptides, 20 chains. Longest chain 15 peptides. Score 0.533 Round 5: 135 peptides, 20 chains. Longest chain 14 peptides. Score 0.504 Taking the results from Round 4 Chains 20, Residues 121, Estimated correctness of the model 21.7 % 2 chains (17 residues) have been docked in sequence ------------------------------------------------------ 4889 reflections ( 99.31 % complete ) and 4655 restraints for refining 2055 atoms. 4134 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2563 (Rfree = 0.000) for 2055 atoms. Found 18 (18 requested) and removed 9 (9 requested) atoms. Cycle 42: After refmac, R = 0.2467 (Rfree = 0.000) for 2064 atoms. Found 2 (18 requested) and removed 12 (9 requested) atoms. Cycle 43: After refmac, R = 0.2419 (Rfree = 0.000) for 2049 atoms. Found 2 (18 requested) and removed 10 (9 requested) atoms. Cycle 44: After refmac, R = 0.2461 (Rfree = 0.000) for 2038 atoms. Found 9 (18 requested) and removed 9 (9 requested) atoms. Cycle 45: After refmac, R = 0.2382 (Rfree = 0.000) for 2036 atoms. Found 8 (18 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.14 3.36 Search for helices and strands: 0 residues in 0 chains, 2047 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 2065 seeds are put forward Round 1: 113 peptides, 22 chains. Longest chain 11 peptides. Score 0.332 Round 2: 119 peptides, 17 chains. Longest chain 17 peptides. Score 0.490 Round 3: 115 peptides, 15 chains. Longest chain 14 peptides. Score 0.515 Round 4: 116 peptides, 15 chains. Longest chain 19 peptides. Score 0.521 Round 5: 116 peptides, 18 chains. Longest chain 9 peptides. Score 0.450 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 16, Residues 101, Estimated correctness of the model 18.0 % 1 chains (9 residues) have been docked in sequence Sequence coverage is 8 % Consider running further cycles of model building using 2ooj-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4889 reflections ( 99.31 % complete ) and 4887 restraints for refining 2060 atoms. 4478 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2525 (Rfree = 0.000) for 2060 atoms. Found 0 (18 requested) and removed 7 (9 requested) atoms. Cycle 47: After refmac, R = 0.2513 (Rfree = 0.000) for 2047 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 48: After refmac, R = 0.2385 (Rfree = 0.000) for 2030 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 49: After refmac, R = 0.2876 (Rfree = 0.000) for 2017 atoms. TimeTaking 28.85