Tue 25 Dec 19:27:57 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2ooj-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ooj-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ooj-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ooj-3.2-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/2ooj-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ooj-3.2-parrot-hancs ############### 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 ============================================================ Tue 25 Dec 19:28:07 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/hancs/ArpWArp/wArpResults/WorkingDir/2ooj-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ooj-3.2-parrot-hancs/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-hancs.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-hancs.fasta_lf Building free atoms model in initial map for 2256 target number of atoms Had to go as low as 0.55 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 2507 atoms. Observations/parameters ratio is 0.49 ------------------------------------------------------ Starting model: R = 0.3503 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2770 (Rfree = 0.000) for 2507 atoms. Found 3 (22 requested) and removed 25 (11 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.10 3.31 Search for helices and strands: 0 residues in 0 chains, 2511 seeds are put forward NCS extension: 0 residues added, 2511 seeds are put forward Round 1: 119 peptides, 23 chains. Longest chain 9 peptides. Score 0.343 Round 2: 136 peptides, 23 chains. Longest chain 10 peptides. Score 0.440 Round 3: 131 peptides, 17 chains. Longest chain 22 peptides. Score 0.550 Round 4: 147 peptides, 20 chains. Longest chain 16 peptides. Score 0.562 Round 5: 143 peptides, 20 chains. Longest chain 17 peptides. Score 0.543 Taking the results from Round 4 Chains 20, Residues 127, Estimated correctness of the model 30.4 % 2 chains (11 residues) have been docked in sequence ------------------------------------------------------ 4889 reflections ( 99.31 % complete ) and 4547 restraints for refining 2059 atoms. 4036 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2855 (Rfree = 0.000) for 2059 atoms. Found 9 (18 requested) and removed 14 (9 requested) atoms. Cycle 2: After refmac, R = 0.2820 (Rfree = 0.000) for 2031 atoms. Found 8 (18 requested) and removed 12 (9 requested) atoms. Cycle 3: After refmac, R = 0.2786 (Rfree = 0.000) for 2022 atoms. Found 1 (18 requested) and removed 12 (9 requested) atoms. Cycle 4: After refmac, R = 0.2795 (Rfree = 0.000) for 2006 atoms. Found 6 (18 requested) and removed 10 (9 requested) atoms. Cycle 5: After refmac, R = 0.2770 (Rfree = 0.000) for 2000 atoms. Found 1 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.14 3.36 Search for helices and strands: 0 residues in 0 chains, 2028 seeds are put forward NCS extension: 0 residues added, 2028 seeds are put forward Round 1: 112 peptides, 17 chains. Longest chain 12 peptides. Score 0.452 Round 2: 153 peptides, 21 chains. Longest chain 16 peptides. Score 0.569 Round 3: 164 peptides, 22 chains. Longest chain 24 peptides. Score 0.598 Round 4: 149 peptides, 21 chains. Longest chain 17 peptides. Score 0.550 Round 5: 162 peptides, 24 chains. Longest chain 20 peptides. Score 0.550 Taking the results from Round 3 Chains 23, Residues 142, Estimated correctness of the model 40.5 % 2 chains (14 residues) have been docked in sequence ------------------------------------------------------ 4889 reflections ( 99.31 % complete ) and 4498 restraints for refining 2030 atoms. 3928 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2938 (Rfree = 0.000) for 2030 atoms. Found 9 (18 requested) and removed 11 (9 requested) atoms. Failed to save intermediate PDB Cycle 7: After refmac, R = 0.2735 (Rfree = 0.000) for 2025 atoms. Found 5 (18 requested) and removed 10 (9 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.2831 (Rfree = 0.000) for 2011 atoms. Found 9 (18 requested) and removed 11 (9 requested) atoms. Cycle 9: After refmac, R = 0.2741 (Rfree = 0.000) for 2006 atoms. Found 5 (18 requested) and removed 9 (9 requested) atoms. Cycle 10: After refmac, R = 0.2667 (Rfree = 0.000) for 1997 atoms. Found 4 (17 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.12 3.34 Search for helices and strands: 0 residues in 0 chains, 2024 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 2042 seeds are put forward Round 1: 150 peptides, 27 chains. Longest chain 13 peptides. Score 0.424 Round 2: 161 peptides, 24 chains. Longest chain 15 peptides. Score 0.545 Round 3: 170 peptides, 25 chains. Longest chain 17 peptides. Score 0.566 Round 4: 170 peptides, 22 chains. Longest chain 16 peptides. Score 0.623 Round 5: 165 peptides, 22 chains. Longest chain 15 peptides. Score 0.602 Taking the results from Round 4 Chains 22, Residues 148, Estimated correctness of the model 47.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4889 reflections ( 99.31 % complete ) and 4621 restraints for refining 2059 atoms. 4051 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2797 (Rfree = 0.000) for 2059 atoms. Found 11 (18 requested) and removed 11 (9 requested) atoms. Failed to save intermediate PDB Cycle 12: After refmac, R = 0.2598 (Rfree = 0.000) for 2056 atoms. Found 2 (18 requested) and removed 10 (9 requested) atoms. Cycle 13: After refmac, R = 0.2594 (Rfree = 0.000) for 2044 atoms. Found 6 (18 requested) and removed 10 (9 requested) atoms. Cycle 14: After refmac, R = 0.2472 (Rfree = 0.000) for 2038 atoms. Found 5 (18 requested) and removed 9 (9 requested) atoms. Failed to save intermediate PDB Cycle 15: After refmac, R = 0.2442 (Rfree = 0.000) for 2034 atoms. Found 2 (18 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.15 3.37 Search for helices and strands: 0 residues in 0 chains, 2066 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 2082 seeds are put forward Round 1: 148 peptides, 27 chains. Longest chain 12 peptides. Score 0.413 Round 2: 145 peptides, 20 chains. Longest chain 13 peptides. Score 0.552 Round 3: 155 peptides, 21 chains. Longest chain 21 peptides. Score 0.578 Round 4: 152 peptides, 21 chains. Longest chain 14 peptides. Score 0.564 Round 5: 159 peptides, 22 chains. Longest chain 14 peptides. Score 0.576 Taking the results from Round 3 Chains 21, Residues 134, Estimated correctness of the model 35.0 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 4889 reflections ( 99.31 % complete ) and 4654 restraints for refining 2060 atoms. 4095 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2696 (Rfree = 0.000) for 2060 atoms. Found 10 (18 requested) and removed 16 (9 requested) atoms. Failed to save intermediate PDB Cycle 17: After refmac, R = 0.2595 (Rfree = 0.000) for 2050 atoms. Found 4 (18 requested) and removed 9 (9 requested) atoms. Cycle 18: After refmac, R = 0.2578 (Rfree = 0.000) for 2044 atoms. Found 3 (18 requested) and removed 9 (9 requested) atoms. Cycle 19: After refmac, R = 0.2566 (Rfree = 0.000) for 2038 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 20: After refmac, R = 0.2553 (Rfree = 0.000) for 2027 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, 2060 seeds are put forward NCS extension: 37 residues added (2 deleted due to clashes), 2097 seeds are put forward Round 1: 136 peptides, 22 chains. Longest chain 12 peptides. Score 0.464 Round 2: 142 peptides, 19 chains. Longest chain 20 peptides. Score 0.559 Round 3: 145 peptides, 20 chains. Longest chain 20 peptides. Score 0.552 Round 4: 159 peptides, 21 chains. Longest chain 15 peptides. Score 0.595 Round 5: 160 peptides, 23 chains. Longest chain 15 peptides. Score 0.561 Taking the results from Round 4 Chains 21, Residues 138, Estimated correctness of the model 39.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 4889 reflections ( 99.31 % complete ) and 4723 restraints for refining 2053 atoms. 4192 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2667 (Rfree = 0.000) for 2053 atoms. Found 10 (18 requested) and removed 10 (9 requested) atoms. Cycle 22: After refmac, R = 0.2618 (Rfree = 0.000) for 2044 atoms. Found 9 (18 requested) and removed 9 (9 requested) atoms. Failed to save intermediate PDB Cycle 23: After refmac, R = 0.2618 (Rfree = 0.000) for 2043 atoms. Found 12 (18 requested) and removed 10 (9 requested) atoms. Failed to save intermediate PDB Cycle 24: After refmac, R = 0.2488 (Rfree = 0.000) for 2045 atoms. Found 5 (18 requested) and removed 9 (9 requested) atoms. Failed to save intermediate PDB Cycle 25: After refmac, R = 0.2505 (Rfree = 0.000) for 2040 atoms. Found 7 (18 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.10 3.31 Search for helices and strands: 0 residues in 0 chains, 2050 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 2072 seeds are put forward Round 1: 134 peptides, 23 chains. Longest chain 11 peptides. Score 0.429 Round 2: 145 peptides, 21 chains. Longest chain 15 peptides. Score 0.531 Round 3: 154 peptides, 23 chains. Longest chain 14 peptides. Score 0.533 Round 4: 151 peptides, 21 chains. Longest chain 15 peptides. Score 0.560 Round 5: 142 peptides, 19 chains. Longest chain 17 peptides. Score 0.559 Taking the results from Round 4 Chains 21, Residues 130, Estimated correctness of the model 29.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 4889 reflections ( 99.31 % complete ) and 4814 restraints for refining 2060 atoms. 4315 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2719 (Rfree = 0.000) for 2060 atoms. Found 9 (18 requested) and removed 11 (9 requested) atoms. Failed to save intermediate PDB Cycle 27: After refmac, R = 0.2593 (Rfree = 0.000) for 2055 atoms. Found 2 (18 requested) and removed 9 (9 requested) atoms. Failed to save intermediate PDB Cycle 28: After refmac, R = 0.2516 (Rfree = 0.000) for 2048 atoms. Found 1 (18 requested) and removed 9 (9 requested) atoms. Cycle 29: After refmac, R = 0.2486 (Rfree = 0.000) for 2038 atoms. Found 2 (18 requested) and removed 9 (9 requested) atoms. Failed to save intermediate PDB Cycle 30: After refmac, R = 0.2468 (Rfree = 0.000) for 2031 atoms. Found 1 (18 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.14 3.36 Search for helices and strands: 0 residues in 0 chains, 2053 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 2072 seeds are put forward Round 1: 138 peptides, 23 chains. Longest chain 16 peptides. Score 0.451 Round 2: 149 peptides, 22 chains. Longest chain 18 peptides. Score 0.530 Round 3: 150 peptides, 22 chains. Longest chain 14 peptides. Score 0.534 Round 4: 144 peptides, 18 chains. Longest chain 18 peptides. Score 0.589 Round 5: 146 peptides, 20 chains. Longest chain 15 peptides. Score 0.557 Taking the results from Round 4 Chains 18, Residues 126, Estimated correctness of the model 38.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4889 reflections ( 99.31 % complete ) and 4935 restraints for refining 2060 atoms. 4449 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2694 (Rfree = 0.000) for 2060 atoms. Found 6 (18 requested) and removed 10 (9 requested) atoms. Cycle 32: After refmac, R = 0.2583 (Rfree = 0.000) for 2053 atoms. Found 3 (18 requested) and removed 9 (9 requested) atoms. Cycle 33: After refmac, R = 0.2554 (Rfree = 0.000) for 2047 atoms. Found 3 (18 requested) and removed 9 (9 requested) atoms. Cycle 34: After refmac, R = 0.2538 (Rfree = 0.000) for 2040 atoms. Found 3 (18 requested) and removed 9 (9 requested) atoms. Failed to save intermediate PDB Cycle 35: After refmac, R = 0.2512 (Rfree = 0.000) for 2033 atoms. Found 1 (18 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.13 3.35 Search for helices and strands: 0 residues in 0 chains, 2070 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 2089 seeds are put forward Round 1: 137 peptides, 25 chains. Longest chain 14 peptides. Score 0.398 Round 2: 132 peptides, 20 chains. Longest chain 13 peptides. Score 0.488 Round 3: 125 peptides, 20 chains. Longest chain 15 peptides. Score 0.451 Round 4: 133 peptides, 16 chains. Longest chain 17 peptides. Score 0.580 Round 5: 138 peptides, 19 chains. Longest chain 21 peptides. Score 0.540 Taking the results from Round 4 Chains 17, Residues 117, Estimated correctness of the model 35.6 % 4 chains (33 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 4889 reflections ( 99.31 % complete ) and 4462 restraints for refining 2060 atoms. 3894 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2676 (Rfree = 0.000) for 2060 atoms. Found 9 (18 requested) and removed 18 (9 requested) atoms. Cycle 37: After refmac, R = 0.2556 (Rfree = 0.000) for 2046 atoms. Found 1 (18 requested) and removed 9 (9 requested) atoms. Cycle 38: After refmac, R = 0.2536 (Rfree = 0.000) for 2034 atoms. Found 2 (18 requested) and removed 9 (9 requested) atoms. Cycle 39: After refmac, R = 0.2583 (Rfree = 0.000) for 2024 atoms. Found 3 (18 requested) and removed 9 (9 requested) atoms. Cycle 40: After refmac, R = 0.2634 (Rfree = 0.000) for 2016 atoms. Found 6 (18 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.17 3.39 Search for helices and strands: 0 residues in 0 chains, 2056 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 2078 seeds are put forward Round 1: 99 peptides, 18 chains. Longest chain 12 peptides. Score 0.350 Round 2: 133 peptides, 19 chains. Longest chain 20 peptides. Score 0.516 Round 3: 133 peptides, 21 chains. Longest chain 15 peptides. Score 0.471 Round 4: 136 peptides, 20 chains. Longest chain 14 peptides. Score 0.509 Round 5: 143 peptides, 19 chains. Longest chain 16 peptides. Score 0.564 Taking the results from Round 5 Chains 19, Residues 124, Estimated correctness of the model 31.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4889 reflections ( 99.31 % complete ) and 4904 restraints for refining 2060 atoms. 4427 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2874 (Rfree = 0.000) for 2060 atoms. Found 18 (18 requested) and removed 9 (9 requested) atoms. Failed to save intermediate PDB Cycle 42: After refmac, R = 0.2608 (Rfree = 0.000) for 2066 atoms. Found 5 (18 requested) and removed 9 (9 requested) atoms. Cycle 43: After refmac, R = 0.2562 (Rfree = 0.000) for 2061 atoms. Found 2 (18 requested) and removed 9 (9 requested) atoms. Cycle 44: After refmac, R = 0.2584 (Rfree = 0.000) for 2053 atoms. Found 2 (18 requested) and removed 9 (9 requested) atoms. Cycle 45: After refmac, R = 0.2544 (Rfree = 0.000) for 2046 atoms. Found 1 (18 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.13 3.35 Search for helices and strands: 0 residues in 0 chains, 2074 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 2096 seeds are put forward Round 1: 112 peptides, 20 chains. Longest chain 14 peptides. Score 0.377 Round 2: 129 peptides, 18 chains. Longest chain 15 peptides. Score 0.518 Round 3: 124 peptides, 18 chains. Longest chain 12 peptides. Score 0.492 Round 4: 131 peptides, 20 chains. Longest chain 19 peptides. Score 0.483 Round 5: 127 peptides, 17 chains. Longest chain 12 peptides. Score 0.530 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 17, Residues 110, Estimated correctness of the model 20.8 % 4 chains (26 residues) have been docked in sequence Sequence coverage is 23 % Consider running further cycles of model building using 2ooj-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 36 A and 45 A 16 chains (117 residues) following loop building 3 chains (34 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4889 reflections ( 99.31 % complete ) and 4586 restraints for refining 2060 atoms. 4060 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2824 (Rfree = 0.000) for 2060 atoms. Found 0 (18 requested) and removed 7 (9 requested) atoms. Cycle 47: After refmac, R = 0.2605 (Rfree = 0.000) for 2048 atoms. Found 0 (18 requested) and removed 3 (9 requested) atoms. Cycle 48: After refmac, R = 0.2501 (Rfree = 0.000) for 2043 atoms. Found 0 (18 requested) and removed 7 (9 requested) atoms. Cycle 49: After refmac, R = 0.2450 (Rfree = 0.000) for 2032 atoms. Found 0 (18 requested) and removed 3 (9 requested) atoms. Writing output files ... TimeTaking 44.61