null Mon 24 Dec 08:01:30 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 2o1q-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2o1q-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2o1q-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2o1q-3.6-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/2o1q-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2o1q-3.6-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 08:01:35 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/2o1q-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2o1q-3.6-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 174 and 0 Target number of residues in the AU: 174 Target solvent content: 0.6315 Checking the provided sequence file Detected sequence length: 145 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 290 Adjusted target solvent content: 0.39 Input MTZ file: 2o1q-3.6-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: 92 Cell parameters: 61.883 61.883 133.475 90.000 90.000 90.000 Input sequence file: 2o1q-3.6-parrot-noncs.fasta_lf Building free atoms model in initial map for 2320 target number of atoms Had to go as low as 0.70 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: 56.142 3.600 Wilson plot Bfac: 67.20 3329 reflections ( 99.70 % complete ) and 0 restraints for refining 2577 atoms. Observations/parameters ratio is 0.32 ------------------------------------------------------ Starting model: R = 0.3471 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3624 (Rfree = 0.000) for 2577 atoms. Found 16 (16 requested) and removed 44 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.28 3.81 Search for helices and strands: 0 residues in 0 chains, 2578 seeds are put forward NCS extension: 0 residues added, 2578 seeds are put forward Round 1: 84 peptides, 17 chains. Longest chain 11 peptides. Score 0.287 Round 2: 99 peptides, 18 chains. Longest chain 11 peptides. Score 0.361 Round 3: 115 peptides, 19 chains. Longest chain 11 peptides. Score 0.434 Round 4: 126 peptides, 20 chains. Longest chain 11 peptides. Score 0.473 Round 5: 134 peptides, 20 chains. Longest chain 11 peptides. Score 0.517 Taking the results from Round 5 Chains 20, Residues 114, Estimated correctness of the model 0.0 % 3 chains (19 residues) have been docked in sequence ------------------------------------------------------ 3329 reflections ( 99.70 % complete ) and 4659 restraints for refining 2100 atoms. 4183 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2601 (Rfree = 0.000) for 2100 atoms. Found 8 (13 requested) and removed 16 (6 requested) atoms. Cycle 2: After refmac, R = 0.2448 (Rfree = 0.000) for 2060 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. Cycle 3: After refmac, R = 0.2248 (Rfree = 0.000) for 2047 atoms. Found 11 (13 requested) and removed 9 (6 requested) atoms. Cycle 4: After refmac, R = 0.2208 (Rfree = 0.000) for 2040 atoms. Found 10 (13 requested) and removed 9 (6 requested) atoms. Cycle 5: After refmac, R = 0.2132 (Rfree = 0.000) for 2029 atoms. Found 11 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.35 3.89 Search for helices and strands: 0 residues in 0 chains, 2071 seeds are put forward NCS extension: 8 residues added (1 deleted due to clashes), 2079 seeds are put forward Round 1: 109 peptides, 23 chains. Longest chain 7 peptides. Score 0.287 Round 2: 123 peptides, 23 chains. Longest chain 9 peptides. Score 0.379 Round 3: 122 peptides, 20 chains. Longest chain 12 peptides. Score 0.450 Round 4: 126 peptides, 19 chains. Longest chain 13 peptides. Score 0.498 Round 5: 139 peptides, 20 chains. Longest chain 13 peptides. Score 0.543 Taking the results from Round 5 Chains 21, Residues 119, Estimated correctness of the model 0.0 % 5 chains (39 residues) have been docked in sequence ------------------------------------------------------ 3329 reflections ( 99.70 % complete ) and 4449 restraints for refining 2103 atoms. 3870 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2015 (Rfree = 0.000) for 2103 atoms. Found 7 (13 requested) and removed 17 (6 requested) atoms. Cycle 7: After refmac, R = 0.1917 (Rfree = 0.000) for 2077 atoms. Found 6 (13 requested) and removed 7 (6 requested) atoms. Cycle 8: After refmac, R = 0.2000 (Rfree = 0.000) for 2072 atoms. Found 11 (13 requested) and removed 9 (6 requested) atoms. Cycle 9: After refmac, R = 0.1898 (Rfree = 0.000) for 2068 atoms. Found 10 (13 requested) and removed 8 (6 requested) atoms. Cycle 10: After refmac, R = 0.1742 (Rfree = 0.000) for 2064 atoms. Found 7 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.40 3.95 Search for helices and strands: 0 residues in 0 chains, 2112 seeds are put forward NCS extension: 0 residues added, 2112 seeds are put forward Round 1: 110 peptides, 23 chains. Longest chain 8 peptides. Score 0.294 Round 2: 133 peptides, 22 chains. Longest chain 11 peptides. Score 0.464 Round 3: 129 peptides, 22 chains. Longest chain 14 peptides. Score 0.441 Round 4: 132 peptides, 18 chains. Longest chain 17 peptides. Score 0.553 Round 5: 140 peptides, 20 chains. Longest chain 12 peptides. Score 0.548 Taking the results from Round 4 Chains 20, Residues 114, Estimated correctness of the model 0.0 % 3 chains (16 residues) have been docked in sequence ------------------------------------------------------ 3329 reflections ( 99.70 % complete ) and 4741 restraints for refining 2102 atoms. 4280 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2137 (Rfree = 0.000) for 2102 atoms. Found 13 (13 requested) and removed 17 (6 requested) atoms. Cycle 12: After refmac, R = 0.2020 (Rfree = 0.000) for 2080 atoms. Found 13 (13 requested) and removed 14 (6 requested) atoms. Cycle 13: After refmac, R = 0.1809 (Rfree = 0.000) for 2072 atoms. Found 13 (13 requested) and removed 13 (6 requested) atoms. Cycle 14: After refmac, R = 0.1663 (Rfree = 0.000) for 2067 atoms. Found 11 (13 requested) and removed 7 (6 requested) atoms. Cycle 15: After refmac, R = 0.1917 (Rfree = 0.000) for 2063 atoms. Found 13 (13 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.34 3.88 Search for helices and strands: 0 residues in 0 chains, 2122 seeds are put forward NCS extension: 29 residues added (1 deleted due to clashes), 2151 seeds are put forward Round 1: 111 peptides, 22 chains. Longest chain 9 peptides. Score 0.328 Round 2: 136 peptides, 24 chains. Longest chain 16 peptides. Score 0.432 Round 3: 122 peptides, 20 chains. Longest chain 16 peptides. Score 0.450 Round 4: 116 peptides, 20 chains. Longest chain 16 peptides. Score 0.414 Round 5: 112 peptides, 21 chains. Longest chain 9 peptides. Score 0.362 Taking the results from Round 3 Chains 21, Residues 102, Estimated correctness of the model 0.0 % 3 chains (20 residues) have been docked in sequence ------------------------------------------------------ 3329 reflections ( 99.70 % complete ) and 4856 restraints for refining 2103 atoms. 4425 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2040 (Rfree = 0.000) for 2103 atoms. Found 12 (13 requested) and removed 19 (6 requested) atoms. Cycle 17: After refmac, R = 0.1779 (Rfree = 0.000) for 2081 atoms. Found 10 (13 requested) and removed 12 (6 requested) atoms. Cycle 18: After refmac, R = 0.1627 (Rfree = 0.000) for 2071 atoms. Found 4 (13 requested) and removed 7 (6 requested) atoms. Cycle 19: After refmac, R = 0.1698 (Rfree = 0.000) for 2066 atoms. Found 6 (13 requested) and removed 7 (6 requested) atoms. Cycle 20: After refmac, R = 0.1701 (Rfree = 0.000) for 2062 atoms. Found 7 (13 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.40 3.95 Search for helices and strands: 0 residues in 0 chains, 2092 seeds are put forward NCS extension: 0 residues added, 2092 seeds are put forward Round 1: 99 peptides, 23 chains. Longest chain 6 peptides. Score 0.218 Round 2: 115 peptides, 20 chains. Longest chain 13 peptides. Score 0.408 Round 3: 130 peptides, 24 chains. Longest chain 11 peptides. Score 0.396 Round 4: 115 peptides, 19 chains. Longest chain 11 peptides. Score 0.434 Round 5: 121 peptides, 20 chains. Longest chain 11 peptides. Score 0.444 Taking the results from Round 5 Chains 21, Residues 101, Estimated correctness of the model 0.0 % 2 chains (16 residues) have been docked in sequence ------------------------------------------------------ 3329 reflections ( 99.70 % complete ) and 4926 restraints for refining 2103 atoms. 4507 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2348 (Rfree = 0.000) for 2103 atoms. Found 13 (13 requested) and removed 15 (6 requested) atoms. Cycle 22: After refmac, R = 0.1756 (Rfree = 0.000) for 2085 atoms. Found 8 (13 requested) and removed 9 (6 requested) atoms. Cycle 23: After refmac, R = 0.1694 (Rfree = 0.000) for 2073 atoms. Found 8 (13 requested) and removed 6 (6 requested) atoms. Cycle 24: After refmac, R = 0.1684 (Rfree = 0.000) for 2071 atoms. Found 7 (13 requested) and removed 8 (6 requested) atoms. Cycle 25: After refmac, R = 0.1342 (Rfree = 0.000) for 2068 atoms. Found 3 (13 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.40 3.95 Search for helices and strands: 0 residues in 0 chains, 2100 seeds are put forward NCS extension: 0 residues added, 2100 seeds are put forward Round 1: 109 peptides, 24 chains. Longest chain 8 peptides. Score 0.259 Round 2: 128 peptides, 27 chains. Longest chain 8 peptides. Score 0.304 Round 3: 135 peptides, 25 chains. Longest chain 9 peptides. Score 0.400 Round 4: 131 peptides, 24 chains. Longest chain 9 peptides. Score 0.402 Round 5: 124 peptides, 22 chains. Longest chain 12 peptides. Score 0.411 Taking the results from Round 5 Chains 22, Residues 102, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 3329 reflections ( 99.70 % complete ) and 4833 restraints for refining 2078 atoms. 4437 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1957 (Rfree = 0.000) for 2078 atoms. Found 12 (13 requested) and removed 13 (6 requested) atoms. Cycle 27: After refmac, R = 0.1785 (Rfree = 0.000) for 2068 atoms. Found 8 (13 requested) and removed 9 (6 requested) atoms. Cycle 28: After refmac, R = 0.1670 (Rfree = 0.000) for 2061 atoms. Found 12 (13 requested) and removed 8 (6 requested) atoms. Cycle 29: After refmac, R = 0.1862 (Rfree = 0.000) for 2061 atoms. Found 13 (13 requested) and removed 7 (6 requested) atoms. Cycle 30: After refmac, R = 0.1615 (Rfree = 0.000) for 2065 atoms. Found 13 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.38 3.92 Search for helices and strands: 0 residues in 0 chains, 2119 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 2134 seeds are put forward Round 1: 100 peptides, 22 chains. Longest chain 9 peptides. Score 0.254 Round 2: 106 peptides, 22 chains. Longest chain 7 peptides. Score 0.295 Round 3: 103 peptides, 19 chains. Longest chain 10 peptides. Score 0.359 Round 4: 95 peptides, 18 chains. Longest chain 11 peptides. Score 0.334 Round 5: 94 peptides, 17 chains. Longest chain 12 peptides. Score 0.356 Taking the results from Round 3 Chains 19, Residues 84, Estimated correctness of the model 0.0 % 3 chains (9 residues) have been docked in sequence ------------------------------------------------------ 3329 reflections ( 99.70 % complete ) and 5008 restraints for refining 2096 atoms. 4677 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1781 (Rfree = 0.000) for 2096 atoms. Found 11 (13 requested) and removed 14 (6 requested) atoms. Cycle 32: After refmac, R = 0.1561 (Rfree = 0.000) for 2090 atoms. Found 9 (13 requested) and removed 10 (6 requested) atoms. Cycle 33: After refmac, R = 0.1614 (Rfree = 0.000) for 2086 atoms. Found 12 (13 requested) and removed 7 (6 requested) atoms. Cycle 34: After refmac, R = 0.1501 (Rfree = 0.000) for 2090 atoms. Found 8 (13 requested) and removed 7 (6 requested) atoms. Cycle 35: After refmac, R = 0.1676 (Rfree = 0.000) for 2088 atoms. Found 13 (13 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.37 3.91 Search for helices and strands: 0 residues in 0 chains, 2133 seeds are put forward NCS extension: 0 residues added, 2133 seeds are put forward Round 1: 102 peptides, 22 chains. Longest chain 10 peptides. Score 0.268 Round 2: 113 peptides, 18 chains. Longest chain 14 peptides. Score 0.448 Round 3: 120 peptides, 21 chains. Longest chain 15 peptides. Score 0.412 Round 4: 118 peptides, 20 chains. Longest chain 15 peptides. Score 0.426 Round 5: 120 peptides, 20 chains. Longest chain 15 peptides. Score 0.438 Taking the results from Round 2 Chains 19, Residues 95, Estimated correctness of the model 0.0 % 3 chains (19 residues) have been docked in sequence ------------------------------------------------------ 3329 reflections ( 99.70 % complete ) and 4741 restraints for refining 2103 atoms. 4325 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1786 (Rfree = 0.000) for 2103 atoms. Found 12 (13 requested) and removed 12 (6 requested) atoms. Cycle 37: After refmac, R = 0.1751 (Rfree = 0.000) for 2098 atoms. Found 13 (13 requested) and removed 12 (6 requested) atoms. Cycle 38: After refmac, R = 0.1734 (Rfree = 0.000) for 2095 atoms. Found 11 (13 requested) and removed 9 (6 requested) atoms. Cycle 39: After refmac, R = 0.1520 (Rfree = 0.000) for 2096 atoms. Found 6 (13 requested) and removed 7 (6 requested) atoms. Cycle 40: After refmac, R = 0.1642 (Rfree = 0.000) for 2093 atoms. Found 10 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.28 3.81 Search for helices and strands: 0 residues in 0 chains, 2131 seeds are put forward NCS extension: 0 residues added, 2131 seeds are put forward Round 1: 92 peptides, 20 chains. Longest chain 6 peptides. Score 0.255 Round 2: 97 peptides, 19 chains. Longest chain 8 peptides. Score 0.319 Round 3: 107 peptides, 21 chains. Longest chain 9 peptides. Score 0.330 Round 4: 103 peptides, 19 chains. Longest chain 9 peptides. Score 0.359 Round 5: 116 peptides, 22 chains. Longest chain 12 peptides. Score 0.361 Taking the results from Round 5 Chains 23, Residues 94, Estimated correctness of the model 0.0 % 3 chains (18 residues) have been docked in sequence ------------------------------------------------------ 3329 reflections ( 99.70 % complete ) and 4748 restraints for refining 2102 atoms. 4338 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1818 (Rfree = 0.000) for 2102 atoms. Found 10 (13 requested) and removed 11 (6 requested) atoms. Cycle 42: After refmac, R = 0.2356 (Rfree = 0.000) for 2091 atoms. Found 13 (13 requested) and removed 11 (6 requested) atoms. Cycle 43: After refmac, R = 0.1659 (Rfree = 0.000) for 2084 atoms. Found 9 (13 requested) and removed 7 (6 requested) atoms. Cycle 44: After refmac, R = 0.1632 (Rfree = 0.000) for 2079 atoms. Found 13 (13 requested) and removed 7 (6 requested) atoms. Cycle 45: After refmac, R = 0.1261 (Rfree = 0.000) for 2082 atoms. Found 5 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.36 3.90 Search for helices and strands: 0 residues in 0 chains, 2124 seeds are put forward NCS extension: 7 residues added (0 deleted due to clashes), 2131 seeds are put forward Round 1: 71 peptides, 14 chains. Longest chain 8 peptides. Score 0.285 Round 2: 82 peptides, 16 chains. Longest chain 9 peptides. Score 0.303 Round 3: 89 peptides, 15 chains. Longest chain 15 peptides. Score 0.380 Round 4: 83 peptides, 14 chains. Longest chain 16 peptides. Score 0.370 Round 5: 93 peptides, 16 chains. Longest chain 16 peptides. Score 0.378 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 15, Residues 74, 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 2o1q-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3329 reflections ( 99.70 % complete ) and 4898 restraints for refining 2032 atoms. 4617 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1627 (Rfree = 0.000) for 2032 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.1642 (Rfree = 0.000) for 2023 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.1598 (Rfree = 0.000) for 2014 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.1648 (Rfree = 0.000) for 2008 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:29:55 GMT 2018 Job finished. TimeTaking 28.41 Used memory is bytes: 18062952