Mon 24 Dec 08:02:36 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-3.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2o1q-3.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2o1q-3.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2o1q-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/2o1q-3.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2o1q-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 08:02:41 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-3.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2o1q-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 169 and 0 Target number of residues in the AU: 169 Target solvent content: 0.6421 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-3.8-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: 92 Cell parameters: 61.883 61.883 133.475 90.000 90.000 90.000 Input sequence file: 2o1q-3.8-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 3.801 Wilson plot Bfac: 72.44 2845 reflections ( 99.65 % complete ) and 0 restraints for refining 2589 atoms. Observations/parameters ratio is 0.27 ------------------------------------------------------ Starting model: R = 0.3605 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3338 (Rfree = 0.000) for 2589 atoms. Found 14 (14 requested) and removed 59 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.42 3.97 Search for helices and strands: 0 residues in 0 chains, 2566 seeds are put forward NCS extension: 0 residues added, 2566 seeds are put forward Round 1: 77 peptides, 16 chains. Longest chain 8 peptides. Score 0.267 Round 2: 99 peptides, 19 chains. Longest chain 8 peptides. Score 0.333 Round 3: 131 peptides, 23 chains. Longest chain 11 peptides. Score 0.427 Round 4: 150 peptides, 25 chains. Longest chain 12 peptides. Score 0.487 Round 5: 143 peptides, 24 chains. Longest chain 12 peptides. Score 0.472 Taking the results from Round 4 Chains 25, Residues 125, Estimated correctness of the model 0.0 % 3 chains (10 residues) have been docked in sequence ------------------------------------------------------ 2845 reflections ( 99.65 % complete ) and 4776 restraints for refining 2097 atoms. 4275 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2509 (Rfree = 0.000) for 2097 atoms. Found 9 (11 requested) and removed 16 (5 requested) atoms. Cycle 2: After refmac, R = 0.2505 (Rfree = 0.000) for 2048 atoms. Found 11 (11 requested) and removed 16 (5 requested) atoms. Cycle 3: After refmac, R = 0.2465 (Rfree = 0.000) for 2020 atoms. Found 9 (11 requested) and removed 12 (5 requested) atoms. Cycle 4: After refmac, R = 0.2646 (Rfree = 0.000) for 2001 atoms. Found 11 (11 requested) and removed 14 (5 requested) atoms. Cycle 5: After refmac, R = 0.2382 (Rfree = 0.000) for 1986 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.37 3.91 Search for helices and strands: 0 residues in 0 chains, 2060 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 2072 seeds are put forward Round 1: 106 peptides, 22 chains. Longest chain 10 peptides. Score 0.295 Round 2: 149 peptides, 29 chains. Longest chain 9 peptides. Score 0.384 Round 3: 131 peptides, 21 chains. Longest chain 11 peptides. Score 0.477 Round 4: 127 peptides, 22 chains. Longest chain 15 peptides. Score 0.429 Round 5: 118 peptides, 18 chains. Longest chain 14 peptides. Score 0.477 Taking the results from Round 5 Chains 18, Residues 100, Estimated correctness of the model 0.0 % 3 chains (16 residues) have been docked in sequence ------------------------------------------------------ 2845 reflections ( 99.65 % complete ) and 4898 restraints for refining 2098 atoms. 4474 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2434 (Rfree = 0.000) for 2098 atoms. Found 11 (11 requested) and removed 23 (5 requested) atoms. Cycle 7: After refmac, R = 0.2264 (Rfree = 0.000) for 2068 atoms. Found 7 (11 requested) and removed 12 (5 requested) atoms. Cycle 8: After refmac, R = 0.2287 (Rfree = 0.000) for 2054 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. Cycle 9: After refmac, R = 0.2301 (Rfree = 0.000) for 2049 atoms. Found 7 (11 requested) and removed 12 (5 requested) atoms. Cycle 10: After refmac, R = 0.2259 (Rfree = 0.000) for 2032 atoms. Found 9 (11 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.39 3.93 Search for helices and strands: 0 residues in 0 chains, 2096 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 2108 seeds are put forward Round 1: 87 peptides, 19 chains. Longest chain 8 peptides. Score 0.249 Round 2: 102 peptides, 20 chains. Longest chain 8 peptides. Score 0.324 Round 3: 96 peptides, 19 chains. Longest chain 8 peptides. Score 0.312 Round 4: 105 peptides, 20 chains. Longest chain 8 peptides. Score 0.344 Round 5: 109 peptides, 19 chains. Longest chain 11 peptides. Score 0.397 Taking the results from Round 5 Chains 19, Residues 90, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 2845 reflections ( 99.65 % complete ) and 4651 restraints for refining 1998 atoms. 4298 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2258 (Rfree = 0.000) for 1998 atoms. Found 6 (10 requested) and removed 26 (5 requested) atoms. Cycle 12: After refmac, R = 0.2058 (Rfree = 0.000) for 1964 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. Cycle 13: After refmac, R = 0.1772 (Rfree = 0.000) for 1964 atoms. Found 5 (10 requested) and removed 7 (5 requested) atoms. Cycle 14: After refmac, R = 0.1647 (Rfree = 0.000) for 1958 atoms. Found 1 (10 requested) and removed 6 (5 requested) atoms. Cycle 15: After refmac, R = 0.1622 (Rfree = 0.000) for 1951 atoms. Found 3 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.38 3.92 Search for helices and strands: 0 residues in 0 chains, 1969 seeds are put forward NCS extension: 7 residues added (0 deleted due to clashes), 1976 seeds are put forward Round 1: 111 peptides, 22 chains. Longest chain 10 peptides. Score 0.328 Round 2: 129 peptides, 25 chains. Longest chain 11 peptides. Score 0.363 Round 3: 121 peptides, 21 chains. Longest chain 11 peptides. Score 0.419 Round 4: 139 peptides, 22 chains. Longest chain 11 peptides. Score 0.497 Round 5: 140 peptides, 24 chains. Longest chain 12 peptides. Score 0.455 Taking the results from Round 4 Chains 22, Residues 117, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 2845 reflections ( 99.65 % complete ) and 4626 restraints for refining 2039 atoms. 4159 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2274 (Rfree = 0.000) for 2039 atoms. Found 9 (11 requested) and removed 19 (5 requested) atoms. Cycle 17: After refmac, R = 0.2101 (Rfree = 0.000) for 2022 atoms. Found 10 (11 requested) and removed 17 (5 requested) atoms. Cycle 18: After refmac, R = 0.1892 (Rfree = 0.000) for 2005 atoms. Found 6 (11 requested) and removed 5 (5 requested) atoms. Cycle 19: After refmac, R = 0.1904 (Rfree = 0.000) for 1998 atoms. Found 10 (11 requested) and removed 5 (5 requested) atoms. Cycle 20: After refmac, R = 0.1680 (Rfree = 0.000) for 1999 atoms. Found 5 (11 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.47 4.03 Search for helices and strands: 0 residues in 0 chains, 2054 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 2067 seeds are put forward Round 1: 83 peptides, 17 chains. Longest chain 10 peptides. Score 0.280 Round 2: 110 peptides, 20 chains. Longest chain 10 peptides. Score 0.377 Round 3: 110 peptides, 18 chains. Longest chain 12 peptides. Score 0.430 Round 4: 113 peptides, 19 chains. Longest chain 16 peptides. Score 0.422 Round 5: 122 peptides, 19 chains. Longest chain 14 peptides. Score 0.475 Taking the results from Round 5 Chains 19, Residues 103, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2845 reflections ( 99.65 % complete ) and 5027 restraints for refining 2098 atoms. 4634 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2038 (Rfree = 0.000) for 2098 atoms. Found 5 (11 requested) and removed 11 (5 requested) atoms. Cycle 22: After refmac, R = 0.2032 (Rfree = 0.000) for 2087 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. Cycle 23: After refmac, R = 0.2130 (Rfree = 0.000) for 2084 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. Cycle 24: After refmac, R = 0.1973 (Rfree = 0.000) for 2076 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 25: After refmac, R = 0.2079 (Rfree = 0.000) for 2073 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.49 4.05 Search for helices and strands: 0 residues in 0 chains, 2107 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 2128 seeds are put forward Round 1: 72 peptides, 16 chains. Longest chain 7 peptides. Score 0.230 Round 2: 89 peptides, 17 chains. Longest chain 10 peptides. Score 0.322 Round 3: 96 peptides, 18 chains. Longest chain 11 peptides. Score 0.341 Round 4: 102 peptides, 18 chains. Longest chain 11 peptides. Score 0.380 Round 5: 101 peptides, 17 chains. Longest chain 11 peptides. Score 0.401 Taking the results from Round 5 Chains 17, Residues 84, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2845 reflections ( 99.65 % complete ) and 5083 restraints for refining 2080 atoms. 4764 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2026 (Rfree = 0.000) for 2080 atoms. Found 10 (11 requested) and removed 14 (5 requested) atoms. Cycle 27: After refmac, R = 0.1825 (Rfree = 0.000) for 2069 atoms. Found 4 (11 requested) and removed 6 (5 requested) atoms. Cycle 28: After refmac, R = 0.1810 (Rfree = 0.000) for 2061 atoms. Found 4 (11 requested) and removed 6 (5 requested) atoms. Cycle 29: After refmac, R = 0.1658 (Rfree = 0.000) for 2058 atoms. Found 2 (11 requested) and removed 5 (5 requested) atoms. Cycle 30: After refmac, R = 0.1829 (Rfree = 0.000) for 2054 atoms. Found 8 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.43 3.98 Search for helices and strands: 0 residues in 0 chains, 2088 seeds are put forward NCS extension: 0 residues added, 2088 seeds are put forward Round 1: 81 peptides, 14 chains. Longest chain 11 peptides. Score 0.356 Round 2: 88 peptides, 15 chains. Longest chain 11 peptides. Score 0.374 Round 3: 80 peptides, 12 chains. Longest chain 9 peptides. Score 0.408 Round 4: 75 peptides, 13 chains. Longest chain 11 peptides. Score 0.345 Round 5: 83 peptides, 13 chains. Longest chain 9 peptides. Score 0.399 Taking the results from Round 3 Chains 12, Residues 68, Estimated correctness of the model 0.0 % 3 chains (17 residues) have been docked in sequence ------------------------------------------------------ 2845 reflections ( 99.65 % complete ) and 5021 restraints for refining 2098 atoms. 4703 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1876 (Rfree = 0.000) for 2098 atoms. Found 4 (11 requested) and removed 7 (5 requested) atoms. Cycle 32: After refmac, R = 0.1701 (Rfree = 0.000) for 2094 atoms. Found 3 (11 requested) and removed 7 (5 requested) atoms. Cycle 33: After refmac, R = 0.1756 (Rfree = 0.000) for 2086 atoms. Found 3 (11 requested) and removed 5 (5 requested) atoms. Cycle 34: After refmac, R = 0.1699 (Rfree = 0.000) for 2082 atoms. Found 3 (11 requested) and removed 5 (5 requested) atoms. Cycle 35: After refmac, R = 0.1797 (Rfree = 0.000) for 2075 atoms. Found 6 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.46 4.02 Search for helices and strands: 0 residues in 0 chains, 2101 seeds are put forward NCS extension: 0 residues added, 2101 seeds are put forward Round 1: 78 peptides, 17 chains. Longest chain 7 peptides. Score 0.244 Round 2: 92 peptides, 17 chains. Longest chain 8 peptides. Score 0.343 Round 3: 99 peptides, 17 chains. Longest chain 9 peptides. Score 0.389 Round 4: 86 peptides, 16 chains. Longest chain 8 peptides. Score 0.331 Round 5: 84 peptides, 15 chains. Longest chain 9 peptides. Score 0.347 Taking the results from Round 3 Chains 17, Residues 82, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 2845 reflections ( 99.65 % complete ) and 5055 restraints for refining 2098 atoms. 4737 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2137 (Rfree = 0.000) for 2098 atoms. Found 11 (11 requested) and removed 20 (5 requested) atoms. Cycle 37: After refmac, R = 0.1625 (Rfree = 0.000) for 2080 atoms. Found 6 (11 requested) and removed 9 (5 requested) atoms. Cycle 38: After refmac, R = 0.1482 (Rfree = 0.000) for 2077 atoms. Found 1 (11 requested) and removed 6 (5 requested) atoms. Cycle 39: After refmac, R = 0.1604 (Rfree = 0.000) for 2070 atoms. Found 4 (11 requested) and removed 9 (5 requested) atoms. Cycle 40: After refmac, R = 0.1418 (Rfree = 0.000) for 2063 atoms. Found 0 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.50 4.06 Search for helices and strands: 0 residues in 0 chains, 2102 seeds are put forward NCS extension: 0 residues added, 2102 seeds are put forward Round 1: 72 peptides, 15 chains. Longest chain 8 peptides. Score 0.261 Round 2: 100 peptides, 20 chains. Longest chain 9 peptides. Score 0.311 Round 3: 95 peptides, 17 chains. Longest chain 9 peptides. Score 0.363 Round 4: 95 peptides, 17 chains. Longest chain 9 peptides. Score 0.363 Round 5: 91 peptides, 16 chains. Longest chain 11 peptides. Score 0.365 Taking the results from Round 5 Chains 16, Residues 75, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2845 reflections ( 99.65 % complete ) and 5067 restraints for refining 2081 atoms. 4783 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1909 (Rfree = 0.000) for 2081 atoms. Found 10 (11 requested) and removed 12 (5 requested) atoms. Cycle 42: After refmac, R = 0.1737 (Rfree = 0.000) for 2079 atoms. Found 2 (11 requested) and removed 7 (5 requested) atoms. Cycle 43: After refmac, R = 0.1658 (Rfree = 0.000) for 2074 atoms. Found 0 (11 requested) and removed 7 (5 requested) atoms. Cycle 44: After refmac, R = 0.1840 (Rfree = 0.000) for 2065 atoms. Found 7 (11 requested) and removed 6 (5 requested) atoms. Cycle 45: After refmac, R = 0.1529 (Rfree = 0.000) for 2066 atoms. Found 2 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.49 4.05 Search for helices and strands: 0 residues in 0 chains, 2099 seeds are put forward NCS extension: 6 residues added (0 deleted due to clashes), 2105 seeds are put forward Round 1: 56 peptides, 13 chains. Longest chain 5 peptides. Score 0.201 Round 2: 70 peptides, 14 chains. Longest chain 8 peptides. Score 0.278 Round 3: 64 peptides, 12 chains. Longest chain 8 peptides. Score 0.297 Round 4: 66 peptides, 12 chains. Longest chain 10 peptides. Score 0.312 Round 5: 65 peptides, 12 chains. Longest chain 10 peptides. Score 0.305 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 12, Residues 54, 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. 2845 reflections ( 99.65 % complete ) and 5175 restraints for refining 2077 atoms. 4971 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1738 (Rfree = 0.000) for 2077 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.1693 (Rfree = 0.000) for 2071 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.1565 (Rfree = 0.000) for 2065 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.1549 (Rfree = 0.000) for 2059 atoms. TimeTaking 28.37