Mon 24 Dec 07:35:30 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-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2o1q-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2o1q-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2o1q-3.4-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-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2o1q-3.4-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 07:35:34 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-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2o1q-3.4-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 178 and 0 Target number of residues in the AU: 178 Target solvent content: 0.6231 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-3.4-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-3.4-parrot-noncs.fasta_lf Building free atoms model in initial map for 2320 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: 56.142 3.400 Wilson plot Bfac: 62.14 3929 reflections ( 99.75 % complete ) and 0 restraints for refining 2578 atoms. Observations/parameters ratio is 0.38 ------------------------------------------------------ Starting model: R = 0.3401 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3299 (Rfree = 0.000) for 2578 atoms. Found 19 (19 requested) and removed 74 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.04 3.53 Search for helices and strands: 0 residues in 0 chains, 2556 seeds are put forward NCS extension: 0 residues added, 2556 seeds are put forward Round 1: 102 peptides, 20 chains. Longest chain 13 peptides. Score 0.324 Round 2: 146 peptides, 27 chains. Longest chain 14 peptides. Score 0.416 Round 3: 154 peptides, 23 chains. Longest chain 13 peptides. Score 0.553 Round 4: 151 peptides, 23 chains. Longest chain 15 peptides. Score 0.538 Round 5: 157 peptides, 23 chains. Longest chain 11 peptides. Score 0.567 Taking the results from Round 5 Chains 23, Residues 134, Estimated correctness of the model 17.5 % 4 chains (19 residues) have been docked in sequence ------------------------------------------------------ 3929 reflections ( 99.75 % complete ) and 4505 restraints for refining 2109 atoms. 3931 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2511 (Rfree = 0.000) for 2109 atoms. Found 9 (15 requested) and removed 20 (7 requested) atoms. Cycle 2: After refmac, R = 0.2349 (Rfree = 0.000) for 2075 atoms. Found 6 (15 requested) and removed 12 (7 requested) atoms. Cycle 3: After refmac, R = 0.2345 (Rfree = 0.000) for 2057 atoms. Found 8 (15 requested) and removed 10 (7 requested) atoms. Cycle 4: After refmac, R = 0.2097 (Rfree = 0.000) for 2049 atoms. Found 1 (15 requested) and removed 8 (7 requested) atoms. Cycle 5: After refmac, R = 0.2116 (Rfree = 0.000) for 2039 atoms. Found 5 (15 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.24 3.76 Search for helices and strands: 0 residues in 0 chains, 2090 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 2101 seeds are put forward Round 1: 134 peptides, 25 chains. Longest chain 10 peptides. Score 0.394 Round 2: 157 peptides, 27 chains. Longest chain 11 peptides. Score 0.479 Round 3: 160 peptides, 26 chains. Longest chain 19 peptides. Score 0.517 Round 4: 164 peptides, 26 chains. Longest chain 12 peptides. Score 0.538 Round 5: 173 peptides, 26 chains. Longest chain 19 peptides. Score 0.581 Taking the results from Round 5 Chains 27, Residues 147, Estimated correctness of the model 22.4 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 3929 reflections ( 99.75 % complete ) and 4643 restraints for refining 2109 atoms. 4041 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2281 (Rfree = 0.000) for 2109 atoms. Found 14 (15 requested) and removed 15 (7 requested) atoms. Cycle 7: After refmac, R = 0.2040 (Rfree = 0.000) for 2100 atoms. Found 2 (15 requested) and removed 9 (7 requested) atoms. Cycle 8: After refmac, R = 0.1984 (Rfree = 0.000) for 2089 atoms. Found 2 (15 requested) and removed 8 (7 requested) atoms. Cycle 9: After refmac, R = 0.1952 (Rfree = 0.000) for 2083 atoms. Found 3 (15 requested) and removed 9 (7 requested) atoms. Cycle 10: After refmac, R = 0.1975 (Rfree = 0.000) for 2076 atoms. Found 4 (15 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.24 3.76 Search for helices and strands: 0 residues in 0 chains, 2119 seeds are put forward NCS extension: 26 residues added (0 deleted due to clashes), 2145 seeds are put forward Round 1: 134 peptides, 25 chains. Longest chain 14 peptides. Score 0.394 Round 2: 152 peptides, 23 chains. Longest chain 16 peptides. Score 0.543 Round 3: 154 peptides, 22 chains. Longest chain 16 peptides. Score 0.574 Round 4: 156 peptides, 23 chains. Longest chain 16 peptides. Score 0.563 Round 5: 158 peptides, 23 chains. Longest chain 16 peptides. Score 0.572 Taking the results from Round 3 Chains 23, Residues 132, Estimated correctness of the model 20.0 % 3 chains (16 residues) have been docked in sequence ------------------------------------------------------ 3929 reflections ( 99.75 % complete ) and 4694 restraints for refining 2109 atoms. 4151 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2080 (Rfree = 0.000) for 2109 atoms. Found 15 (15 requested) and removed 9 (7 requested) atoms. Cycle 12: After refmac, R = 0.1905 (Rfree = 0.000) for 2107 atoms. Found 7 (15 requested) and removed 8 (7 requested) atoms. Cycle 13: After refmac, R = 0.1889 (Rfree = 0.000) for 2106 atoms. Found 7 (15 requested) and removed 7 (7 requested) atoms. Cycle 14: After refmac, R = 0.1934 (Rfree = 0.000) for 2104 atoms. Found 8 (15 requested) and removed 10 (7 requested) atoms. Cycle 15: After refmac, R = 0.1661 (Rfree = 0.000) for 2100 atoms. Found 2 (15 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.24 3.76 Search for helices and strands: 0 residues in 0 chains, 2135 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 2152 seeds are put forward Round 1: 121 peptides, 22 chains. Longest chain 14 peptides. Score 0.392 Round 2: 143 peptides, 22 chains. Longest chain 17 peptides. Score 0.519 Round 3: 159 peptides, 24 chains. Longest chain 16 peptides. Score 0.556 Round 4: 159 peptides, 23 chains. Longest chain 17 peptides. Score 0.577 Round 5: 154 peptides, 20 chains. Longest chain 26 peptides. Score 0.615 Taking the results from Round 5 Chains 22, Residues 134, Estimated correctness of the model 33.5 % 1 chains (16 residues) have been docked in sequence ------------------------------------------------------ 3929 reflections ( 99.75 % complete ) and 4527 restraints for refining 2109 atoms. 3949 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2197 (Rfree = 0.000) for 2109 atoms. Found 15 (15 requested) and removed 15 (7 requested) atoms. Cycle 17: After refmac, R = 0.1977 (Rfree = 0.000) for 2100 atoms. Found 7 (15 requested) and removed 8 (7 requested) atoms. Cycle 18: After refmac, R = 0.1812 (Rfree = 0.000) for 2096 atoms. Found 5 (15 requested) and removed 7 (7 requested) atoms. Cycle 19: After refmac, R = 0.1765 (Rfree = 0.000) for 2089 atoms. Found 3 (15 requested) and removed 7 (7 requested) atoms. Cycle 20: After refmac, R = 0.1703 (Rfree = 0.000) for 2077 atoms. Found 7 (15 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.21 3.73 Search for helices and strands: 0 residues in 0 chains, 2105 seeds are put forward NCS extension: 41 residues added (4 deleted due to clashes), 2146 seeds are put forward Round 1: 125 peptides, 24 chains. Longest chain 9 peptides. Score 0.365 Round 2: 145 peptides, 23 chains. Longest chain 14 peptides. Score 0.506 Round 3: 151 peptides, 22 chains. Longest chain 14 peptides. Score 0.559 Round 4: 146 peptides, 20 chains. Longest chain 20 peptides. Score 0.578 Round 5: 156 peptides, 25 chains. Longest chain 13 peptides. Score 0.519 Taking the results from Round 4 Chains 20, Residues 126, Estimated correctness of the model 21.3 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 3929 reflections ( 99.75 % complete ) and 4738 restraints for refining 2108 atoms. 4211 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2010 (Rfree = 0.000) for 2108 atoms. Found 15 (15 requested) and removed 8 (7 requested) atoms. Cycle 22: After refmac, R = 0.1761 (Rfree = 0.000) for 2112 atoms. Found 6 (15 requested) and removed 7 (7 requested) atoms. Cycle 23: After refmac, R = 0.1682 (Rfree = 0.000) for 2107 atoms. Found 8 (15 requested) and removed 8 (7 requested) atoms. Cycle 24: After refmac, R = 0.1622 (Rfree = 0.000) for 2107 atoms. Found 5 (15 requested) and removed 8 (7 requested) atoms. Cycle 25: After refmac, R = 0.1617 (Rfree = 0.000) for 2102 atoms. Found 4 (15 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.24 3.76 Search for helices and strands: 0 residues in 0 chains, 2139 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 2165 seeds are put forward Round 1: 130 peptides, 22 chains. Longest chain 13 peptides. Score 0.447 Round 2: 148 peptides, 23 chains. Longest chain 14 peptides. Score 0.522 Round 3: 155 peptides, 23 chains. Longest chain 15 peptides. Score 0.558 Round 4: 150 peptides, 24 chains. Longest chain 9 peptides. Score 0.510 Round 5: 151 peptides, 23 chains. Longest chain 15 peptides. Score 0.538 Taking the results from Round 3 Chains 23, Residues 132, Estimated correctness of the model 14.4 % 2 chains (10 residues) have been docked in sequence ------------------------------------------------------ 3929 reflections ( 99.75 % complete ) and 4777 restraints for refining 2109 atoms. 4262 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1956 (Rfree = 0.000) for 2109 atoms. Found 7 (15 requested) and removed 8 (7 requested) atoms. Cycle 27: After refmac, R = 0.1884 (Rfree = 0.000) for 2104 atoms. Found 5 (15 requested) and removed 7 (7 requested) atoms. Cycle 28: After refmac, R = 0.1863 (Rfree = 0.000) for 2100 atoms. Found 4 (15 requested) and removed 7 (7 requested) atoms. Cycle 29: After refmac, R = 0.1840 (Rfree = 0.000) for 2097 atoms. Found 3 (15 requested) and removed 7 (7 requested) atoms. Cycle 30: After refmac, R = 0.1814 (Rfree = 0.000) for 2093 atoms. Found 3 (15 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.25 3.77 Search for helices and strands: 0 residues in 0 chains, 2127 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 2146 seeds are put forward Round 1: 107 peptides, 19 chains. Longest chain 13 peptides. Score 0.385 Round 2: 124 peptides, 18 chains. Longest chain 22 peptides. Score 0.511 Round 3: 115 peptides, 18 chains. Longest chain 11 peptides. Score 0.460 Round 4: 129 peptides, 18 chains. Longest chain 21 peptides. Score 0.537 Round 5: 140 peptides, 21 chains. Longest chain 18 peptides. Score 0.526 Taking the results from Round 4 Chains 18, Residues 111, Estimated correctness of the model 6.8 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 3929 reflections ( 99.75 % complete ) and 4891 restraints for refining 2108 atoms. 4455 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1904 (Rfree = 0.000) for 2108 atoms. Found 14 (15 requested) and removed 10 (7 requested) atoms. Cycle 32: After refmac, R = 0.1788 (Rfree = 0.000) for 2107 atoms. Found 6 (15 requested) and removed 7 (7 requested) atoms. Cycle 33: After refmac, R = 0.1762 (Rfree = 0.000) for 2104 atoms. Found 4 (15 requested) and removed 7 (7 requested) atoms. Cycle 34: After refmac, R = 0.1733 (Rfree = 0.000) for 2101 atoms. Found 3 (15 requested) and removed 7 (7 requested) atoms. Cycle 35: After refmac, R = 0.1720 (Rfree = 0.000) for 2095 atoms. Found 4 (15 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.24 3.76 Search for helices and strands: 0 residues in 0 chains, 2123 seeds are put forward NCS extension: 39 residues added (0 deleted due to clashes), 2162 seeds are put forward Round 1: 124 peptides, 23 chains. Longest chain 13 peptides. Score 0.385 Round 2: 132 peptides, 21 chains. Longest chain 19 peptides. Score 0.482 Round 3: 138 peptides, 22 chains. Longest chain 10 peptides. Score 0.492 Round 4: 144 peptides, 21 chains. Longest chain 19 peptides. Score 0.546 Round 5: 143 peptides, 23 chains. Longest chain 19 peptides. Score 0.495 Taking the results from Round 4 Chains 21, Residues 123, Estimated correctness of the model 10.1 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 3929 reflections ( 99.75 % complete ) and 4738 restraints for refining 2103 atoms. 4257 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1875 (Rfree = 0.000) for 2103 atoms. Found 15 (15 requested) and removed 7 (7 requested) atoms. Cycle 37: After refmac, R = 0.1736 (Rfree = 0.000) for 2108 atoms. Found 7 (15 requested) and removed 7 (7 requested) atoms. Cycle 38: After refmac, R = 0.1695 (Rfree = 0.000) for 2105 atoms. Found 6 (15 requested) and removed 7 (7 requested) atoms. Cycle 39: After refmac, R = 0.1644 (Rfree = 0.000) for 2102 atoms. Found 5 (15 requested) and removed 8 (7 requested) atoms. Cycle 40: After refmac, R = 0.1619 (Rfree = 0.000) for 2097 atoms. Found 4 (15 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.22 3.74 Search for helices and strands: 0 residues in 0 chains, 2127 seeds are put forward NCS extension: 36 residues added (2 deleted due to clashes), 2163 seeds are put forward Round 1: 97 peptides, 20 chains. Longest chain 10 peptides. Score 0.290 Round 2: 117 peptides, 21 chains. Longest chain 10 peptides. Score 0.394 Round 3: 137 peptides, 23 chains. Longest chain 15 peptides. Score 0.462 Round 4: 134 peptides, 22 chains. Longest chain 14 peptides. Score 0.469 Round 5: 121 peptides, 20 chains. Longest chain 13 peptides. Score 0.444 Taking the results from Round 4 Chains 22, Residues 112, Estimated correctness of the model 0.0 % 3 chains (16 residues) have been docked in sequence ------------------------------------------------------ 3929 reflections ( 99.75 % complete ) and 4698 restraints for refining 2109 atoms. 4235 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1809 (Rfree = 0.000) for 2109 atoms. Found 7 (15 requested) and removed 7 (7 requested) atoms. Cycle 42: After refmac, R = 0.1703 (Rfree = 0.000) for 2106 atoms. Found 1 (15 requested) and removed 7 (7 requested) atoms. Cycle 43: After refmac, R = 0.1750 (Rfree = 0.000) for 2095 atoms. Found 10 (15 requested) and removed 7 (7 requested) atoms. Cycle 44: After refmac, R = 0.1762 (Rfree = 0.000) for 2094 atoms. Found 11 (15 requested) and removed 7 (7 requested) atoms. Cycle 45: After refmac, R = 0.1760 (Rfree = 0.000) for 2092 atoms. Found 12 (15 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.24 3.76 Search for helices and strands: 0 residues in 0 chains, 2136 seeds are put forward NCS extension: 0 residues added, 2136 seeds are put forward Round 1: 97 peptides, 21 chains. Longest chain 7 peptides. Score 0.262 Round 2: 115 peptides, 22 chains. Longest chain 15 peptides. Score 0.355 Round 3: 116 peptides, 22 chains. Longest chain 10 peptides. Score 0.361 Round 4: 100 peptides, 19 chains. Longest chain 14 peptides. Score 0.339 Round 5: 110 peptides, 20 chains. Longest chain 10 peptides. Score 0.377 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 20, Residues 90, Estimated correctness of the model 0.0 % 5 chains (18 residues) have been docked in sequence Sequence coverage is 19 % Consider running further cycles of model building using 2o1q-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 84 A and 92 A 18 chains (93 residues) following loop building 4 chains (25 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3929 reflections ( 99.75 % complete ) and 4681 restraints for refining 2109 atoms. 4287 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1914 (Rfree = 0.000) for 2109 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.1793 (Rfree = 0.000) for 2098 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.1889 (Rfree = 0.000) for 2091 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.1751 (Rfree = 0.000) for 2082 atoms. TimeTaking 25.68