null Mon 24 Dec 07:29:23 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 2ig6-4.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2ig6-4.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2ig6-4.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ig6-4.0-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/2ig6-4.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ig6-4.0-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 07:29:28 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/2ig6-4.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ig6-4.0-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 240 and 0 Target number of residues in the AU: 240 Target solvent content: 0.6509 Checking the provided sequence file Detected sequence length: 150 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 300 Adjusted target solvent content: 0.56 Input MTZ file: 2ig6-4.0-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: 19 Cell parameters: 52.413 65.299 108.709 90.000 90.000 90.000 Input sequence file: 2ig6-4.0-parrot-noncs.fasta_lf Building free atoms model in initial map for 2400 target number of atoms Had to go as low as 0.80 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: 55.977 4.001 Wilson plot Bfac: 78.18 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 3336 reflections ( 97.60 % complete ) and 0 restraints for refining 2669 atoms. Observations/parameters ratio is 0.31 ------------------------------------------------------ Starting model: R = 0.3613 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3368 (Rfree = 0.000) for 2669 atoms. Found 12 (12 requested) and removed 94 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.55 3.28 Search for helices and strands: 0 residues in 0 chains, 2613 seeds are put forward NCS extension: 0 residues added, 2613 seeds are put forward Round 1: 86 peptides, 17 chains. Longest chain 9 peptides. Score 0.271 Round 2: 130 peptides, 23 chains. Longest chain 10 peptides. Score 0.360 Round 3: 147 peptides, 23 chains. Longest chain 11 peptides. Score 0.434 Round 4: 147 peptides, 24 chains. Longest chain 12 peptides. Score 0.415 Round 5: 151 peptides, 24 chains. Longest chain 12 peptides. Score 0.432 Taking the results from Round 3 Chains 23, Residues 124, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3336 reflections ( 97.60 % complete ) and 4971 restraints for refining 2167 atoms. 4498 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2452 (Rfree = 0.000) for 2167 atoms. Found 9 (10 requested) and removed 10 (5 requested) atoms. Cycle 2: After refmac, R = 0.2508 (Rfree = 0.000) for 2116 atoms. Found 10 (10 requested) and removed 38 (5 requested) atoms. Cycle 3: After refmac, R = 0.2364 (Rfree = 0.000) for 2065 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. Cycle 4: After refmac, R = 0.2323 (Rfree = 0.000) for 2042 atoms. Found 9 (9 requested) and removed 5 (4 requested) atoms. Cycle 5: After refmac, R = 0.2271 (Rfree = 0.000) for 2033 atoms. Found 4 (9 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.59 3.31 Search for helices and strands: 0 residues in 0 chains, 2106 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 2121 seeds are put forward Round 1: 134 peptides, 26 chains. Longest chain 9 peptides. Score 0.318 Round 2: 157 peptides, 26 chains. Longest chain 15 peptides. Score 0.421 Round 3: 168 peptides, 28 chains. Longest chain 20 peptides. Score 0.431 Round 4: 170 peptides, 26 chains. Longest chain 18 peptides. Score 0.474 Round 5: 155 peptides, 24 chains. Longest chain 16 peptides. Score 0.449 Taking the results from Round 4 Chains 26, Residues 144, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3336 reflections ( 97.60 % complete ) and 4594 restraints for refining 2121 atoms. 4044 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2103 (Rfree = 0.000) for 2121 atoms. Found 8 (10 requested) and removed 11 (5 requested) atoms. Cycle 7: After refmac, R = 0.1994 (Rfree = 0.000) for 2097 atoms. Found 4 (10 requested) and removed 9 (5 requested) atoms. Cycle 8: After refmac, R = 0.2054 (Rfree = 0.000) for 2086 atoms. Found 7 (9 requested) and removed 13 (4 requested) atoms. Cycle 9: After refmac, R = 0.2123 (Rfree = 0.000) for 2074 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. Cycle 10: After refmac, R = 0.2142 (Rfree = 0.000) for 2067 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.67 3.39 Search for helices and strands: 0 residues in 0 chains, 2132 seeds are put forward NCS extension: 38 residues added (2 deleted due to clashes), 2170 seeds are put forward Round 1: 146 peptides, 27 chains. Longest chain 9 peptides. Score 0.354 Round 2: 156 peptides, 25 chains. Longest chain 10 peptides. Score 0.435 Round 3: 169 peptides, 25 chains. Longest chain 17 peptides. Score 0.487 Round 4: 162 peptides, 24 chains. Longest chain 20 peptides. Score 0.477 Round 5: 168 peptides, 23 chains. Longest chain 23 peptides. Score 0.517 Taking the results from Round 5 Chains 23, Residues 145, Estimated correctness of the model 0.0 % 2 chains (25 residues) have been docked in sequence ------------------------------------------------------ 3336 reflections ( 97.60 % complete ) and 4486 restraints for refining 2168 atoms. 3823 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2227 (Rfree = 0.000) for 2168 atoms. Found 9 (10 requested) and removed 86 (5 requested) atoms. Cycle 12: After refmac, R = 0.2065 (Rfree = 0.000) for 2071 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. Cycle 13: After refmac, R = 0.1923 (Rfree = 0.000) for 2054 atoms. Found 5 (9 requested) and removed 7 (4 requested) atoms. Cycle 14: After refmac, R = 0.1939 (Rfree = 0.000) for 2042 atoms. Found 8 (9 requested) and removed 8 (4 requested) atoms. Cycle 15: After refmac, R = 0.1871 (Rfree = 0.000) for 2035 atoms. Found 7 (9 requested) and removed 10 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.67 3.39 Search for helices and strands: 0 residues in 0 chains, 2071 seeds are put forward NCS extension: 0 residues added, 2071 seeds are put forward Round 1: 142 peptides, 28 chains. Longest chain 13 peptides. Score 0.316 Round 2: 143 peptides, 23 chains. Longest chain 17 peptides. Score 0.417 Round 3: 154 peptides, 23 chains. Longest chain 13 peptides. Score 0.463 Round 4: 161 peptides, 23 chains. Longest chain 26 peptides. Score 0.491 Round 5: 166 peptides, 25 chains. Longest chain 21 peptides. Score 0.476 Taking the results from Round 4 Chains 23, Residues 138, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 3336 reflections ( 97.60 % complete ) and 4722 restraints for refining 2168 atoms. 4165 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2276 (Rfree = 0.000) for 2168 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 17: After refmac, R = 0.2378 (Rfree = 0.000) for 2153 atoms. Found 10 (10 requested) and removed 23 (5 requested) atoms. Cycle 18: After refmac, R = 0.2136 (Rfree = 0.000) for 2123 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. Cycle 19: After refmac, R = 0.2111 (Rfree = 0.000) for 2114 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Cycle 20: After refmac, R = 0.1961 (Rfree = 0.000) for 2109 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.68 3.40 Search for helices and strands: 0 residues in 0 chains, 2184 seeds are put forward NCS extension: 33 residues added (1 deleted due to clashes), 2217 seeds are put forward Round 1: 129 peptides, 23 chains. Longest chain 11 peptides. Score 0.355 Round 2: 143 peptides, 25 chains. Longest chain 16 peptides. Score 0.379 Round 3: 148 peptides, 23 chains. Longest chain 18 peptides. Score 0.438 Round 4: 153 peptides, 22 chains. Longest chain 21 peptides. Score 0.477 Round 5: 156 peptides, 20 chains. Longest chain 26 peptides. Score 0.523 Taking the results from Round 5 Chains 22, Residues 136, Estimated correctness of the model 0.0 % 2 chains (24 residues) have been docked in sequence ------------------------------------------------------ 3336 reflections ( 97.60 % complete ) and 4576 restraints for refining 2168 atoms. 3954 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2339 (Rfree = 0.000) for 2168 atoms. Found 5 (10 requested) and removed 7 (5 requested) atoms. Cycle 22: After refmac, R = 0.2149 (Rfree = 0.000) for 2145 atoms. Found 7 (10 requested) and removed 7 (5 requested) atoms. Cycle 23: After refmac, R = 0.2078 (Rfree = 0.000) for 2128 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. Cycle 24: After refmac, R = 0.1915 (Rfree = 0.000) for 2120 atoms. Found 6 (10 requested) and removed 6 (5 requested) atoms. Cycle 25: After refmac, R = 0.1980 (Rfree = 0.000) for 2113 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.64 3.36 Search for helices and strands: 0 residues in 0 chains, 2152 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 2174 seeds are put forward Round 1: 127 peptides, 27 chains. Longest chain 9 peptides. Score 0.265 Round 2: 154 peptides, 27 chains. Longest chain 12 peptides. Score 0.390 Round 3: 149 peptides, 27 chains. Longest chain 10 peptides. Score 0.368 Round 4: 152 peptides, 25 chains. Longest chain 12 peptides. Score 0.418 Round 5: 153 peptides, 26 chains. Longest chain 10 peptides. Score 0.404 Taking the results from Round 4 Chains 25, Residues 127, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3336 reflections ( 97.60 % complete ) and 4985 restraints for refining 2167 atoms. 4502 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1956 (Rfree = 0.000) for 2167 atoms. Found 6 (10 requested) and removed 6 (5 requested) atoms. Cycle 27: After refmac, R = 0.1756 (Rfree = 0.000) for 2156 atoms. Found 6 (10 requested) and removed 7 (5 requested) atoms. Cycle 28: After refmac, R = 0.1661 (Rfree = 0.000) for 2146 atoms. Found 1 (10 requested) and removed 10 (5 requested) atoms. Cycle 29: After refmac, R = 0.1670 (Rfree = 0.000) for 2131 atoms. Found 1 (10 requested) and removed 5 (5 requested) atoms. Cycle 30: After refmac, R = 0.1620 (Rfree = 0.000) for 2125 atoms. Found 1 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.67 3.39 Search for helices and strands: 0 residues in 0 chains, 2174 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 2188 seeds are put forward Round 1: 136 peptides, 30 chains. Longest chain 7 peptides. Score 0.248 Round 2: 142 peptides, 26 chains. Longest chain 12 peptides. Score 0.355 Round 3: 136 peptides, 26 chains. Longest chain 9 peptides. Score 0.328 Round 4: 134 peptides, 23 chains. Longest chain 10 peptides. Score 0.378 Round 5: 136 peptides, 23 chains. Longest chain 11 peptides. Score 0.387 Taking the results from Round 5 Chains 23, Residues 113, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3336 reflections ( 97.60 % complete ) and 5195 restraints for refining 2168 atoms. 4766 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2125 (Rfree = 0.000) for 2168 atoms. Found 10 (10 requested) and removed 5 (5 requested) atoms. Cycle 32: After refmac, R = 0.1984 (Rfree = 0.000) for 2157 atoms. Found 2 (10 requested) and removed 5 (5 requested) atoms. Cycle 33: After refmac, R = 0.1896 (Rfree = 0.000) for 2149 atoms. Found 3 (10 requested) and removed 5 (5 requested) atoms. Cycle 34: After refmac, R = 0.2008 (Rfree = 0.000) for 2144 atoms. Found 5 (10 requested) and removed 6 (5 requested) atoms. Cycle 35: After refmac, R = 0.2025 (Rfree = 0.000) for 2138 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.64 3.36 Search for helices and strands: 0 residues in 0 chains, 2165 seeds are put forward NCS extension: 0 residues added, 2165 seeds are put forward Round 1: 102 peptides, 21 chains. Longest chain 8 peptides. Score 0.265 Round 2: 106 peptides, 17 chains. Longest chain 10 peptides. Score 0.371 Round 3: 114 peptides, 21 chains. Longest chain 8 peptides. Score 0.325 Round 4: 111 peptides, 20 chains. Longest chain 8 peptides. Score 0.331 Round 5: 103 peptides, 18 chains. Longest chain 11 peptides. Score 0.335 Taking the results from Round 2 Chains 17, Residues 89, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3336 reflections ( 97.60 % complete ) and 5144 restraints for refining 2144 atoms. 4805 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2101 (Rfree = 0.000) for 2144 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. Cycle 37: After refmac, R = 0.2144 (Rfree = 0.000) for 2135 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Cycle 38: After refmac, R = 0.2023 (Rfree = 0.000) for 2124 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 39: After refmac, R = 0.2083 (Rfree = 0.000) for 2108 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Cycle 40: After refmac, R = 0.2097 (Rfree = 0.000) for 2094 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.63 3.35 Search for helices and strands: 0 residues in 0 chains, 2166 seeds are put forward NCS extension: 9 residues added (0 deleted due to clashes), 2175 seeds are put forward Round 1: 96 peptides, 21 chains. Longest chain 7 peptides. Score 0.234 Round 2: 108 peptides, 21 chains. Longest chain 10 peptides. Score 0.296 Round 3: 117 peptides, 22 chains. Longest chain 11 peptides. Score 0.319 Round 4: 111 peptides, 21 chains. Longest chain 10 peptides. Score 0.310 Round 5: 111 peptides, 19 chains. Longest chain 14 peptides. Score 0.352 Taking the results from Round 5 Chains 19, Residues 92, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3336 reflections ( 97.60 % complete ) and 4933 restraints for refining 2103 atoms. 4584 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2028 (Rfree = 0.000) for 2103 atoms. Found 9 (9 requested) and removed 15 (4 requested) atoms. Cycle 42: After refmac, R = 0.2100 (Rfree = 0.000) for 2083 atoms. Found 9 (9 requested) and removed 65 (4 requested) atoms. Cycle 43: After refmac, R = 0.1960 (Rfree = 0.000) for 2014 atoms. Found 9 (9 requested) and removed 23 (4 requested) atoms. Cycle 44: After refmac, R = 0.2010 (Rfree = 0.000) for 1989 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. Cycle 45: After refmac, R = 0.1939 (Rfree = 0.000) for 1987 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.59 3.31 Search for helices and strands: 0 residues in 0 chains, 2052 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 2074 seeds are put forward Round 1: 75 peptides, 18 chains. Longest chain 5 peptides. Score 0.185 Round 2: 96 peptides, 20 chains. Longest chain 6 peptides. Score 0.256 Round 3: 94 peptides, 17 chains. Longest chain 10 peptides. Score 0.312 Round 4: 97 peptides, 18 chains. Longest chain 9 peptides. Score 0.305 Round 5: 103 peptides, 18 chains. Longest chain 10 peptides. Score 0.335 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 18, Residues 85, 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 2ig6-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3336 reflections ( 97.60 % complete ) and 4503 restraints for refining 2013 atoms. 4181 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2193 (Rfree = 0.000) for 2013 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.2183 (Rfree = 0.000) for 1988 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.2142 (Rfree = 0.000) for 1970 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.1989 (Rfree = 0.000) for 1953 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 07:58:00 GMT 2018 Job finished. TimeTaking 28.61 Used memory is bytes: 22307536