null Sun 23 Dec 22:22:46 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 2gno-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2gno-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2gno-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gno-3.6-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/2gno-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gno-3.6-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 ============================================================ Sun 23 Dec 22:22:56 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/2gno-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gno-3.6-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 197 and 0 Target number of residues in the AU: 197 Target solvent content: 0.6737 Checking the provided sequence file Detected sequence length: 305 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 305 Adjusted target solvent content: 0.49 Input MTZ file: 2gno-3.6-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: 79 Cell parameters: 135.560 135.560 35.560 90.000 90.000 90.000 Input sequence file: 2gno-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 2440 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 Loops will be built when appropriate and at the last cycle Resolution range: 95.855 3.602 Wilson plot Bfac: 94.61 3896 reflections ( 98.93 % complete ) and 0 restraints for refining 2711 atoms. Observations/parameters ratio is 0.36 ------------------------------------------------------ Starting model: R = 0.3441 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3557 (Rfree = 0.000) for 2711 atoms. Found 6 (17 requested) and removed 16 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.80 3.85 Search for helices and strands: 0 residues in 0 chains, 2753 seeds are put forward Round 1: 104 peptides, 20 chains. Longest chain 11 peptides. Score 0.310 Round 2: 145 peptides, 22 chains. Longest chain 17 peptides. Score 0.471 Round 3: 152 peptides, 24 chains. Longest chain 11 peptides. Score 0.463 Round 4: 176 peptides, 22 chains. Longest chain 20 peptides. Score 0.598 Round 5: 185 peptides, 23 chains. Longest chain 20 peptides. Score 0.614 Taking the results from Round 5 Chains 23, Residues 162, Estimated correctness of the model 19.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3896 reflections ( 98.93 % complete ) and 4963 restraints for refining 2212 atoms. 4338 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2655 (Rfree = 0.000) for 2212 atoms. Found 6 (14 requested) and removed 17 (7 requested) atoms. Cycle 2: After refmac, R = 0.2468 (Rfree = 0.000) for 2184 atoms. Found 2 (14 requested) and removed 10 (7 requested) atoms. Cycle 3: After refmac, R = 0.2409 (Rfree = 0.000) for 2154 atoms. Found 0 (13 requested) and removed 8 (6 requested) atoms. Cycle 4: After refmac, R = 0.2149 (Rfree = 0.000) for 2134 atoms. Found 2 (13 requested) and removed 7 (6 requested) atoms. Cycle 5: After refmac, R = 0.2075 (Rfree = 0.000) for 2122 atoms. Found 0 (13 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.70 3.75 Search for helices and strands: 0 residues in 0 chains, 2200 seeds are put forward Round 1: 146 peptides, 24 chains. Longest chain 16 peptides. Score 0.435 Round 2: 170 peptides, 21 chains. Longest chain 23 peptides. Score 0.592 Round 3: 176 peptides, 23 chains. Longest chain 24 peptides. Score 0.581 Round 4: 175 peptides, 24 chains. Longest chain 25 peptides. Score 0.560 Round 5: 181 peptides, 21 chains. Longest chain 27 peptides. Score 0.632 Taking the results from Round 5 Chains 21, Residues 160, Estimated correctness of the model 26.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3896 reflections ( 98.93 % complete ) and 4898 restraints for refining 2212 atoms. 4279 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2273 (Rfree = 0.000) for 2212 atoms. Found 5 (14 requested) and removed 12 (7 requested) atoms. Cycle 7: After refmac, R = 0.1984 (Rfree = 0.000) for 2185 atoms. Found 1 (14 requested) and removed 13 (7 requested) atoms. Cycle 8: After refmac, R = 0.2016 (Rfree = 0.000) for 2164 atoms. Found 1 (13 requested) and removed 10 (6 requested) atoms. Cycle 9: After refmac, R = 0.2065 (Rfree = 0.000) for 2145 atoms. Found 1 (13 requested) and removed 8 (6 requested) atoms. Cycle 10: After refmac, R = 0.2031 (Rfree = 0.000) for 2133 atoms. Found 1 (13 requested) and removed 12 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.63 3.68 Search for helices and strands: 0 residues in 0 chains, 2195 seeds are put forward Round 1: 134 peptides, 25 chains. Longest chain 12 peptides. Score 0.356 Round 2: 158 peptides, 23 chains. Longest chain 14 peptides. Score 0.509 Round 3: 155 peptides, 22 chains. Longest chain 14 peptides. Score 0.515 Round 4: 156 peptides, 19 chains. Longest chain 15 peptides. Score 0.574 Round 5: 146 peptides, 19 chains. Longest chain 15 peptides. Score 0.534 Taking the results from Round 4 Chains 19, Residues 137, Estimated correctness of the model 4.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3896 reflections ( 98.93 % complete ) and 5003 restraints for refining 2211 atoms. 4474 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2254 (Rfree = 0.000) for 2211 atoms. Found 7 (14 requested) and removed 12 (7 requested) atoms. Cycle 12: After refmac, R = 0.2156 (Rfree = 0.000) for 2196 atoms. Found 5 (14 requested) and removed 7 (7 requested) atoms. Cycle 13: After refmac, R = 0.2136 (Rfree = 0.000) for 2189 atoms. Found 4 (14 requested) and removed 7 (7 requested) atoms. Cycle 14: After refmac, R = 0.2304 (Rfree = 0.000) for 2180 atoms. Found 8 (14 requested) and removed 10 (7 requested) atoms. Cycle 15: After refmac, R = 0.2383 (Rfree = 0.000) for 2165 atoms. Found 10 (13 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.64 3.69 Search for helices and strands: 0 residues in 0 chains, 2255 seeds are put forward Round 1: 124 peptides, 22 chains. Longest chain 12 peptides. Score 0.370 Round 2: 146 peptides, 25 chains. Longest chain 12 peptides. Score 0.415 Round 3: 160 peptides, 25 chains. Longest chain 12 peptides. Score 0.479 Round 4: 163 peptides, 23 chains. Longest chain 15 peptides. Score 0.530 Round 5: 167 peptides, 24 chains. Longest chain 17 peptides. Score 0.528 Taking the results from Round 4 Chains 23, Residues 140, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3896 reflections ( 98.93 % complete ) and 4947 restraints for refining 2212 atoms. 4410 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2142 (Rfree = 0.000) for 2212 atoms. Found 8 (14 requested) and removed 11 (7 requested) atoms. Cycle 17: After refmac, R = 0.2049 (Rfree = 0.000) for 2188 atoms. Found 7 (14 requested) and removed 13 (7 requested) atoms. Cycle 18: After refmac, R = 0.2521 (Rfree = 0.000) for 2173 atoms. Found 13 (13 requested) and removed 105 (6 requested) atoms. Cycle 19: After refmac, R = 0.2036 (Rfree = 0.000) for 2071 atoms. Found 6 (13 requested) and removed 8 (6 requested) atoms. Cycle 20: After refmac, R = 0.1777 (Rfree = 0.000) for 2057 atoms. Found 3 (13 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.63 3.68 Search for helices and strands: 0 residues in 0 chains, 2130 seeds are put forward Round 1: 116 peptides, 24 chains. Longest chain 11 peptides. Score 0.283 Round 2: 137 peptides, 27 chains. Longest chain 11 peptides. Score 0.328 Round 3: 127 peptides, 22 chains. Longest chain 13 peptides. Score 0.385 Round 4: 117 peptides, 20 chains. Longest chain 14 peptides. Score 0.379 Round 5: 118 peptides, 20 chains. Longest chain 11 peptides. Score 0.384 Taking the results from Round 3 Chains 22, Residues 105, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3896 reflections ( 98.93 % complete ) and 4823 restraints for refining 2128 atoms. 4425 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2132 (Rfree = 0.000) for 2128 atoms. Found 11 (13 requested) and removed 10 (6 requested) atoms. Cycle 22: After refmac, R = 0.1974 (Rfree = 0.000) for 2120 atoms. Found 5 (13 requested) and removed 9 (6 requested) atoms. Cycle 23: After refmac, R = 0.1958 (Rfree = 0.000) for 2109 atoms. Found 5 (13 requested) and removed 9 (6 requested) atoms. Cycle 24: After refmac, R = 0.1815 (Rfree = 0.000) for 2099 atoms. Found 3 (13 requested) and removed 7 (6 requested) atoms. Cycle 25: After refmac, R = 0.1629 (Rfree = 0.000) for 2091 atoms. Found 3 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.67 3.72 Search for helices and strands: 0 residues in 0 chains, 2156 seeds are put forward Round 1: 108 peptides, 23 chains. Longest chain 7 peptides. Score 0.261 Round 2: 129 peptides, 23 chains. Longest chain 9 peptides. Score 0.374 Round 3: 128 peptides, 21 chains. Longest chain 16 peptides. Score 0.412 Round 4: 134 peptides, 21 chains. Longest chain 13 peptides. Score 0.441 Round 5: 131 peptides, 20 chains. Longest chain 11 peptides. Score 0.447 Taking the results from Round 5 Chains 20, Residues 111, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3896 reflections ( 98.93 % complete ) and 4923 restraints for refining 2194 atoms. 4499 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2329 (Rfree = 0.000) for 2194 atoms. Found 6 (14 requested) and removed 17 (7 requested) atoms. Cycle 27: After refmac, R = 0.2161 (Rfree = 0.000) for 2167 atoms. Found 8 (13 requested) and removed 10 (6 requested) atoms. Cycle 28: After refmac, R = 0.2162 (Rfree = 0.000) for 2155 atoms. Found 6 (13 requested) and removed 9 (6 requested) atoms. Cycle 29: After refmac, R = 0.2393 (Rfree = 0.000) for 2143 atoms. Found 8 (13 requested) and removed 9 (6 requested) atoms. Cycle 30: After refmac, R = 0.1957 (Rfree = 0.000) for 2125 atoms. Found 6 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.67 3.72 Search for helices and strands: 0 residues in 0 chains, 2196 seeds are put forward Round 1: 81 peptides, 17 chains. Longest chain 8 peptides. Score 0.250 Round 2: 108 peptides, 22 chains. Longest chain 8 peptides. Score 0.285 Round 3: 118 peptides, 22 chains. Longest chain 9 peptides. Score 0.339 Round 4: 115 peptides, 20 chains. Longest chain 13 peptides. Score 0.368 Round 5: 117 peptides, 21 chains. Longest chain 9 peptides. Score 0.356 Taking the results from Round 4 Chains 20, Residues 95, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3896 reflections ( 98.93 % complete ) and 4900 restraints for refining 2155 atoms. 4540 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1973 (Rfree = 0.000) for 2155 atoms. Found 4 (13 requested) and removed 9 (6 requested) atoms. Cycle 32: After refmac, R = 0.2094 (Rfree = 0.000) for 2138 atoms. Found 2 (13 requested) and removed 7 (6 requested) atoms. Cycle 33: After refmac, R = 0.2066 (Rfree = 0.000) for 2124 atoms. Found 1 (13 requested) and removed 11 (6 requested) atoms. Cycle 34: After refmac, R = 0.1957 (Rfree = 0.000) for 2102 atoms. Found 2 (13 requested) and removed 7 (6 requested) atoms. Cycle 35: After refmac, R = 0.1999 (Rfree = 0.000) for 2093 atoms. Found 4 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.66 3.71 Search for helices and strands: 0 residues in 0 chains, 2149 seeds are put forward Round 1: 99 peptides, 21 chains. Longest chain 8 peptides. Score 0.258 Round 2: 116 peptides, 21 chains. Longest chain 9 peptides. Score 0.351 Round 3: 125 peptides, 23 chains. Longest chain 11 peptides. Score 0.353 Round 4: 104 peptides, 19 chains. Longest chain 10 peptides. Score 0.333 Round 5: 109 peptides, 19 chains. Longest chain 12 peptides. Score 0.360 Taking the results from Round 5 Chains 19, Residues 90, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3896 reflections ( 98.93 % complete ) and 4719 restraints for refining 2109 atoms. 4378 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2131 (Rfree = 0.000) for 2109 atoms. Found 13 (13 requested) and removed 23 (6 requested) atoms. Cycle 37: After refmac, R = 0.1963 (Rfree = 0.000) for 2091 atoms. Found 1 (13 requested) and removed 8 (6 requested) atoms. Cycle 38: After refmac, R = 0.2007 (Rfree = 0.000) for 2081 atoms. Found 5 (13 requested) and removed 8 (6 requested) atoms. Cycle 39: After refmac, R = 0.1957 (Rfree = 0.000) for 2074 atoms. Found 4 (13 requested) and removed 7 (6 requested) atoms. Cycle 40: After refmac, R = 0.1879 (Rfree = 0.000) for 2067 atoms. Found 2 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.65 3.70 Search for helices and strands: 0 residues in 0 chains, 2122 seeds are put forward Round 1: 83 peptides, 19 chains. Longest chain 7 peptides. Score 0.211 Round 2: 100 peptides, 20 chains. Longest chain 8 peptides. Score 0.287 Round 3: 116 peptides, 20 chains. Longest chain 11 peptides. Score 0.373 Round 4: 113 peptides, 21 chains. Longest chain 9 peptides. Score 0.335 Round 5: 112 peptides, 21 chains. Longest chain 10 peptides. Score 0.330 Taking the results from Round 3 Chains 20, Residues 96, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3896 reflections ( 98.93 % complete ) and 4723 restraints for refining 2104 atoms. 4359 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2046 (Rfree = 0.000) for 2104 atoms. Found 7 (13 requested) and removed 11 (6 requested) atoms. Cycle 42: After refmac, R = 0.1831 (Rfree = 0.000) for 2094 atoms. Found 2 (13 requested) and removed 7 (6 requested) atoms. Cycle 43: After refmac, R = 0.1789 (Rfree = 0.000) for 2088 atoms. Found 2 (13 requested) and removed 6 (6 requested) atoms. Cycle 44: After refmac, R = 0.1770 (Rfree = 0.000) for 2083 atoms. Found 1 (13 requested) and removed 6 (6 requested) atoms. Cycle 45: After refmac, R = 0.1753 (Rfree = 0.000) for 2078 atoms. Found 1 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.68 3.73 Search for helices and strands: 0 residues in 0 chains, 2125 seeds are put forward Round 1: 91 peptides, 20 chains. Longest chain 7 peptides. Score 0.235 Round 2: 106 peptides, 20 chains. Longest chain 8 peptides. Score 0.320 Round 3: 109 peptides, 21 chains. Longest chain 7 peptides. Score 0.314 Round 4: 120 peptides, 21 chains. Longest chain 9 peptides. Score 0.372 Round 5: 115 peptides, 21 chains. Longest chain 9 peptides. Score 0.346 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 21, Residues 99, 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 2gno-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3896 reflections ( 98.93 % complete ) and 4825 restraints for refining 2166 atoms. 4450 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2034 (Rfree = 0.000) for 2166 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.2162 (Rfree = 0.000) for 2145 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.2319 (Rfree = 0.000) for 2137 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.2337 (Rfree = 0.000) for 2123 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:09:08 GMT 2018 Job finished. TimeTaking 46.36 Used memory is bytes: 6340152