Tue 25 Dec 19:27:57 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 1vpy-2.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vpy-2.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vpy-2.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vpy-2.4-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/1vpy-2.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vpy-2.4-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 ============================================================ Tue 25 Dec 19:28:06 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/1vpy-2.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vpy-2.4-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 328 and 0 Target number of residues in the AU: 328 Target solvent content: 0.5490 Checking the provided sequence file Detected sequence length: 289 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 289 Adjusted target solvent content: 0.60 Input MTZ file: 1vpy-2.4-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: 170 Cell parameters: 114.136 114.136 52.333 90.000 90.000 120.000 Input sequence file: 1vpy-2.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 2312 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 Loops will be built when appropriate and at the last cycle Resolution range: 98.845 2.400 Wilson plot Bfac: 35.21 15417 reflections ( 99.92 % complete ) and 0 restraints for refining 2547 atoms. Observations/parameters ratio is 1.51 ------------------------------------------------------ Starting model: R = 0.3099 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2505 (Rfree = 0.000) for 2547 atoms. Found 47 (51 requested) and removed 38 (25 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.53 2.21 Round 1: 173 peptides, 26 chains. Longest chain 13 peptides. Score 0.473 Round 2: 186 peptides, 21 chains. Longest chain 18 peptides. Score 0.595 Round 3: 185 peptides, 16 chains. Longest chain 21 peptides. Score 0.662 Round 4: 196 peptides, 17 chains. Longest chain 24 peptides. Score 0.678 Round 5: 207 peptides, 16 chains. Longest chain 32 peptides. Score 0.717 Taking the results from Round 5 Chains 16, Residues 191, Estimated correctness of the model 87.4 % 5 chains (87 residues) have been docked in sequence Building loops using Loopy2018 16 chains (191 residues) following loop building 5 chains (87 residues) in sequence following loop building ------------------------------------------------------ 15417 reflections ( 99.92 % complete ) and 3738 restraints for refining 2178 atoms. 2623 conditional restraints added. Observations/parameters ratio is 1.77 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2924 (Rfree = 0.000) for 2178 atoms. Found 44 (44 requested) and removed 24 (22 requested) atoms. Cycle 2: After refmac, R = 0.2800 (Rfree = 0.000) for 2193 atoms. Found 38 (43 requested) and removed 23 (22 requested) atoms. Cycle 3: After refmac, R = 0.2757 (Rfree = 0.000) for 2202 atoms. Found 31 (42 requested) and removed 28 (22 requested) atoms. Cycle 4: After refmac, R = 0.2589 (Rfree = 0.000) for 2199 atoms. Found 30 (41 requested) and removed 25 (22 requested) atoms. Cycle 5: After refmac, R = 0.2549 (Rfree = 0.000) for 2200 atoms. Found 32 (40 requested) and removed 25 (22 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.50 2.18 Round 1: 203 peptides, 18 chains. Longest chain 25 peptides. Score 0.684 Round 2: 213 peptides, 13 chains. Longest chain 32 peptides. Score 0.764 Round 3: 220 peptides, 12 chains. Longest chain 32 peptides. Score 0.787 Round 4: 226 peptides, 13 chains. Longest chain 41 peptides. Score 0.788 Round 5: 217 peptides, 11 chains. Longest chain 51 peptides. Score 0.791 Taking the results from Round 5 Chains 16, Residues 206, Estimated correctness of the model 92.8 % 7 chains (166 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 53 A and 59 A Built loop between residues 125 A and 136 A Built loop between residues 152 A and 163 A 9 chains (220 residues) following loop building 4 chains (191 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 15417 reflections ( 99.92 % complete ) and 2684 restraints for refining 2254 atoms. 1022 conditional restraints added. Observations/parameters ratio is 1.71 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2824 (Rfree = 0.000) for 2254 atoms. Found 40 (40 requested) and removed 37 (22 requested) atoms. Cycle 7: After refmac, R = 0.2588 (Rfree = 0.000) for 2249 atoms. Found 40 (40 requested) and removed 27 (22 requested) atoms. Cycle 8: After refmac, R = 0.2446 (Rfree = 0.000) for 2260 atoms. Found 37 (40 requested) and removed 26 (23 requested) atoms. Cycle 9: After refmac, R = 0.2369 (Rfree = 0.000) for 2268 atoms. Found 39 (39 requested) and removed 24 (23 requested) atoms. Cycle 10: After refmac, R = 0.2345 (Rfree = 0.000) for 2281 atoms. Found 38 (38 requested) and removed 26 (23 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.52 2.20 Round 1: 214 peptides, 14 chains. Longest chain 36 peptides. Score 0.755 Round 2: 221 peptides, 12 chains. Longest chain 51 peptides. Score 0.789 Round 3: 226 peptides, 10 chains. Longest chain 38 peptides. Score 0.816 Round 4: 230 peptides, 13 chains. Longest chain 39 peptides. Score 0.796 Round 5: 228 peptides, 13 chains. Longest chain 36 peptides. Score 0.792 Taking the results from Round 3 Chains 10, Residues 216, Estimated correctness of the model 94.3 % 8 chains (201 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 55 A and 59 A Built loop between residues 91 A and 95 A Built loop between residues 127 A and 136 A Built loop between residues 156 A and 162 A Built loop between residues 239 A and 242 A 5 chains (237 residues) following loop building 3 chains (222 residues) in sequence following loop building ------------------------------------------------------ 15417 reflections ( 99.92 % complete ) and 2458 restraints for refining 2305 atoms. 534 conditional restraints added. Observations/parameters ratio is 1.67 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2598 (Rfree = 0.000) for 2305 atoms. Found 37 (37 requested) and removed 35 (23 requested) atoms. Failed to save intermediate PDB Cycle 12: After refmac, R = 0.2418 (Rfree = 0.000) for 2304 atoms. Found 37 (37 requested) and removed 27 (23 requested) atoms. Failed to save intermediate PDB Cycle 13: After refmac, R = 0.2330 (Rfree = 0.000) for 2311 atoms. Found 36 (36 requested) and removed 24 (23 requested) atoms. Failed to save intermediate PDB Cycle 14: After refmac, R = 0.2259 (Rfree = 0.000) for 2321 atoms. Found 35 (35 requested) and removed 28 (23 requested) atoms. Cycle 15: After refmac, R = 0.2186 (Rfree = 0.000) for 2326 atoms. Found 34 (34 requested) and removed 29 (23 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.50 2.18 Round 1: 227 peptides, 12 chains. Longest chain 37 peptides. Score 0.800 Round 2: 230 peptides, 11 chains. Longest chain 53 peptides. Score 0.814 Round 3: 229 peptides, 10 chains. Longest chain 51 peptides. Score 0.821 Round 4: 235 peptides, 8 chains. Longest chain 56 peptides. Score 0.846 Round 5: 226 peptides, 11 chains. Longest chain 54 peptides. Score 0.807 Taking the results from Round 4 Chains 11, Residues 227, Estimated correctness of the model 95.9 % 7 chains (207 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 62 A and 68 A Built loop between residues 77 A and 80 A Built loop between residues 106 A and 113 A Built loop between residues 167 A and 172 A Built loop between residues 258 A and 261 A 4 chains (241 residues) following loop building 2 chains (226 residues) in sequence following loop building ------------------------------------------------------ 15417 reflections ( 99.92 % complete ) and 2369 restraints for refining 2265 atoms. 414 conditional restraints added. Observations/parameters ratio is 1.70 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2289 (Rfree = 0.000) for 2265 atoms. Found 32 (32 requested) and removed 27 (23 requested) atoms. Cycle 17: After refmac, R = 0.2110 (Rfree = 0.000) for 2266 atoms. Found 31 (31 requested) and removed 24 (23 requested) atoms. Cycle 18: After refmac, R = 0.2058 (Rfree = 0.000) for 2270 atoms. Found 30 (30 requested) and removed 24 (23 requested) atoms. Cycle 19: After refmac, R = 0.1981 (Rfree = 0.000) for 2273 atoms. Found 29 (29 requested) and removed 24 (23 requested) atoms. Cycle 20: After refmac, R = 0.1912 (Rfree = 0.000) for 2277 atoms. Found 29 (29 requested) and removed 26 (23 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.50 2.18 Round 1: 235 peptides, 11 chains. Longest chain 46 peptides. Score 0.822 Round 2: 239 peptides, 8 chains. Longest chain 54 peptides. Score 0.852 Round 3: 239 peptides, 10 chains. Longest chain 47 peptides. Score 0.836 Round 4: 237 peptides, 11 chains. Longest chain 36 peptides. Score 0.825 Round 5: 240 peptides, 7 chains. Longest chain 78 peptides. Score 0.861 Taking the results from Round 5 Chains 8, Residues 233, Estimated correctness of the model 96.6 % 6 chains (221 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 58 A and 61 A Built loop between residues 105 A and 108 A Built loop between residues 184 A and 187 A Built loop between residues 259 A and 263 A 4 chains (242 residues) following loop building 2 chains (230 residues) in sequence following loop building ------------------------------------------------------ 15417 reflections ( 99.92 % complete ) and 2400 restraints for refining 2284 atoms. 420 conditional restraints added. Observations/parameters ratio is 1.69 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2337 (Rfree = 0.000) for 2284 atoms. Found 28 (28 requested) and removed 32 (23 requested) atoms. Failed to save intermediate PDB Cycle 22: After refmac, R = 0.2157 (Rfree = 0.000) for 2279 atoms. Found 27 (27 requested) and removed 25 (23 requested) atoms. Failed to save intermediate PDB Cycle 23: After refmac, R = 0.2070 (Rfree = 0.000) for 2278 atoms. Found 26 (26 requested) and removed 25 (23 requested) atoms. Cycle 24: After refmac, R = 0.2023 (Rfree = 0.000) for 2278 atoms. Found 25 (25 requested) and removed 24 (23 requested) atoms. Cycle 25: After refmac, R = 0.1978 (Rfree = 0.000) for 2279 atoms. Found 24 (24 requested) and removed 26 (23 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.49 2.18 Round 1: 236 peptides, 10 chains. Longest chain 67 peptides. Score 0.832 Round 2: 244 peptides, 5 chains. Longest chain 133 peptides. Score 0.880 Round 3: 238 peptides, 9 chains. Longest chain 39 peptides. Score 0.843 Round 4: 238 peptides, 7 chains. Longest chain 67 peptides. Score 0.858 Round 5: 236 peptides, 10 chains. Longest chain 59 peptides. Score 0.832 Taking the results from Round 2 Chains 6, Residues 239, Estimated correctness of the model 97.4 % 4 chains (227 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 165 A and 168 A Built loop between residues 192 A and 195 A Built loop between residues 211 A and 222 A 2 chains (252 residues) following loop building 1 chains (241 residues) in sequence following loop building ------------------------------------------------------ 15417 reflections ( 99.92 % complete ) and 2396 restraints for refining 2320 atoms. 324 conditional restraints added. Observations/parameters ratio is 1.66 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2299 (Rfree = 0.000) for 2320 atoms. Found 23 (23 requested) and removed 32 (23 requested) atoms. Cycle 27: After refmac, R = 0.2063 (Rfree = 0.000) for 2308 atoms. Found 23 (23 requested) and removed 27 (23 requested) atoms. Cycle 28: After refmac, R = 0.1986 (Rfree = 0.000) for 2303 atoms. Found 23 (23 requested) and removed 28 (23 requested) atoms. Cycle 29: After refmac, R = 0.1953 (Rfree = 0.000) for 2297 atoms. Found 23 (23 requested) and removed 24 (23 requested) atoms. Cycle 30: After refmac, R = 0.1942 (Rfree = 0.000) for 2294 atoms. Found 23 (23 requested) and removed 25 (23 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.48 2.17 Round 1: 239 peptides, 8 chains. Longest chain 56 peptides. Score 0.852 Round 2: 237 peptides, 11 chains. Longest chain 54 peptides. Score 0.825 Round 3: 238 peptides, 6 chains. Longest chain 74 peptides. Score 0.866 Round 4: 231 peptides, 13 chains. Longest chain 51 peptides. Score 0.797 Round 5: 236 peptides, 7 chains. Longest chain 51 peptides. Score 0.856 Taking the results from Round 3 Chains 7, Residues 232, Estimated correctness of the model 96.8 % 5 chains (223 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 90 A and 93 A Built loop between residues 165 A and 168 A Built loop between residues 192 A and 195 A 4 chains (238 residues) following loop building 2 chains (229 residues) in sequence following loop building ------------------------------------------------------ 15417 reflections ( 99.92 % complete ) and 2395 restraints for refining 2244 atoms. 441 conditional restraints added. Observations/parameters ratio is 1.72 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2227 (Rfree = 0.000) for 2244 atoms. Found 22 (22 requested) and removed 24 (22 requested) atoms. Cycle 32: After refmac, R = 0.2124 (Rfree = 0.000) for 2241 atoms. Found 22 (22 requested) and removed 26 (22 requested) atoms. Cycle 33: After refmac, R = 0.2058 (Rfree = 0.000) for 2236 atoms. Found 22 (22 requested) and removed 26 (22 requested) atoms. Cycle 34: After refmac, R = 0.2021 (Rfree = 0.000) for 2232 atoms. Found 22 (22 requested) and removed 24 (22 requested) atoms. Failed to save intermediate PDB Cycle 35: After refmac, R = 0.1976 (Rfree = 0.000) for 2229 atoms. Found 22 (22 requested) and removed 26 (22 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.50 2.18 Round 1: 230 peptides, 9 chains. Longest chain 51 peptides. Score 0.831 Round 2: 233 peptides, 8 chains. Longest chain 55 peptides. Score 0.844 Round 3: 233 peptides, 10 chains. Longest chain 52 peptides. Score 0.827 Round 4: 235 peptides, 11 chains. Longest chain 61 peptides. Score 0.822 Round 5: 237 peptides, 9 chains. Longest chain 54 peptides. Score 0.841 Taking the results from Round 2 Chains 14, Residues 225, Estimated correctness of the model 95.8 % 7 chains (201 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 55 A and 58 A Built loop between residues 84 A and 87 A Built loop between residues 140 A and 144 A Built loop between residues 257 A and 264 A 8 chains (232 residues) following loop building 3 chains (214 residues) in sequence following loop building ------------------------------------------------------ 15417 reflections ( 99.92 % complete ) and 2450 restraints for refining 2193 atoms. 595 conditional restraints added. Observations/parameters ratio is 1.76 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2195 (Rfree = 0.000) for 2193 atoms. Found 22 (22 requested) and removed 25 (22 requested) atoms. Cycle 37: After refmac, R = 0.2085 (Rfree = 0.000) for 2189 atoms. Found 22 (22 requested) and removed 23 (22 requested) atoms. Cycle 38: After refmac, R = 0.2044 (Rfree = 0.000) for 2188 atoms. Found 22 (22 requested) and removed 27 (22 requested) atoms. Cycle 39: After refmac, R = 0.2002 (Rfree = 0.000) for 2183 atoms. Found 22 (22 requested) and removed 26 (22 requested) atoms. Cycle 40: After refmac, R = 0.1936 (Rfree = 0.000) for 2179 atoms. Found 22 (22 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.50 2.18 Round 1: 228 peptides, 7 chains. Longest chain 62 peptides. Score 0.845 Round 2: 234 peptides, 9 chains. Longest chain 51 peptides. Score 0.837 Round 3: 232 peptides, 7 chains. Longest chain 74 peptides. Score 0.850 Round 4: 234 peptides, 12 chains. Longest chain 53 peptides. Score 0.811 Round 5: 239 peptides, 6 chains. Longest chain 86 peptides. Score 0.867 Taking the results from Round 5 Chains 6, Residues 233, Estimated correctness of the model 96.8 % 4 chains (208 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 192 A and 195 A Built loop between residues 211 A and 222 A 4 chains (245 residues) following loop building 2 chains (220 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 15417 reflections ( 99.92 % complete ) and 2501 restraints for refining 2264 atoms. 555 conditional restraints added. Observations/parameters ratio is 1.70 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2268 (Rfree = 0.000) for 2264 atoms. Found 23 (23 requested) and removed 27 (23 requested) atoms. Cycle 42: After refmac, R = 0.2120 (Rfree = 0.000) for 2260 atoms. Found 23 (23 requested) and removed 25 (23 requested) atoms. Cycle 43: After refmac, R = 0.2060 (Rfree = 0.000) for 2258 atoms. Found 23 (23 requested) and removed 26 (23 requested) atoms. Cycle 44: After refmac, R = 0.2024 (Rfree = 0.000) for 2254 atoms. Found 22 (22 requested) and removed 27 (22 requested) atoms. Cycle 45: After refmac, R = 0.1975 (Rfree = 0.000) for 2249 atoms. Found 22 (22 requested) and removed 23 (22 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.50 2.18 Round 1: 231 peptides, 11 chains. Longest chain 72 peptides. Score 0.815 Round 2: 233 peptides, 8 chains. Longest chain 55 peptides. Score 0.844 Round 3: 235 peptides, 10 chains. Longest chain 73 peptides. Score 0.830 Round 4: 230 peptides, 10 chains. Longest chain 63 peptides. Score 0.822 Round 5: 233 peptides, 13 chains. Longest chain 42 peptides. Score 0.801 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 9, Residues 225, Estimated correctness of the model 95.8 % 6 chains (206 residues) have been docked in sequence Sequence coverage is 91 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 21 A and 34 A Built loop between residues 128 A and 131 A Built loop between residues 184 A and 187 A Built loop between residues 209 A and 222 A 4 chains (251 residues) following loop building 2 chains (234 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 15417 reflections ( 99.92 % complete ) and 2047 restraints for refining 1995 atoms. Observations/parameters ratio is 1.93 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3092 (Rfree = 0.000) for 1995 atoms. Found 15 (20 requested) and removed 0 (20 requested) atoms. Cycle 47: After refmac, R = 0.2849 (Rfree = 0.000) for 1995 atoms. Found 6 (20 requested) and removed 2 (20 requested) atoms. Cycle 48: After refmac, R = 0.2776 (Rfree = 0.000) for 1995 atoms. Found 5 (20 requested) and removed 2 (20 requested) atoms. Cycle 49: After refmac, R = 0.2746 (Rfree = 0.000) for 1995 atoms. Found 1 (20 requested) and removed 1 (20 requested) atoms. Writing output files ... TimeTaking 57.05