Sun 23 Dec 22:23:02 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 1vlm-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vlm-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vlm-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vlm-3.4-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/1vlm-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vlm-3.4-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 ============================================================ Sun 23 Dec 22:23:12 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/1vlm-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vlm-3.4-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 307 and 0 Target number of residues in the AU: 307 Target solvent content: 0.6190 Checking the provided sequence file Detected sequence length: 219 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 438 Adjusted target solvent content: 0.46 Input MTZ file: 1vlm-3.4-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: 18 Cell parameters: 65.648 70.734 93.922 90.000 90.000 90.000 Input sequence file: 1vlm-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 3504 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: 93.922 3.400 Wilson plot Bfac: 60.57 6393 reflections ( 99.72 % complete ) and 0 restraints for refining 3898 atoms. Observations/parameters ratio is 0.41 ------------------------------------------------------ Starting model: R = 0.3170 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2898 (Rfree = 0.000) for 3898 atoms. Found 29 (29 requested) and removed 112 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.24 3.42 Search for helices and strands: 0 residues in 0 chains, 3880 seeds are put forward NCS extension: 0 residues added, 3880 seeds are put forward Round 1: 175 peptides, 35 chains. Longest chain 16 peptides. Score 0.314 Round 2: 217 peptides, 35 chains. Longest chain 16 peptides. Score 0.467 Round 3: 223 peptides, 33 chains. Longest chain 19 peptides. Score 0.515 Round 4: 248 peptides, 34 chains. Longest chain 21 peptides. Score 0.576 Round 5: 245 peptides, 35 chains. Longest chain 25 peptides. Score 0.555 Taking the results from Round 4 Chains 34, Residues 214, Estimated correctness of the model 20.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6393 reflections ( 99.72 % complete ) and 7086 restraints for refining 3186 atoms. 6264 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2471 (Rfree = 0.000) for 3186 atoms. Found 22 (24 requested) and removed 42 (12 requested) atoms. Cycle 2: After refmac, R = 0.2356 (Rfree = 0.000) for 3136 atoms. Found 8 (23 requested) and removed 30 (11 requested) atoms. Cycle 3: After refmac, R = 0.2270 (Rfree = 0.000) for 3098 atoms. Found 8 (23 requested) and removed 25 (11 requested) atoms. Cycle 4: After refmac, R = 0.2265 (Rfree = 0.000) for 3067 atoms. Found 17 (23 requested) and removed 18 (11 requested) atoms. Failed to save intermediate PDB Cycle 5: After refmac, R = 0.2116 (Rfree = 0.000) for 3059 atoms. Found 12 (23 requested) and removed 27 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.23 3.41 Search for helices and strands: 0 residues in 0 chains, 3165 seeds are put forward NCS extension: 34 residues added (0 deleted due to clashes), 3199 seeds are put forward Round 1: 201 peptides, 35 chains. Longest chain 13 peptides. Score 0.412 Round 2: 225 peptides, 32 chains. Longest chain 23 peptides. Score 0.535 Round 3: 225 peptides, 28 chains. Longest chain 31 peptides. Score 0.587 Round 4: 235 peptides, 30 chains. Longest chain 18 peptides. Score 0.590 Round 5: 222 peptides, 31 chains. Longest chain 28 peptides. Score 0.539 Taking the results from Round 4 Chains 31, Residues 205, Estimated correctness of the model 25.4 % 3 chains (22 residues) have been docked in sequence ------------------------------------------------------ 6393 reflections ( 99.72 % complete ) and 6897 restraints for refining 3155 atoms. 6017 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2338 (Rfree = 0.000) for 3155 atoms. Found 13 (23 requested) and removed 33 (11 requested) atoms. Cycle 7: After refmac, R = 0.2333 (Rfree = 0.000) for 3117 atoms. Found 23 (23 requested) and removed 30 (11 requested) atoms. Cycle 8: After refmac, R = 0.2245 (Rfree = 0.000) for 3105 atoms. Found 12 (23 requested) and removed 26 (11 requested) atoms. Cycle 9: After refmac, R = 0.2245 (Rfree = 0.000) for 3088 atoms. Found 12 (23 requested) and removed 20 (11 requested) atoms. Cycle 10: After refmac, R = 0.2180 (Rfree = 0.000) for 3076 atoms. Found 11 (23 requested) and removed 22 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.23 3.41 Search for helices and strands: 0 residues in 0 chains, 3166 seeds are put forward NCS extension: 11 residues added (3 deleted due to clashes), 3177 seeds are put forward Round 1: 196 peptides, 31 chains. Longest chain 18 peptides. Score 0.455 Round 2: 224 peptides, 35 chains. Longest chain 16 peptides. Score 0.490 Round 3: 230 peptides, 33 chains. Longest chain 21 peptides. Score 0.537 Round 4: 218 peptides, 31 chains. Longest chain 19 peptides. Score 0.527 Round 5: 227 peptides, 35 chains. Longest chain 15 peptides. Score 0.500 Taking the results from Round 3 Chains 33, Residues 197, Estimated correctness of the model 6.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6393 reflections ( 99.72 % complete ) and 7199 restraints for refining 3163 atoms. 6444 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2184 (Rfree = 0.000) for 3163 atoms. Found 12 (23 requested) and removed 34 (11 requested) atoms. Cycle 12: After refmac, R = 0.2252 (Rfree = 0.000) for 3136 atoms. Found 12 (23 requested) and removed 26 (11 requested) atoms. Cycle 13: After refmac, R = 0.2239 (Rfree = 0.000) for 3117 atoms. Found 10 (23 requested) and removed 20 (11 requested) atoms. Cycle 14: After refmac, R = 0.2240 (Rfree = 0.000) for 3105 atoms. Found 18 (23 requested) and removed 15 (11 requested) atoms. Cycle 15: After refmac, R = 0.2202 (Rfree = 0.000) for 3103 atoms. Found 13 (23 requested) and removed 16 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.22 3.40 Search for helices and strands: 0 residues in 0 chains, 3236 seeds are put forward NCS extension: 27 residues added (1 deleted due to clashes), 3263 seeds are put forward Round 1: 204 peptides, 34 chains. Longest chain 13 peptides. Score 0.438 Round 2: 226 peptides, 32 chains. Longest chain 19 peptides. Score 0.538 Round 3: 223 peptides, 30 chains. Longest chain 15 peptides. Score 0.556 Round 4: 229 peptides, 31 chains. Longest chain 20 peptides. Score 0.560 Round 5: 241 peptides, 33 chains. Longest chain 15 peptides. Score 0.569 Taking the results from Round 5 Chains 34, Residues 208, Estimated correctness of the model 18.2 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 6393 reflections ( 99.72 % complete ) and 7088 restraints for refining 3186 atoms. 6244 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2388 (Rfree = 0.000) for 3186 atoms. Found 24 (24 requested) and removed 28 (12 requested) atoms. Cycle 17: After refmac, R = 0.2235 (Rfree = 0.000) for 3172 atoms. Found 8 (24 requested) and removed 31 (12 requested) atoms. Cycle 18: After refmac, R = 0.2160 (Rfree = 0.000) for 3143 atoms. Found 23 (23 requested) and removed 40 (11 requested) atoms. Cycle 19: After refmac, R = 0.2147 (Rfree = 0.000) for 3121 atoms. Found 9 (23 requested) and removed 20 (11 requested) atoms. Cycle 20: After refmac, R = 0.2130 (Rfree = 0.000) for 3105 atoms. Found 10 (23 requested) and removed 20 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.24 3.42 Search for helices and strands: 0 residues in 0 chains, 3195 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 3208 seeds are put forward Round 1: 174 peptides, 32 chains. Longest chain 14 peptides. Score 0.359 Round 2: 199 peptides, 30 chains. Longest chain 13 peptides. Score 0.480 Round 3: 199 peptides, 30 chains. Longest chain 14 peptides. Score 0.480 Round 4: 203 peptides, 31 chains. Longest chain 18 peptides. Score 0.479 Round 5: 211 peptides, 31 chains. Longest chain 12 peptides. Score 0.505 Taking the results from Round 5 Chains 31, Residues 180, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6393 reflections ( 99.72 % complete ) and 7487 restraints for refining 3186 atoms. 6798 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2313 (Rfree = 0.000) for 3186 atoms. Found 24 (24 requested) and removed 28 (12 requested) atoms. Cycle 22: After refmac, R = 0.2213 (Rfree = 0.000) for 3174 atoms. Found 21 (24 requested) and removed 26 (12 requested) atoms. Cycle 23: After refmac, R = 0.2141 (Rfree = 0.000) for 3163 atoms. Found 15 (23 requested) and removed 26 (11 requested) atoms. Cycle 24: After refmac, R = 0.2160 (Rfree = 0.000) for 3150 atoms. Found 16 (23 requested) and removed 25 (11 requested) atoms. Cycle 25: After refmac, R = 0.2169 (Rfree = 0.000) for 3138 atoms. Found 15 (23 requested) and removed 19 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.22 3.40 Search for helices and strands: 0 residues in 0 chains, 3226 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 3238 seeds are put forward Round 1: 175 peptides, 36 chains. Longest chain 12 peptides. Score 0.297 Round 2: 206 peptides, 32 chains. Longest chain 14 peptides. Score 0.474 Round 3: 207 peptides, 34 chains. Longest chain 14 peptides. Score 0.448 Round 4: 208 peptides, 34 chains. Longest chain 13 peptides. Score 0.451 Round 5: 224 peptides, 33 chains. Longest chain 20 peptides. Score 0.518 Taking the results from Round 5 Chains 33, Residues 191, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 6393 reflections ( 99.72 % complete ) and 7317 restraints for refining 3186 atoms. 6562 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2443 (Rfree = 0.000) for 3186 atoms. Found 24 (24 requested) and removed 35 (12 requested) atoms. Cycle 27: After refmac, R = 0.2229 (Rfree = 0.000) for 3157 atoms. Found 15 (23 requested) and removed 21 (11 requested) atoms. Cycle 28: After refmac, R = 0.2176 (Rfree = 0.000) for 3138 atoms. Found 16 (23 requested) and removed 19 (11 requested) atoms. Cycle 29: After refmac, R = 0.2092 (Rfree = 0.000) for 3126 atoms. Found 13 (23 requested) and removed 12 (11 requested) atoms. Cycle 30: After refmac, R = 0.2088 (Rfree = 0.000) for 3124 atoms. Found 22 (23 requested) and removed 18 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.24 3.42 Search for helices and strands: 0 residues in 0 chains, 3214 seeds are put forward NCS extension: 18 residues added (4 deleted due to clashes), 3232 seeds are put forward Round 1: 160 peptides, 32 chains. Longest chain 8 peptides. Score 0.304 Round 2: 176 peptides, 34 chains. Longest chain 12 peptides. Score 0.334 Round 3: 177 peptides, 31 chains. Longest chain 10 peptides. Score 0.387 Round 4: 169 peptides, 32 chains. Longest chain 9 peptides. Score 0.340 Round 5: 176 peptides, 32 chains. Longest chain 9 peptides. Score 0.367 Taking the results from Round 3 Chains 31, Residues 146, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 6393 reflections ( 99.72 % complete ) and 7663 restraints for refining 3186 atoms. 7079 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2246 (Rfree = 0.000) for 3186 atoms. Found 19 (24 requested) and removed 28 (12 requested) atoms. Cycle 32: After refmac, R = 0.2118 (Rfree = 0.000) for 3173 atoms. Found 17 (23 requested) and removed 13 (11 requested) atoms. Cycle 33: After refmac, R = 0.2234 (Rfree = 0.000) for 3171 atoms. Found 23 (23 requested) and removed 19 (11 requested) atoms. Cycle 34: After refmac, R = 0.2049 (Rfree = 0.000) for 3173 atoms. Found 12 (23 requested) and removed 16 (11 requested) atoms. Cycle 35: After refmac, R = 0.2101 (Rfree = 0.000) for 3166 atoms. Found 18 (23 requested) and removed 17 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.23 3.41 Search for helices and strands: 0 residues in 0 chains, 3270 seeds are put forward NCS extension: 9 residues added (0 deleted due to clashes), 3279 seeds are put forward Round 1: 156 peptides, 31 chains. Longest chain 10 peptides. Score 0.305 Round 2: 179 peptides, 31 chains. Longest chain 12 peptides. Score 0.394 Round 3: 182 peptides, 30 chains. Longest chain 10 peptides. Score 0.421 Round 4: 181 peptides, 31 chains. Longest chain 12 peptides. Score 0.402 Round 5: 198 peptides, 34 chains. Longest chain 11 peptides. Score 0.416 Taking the results from Round 3 Chains 30, Residues 152, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6393 reflections ( 99.72 % complete ) and 7519 restraints for refining 3186 atoms. 6941 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2161 (Rfree = 0.000) for 3186 atoms. Found 15 (24 requested) and removed 33 (12 requested) atoms. Cycle 37: After refmac, R = 0.2111 (Rfree = 0.000) for 3157 atoms. Found 23 (23 requested) and removed 25 (11 requested) atoms. Cycle 38: After refmac, R = 0.2014 (Rfree = 0.000) for 3152 atoms. Found 15 (23 requested) and removed 20 (11 requested) atoms. Cycle 39: After refmac, R = 0.1974 (Rfree = 0.000) for 3142 atoms. Found 19 (23 requested) and removed 12 (11 requested) atoms. Cycle 40: After refmac, R = 0.1994 (Rfree = 0.000) for 3145 atoms. Found 13 (23 requested) and removed 21 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.20 3.38 Search for helices and strands: 0 residues in 0 chains, 3221 seeds are put forward NCS extension: 10 residues added (2 deleted due to clashes), 3231 seeds are put forward Round 1: 153 peptides, 27 chains. Longest chain 13 peptides. Score 0.361 Round 2: 156 peptides, 29 chains. Longest chain 9 peptides. Score 0.339 Round 3: 163 peptides, 27 chains. Longest chain 12 peptides. Score 0.399 Round 4: 170 peptides, 27 chains. Longest chain 14 peptides. Score 0.425 Round 5: 180 peptides, 28 chains. Longest chain 13 peptides. Score 0.445 Taking the results from Round 5 Chains 28, Residues 152, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6393 reflections ( 99.72 % complete ) and 7528 restraints for refining 3186 atoms. 6948 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2261 (Rfree = 0.000) for 3186 atoms. Found 20 (24 requested) and removed 23 (12 requested) atoms. Cycle 42: After refmac, R = 0.2052 (Rfree = 0.000) for 3179 atoms. Found 22 (24 requested) and removed 20 (12 requested) atoms. Cycle 43: After refmac, R = 0.1985 (Rfree = 0.000) for 3174 atoms. Found 22 (24 requested) and removed 28 (12 requested) atoms. Cycle 44: After refmac, R = 0.1854 (Rfree = 0.000) for 3166 atoms. Found 11 (23 requested) and removed 17 (11 requested) atoms. Cycle 45: After refmac, R = 0.1855 (Rfree = 0.000) for 3156 atoms. Found 10 (23 requested) and removed 16 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.22 3.40 Search for helices and strands: 0 residues in 0 chains, 3229 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 3247 seeds are put forward Round 1: 124 peptides, 26 chains. Longest chain 9 peptides. Score 0.259 Round 2: 134 peptides, 26 chains. Longest chain 10 peptides. Score 0.302 Round 3: 136 peptides, 25 chains. Longest chain 10 peptides. Score 0.328 Round 4: 153 peptides, 26 chains. Longest chain 14 peptides. Score 0.378 Round 5: 162 peptides, 26 chains. Longest chain 11 peptides. Score 0.412 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 26, Residues 136, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence Sequence coverage is 6 % Consider running further cycles of model building using 1vlm-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 51 A and 59 A 25 chains (142 residues) following loop building 1 chains (16 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6393 reflections ( 99.72 % complete ) and 7583 restraints for refining 3186 atoms. 7014 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2251 (Rfree = 0.000) for 3186 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 47: After refmac, R = 0.2248 (Rfree = 0.000) for 3165 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 48: After refmac, R = 0.2084 (Rfree = 0.000) for 3151 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 49: After refmac, R = 0.1970 (Rfree = 0.000) for 3136 atoms. TimeTaking 52.73