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 1vjn-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vjn-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vjn-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjn-3.8-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/1vjn-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjn-3.8-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 19:28:12 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/1vjn-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjn-3.8-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 331 and 0 Target number of residues in the AU: 331 Target solvent content: 0.5837 Checking the provided sequence file Detected sequence length: 220 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 440 Adjusted target solvent content: 0.45 Input MTZ file: 1vjn-3.8-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: 1 Cell parameters: 43.059 45.719 63.384 73.681 89.271 64.860 Input sequence file: 1vjn-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 3520 target number of atoms Had to go as low as 0.60 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: 60.370 3.800 Wilson plot Bfac: 46.27 4023 reflections ( 98.05 % complete ) and 0 restraints for refining 3901 atoms. Observations/parameters ratio is 0.26 ------------------------------------------------------ Starting model: R = 0.2827 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2817 (Rfree = 0.000) for 3901 atoms. Found 21 (21 requested) and removed 38 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.18 3.40 Search for helices and strands: 0 residues in 0 chains, 3938 seeds are put forward NCS extension: 0 residues added, 3938 seeds are put forward Round 1: 127 peptides, 27 chains. Longest chain 7 peptides. Score 0.255 Round 2: 178 peptides, 32 chains. Longest chain 11 peptides. Score 0.377 Round 3: 202 peptides, 34 chains. Longest chain 11 peptides. Score 0.433 Round 4: 205 peptides, 35 chains. Longest chain 12 peptides. Score 0.429 Round 5: 205 peptides, 34 chains. Longest chain 11 peptides. Score 0.444 Taking the results from Round 5 Chains 34, Residues 171, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4023 reflections ( 98.05 % complete ) and 7602 restraints for refining 3169 atoms. 6952 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2269 (Rfree = 0.000) for 3169 atoms. Found 17 (17 requested) and removed 37 (8 requested) atoms. Failed to save intermediate PDB Cycle 2: After refmac, R = 0.1981 (Rfree = 0.000) for 3097 atoms. Found 17 (17 requested) and removed 33 (8 requested) atoms. Cycle 3: After refmac, R = 0.1839 (Rfree = 0.000) for 3055 atoms. Found 6 (16 requested) and removed 30 (8 requested) atoms. Cycle 4: After refmac, R = 0.1436 (Rfree = 0.000) for 3024 atoms. Found 6 (16 requested) and removed 18 (8 requested) atoms. Cycle 5: After refmac, R = 0.1541 (Rfree = 0.000) for 3007 atoms. Found 5 (16 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.14 3.36 Search for helices and strands: 0 residues in 0 chains, 3099 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 3113 seeds are put forward Round 1: 163 peptides, 33 chains. Longest chain 11 peptides. Score 0.301 Round 2: 201 peptides, 38 chains. Longest chain 9 peptides. Score 0.367 Round 3: 201 peptides, 37 chains. Longest chain 10 peptides. Score 0.383 Round 4: 206 peptides, 35 chains. Longest chain 12 peptides. Score 0.432 Round 5: 202 peptides, 35 chains. Longest chain 11 peptides. Score 0.418 Taking the results from Round 4 Chains 35, Residues 171, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4023 reflections ( 98.05 % complete ) and 7407 restraints for refining 3085 atoms. 6758 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2007 (Rfree = 0.000) for 3085 atoms. Found 15 (16 requested) and removed 28 (8 requested) atoms. Cycle 7: After refmac, R = 0.1928 (Rfree = 0.000) for 3052 atoms. Found 16 (16 requested) and removed 24 (8 requested) atoms. Cycle 8: After refmac, R = 0.1742 (Rfree = 0.000) for 3028 atoms. Found 12 (16 requested) and removed 23 (8 requested) atoms. Cycle 9: After refmac, R = 0.1661 (Rfree = 0.000) for 3012 atoms. Found 10 (16 requested) and removed 21 (8 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.1331 (Rfree = 0.000) for 2996 atoms. Found 5 (16 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.13 3.35 Search for helices and strands: 0 residues in 0 chains, 3054 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 3068 seeds are put forward Round 1: 182 peptides, 38 chains. Longest chain 10 peptides. Score 0.293 Round 2: 209 peptides, 36 chains. Longest chain 20 peptides. Score 0.428 Round 3: 204 peptides, 36 chains. Longest chain 13 peptides. Score 0.410 Round 4: 209 peptides, 33 chains. Longest chain 14 peptides. Score 0.473 Round 5: 191 peptides, 31 chains. Longest chain 17 peptides. Score 0.440 Taking the results from Round 4 Chains 33, Residues 176, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 4023 reflections ( 98.05 % complete ) and 7152 restraints for refining 3103 atoms. 6481 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1933 (Rfree = 0.000) for 3103 atoms. Found 17 (17 requested) and removed 26 (8 requested) atoms. Cycle 12: After refmac, R = 0.1859 (Rfree = 0.000) for 3080 atoms. Found 10 (17 requested) and removed 14 (8 requested) atoms. Failed to save intermediate PDB Cycle 13: After refmac, R = 0.1841 (Rfree = 0.000) for 3059 atoms. Found 16 (16 requested) and removed 21 (8 requested) atoms. Cycle 14: After refmac, R = 0.1505 (Rfree = 0.000) for 3033 atoms. Found 10 (16 requested) and removed 15 (8 requested) atoms. Failed to save intermediate PDB Cycle 15: After refmac, R = 0.1592 (Rfree = 0.000) for 3018 atoms. Found 13 (16 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.09 3.30 Search for helices and strands: 0 residues in 0 chains, 3097 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 3113 seeds are put forward Round 1: 169 peptides, 34 chains. Longest chain 8 peptides. Score 0.308 Round 2: 209 peptides, 36 chains. Longest chain 12 peptides. Score 0.428 Round 3: 201 peptides, 37 chains. Longest chain 10 peptides. Score 0.383 Round 4: 208 peptides, 34 chains. Longest chain 12 peptides. Score 0.455 Round 5: 205 peptides, 34 chains. Longest chain 12 peptides. Score 0.444 Taking the results from Round 4 Chains 34, Residues 174, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4023 reflections ( 98.05 % complete ) and 7273 restraints for refining 3115 atoms. 6611 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2048 (Rfree = 0.000) for 3115 atoms. Found 17 (17 requested) and removed 27 (8 requested) atoms. Failed to save intermediate PDB Cycle 17: After refmac, R = 0.1880 (Rfree = 0.000) for 3086 atoms. Found 17 (17 requested) and removed 23 (8 requested) atoms. Failed to save intermediate PDB Cycle 18: After refmac, R = 0.1866 (Rfree = 0.000) for 3072 atoms. Found 16 (16 requested) and removed 12 (8 requested) atoms. Cycle 19: After refmac, R = 0.1433 (Rfree = 0.000) for 3071 atoms. Found 7 (16 requested) and removed 12 (8 requested) atoms. Cycle 20: After refmac, R = 0.1369 (Rfree = 0.000) for 3063 atoms. Found 2 (16 requested) and removed 17 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.14 3.36 Search for helices and strands: 0 residues in 0 chains, 3120 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 3137 seeds are put forward Round 1: 166 peptides, 33 chains. Longest chain 12 peptides. Score 0.313 Round 2: 198 peptides, 35 chains. Longest chain 11 peptides. Score 0.404 Round 3: 193 peptides, 33 chains. Longest chain 10 peptides. Score 0.417 Round 4: 198 peptides, 35 chains. Longest chain 10 peptides. Score 0.404 Round 5: 191 peptides, 32 chains. Longest chain 13 peptides. Score 0.425 Taking the results from Round 5 Chains 33, Residues 159, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 4023 reflections ( 98.05 % complete ) and 7471 restraints for refining 3184 atoms. 6835 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1966 (Rfree = 0.000) for 3184 atoms. Found 17 (17 requested) and removed 29 (8 requested) atoms. Failed to save intermediate PDB Cycle 22: After refmac, R = 0.1852 (Rfree = 0.000) for 3149 atoms. Found 17 (17 requested) and removed 17 (8 requested) atoms. Cycle 23: After refmac, R = 0.1616 (Rfree = 0.000) for 3136 atoms. Found 11 (17 requested) and removed 22 (8 requested) atoms. Cycle 24: After refmac, R = 0.1285 (Rfree = 0.000) for 3122 atoms. Found 3 (17 requested) and removed 10 (8 requested) atoms. Cycle 25: After refmac, R = 0.1172 (Rfree = 0.000) for 3111 atoms. Found 3 (17 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.09 3.30 Search for helices and strands: 0 residues in 0 chains, 3187 seeds are put forward NCS extension: 11 residues added (2 deleted due to clashes), 3198 seeds are put forward Round 1: 171 peptides, 36 chains. Longest chain 9 peptides. Score 0.282 Round 2: 183 peptides, 33 chains. Longest chain 11 peptides. Score 0.380 Round 3: 183 peptides, 31 chains. Longest chain 14 peptides. Score 0.412 Round 4: 183 peptides, 29 chains. Longest chain 13 peptides. Score 0.443 Round 5: 196 peptides, 34 chains. Longest chain 12 peptides. Score 0.412 Taking the results from Round 4 Chains 29, Residues 154, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4023 reflections ( 98.05 % complete ) and 7486 restraints for refining 3184 atoms. 6899 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1661 (Rfree = 0.000) for 3184 atoms. Found 11 (17 requested) and removed 15 (8 requested) atoms. Cycle 27: After refmac, R = 0.1710 (Rfree = 0.000) for 3163 atoms. Found 17 (17 requested) and removed 14 (8 requested) atoms. Cycle 28: After refmac, R = 0.1550 (Rfree = 0.000) for 3160 atoms. Found 11 (17 requested) and removed 13 (8 requested) atoms. Cycle 29: After refmac, R = 0.1464 (Rfree = 0.000) for 3153 atoms. Found 9 (17 requested) and removed 10 (8 requested) atoms. Cycle 30: After refmac, R = 0.1424 (Rfree = 0.000) for 3140 atoms. Found 10 (17 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.07 3.28 Search for helices and strands: 0 residues in 0 chains, 3199 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 3215 seeds are put forward Round 1: 159 peptides, 35 chains. Longest chain 8 peptides. Score 0.250 Round 2: 182 peptides, 31 chains. Longest chain 13 peptides. Score 0.408 Round 3: 173 peptides, 28 chains. Longest chain 12 peptides. Score 0.423 Round 4: 169 peptides, 29 chains. Longest chain 14 peptides. Score 0.392 Round 5: 173 peptides, 30 chains. Longest chain 11 peptides. Score 0.390 Taking the results from Round 3 Chains 28, Residues 145, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 4023 reflections ( 98.05 % complete ) and 7510 restraints for refining 3167 atoms. 6958 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1723 (Rfree = 0.000) for 3167 atoms. Found 17 (17 requested) and removed 24 (8 requested) atoms. Cycle 32: After refmac, R = 0.1805 (Rfree = 0.000) for 3146 atoms. Found 17 (17 requested) and removed 18 (8 requested) atoms. Failed to save intermediate PDB Cycle 33: After refmac, R = 0.1285 (Rfree = 0.000) for 3135 atoms. Found 4 (17 requested) and removed 12 (8 requested) atoms. Failed to save intermediate PDB Cycle 34: After refmac, R = 0.1222 (Rfree = 0.000) for 3123 atoms. Found 0 (17 requested) and removed 12 (8 requested) atoms. Cycle 35: After refmac, R = 0.1217 (Rfree = 0.000) for 3110 atoms. Found 3 (17 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.14 3.36 Search for helices and strands: 0 residues in 0 chains, 3152 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 3165 seeds are put forward Round 1: 126 peptides, 26 chains. Longest chain 10 peptides. Score 0.269 Round 2: 148 peptides, 26 chains. Longest chain 10 peptides. Score 0.361 Round 3: 164 peptides, 28 chains. Longest chain 12 peptides. Score 0.389 Round 4: 170 peptides, 31 chains. Longest chain 12 peptides. Score 0.362 Round 5: 162 peptides, 27 chains. Longest chain 12 peptides. Score 0.398 Taking the results from Round 5 Chains 27, Residues 135, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 4023 reflections ( 98.05 % complete ) and 7349 restraints for refining 3171 atoms. 6812 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1631 (Rfree = 0.000) for 3171 atoms. Found 10 (17 requested) and removed 22 (8 requested) atoms. Cycle 37: After refmac, R = 0.1399 (Rfree = 0.000) for 3151 atoms. Found 3 (17 requested) and removed 12 (8 requested) atoms. Cycle 38: After refmac, R = 0.1475 (Rfree = 0.000) for 3133 atoms. Found 13 (17 requested) and removed 11 (8 requested) atoms. Failed to save intermediate PDB Cycle 39: After refmac, R = 0.1320 (Rfree = 0.000) for 3133 atoms. Found 2 (17 requested) and removed 9 (8 requested) atoms. Cycle 40: After refmac, R = 0.1305 (Rfree = 0.000) for 3120 atoms. Found 4 (17 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.15 3.37 Search for helices and strands: 0 residues in 0 chains, 3179 seeds are put forward NCS extension: 4 residues added (2 deleted due to clashes), 3183 seeds are put forward Round 1: 146 peptides, 31 chains. Longest chain 9 peptides. Score 0.265 Round 2: 164 peptides, 31 chains. Longest chain 10 peptides. Score 0.339 Round 3: 156 peptides, 28 chains. Longest chain 10 peptides. Score 0.358 Round 4: 157 peptides, 27 chains. Longest chain 14 peptides. Score 0.379 Round 5: 147 peptides, 24 chains. Longest chain 10 peptides. Score 0.391 Taking the results from Round 5 Chains 24, Residues 123, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4023 reflections ( 98.05 % complete ) and 7734 restraints for refining 3184 atoms. 7266 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1987 (Rfree = 0.000) for 3184 atoms. Found 17 (17 requested) and removed 25 (8 requested) atoms. Cycle 42: After refmac, R = 0.1891 (Rfree = 0.000) for 3164 atoms. Found 17 (17 requested) and removed 23 (8 requested) atoms. Failed to save intermediate PDB Cycle 43: After refmac, R = 0.1558 (Rfree = 0.000) for 3145 atoms. Found 14 (17 requested) and removed 16 (8 requested) atoms. Cycle 44: After refmac, R = 0.1136 (Rfree = 0.000) for 3138 atoms. Found 5 (17 requested) and removed 13 (8 requested) atoms. Cycle 45: After refmac, R = 0.1225 (Rfree = 0.000) for 3124 atoms. Found 10 (17 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.09 3.30 Search for helices and strands: 0 residues in 0 chains, 3194 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 3206 seeds are put forward Round 1: 111 peptides, 25 chains. Longest chain 6 peptides. Score 0.220 Round 2: 133 peptides, 25 chains. Longest chain 12 peptides. Score 0.317 Round 3: 141 peptides, 25 chains. Longest chain 10 peptides. Score 0.350 Round 4: 139 peptides, 27 chains. Longest chain 12 peptides. Score 0.306 Round 5: 141 peptides, 26 chains. Longest chain 11 peptides. Score 0.332 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 25, Residues 116, 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 1vjn-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4023 reflections ( 98.05 % complete ) and 7506 restraints for refining 3134 atoms. 7067 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1698 (Rfree = 0.000) for 3134 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Failed to save intermediate PDB Cycle 47: After refmac, R = 0.1525 (Rfree = 0.000) for 3122 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.1461 (Rfree = 0.000) for 3107 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.1353 (Rfree = 0.000) for 3098 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Writing output files ... Failed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDB TimeTaking 68.2