null Mon 24 Dec 07:30:23 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 1vmf-3.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vmf-3.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vmf-3.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vmf-3.8-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/1vmf-3.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vmf-3.8-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 07:30:28 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/1vmf-3.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vmf-3.8-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 306 and 0 Target number of residues in the AU: 306 Target solvent content: 0.6357 Checking the provided sequence file Detected sequence length: 145 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 3 Adjusted target number of residues: 435 Adjusted target solvent content: 0.48 Input MTZ file: 1vmf-3.8-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: 57.443 58.601 135.061 90.000 90.000 90.000 Input sequence file: 1vmf-3.8-parrot-noncs.fasta_lf Building free atoms model in initial map for 3480 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 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: 67.531 3.800 Wilson plot Bfac: 69.06 4824 reflections ( 99.61 % complete ) and 0 restraints for refining 3868 atoms. Observations/parameters ratio is 0.31 ------------------------------------------------------ Starting model: R = 0.3194 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3017 (Rfree = 0.000) for 3868 atoms. Found 21 (21 requested) and removed 43 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.57 3.67 Search for helices and strands: 0 residues in 0 chains, 3922 seeds are put forward NCS extension: 0 residues added, 3922 seeds are put forward Round 1: 208 peptides, 38 chains. Longest chain 12 peptides. Score 0.384 Round 2: 228 peptides, 34 chains. Longest chain 21 peptides. Score 0.507 Round 3: 244 peptides, 34 chains. Longest chain 26 peptides. Score 0.554 Round 4: 246 peptides, 29 chains. Longest chain 24 peptides. Score 0.620 Round 5: 251 peptides, 28 chains. Longest chain 21 peptides. Score 0.643 Taking the results from Round 5 Chains 28, Residues 223, Estimated correctness of the model 17.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4824 reflections ( 99.61 % complete ) and 7201 restraints for refining 3148 atoms. 6337 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2565 (Rfree = 0.000) for 3148 atoms. Found 17 (17 requested) and removed 19 (8 requested) atoms. Cycle 2: After refmac, R = 0.2447 (Rfree = 0.000) for 3104 atoms. Found 17 (17 requested) and removed 17 (8 requested) atoms. Cycle 3: After refmac, R = 0.2125 (Rfree = 0.000) for 3085 atoms. Found 5 (17 requested) and removed 16 (8 requested) atoms. Cycle 4: After refmac, R = 0.1879 (Rfree = 0.000) for 3060 atoms. Found 5 (16 requested) and removed 14 (8 requested) atoms. Cycle 5: After refmac, R = 0.1790 (Rfree = 0.000) for 3046 atoms. Found 1 (16 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.50 3.59 Search for helices and strands: 0 residues in 0 chains, 3131 seeds are put forward NCS extension: 26 residues added (3 deleted due to clashes), 3157 seeds are put forward Round 1: 226 peptides, 38 chains. Longest chain 17 peptides. Score 0.445 Round 2: 247 peptides, 36 chains. Longest chain 19 peptides. Score 0.537 Round 3: 239 peptides, 34 chains. Longest chain 21 peptides. Score 0.540 Round 4: 258 peptides, 38 chains. Longest chain 15 peptides. Score 0.544 Round 5: 260 peptides, 35 chains. Longest chain 28 peptides. Score 0.586 Taking the results from Round 5 Chains 36, Residues 225, Estimated correctness of the model 0.0 % 1 chains (21 residues) have been docked in sequence ------------------------------------------------------ 4824 reflections ( 99.61 % complete ) and 6983 restraints for refining 3148 atoms. 6043 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2417 (Rfree = 0.000) for 3148 atoms. Found 9 (17 requested) and removed 18 (8 requested) atoms. Cycle 7: After refmac, R = 0.2361 (Rfree = 0.000) for 3113 atoms. Found 9 (17 requested) and removed 14 (8 requested) atoms. Cycle 8: After refmac, R = 0.2048 (Rfree = 0.000) for 3096 atoms. Found 3 (17 requested) and removed 14 (8 requested) atoms. Cycle 9: After refmac, R = 0.2029 (Rfree = 0.000) for 3073 atoms. Found 11 (16 requested) and removed 11 (8 requested) atoms. Cycle 10: After refmac, R = 0.2038 (Rfree = 0.000) for 3067 atoms. Found 11 (16 requested) and removed 14 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.48 3.57 Search for helices and strands: 0 residues in 0 chains, 3181 seeds are put forward NCS extension: 29 residues added (4 deleted due to clashes), 3210 seeds are put forward Round 1: 217 peptides, 40 chains. Longest chain 11 peptides. Score 0.386 Round 2: 235 peptides, 29 chains. Longest chain 20 peptides. Score 0.591 Round 3: 247 peptides, 31 chains. Longest chain 21 peptides. Score 0.599 Round 4: 247 peptides, 32 chains. Longest chain 22 peptides. Score 0.587 Round 5: 252 peptides, 36 chains. Longest chain 22 peptides. Score 0.552 Taking the results from Round 3 Chains 31, Residues 216, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4824 reflections ( 99.61 % complete ) and 7293 restraints for refining 3148 atoms. 6460 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2265 (Rfree = 0.000) for 3148 atoms. Found 16 (17 requested) and removed 28 (8 requested) atoms. Cycle 12: After refmac, R = 0.2234 (Rfree = 0.000) for 3120 atoms. Found 14 (17 requested) and removed 14 (8 requested) atoms. Cycle 13: After refmac, R = 0.2083 (Rfree = 0.000) for 3109 atoms. Found 15 (17 requested) and removed 14 (8 requested) atoms. Cycle 14: After refmac, R = 0.1731 (Rfree = 0.000) for 3100 atoms. Found 2 (17 requested) and removed 9 (8 requested) atoms. Cycle 15: After refmac, R = 0.1674 (Rfree = 0.000) for 3088 atoms. Found 2 (17 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.54 3.64 Search for helices and strands: 0 residues in 0 chains, 3165 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 3186 seeds are put forward Round 1: 196 peptides, 35 chains. Longest chain 14 peptides. Score 0.387 Round 2: 225 peptides, 36 chains. Longest chain 16 peptides. Score 0.470 Round 3: 226 peptides, 34 chains. Longest chain 12 peptides. Score 0.501 Round 4: 242 peptides, 32 chains. Longest chain 19 peptides. Score 0.573 Round 5: 241 peptides, 31 chains. Longest chain 13 peptides. Score 0.583 Taking the results from Round 5 Chains 31, Residues 210, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4824 reflections ( 99.61 % complete ) and 7177 restraints for refining 3145 atoms. 6368 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2144 (Rfree = 0.000) for 3145 atoms. Found 17 (17 requested) and removed 14 (8 requested) atoms. Cycle 17: After refmac, R = 0.1941 (Rfree = 0.000) for 3128 atoms. Found 4 (17 requested) and removed 9 (8 requested) atoms. Cycle 18: After refmac, R = 0.1963 (Rfree = 0.000) for 3113 atoms. Found 3 (17 requested) and removed 14 (8 requested) atoms. Cycle 19: After refmac, R = 0.1965 (Rfree = 0.000) for 3098 atoms. Found 2 (17 requested) and removed 10 (8 requested) atoms. Cycle 20: After refmac, R = 0.1936 (Rfree = 0.000) for 3089 atoms. Found 4 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.54 3.64 Search for helices and strands: 0 residues in 0 chains, 3174 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 3186 seeds are put forward Round 1: 194 peptides, 36 chains. Longest chain 10 peptides. Score 0.364 Round 2: 223 peptides, 31 chains. Longest chain 16 peptides. Score 0.532 Round 3: 233 peptides, 32 chains. Longest chain 22 peptides. Score 0.548 Round 4: 223 peptides, 30 chains. Longest chain 19 peptides. Score 0.545 Round 5: 221 peptides, 28 chains. Longest chain 19 peptides. Score 0.565 Taking the results from Round 5 Chains 28, Residues 193, Estimated correctness of the model 0.0 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 4824 reflections ( 99.61 % complete ) and 7252 restraints for refining 3148 atoms. 6460 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2219 (Rfree = 0.000) for 3148 atoms. Found 14 (17 requested) and removed 20 (8 requested) atoms. Cycle 22: After refmac, R = 0.1952 (Rfree = 0.000) for 3132 atoms. Found 5 (17 requested) and removed 11 (8 requested) atoms. Cycle 23: After refmac, R = 0.1936 (Rfree = 0.000) for 3122 atoms. Found 0 (17 requested) and removed 10 (8 requested) atoms. Cycle 24: After refmac, R = 0.1948 (Rfree = 0.000) for 3111 atoms. Found 4 (17 requested) and removed 8 (8 requested) atoms. Cycle 25: After refmac, R = 0.1950 (Rfree = 0.000) for 3105 atoms. Found 1 (17 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.49 3.58 Search for helices and strands: 0 residues in 0 chains, 3199 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 3219 seeds are put forward Round 1: 193 peptides, 35 chains. Longest chain 9 peptides. Score 0.376 Round 2: 209 peptides, 32 chains. Longest chain 14 peptides. Score 0.475 Round 3: 195 peptides, 26 chains. Longest chain 20 peptides. Score 0.515 Round 4: 215 peptides, 32 chains. Longest chain 16 peptides. Score 0.494 Round 5: 204 peptides, 30 chains. Longest chain 13 peptides. Score 0.487 Taking the results from Round 3 Chains 26, Residues 169, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4824 reflections ( 99.61 % complete ) and 7515 restraints for refining 3148 atoms. 6865 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2232 (Rfree = 0.000) for 3148 atoms. Found 14 (17 requested) and removed 15 (8 requested) atoms. Cycle 27: After refmac, R = 0.2083 (Rfree = 0.000) for 3141 atoms. Found 0 (17 requested) and removed 12 (8 requested) atoms. Cycle 28: After refmac, R = 0.2084 (Rfree = 0.000) for 3126 atoms. Found 6 (17 requested) and removed 13 (8 requested) atoms. Cycle 29: After refmac, R = 0.2290 (Rfree = 0.000) for 3119 atoms. Found 4 (17 requested) and removed 9 (8 requested) atoms. Cycle 30: After refmac, R = 0.2129 (Rfree = 0.000) for 3111 atoms. Found 1 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.52 3.62 Search for helices and strands: 0 residues in 0 chains, 3183 seeds are put forward NCS extension: 31 residues added (1 deleted due to clashes), 3214 seeds are put forward Round 1: 175 peptides, 34 chains. Longest chain 8 peptides. Score 0.325 Round 2: 197 peptides, 33 chains. Longest chain 11 peptides. Score 0.420 Round 3: 185 peptides, 27 chains. Longest chain 12 peptides. Score 0.469 Round 4: 191 peptides, 29 chains. Longest chain 14 peptides. Score 0.459 Round 5: 188 peptides, 29 chains. Longest chain 15 peptides. Score 0.449 Taking the results from Round 3 Chains 27, Residues 158, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4824 reflections ( 99.61 % complete ) and 7555 restraints for refining 3147 atoms. 6950 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2213 (Rfree = 0.000) for 3147 atoms. Found 7 (17 requested) and removed 10 (8 requested) atoms. Cycle 32: After refmac, R = 0.2318 (Rfree = 0.000) for 3136 atoms. Found 17 (17 requested) and removed 14 (8 requested) atoms. Cycle 33: After refmac, R = 0.2107 (Rfree = 0.000) for 3137 atoms. Found 17 (17 requested) and removed 16 (8 requested) atoms. Cycle 34: After refmac, R = 0.1772 (Rfree = 0.000) for 3135 atoms. Found 4 (17 requested) and removed 11 (8 requested) atoms. Cycle 35: After refmac, R = 0.1836 (Rfree = 0.000) for 3123 atoms. Found 5 (17 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.49 3.58 Search for helices and strands: 0 residues in 0 chains, 3200 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 3214 seeds are put forward Round 1: 153 peptides, 29 chains. Longest chain 9 peptides. Score 0.322 Round 2: 165 peptides, 28 chains. Longest chain 15 peptides. Score 0.384 Round 3: 163 peptides, 26 chains. Longest chain 16 peptides. Score 0.408 Round 4: 177 peptides, 29 chains. Longest chain 11 peptides. Score 0.411 Round 5: 196 peptides, 29 chains. Longest chain 18 peptides. Score 0.475 Taking the results from Round 5 Chains 29, Residues 167, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4824 reflections ( 99.61 % complete ) and 7462 restraints for refining 3148 atoms. 6823 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2423 (Rfree = 0.000) for 3148 atoms. Found 17 (17 requested) and removed 20 (8 requested) atoms. Cycle 37: After refmac, R = 0.2085 (Rfree = 0.000) for 3131 atoms. Found 11 (17 requested) and removed 17 (8 requested) atoms. Cycle 38: After refmac, R = 0.1942 (Rfree = 0.000) for 3120 atoms. Found 11 (17 requested) and removed 12 (8 requested) atoms. Cycle 39: After refmac, R = 0.1873 (Rfree = 0.000) for 3115 atoms. Found 10 (17 requested) and removed 13 (8 requested) atoms. Cycle 40: After refmac, R = 0.1739 (Rfree = 0.000) for 3111 atoms. Found 6 (17 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.43 3.52 Search for helices and strands: 0 residues in 0 chains, 3167 seeds are put forward NCS extension: 28 residues added (3 deleted due to clashes), 3195 seeds are put forward Round 1: 134 peptides, 26 chains. Longest chain 8 peptides. Score 0.298 Round 2: 147 peptides, 25 chains. Longest chain 13 peptides. Score 0.366 Round 3: 159 peptides, 25 chains. Longest chain 13 peptides. Score 0.410 Round 4: 159 peptides, 23 chains. Longest chain 26 peptides. Score 0.441 Round 5: 158 peptides, 25 chains. Longest chain 16 peptides. Score 0.406 Taking the results from Round 4 Chains 23, Residues 136, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4824 reflections ( 99.61 % complete ) and 7635 restraints for refining 3148 atoms. 7114 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2204 (Rfree = 0.000) for 3148 atoms. Found 17 (17 requested) and removed 13 (8 requested) atoms. Cycle 42: After refmac, R = 0.2121 (Rfree = 0.000) for 3141 atoms. Found 17 (17 requested) and removed 16 (8 requested) atoms. Cycle 43: After refmac, R = 0.1642 (Rfree = 0.000) for 3134 atoms. Found 2 (17 requested) and removed 8 (8 requested) atoms. Cycle 44: After refmac, R = 0.1697 (Rfree = 0.000) for 3124 atoms. Found 9 (17 requested) and removed 8 (8 requested) atoms. Cycle 45: After refmac, R = 0.1508 (Rfree = 0.000) for 3124 atoms. Found 0 (17 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.46 3.55 Search for helices and strands: 0 residues in 0 chains, 3190 seeds are put forward NCS extension: 36 residues added (6 deleted due to clashes), 3226 seeds are put forward Round 1: 138 peptides, 28 chains. Longest chain 8 peptides. Score 0.280 Round 2: 147 peptides, 21 chains. Longest chain 15 peptides. Score 0.431 Round 3: 162 peptides, 28 chains. Longest chain 12 peptides. Score 0.373 Round 4: 169 peptides, 24 chains. Longest chain 21 peptides. Score 0.460 Round 5: 168 peptides, 26 chains. Longest chain 16 peptides. Score 0.426 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 24, Residues 145, 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 1vmf-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4824 reflections ( 99.61 % complete ) and 7626 restraints for refining 3148 atoms. 7070 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2193 (Rfree = 0.000) for 3148 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.2036 (Rfree = 0.000) for 3129 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.2059 (Rfree = 0.000) for 3113 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.1553 (Rfree = 0.000) for 3104 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:10:58 GMT 2018 Job finished. TimeTaking 40.57 Used memory is bytes: 14025416