Mon 24 Dec 07:50:09 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-4.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vmf-4.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vmf-4.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vmf-4.0-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-4.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vmf-4.0-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 07:50:14 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-4.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vmf-4.0-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 300 and 0 Target number of residues in the AU: 300 Target solvent content: 0.6429 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-4.0-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-4.0-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 4.000 Wilson plot Bfac: 73.23 4162 reflections ( 99.55 % complete ) and 0 restraints for refining 3868 atoms. Observations/parameters ratio is 0.27 ------------------------------------------------------ Starting model: R = 0.3223 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3182 (Rfree = 0.000) for 3868 atoms. Found 18 (18 requested) and removed 24 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.69 3.79 Search for helices and strands: 0 residues in 0 chains, 3929 seeds are put forward NCS extension: 0 residues added, 3929 seeds are put forward Round 1: 158 peptides, 31 chains. Longest chain 9 peptides. Score 0.309 Round 2: 215 peptides, 36 chains. Longest chain 12 peptides. Score 0.437 Round 3: 219 peptides, 30 chains. Longest chain 17 peptides. Score 0.533 Round 4: 237 peptides, 34 chains. Longest chain 18 peptides. Score 0.534 Round 5: 239 peptides, 33 chains. Longest chain 18 peptides. Score 0.552 Taking the results from Round 5 Chains 35, Residues 206, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 4162 reflections ( 99.55 % complete ) and 7170 restraints for refining 3140 atoms. 6348 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2191 (Rfree = 0.000) for 3140 atoms. Found 8 (14 requested) and removed 15 (7 requested) atoms. Cycle 2: After refmac, R = 0.2228 (Rfree = 0.000) for 3081 atoms. Found 14 (14 requested) and removed 19 (7 requested) atoms. Cycle 3: After refmac, R = 0.2185 (Rfree = 0.000) for 3045 atoms. Found 14 (14 requested) and removed 17 (7 requested) atoms. Cycle 4: After refmac, R = 0.2015 (Rfree = 0.000) for 3024 atoms. Found 14 (14 requested) and removed 14 (7 requested) atoms. Cycle 5: After refmac, R = 0.1937 (Rfree = 0.000) for 3015 atoms. Found 14 (14 requested) and removed 16 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.63 3.73 Search for helices and strands: 0 residues in 0 chains, 3097 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 3115 seeds are put forward Round 1: 183 peptides, 35 chains. Longest chain 11 peptides. Score 0.340 Round 2: 188 peptides, 30 chains. Longest chain 15 peptides. Score 0.434 Round 3: 206 peptides, 31 chains. Longest chain 19 peptides. Score 0.479 Round 4: 200 peptides, 31 chains. Longest chain 15 peptides. Score 0.460 Round 5: 185 peptides, 28 chains. Longest chain 16 peptides. Score 0.454 Taking the results from Round 3 Chains 31, Residues 175, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4162 reflections ( 99.55 % complete ) and 7586 restraints for refining 3139 atoms. 6917 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2044 (Rfree = 0.000) for 3139 atoms. Found 8 (14 requested) and removed 14 (7 requested) atoms. Cycle 7: After refmac, R = 0.1970 (Rfree = 0.000) for 3111 atoms. Found 14 (14 requested) and removed 18 (7 requested) atoms. Cycle 8: After refmac, R = 0.2431 (Rfree = 0.000) for 3092 atoms. Found 14 (14 requested) and removed 23 (7 requested) atoms. Cycle 9: After refmac, R = 0.1970 (Rfree = 0.000) for 3066 atoms. Found 14 (14 requested) and removed 16 (7 requested) atoms. Cycle 10: After refmac, R = 0.2173 (Rfree = 0.000) for 3051 atoms. Found 14 (14 requested) and removed 14 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.62 3.72 Search for helices and strands: 0 residues in 0 chains, 3161 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 3177 seeds are put forward Round 1: 171 peptides, 33 chains. Longest chain 10 peptides. Score 0.326 Round 2: 209 peptides, 35 chains. Longest chain 16 peptides. Score 0.432 Round 3: 205 peptides, 34 chains. Longest chain 15 peptides. Score 0.433 Round 4: 215 peptides, 35 chains. Longest chain 14 peptides. Score 0.452 Round 5: 206 peptides, 32 chains. Longest chain 15 peptides. Score 0.465 Taking the results from Round 5 Chains 32, Residues 174, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4162 reflections ( 99.55 % complete ) and 7447 restraints for refining 3142 atoms. 6783 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2489 (Rfree = 0.000) for 3142 atoms. Found 14 (14 requested) and removed 15 (7 requested) atoms. Cycle 12: After refmac, R = 0.2105 (Rfree = 0.000) for 3115 atoms. Found 9 (14 requested) and removed 15 (7 requested) atoms. Cycle 13: After refmac, R = 0.1872 (Rfree = 0.000) for 3095 atoms. Found 5 (14 requested) and removed 9 (7 requested) atoms. Cycle 14: After refmac, R = 0.1546 (Rfree = 0.000) for 3083 atoms. Found 2 (14 requested) and removed 12 (7 requested) atoms. Cycle 15: After refmac, R = 0.1474 (Rfree = 0.000) for 3069 atoms. Found 3 (14 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.59 3.69 Search for helices and strands: 0 residues in 0 chains, 3158 seeds are put forward NCS extension: 17 residues added (3 deleted due to clashes), 3175 seeds are put forward Round 1: 180 peptides, 34 chains. Longest chain 10 peptides. Score 0.344 Round 2: 212 peptides, 34 chains. Longest chain 13 peptides. Score 0.456 Round 3: 204 peptides, 31 chains. Longest chain 13 peptides. Score 0.473 Round 4: 220 peptides, 33 chains. Longest chain 15 peptides. Score 0.496 Round 5: 219 peptides, 34 chains. Longest chain 14 peptides. Score 0.479 Taking the results from Round 4 Chains 33, Residues 187, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4162 reflections ( 99.55 % complete ) and 7331 restraints for refining 3141 atoms. 6616 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2215 (Rfree = 0.000) for 3141 atoms. Found 6 (14 requested) and removed 10 (7 requested) atoms. Cycle 17: After refmac, R = 0.2104 (Rfree = 0.000) for 3116 atoms. Found 13 (14 requested) and removed 18 (7 requested) atoms. Cycle 18: After refmac, R = 0.2016 (Rfree = 0.000) for 3101 atoms. Found 14 (14 requested) and removed 14 (7 requested) atoms. Cycle 19: After refmac, R = 0.1987 (Rfree = 0.000) for 3094 atoms. Found 13 (14 requested) and removed 16 (7 requested) atoms. Cycle 20: After refmac, R = 0.1444 (Rfree = 0.000) for 3086 atoms. Found 2 (14 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.56 3.66 Search for helices and strands: 0 residues in 0 chains, 3163 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 3183 seeds are put forward Round 1: 179 peptides, 35 chains. Longest chain 9 peptides. Score 0.325 Round 2: 200 peptides, 34 chains. Longest chain 20 peptides. Score 0.416 Round 3: 214 peptides, 35 chains. Longest chain 15 peptides. Score 0.448 Round 4: 216 peptides, 35 chains. Longest chain 16 peptides. Score 0.455 Round 5: 203 peptides, 33 chains. Longest chain 12 peptides. Score 0.441 Taking the results from Round 4 Chains 35, Residues 181, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4162 reflections ( 99.55 % complete ) and 7485 restraints for refining 3142 atoms. 6796 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2504 (Rfree = 0.000) for 3142 atoms. Found 14 (14 requested) and removed 16 (7 requested) atoms. Cycle 22: After refmac, R = 0.2176 (Rfree = 0.000) for 3119 atoms. Found 14 (14 requested) and removed 15 (7 requested) atoms. Cycle 23: After refmac, R = 0.1864 (Rfree = 0.000) for 3102 atoms. Found 4 (14 requested) and removed 10 (7 requested) atoms. Cycle 24: After refmac, R = 0.1649 (Rfree = 0.000) for 3091 atoms. Found 3 (14 requested) and removed 9 (7 requested) atoms. Cycle 25: After refmac, R = 0.1792 (Rfree = 0.000) for 3080 atoms. Found 6 (14 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.57 3.67 Search for helices and strands: 0 residues in 0 chains, 3152 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 3171 seeds are put forward Round 1: 189 peptides, 37 chains. Longest chain 8 peptides. Score 0.331 Round 2: 198 peptides, 31 chains. Longest chain 11 peptides. Score 0.453 Round 3: 194 peptides, 31 chains. Longest chain 13 peptides. Score 0.440 Round 4: 204 peptides, 32 chains. Longest chain 15 peptides. Score 0.459 Round 5: 191 peptides, 27 chains. Longest chain 22 peptides. Score 0.488 Taking the results from Round 5 Chains 27, Residues 164, Estimated correctness of the model 0.0 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ 4162 reflections ( 99.55 % complete ) and 7392 restraints for refining 3142 atoms. 6688 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2020 (Rfree = 0.000) for 3142 atoms. Found 8 (14 requested) and removed 15 (7 requested) atoms. Cycle 27: After refmac, R = 0.2036 (Rfree = 0.000) for 3118 atoms. Found 14 (14 requested) and removed 10 (7 requested) atoms. Cycle 28: After refmac, R = 0.1986 (Rfree = 0.000) for 3115 atoms. Found 14 (14 requested) and removed 14 (7 requested) atoms. Cycle 29: After refmac, R = 0.1514 (Rfree = 0.000) for 3102 atoms. Found 9 (14 requested) and removed 8 (7 requested) atoms. Cycle 30: After refmac, R = 0.1779 (Rfree = 0.000) for 3098 atoms. Found 14 (14 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.57 3.67 Search for helices and strands: 0 residues in 0 chains, 3184 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 3200 seeds are put forward Round 1: 172 peptides, 36 chains. Longest chain 8 peptides. Score 0.282 Round 2: 191 peptides, 33 chains. Longest chain 13 peptides. Score 0.399 Round 3: 178 peptides, 30 chains. Longest chain 13 peptides. Score 0.399 Round 4: 170 peptides, 29 chains. Longest chain 13 peptides. Score 0.386 Round 5: 169 peptides, 30 chains. Longest chain 13 peptides. Score 0.367 Taking the results from Round 3 Chains 30, Residues 148, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4162 reflections ( 99.55 % complete ) and 7554 restraints for refining 3142 atoms. 6992 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2222 (Rfree = 0.000) for 3142 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. Cycle 32: After refmac, R = 0.2036 (Rfree = 0.000) for 3126 atoms. Found 14 (14 requested) and removed 19 (7 requested) atoms. Cycle 33: After refmac, R = 0.2216 (Rfree = 0.000) for 3103 atoms. Found 14 (14 requested) and removed 12 (7 requested) atoms. Cycle 34: After refmac, R = 0.2007 (Rfree = 0.000) for 3091 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. Cycle 35: After refmac, R = 0.2278 (Rfree = 0.000) for 3088 atoms. Found 14 (14 requested) and removed 18 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.60 3.70 Search for helices and strands: 0 residues in 0 chains, 3178 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 3196 seeds are put forward Round 1: 151 peptides, 31 chains. Longest chain 14 peptides. Score 0.281 Round 2: 167 peptides, 29 chains. Longest chain 13 peptides. Score 0.375 Round 3: 165 peptides, 31 chains. Longest chain 15 peptides. Score 0.336 Round 4: 161 peptides, 26 chains. Longest chain 12 peptides. Score 0.401 Round 5: 159 peptides, 27 chains. Longest chain 14 peptides. Score 0.378 Taking the results from Round 4 Chains 26, Residues 135, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4162 reflections ( 99.55 % complete ) and 7879 restraints for refining 3142 atoms. 7365 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2250 (Rfree = 0.000) for 3142 atoms. Found 14 (14 requested) and removed 23 (7 requested) atoms. Cycle 37: After refmac, R = 0.2230 (Rfree = 0.000) for 3116 atoms. Found 14 (14 requested) and removed 15 (7 requested) atoms. Cycle 38: After refmac, R = 0.2035 (Rfree = 0.000) for 3108 atoms. Found 14 (14 requested) and removed 24 (7 requested) atoms. Cycle 39: After refmac, R = 0.1636 (Rfree = 0.000) for 3090 atoms. Found 8 (14 requested) and removed 10 (7 requested) atoms. Cycle 40: After refmac, R = 0.1422 (Rfree = 0.000) for 3078 atoms. Found 6 (14 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.61 3.71 Search for helices and strands: 0 residues in 0 chains, 3162 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 3176 seeds are put forward Round 1: 149 peptides, 32 chains. Longest chain 9 peptides. Score 0.256 Round 2: 164 peptides, 29 chains. Longest chain 11 peptides. Score 0.364 Round 3: 182 peptides, 33 chains. Longest chain 11 peptides. Score 0.367 Round 4: 186 peptides, 31 chains. Longest chain 12 peptides. Score 0.412 Round 5: 173 peptides, 30 chains. Longest chain 16 peptides. Score 0.381 Taking the results from Round 4 Chains 31, Residues 155, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4162 reflections ( 99.55 % complete ) and 7524 restraints for refining 3142 atoms. 6935 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2039 (Rfree = 0.000) for 3142 atoms. Found 14 (14 requested) and removed 8 (7 requested) atoms. Cycle 42: After refmac, R = 0.2072 (Rfree = 0.000) for 3134 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. Cycle 43: After refmac, R = 0.1863 (Rfree = 0.000) for 3127 atoms. Found 14 (14 requested) and removed 11 (7 requested) atoms. Cycle 44: After refmac, R = 0.1419 (Rfree = 0.000) for 3117 atoms. Found 9 (14 requested) and removed 8 (7 requested) atoms. Cycle 45: After refmac, R = 0.1218 (Rfree = 0.000) for 3115 atoms. Found 3 (14 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.59 3.69 Search for helices and strands: 0 residues in 0 chains, 3182 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 3197 seeds are put forward Round 1: 134 peptides, 29 chains. Longest chain 8 peptides. Score 0.246 Round 2: 147 peptides, 26 chains. Longest chain 11 peptides. Score 0.349 Round 3: 152 peptides, 24 chains. Longest chain 14 peptides. Score 0.401 Round 4: 151 peptides, 24 chains. Longest chain 10 peptides. Score 0.397 Round 5: 156 peptides, 22 chains. Longest chain 19 peptides. Score 0.447 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 22, Residues 134, 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-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4162 reflections ( 99.55 % complete ) and 7605 restraints for refining 3141 atoms. 7091 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1954 (Rfree = 0.000) for 3141 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.2042 (Rfree = 0.000) for 3118 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.2298 (Rfree = 0.000) for 3102 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.1538 (Rfree = 0.000) for 3082 atoms. TimeTaking 40.43