Mon 24 Dec 00:04:11 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vmf-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vmf-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vmf-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vmf-4.0-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/1vmf-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vmf-4.0-parrot-mrncs ############### 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 00:04:15 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/mrncs/ArpWArp/wArpResults/WorkingDir/1vmf-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vmf-4.0-parrot-mrncs/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-mrncs.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-mrncs.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 3842 atoms. Observations/parameters ratio is 0.27 ------------------------------------------------------ Starting model: R = 0.3211 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3115 (Rfree = 0.000) for 3842 atoms. Found 18 (18 requested) and removed 37 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.63 3.73 Search for helices and strands: 0 residues in 0 chains, 3890 seeds are put forward NCS extension: 0 residues added, 3890 seeds are put forward Round 1: 159 peptides, 30 chains. Longest chain 9 peptides. Score 0.329 Round 2: 214 peptides, 34 chains. Longest chain 15 peptides. Score 0.463 Round 3: 231 peptides, 34 chains. Longest chain 15 peptides. Score 0.516 Round 4: 245 peptides, 35 chains. Longest chain 20 peptides. Score 0.544 Round 5: 245 peptides, 32 chains. Longest chain 26 peptides. Score 0.582 Taking the results from Round 5 Chains 32, Residues 213, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4162 reflections ( 99.55 % complete ) and 7307 restraints for refining 3141 atoms. 6487 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2772 (Rfree = 0.000) for 3141 atoms. Found 14 (14 requested) and removed 29 (7 requested) atoms. Cycle 2: After refmac, R = 0.2259 (Rfree = 0.000) for 3074 atoms. Found 6 (14 requested) and removed 18 (7 requested) atoms. Cycle 3: After refmac, R = 0.1837 (Rfree = 0.000) for 3039 atoms. Found 5 (14 requested) and removed 20 (7 requested) atoms. Cycle 4: After refmac, R = 0.1873 (Rfree = 0.000) for 3016 atoms. Found 8 (14 requested) and removed 9 (7 requested) atoms. Cycle 5: After refmac, R = 0.2273 (Rfree = 0.000) for 3009 atoms. Found 13 (14 requested) and removed 18 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.54 3.64 Search for helices and strands: 0 residues in 0 chains, 3102 seeds are put forward NCS extension: 41 residues added (5 deleted due to clashes), 3143 seeds are put forward Round 1: 201 peptides, 35 chains. Longest chain 14 peptides. Score 0.404 Round 2: 242 peptides, 35 chains. Longest chain 16 peptides. Score 0.536 Round 3: 237 peptides, 35 chains. Longest chain 15 peptides. Score 0.521 Round 4: 232 peptides, 33 chains. Longest chain 15 peptides. Score 0.532 Round 5: 242 peptides, 34 chains. Longest chain 15 peptides. Score 0.548 Taking the results from Round 5 Chains 34, Residues 208, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4162 reflections ( 99.55 % complete ) and 7292 restraints for refining 3141 atoms. 6494 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3156 (Rfree = 0.000) for 3141 atoms. Found 14 (14 requested) and removed 91 (7 requested) atoms. Cycle 7: After refmac, R = 0.2619 (Rfree = 0.000) for 3047 atoms. Found 14 (14 requested) and removed 29 (7 requested) atoms. Cycle 8: After refmac, R = 0.1982 (Rfree = 0.000) for 3019 atoms. Found 8 (14 requested) and removed 12 (7 requested) atoms. Cycle 9: After refmac, R = 0.1881 (Rfree = 0.000) for 3011 atoms. Found 4 (14 requested) and removed 10 (7 requested) atoms. Cycle 10: After refmac, R = 0.1839 (Rfree = 0.000) for 3002 atoms. Found 6 (14 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.64 3.74 Search for helices and strands: 0 residues in 0 chains, 3106 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 3117 seeds are put forward Round 1: 200 peptides, 38 chains. Longest chain 10 peptides. Score 0.355 Round 2: 208 peptides, 31 chains. Longest chain 15 peptides. Score 0.486 Round 3: 207 peptides, 30 chains. Longest chain 21 peptides. Score 0.496 Round 4: 211 peptides, 33 chains. Longest chain 14 peptides. Score 0.467 Round 5: 211 peptides, 30 chains. Longest chain 19 peptides. Score 0.509 Taking the results from Round 5 Chains 30, Residues 181, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4162 reflections ( 99.55 % complete ) and 7569 restraints for refining 3142 atoms. 6875 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2354 (Rfree = 0.000) for 3142 atoms. Found 8 (14 requested) and removed 21 (7 requested) atoms. Cycle 12: After refmac, R = 0.2106 (Rfree = 0.000) for 3119 atoms. Found 5 (14 requested) and removed 13 (7 requested) atoms. Cycle 13: After refmac, R = 0.1990 (Rfree = 0.000) for 3107 atoms. Found 2 (14 requested) and removed 11 (7 requested) atoms. Cycle 14: After refmac, R = 0.1985 (Rfree = 0.000) for 3097 atoms. Found 2 (14 requested) and removed 8 (7 requested) atoms. Cycle 15: After refmac, R = 0.1985 (Rfree = 0.000) for 3090 atoms. Found 1 (14 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.65 3.75 Search for helices and strands: 0 residues in 0 chains, 3189 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 3206 seeds are put forward Round 1: 183 peptides, 35 chains. Longest chain 11 peptides. Score 0.340 Round 2: 224 peptides, 36 chains. Longest chain 14 peptides. Score 0.467 Round 3: 220 peptides, 32 chains. Longest chain 15 peptides. Score 0.509 Round 4: 204 peptides, 31 chains. Longest chain 17 peptides. Score 0.473 Round 5: 204 peptides, 28 chains. Longest chain 20 peptides. Score 0.515 Taking the results from Round 5 Chains 28, Residues 176, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 4162 reflections ( 99.55 % complete ) and 7488 restraints for refining 3142 atoms. 6776 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2206 (Rfree = 0.000) for 3142 atoms. Found 10 (14 requested) and removed 15 (7 requested) atoms. Cycle 17: After refmac, R = 0.2097 (Rfree = 0.000) for 3129 atoms. Found 13 (14 requested) and removed 14 (7 requested) atoms. Cycle 18: After refmac, R = 0.1994 (Rfree = 0.000) for 3127 atoms. Found 5 (14 requested) and removed 11 (7 requested) atoms. Cycle 19: After refmac, R = 0.2304 (Rfree = 0.000) for 3115 atoms. Found 14 (14 requested) and removed 21 (7 requested) atoms. Cycle 20: After refmac, R = 0.2028 (Rfree = 0.000) for 3103 atoms. Found 14 (14 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.63 3.73 Search for helices and strands: 0 residues in 0 chains, 3213 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 3236 seeds are put forward Round 1: 158 peptides, 32 chains. Longest chain 8 peptides. Score 0.292 Round 2: 169 peptides, 26 chains. Longest chain 13 peptides. Score 0.429 Round 3: 176 peptides, 28 chains. Longest chain 18 peptides. Score 0.423 Round 4: 192 peptides, 31 chains. Longest chain 15 peptides. Score 0.433 Round 5: 196 peptides, 29 chains. Longest chain 19 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 ------------------------------------------------------ 4162 reflections ( 99.55 % complete ) and 7774 restraints for refining 3142 atoms. 7135 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2179 (Rfree = 0.000) for 3142 atoms. Found 13 (14 requested) and removed 12 (7 requested) atoms. Cycle 22: After refmac, R = 0.2224 (Rfree = 0.000) for 3131 atoms. Found 14 (14 requested) and removed 15 (7 requested) atoms. Cycle 23: After refmac, R = 0.2089 (Rfree = 0.000) for 3116 atoms. Found 14 (14 requested) and removed 18 (7 requested) atoms. Cycle 24: After refmac, R = 0.1895 (Rfree = 0.000) for 3108 atoms. Found 7 (14 requested) and removed 34 (7 requested) atoms. Cycle 25: After refmac, R = 0.1750 (Rfree = 0.000) for 3079 atoms. Found 12 (14 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.60 3.70 Search for helices and strands: 0 residues in 0 chains, 3176 seeds are put forward NCS extension: 30 residues added (0 deleted due to clashes), 3206 seeds are put forward Round 1: 153 peptides, 29 chains. Longest chain 11 peptides. Score 0.322 Round 2: 165 peptides, 28 chains. Longest chain 12 peptides. Score 0.384 Round 3: 166 peptides, 26 chains. Longest chain 11 peptides. Score 0.419 Round 4: 173 peptides, 25 chains. Longest chain 12 peptides. Score 0.458 Round 5: 180 peptides, 28 chains. Longest chain 17 peptides. Score 0.437 Taking the results from Round 4 Chains 26, Residues 148, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4162 reflections ( 99.55 % complete ) and 7740 restraints for refining 3142 atoms. 7142 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2413 (Rfree = 0.000) for 3142 atoms. Found 14 (14 requested) and removed 23 (7 requested) atoms. Cycle 27: After refmac, R = 0.2070 (Rfree = 0.000) for 3113 atoms. Found 14 (14 requested) and removed 18 (7 requested) atoms. Cycle 28: After refmac, R = 0.1519 (Rfree = 0.000) for 3105 atoms. Found 4 (14 requested) and removed 11 (7 requested) atoms. Cycle 29: After refmac, R = 0.1367 (Rfree = 0.000) for 3093 atoms. Found 2 (14 requested) and removed 10 (7 requested) atoms. Cycle 30: After refmac, R = 0.1362 (Rfree = 0.000) for 3079 atoms. Found 3 (14 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.60 3.70 Search for helices and strands: 0 residues in 0 chains, 3165 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 3178 seeds are put forward Round 1: 168 peptides, 32 chains. Longest chain 12 peptides. Score 0.331 Round 2: 171 peptides, 28 chains. Longest chain 15 peptides. Score 0.405 Round 3: 181 peptides, 28 chains. Longest chain 17 peptides. Score 0.440 Round 4: 178 peptides, 29 chains. Longest chain 13 peptides. Score 0.415 Round 5: 175 peptides, 28 chains. Longest chain 13 peptides. Score 0.420 Taking the results from Round 3 Chains 28, Residues 153, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4162 reflections ( 99.55 % complete ) and 7799 restraints for refining 3142 atoms. 7215 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2283 (Rfree = 0.000) for 3142 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. Cycle 32: After refmac, R = 0.2096 (Rfree = 0.000) for 3130 atoms. Found 14 (14 requested) and removed 23 (7 requested) atoms. Cycle 33: After refmac, R = 0.1561 (Rfree = 0.000) for 3107 atoms. Found 9 (14 requested) and removed 13 (7 requested) atoms. Cycle 34: After refmac, R = 0.1315 (Rfree = 0.000) for 3098 atoms. Found 4 (14 requested) and removed 8 (7 requested) atoms. Cycle 35: After refmac, R = 0.1251 (Rfree = 0.000) for 3089 atoms. Found 3 (14 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.60 3.70 Search for helices and strands: 0 residues in 0 chains, 3188 seeds are put forward NCS extension: 30 residues added (0 deleted due to clashes), 3218 seeds are put forward Round 1: 136 peptides, 30 chains. Longest chain 12 peptides. Score 0.237 Round 2: 167 peptides, 33 chains. Longest chain 10 peptides. Score 0.311 Round 3: 161 peptides, 30 chains. Longest chain 10 peptides. Score 0.337 Round 4: 156 peptides, 27 chains. Longest chain 10 peptides. Score 0.367 Round 5: 163 peptides, 28 chains. Longest chain 12 peptides. Score 0.377 Taking the results from Round 5 Chains 28, Residues 135, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 4162 reflections ( 99.55 % complete ) and 7816 restraints for refining 3141 atoms. 7268 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2133 (Rfree = 0.000) for 3141 atoms. Found 14 (14 requested) and removed 10 (7 requested) atoms. Cycle 37: After refmac, R = 0.2104 (Rfree = 0.000) for 3124 atoms. Found 14 (14 requested) and removed 8 (7 requested) atoms. Cycle 38: After refmac, R = 0.2223 (Rfree = 0.000) for 3125 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. Cycle 39: After refmac, R = 0.2081 (Rfree = 0.000) for 3114 atoms. Found 14 (14 requested) and removed 17 (7 requested) atoms. Cycle 40: After refmac, R = 0.2044 (Rfree = 0.000) for 3098 atoms. Found 14 (14 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.59 3.69 Search for helices and strands: 0 residues in 0 chains, 3191 seeds are put forward NCS extension: 0 residues added, 3191 seeds are put forward Round 1: 116 peptides, 25 chains. Longest chain 7 peptides. Score 0.240 Round 2: 158 peptides, 29 chains. Longest chain 8 peptides. Score 0.342 Round 3: 157 peptides, 29 chains. Longest chain 8 peptides. Score 0.338 Round 4: 165 peptides, 29 chains. Longest chain 11 peptides. Score 0.368 Round 5: 153 peptides, 28 chains. Longest chain 9 peptides. Score 0.339 Taking the results from Round 4 Chains 29, Residues 136, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4162 reflections ( 99.55 % complete ) and 7834 restraints for refining 3142 atoms. 7319 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2239 (Rfree = 0.000) for 3142 atoms. Found 14 (14 requested) and removed 16 (7 requested) atoms. Cycle 42: After refmac, R = 0.2035 (Rfree = 0.000) for 3125 atoms. Found 14 (14 requested) and removed 19 (7 requested) atoms. Cycle 43: After refmac, R = 0.1549 (Rfree = 0.000) for 3113 atoms. Found 5 (14 requested) and removed 44 (7 requested) atoms. Cycle 44: After refmac, R = 0.1404 (Rfree = 0.000) for 3069 atoms. Found 3 (14 requested) and removed 8 (7 requested) atoms. Cycle 45: After refmac, R = 0.1403 (Rfree = 0.000) for 3057 atoms. Found 8 (14 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.58 3.68 Search for helices and strands: 0 residues in 0 chains, 3125 seeds are put forward NCS extension: 7 residues added (0 deleted due to clashes), 3132 seeds are put forward Round 1: 108 peptides, 24 chains. Longest chain 7 peptides. Score 0.223 Round 2: 123 peptides, 25 chains. Longest chain 8 peptides. Score 0.270 Round 3: 133 peptides, 23 chains. Longest chain 11 peptides. Score 0.346 Round 4: 131 peptides, 24 chains. Longest chain 10 peptides. Score 0.321 Round 5: 121 peptides, 24 chains. Longest chain 9 peptides. Score 0.280 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 23, Residues 110, 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 ------------------------------------------------------ Failed to save intermediate PDB ---> Final restrained refinement block. No atom update. 4162 reflections ( 99.55 % complete ) and 7684 restraints for refining 3092 atoms. 7267 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2137 (Rfree = 0.000) for 3092 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.2126 (Rfree = 0.000) for 3074 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.1592 (Rfree = 0.000) for 3059 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.1356 (Rfree = 0.000) for 3046 atoms. TimeTaking 37.47