Sun 23 Dec 22:22:56 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 1vmf-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vmf-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vmf-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vmf-4.0-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/1vmf-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vmf-4.0-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 22:23:05 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/1vmf-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vmf-4.0-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 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-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: 19 Cell parameters: 57.443 58.601 135.061 90.000 90.000 90.000 Input sequence file: 1vmf-4.0-parrot-hancs.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 Failed to save intermediate PDB 4162 reflections ( 99.55 % complete ) and 0 restraints for refining 3874 atoms. Observations/parameters ratio is 0.27 ------------------------------------------------------ Starting model: R = 0.3212 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3096 (Rfree = 0.000) for 3874 atoms. Found 18 (18 requested) and removed 28 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.65 3.75 Search for helices and strands: 0 residues in 0 chains, 3936 seeds are put forward NCS extension: 0 residues added, 3936 seeds are put forward Round 1: 156 peptides, 32 chains. Longest chain 8 peptides. Score 0.284 Round 2: 201 peptides, 33 chains. Longest chain 15 peptides. Score 0.434 Round 3: 210 peptides, 27 chains. Longest chain 15 peptides. Score 0.546 Round 4: 217 peptides, 26 chains. Longest chain 22 peptides. Score 0.579 Round 5: 221 peptides, 26 chains. Longest chain 22 peptides. Score 0.590 Taking the results from Round 5 Chains 26, Residues 195, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4162 reflections ( 99.55 % complete ) and 7263 restraints for refining 3140 atoms. 6509 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2782 (Rfree = 0.000) for 3140 atoms. Found 14 (14 requested) and removed 17 (7 requested) atoms. Cycle 2: After refmac, R = 0.2161 (Rfree = 0.000) for 3078 atoms. Found 9 (14 requested) and removed 17 (7 requested) atoms. Cycle 3: After refmac, R = 0.2200 (Rfree = 0.000) for 3048 atoms. Found 7 (14 requested) and removed 13 (7 requested) atoms. Cycle 4: After refmac, R = 0.2151 (Rfree = 0.000) for 3034 atoms. Found 2 (14 requested) and removed 13 (7 requested) atoms. Cycle 5: After refmac, R = 0.1956 (Rfree = 0.000) for 3015 atoms. Found 7 (14 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.60 3.70 Search for helices and strands: 0 residues in 0 chains, 3111 seeds are put forward NCS extension: 27 residues added (4 deleted due to clashes), 3138 seeds are put forward Round 1: 198 peptides, 38 chains. Longest chain 14 peptides. Score 0.348 Round 2: 221 peptides, 32 chains. Longest chain 20 peptides. Score 0.512 Round 3: 232 peptides, 31 chains. Longest chain 14 peptides. Score 0.558 Round 4: 243 peptides, 32 chains. Longest chain 13 peptides. Score 0.576 Round 5: 239 peptides, 33 chains. Longest chain 14 peptides. Score 0.552 Taking the results from Round 4 Chains 33, Residues 211, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4162 reflections ( 99.55 % complete ) and 7230 restraints for refining 3140 atoms. 6387 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2123 (Rfree = 0.000) for 3140 atoms. Found 9 (14 requested) and removed 16 (7 requested) atoms. Cycle 7: After refmac, R = 0.1948 (Rfree = 0.000) for 3102 atoms. Found 7 (14 requested) and removed 14 (7 requested) atoms. Cycle 8: After refmac, R = 0.1858 (Rfree = 0.000) for 3081 atoms. Found 5 (14 requested) and removed 8 (7 requested) atoms. Cycle 9: After refmac, R = 0.1797 (Rfree = 0.000) for 3066 atoms. Found 5 (14 requested) and removed 8 (7 requested) atoms. Cycle 10: After refmac, R = 0.1737 (Rfree = 0.000) for 3060 atoms. Found 4 (14 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.64 3.74 Search for helices and strands: 0 residues in 0 chains, 3157 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 3171 seeds are put forward Round 1: 203 peptides, 36 chains. Longest chain 12 peptides. Score 0.396 Round 2: 222 peptides, 34 chains. Longest chain 15 peptides. Score 0.488 Round 3: 226 peptides, 32 chains. Longest chain 14 peptides. Score 0.527 Round 4: 236 peptides, 35 chains. Longest chain 14 peptides. Score 0.518 Round 5: 236 peptides, 33 chains. Longest chain 16 peptides. Score 0.544 Taking the results from Round 5 Chains 33, Residues 203, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4162 reflections ( 99.55 % complete ) and 7313 restraints for refining 3142 atoms. 6534 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2176 (Rfree = 0.000) for 3142 atoms. Found 7 (14 requested) and removed 16 (7 requested) atoms. Cycle 12: After refmac, R = 0.1956 (Rfree = 0.000) for 3106 atoms. Found 2 (14 requested) and removed 16 (7 requested) atoms. Failed to save intermediate PDB Cycle 13: After refmac, R = 0.1978 (Rfree = 0.000) for 3084 atoms. Found 10 (14 requested) and removed 16 (7 requested) atoms. Cycle 14: After refmac, R = 0.1969 (Rfree = 0.000) for 3072 atoms. Found 14 (14 requested) and removed 11 (7 requested) atoms. Cycle 15: After refmac, R = 0.2029 (Rfree = 0.000) for 3066 atoms. Found 14 (14 requested) and removed 16 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.56 3.66 Search for helices and strands: 0 residues in 0 chains, 3185 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 3204 seeds are put forward Round 1: 181 peptides, 37 chains. Longest chain 9 peptides. Score 0.300 Round 2: 197 peptides, 34 chains. Longest chain 11 peptides. Score 0.405 Round 3: 214 peptides, 36 chains. Longest chain 13 peptides. Score 0.434 Round 4: 208 peptides, 35 chains. Longest chain 13 peptides. Score 0.428 Round 5: 219 peptides, 39 chains. Longest chain 11 peptides. Score 0.408 Taking the results from Round 3 Chains 36, Residues 178, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4162 reflections ( 99.55 % complete ) and 7323 restraints for refining 3138 atoms. 6647 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2118 (Rfree = 0.000) for 3138 atoms. Found 14 (14 requested) and removed 24 (7 requested) atoms. Cycle 17: After refmac, R = 0.2113 (Rfree = 0.000) for 3099 atoms. Found 14 (14 requested) and removed 16 (7 requested) atoms. Cycle 18: After refmac, R = 0.1969 (Rfree = 0.000) for 3081 atoms. Found 14 (14 requested) and removed 14 (7 requested) atoms. Cycle 19: After refmac, R = 0.2037 (Rfree = 0.000) for 3072 atoms. Found 14 (14 requested) and removed 12 (7 requested) atoms. Cycle 20: After refmac, R = 0.1856 (Rfree = 0.000) for 3066 atoms. Found 14 (14 requested) and removed 16 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.63 3.73 Search for helices and strands: 0 residues in 0 chains, 3184 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 3201 seeds are put forward Round 1: 181 peptides, 37 chains. Longest chain 12 peptides. Score 0.300 Round 2: 209 peptides, 35 chains. Longest chain 16 peptides. Score 0.432 Round 3: 204 peptides, 36 chains. Longest chain 12 peptides. Score 0.400 Round 4: 204 peptides, 32 chains. Longest chain 15 peptides. Score 0.459 Round 5: 221 peptides, 36 chains. Longest chain 15 peptides. Score 0.457 Taking the results from Round 4 Chains 32, Residues 172, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4162 reflections ( 99.55 % complete ) and 7672 restraints for refining 3142 atoms. 7016 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2119 (Rfree = 0.000) for 3142 atoms. Found 14 (14 requested) and removed 17 (7 requested) atoms. Cycle 22: After refmac, R = 0.2196 (Rfree = 0.000) for 3126 atoms. Found 14 (14 requested) and removed 15 (7 requested) atoms. Cycle 23: After refmac, R = 0.1958 (Rfree = 0.000) for 3114 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. Cycle 24: After refmac, R = 0.1600 (Rfree = 0.000) for 3109 atoms. Found 4 (14 requested) and removed 9 (7 requested) atoms. Cycle 25: After refmac, R = 0.1399 (Rfree = 0.000) for 3100 atoms. Found 5 (14 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.62 3.72 Search for helices and strands: 0 residues in 0 chains, 3190 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 3205 seeds are put forward Round 1: 174 peptides, 34 chains. Longest chain 12 peptides. Score 0.322 Round 2: 175 peptides, 27 chains. Longest chain 13 peptides. Score 0.435 Round 3: 179 peptides, 31 chains. Longest chain 14 peptides. Score 0.387 Round 4: 181 peptides, 29 chains. Longest chain 12 peptides. Score 0.425 Round 5: 169 peptides, 27 chains. Longest chain 13 peptides. Score 0.414 Taking the results from Round 2 Chains 27, Residues 148, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4162 reflections ( 99.55 % complete ) and 7637 restraints for refining 3141 atoms. 7072 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2188 (Rfree = 0.000) for 3141 atoms. Found 14 (14 requested) and removed 14 (7 requested) atoms. Cycle 27: After refmac, R = 0.2140 (Rfree = 0.000) for 3126 atoms. Found 14 (14 requested) and removed 20 (7 requested) atoms. Cycle 28: After refmac, R = 0.1495 (Rfree = 0.000) for 3117 atoms. Found 5 (14 requested) and removed 10 (7 requested) atoms. Cycle 29: After refmac, R = 0.1845 (Rfree = 0.000) for 3108 atoms. Found 14 (14 requested) and removed 14 (7 requested) atoms. Cycle 30: After refmac, R = 0.1715 (Rfree = 0.000) for 3103 atoms. Found 14 (14 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.62 3.72 Search for helices and strands: 0 residues in 0 chains, 3204 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 3222 seeds are put forward Round 1: 155 peptides, 31 chains. Longest chain 9 peptides. Score 0.297 Round 2: 175 peptides, 29 chains. Longest chain 11 peptides. Score 0.404 Round 3: 173 peptides, 31 chains. Longest chain 12 peptides. Score 0.366 Round 4: 179 peptides, 29 chains. Longest chain 14 peptides. Score 0.418 Round 5: 180 peptides, 31 chains. Longest chain 15 peptides. Score 0.391 Taking the results from Round 4 Chains 29, Residues 150, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4162 reflections ( 99.55 % complete ) and 7698 restraints for refining 3141 atoms. 7127 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2200 (Rfree = 0.000) for 3141 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. Cycle 32: After refmac, R = 0.2019 (Rfree = 0.000) for 3129 atoms. Found 14 (14 requested) and removed 12 (7 requested) atoms. Cycle 33: After refmac, R = 0.1875 (Rfree = 0.000) for 3123 atoms. Found 14 (14 requested) and removed 10 (7 requested) atoms. Cycle 34: After refmac, R = 0.1572 (Rfree = 0.000) for 3114 atoms. Found 5 (14 requested) and removed 13 (7 requested) atoms. Cycle 35: After refmac, R = 0.1369 (Rfree = 0.000) for 3102 atoms. Found 4 (14 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.57 3.67 Search for helices and strands: 0 residues in 0 chains, 3183 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 3204 seeds are put forward Round 1: 159 peptides, 31 chains. Longest chain 12 peptides. Score 0.313 Round 2: 173 peptides, 32 chains. Longest chain 11 peptides. Score 0.350 Round 3: 179 peptides, 32 chains. Longest chain 11 peptides. Score 0.372 Round 4: 178 peptides, 28 chains. Longest chain 13 peptides. Score 0.430 Round 5: 178 peptides, 29 chains. Longest chain 11 peptides. Score 0.415 Taking the results from Round 4 Chains 28, Residues 150, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4162 reflections ( 99.55 % complete ) and 7590 restraints for refining 3142 atoms. 7018 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2075 (Rfree = 0.000) for 3142 atoms. Found 14 (14 requested) and removed 11 (7 requested) atoms. Cycle 37: After refmac, R = 0.2287 (Rfree = 0.000) for 3133 atoms. Found 14 (14 requested) and removed 24 (7 requested) atoms. Cycle 38: After refmac, R = 0.1945 (Rfree = 0.000) for 3113 atoms. Found 14 (14 requested) and removed 20 (7 requested) atoms. Cycle 39: After refmac, R = 0.1554 (Rfree = 0.000) for 3103 atoms. Found 5 (14 requested) and removed 11 (7 requested) atoms. Cycle 40: After refmac, R = 0.1474 (Rfree = 0.000) for 3092 atoms. Found 2 (14 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.61 3.71 Search for helices and strands: 0 residues in 0 chains, 3191 seeds are put forward NCS extension: 12 residues added (2 deleted due to clashes), 3203 seeds are put forward Round 1: 143 peptides, 28 chains. Longest chain 12 peptides. Score 0.300 Round 2: 159 peptides, 28 chains. Longest chain 14 peptides. Score 0.362 Round 3: 160 peptides, 28 chains. Longest chain 11 peptides. Score 0.365 Round 4: 163 peptides, 25 chains. Longest chain 15 peptides. Score 0.424 Round 5: 173 peptides, 30 chains. Longest chain 12 peptides. Score 0.381 Taking the results from Round 4 Chains 25, Residues 138, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4162 reflections ( 99.55 % complete ) and 7606 restraints for refining 3141 atoms. 7079 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2063 (Rfree = 0.000) for 3141 atoms. Found 14 (14 requested) and removed 11 (7 requested) atoms. Cycle 42: After refmac, R = 0.1648 (Rfree = 0.000) for 3133 atoms. Found 8 (14 requested) and removed 12 (7 requested) atoms. Cycle 43: After refmac, R = 0.1477 (Rfree = 0.000) for 3120 atoms. Found 2 (14 requested) and removed 9 (7 requested) atoms. Cycle 44: After refmac, R = 0.1444 (Rfree = 0.000) for 3109 atoms. Found 2 (14 requested) and removed 9 (7 requested) atoms. Cycle 45: After refmac, R = 0.1423 (Rfree = 0.000) for 3102 atoms. Found 2 (14 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.62 3.72 Search for helices and strands: 0 residues in 0 chains, 3188 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 3204 seeds are put forward Round 1: 112 peptides, 22 chains. Longest chain 10 peptides. Score 0.278 Round 2: 133 peptides, 25 chains. Longest chain 10 peptides. Score 0.311 Round 3: 144 peptides, 23 chains. Longest chain 10 peptides. Score 0.388 Round 4: 149 peptides, 22 chains. Longest chain 13 peptides. Score 0.422 Round 5: 150 peptides, 20 chains. Longest chain 23 peptides. Score 0.457 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 20, Residues 130, 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 7726 restraints for refining 3141 atoms. 7226 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1886 (Rfree = 0.000) for 3141 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.2386 (Rfree = 0.000) for 3121 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.1953 (Rfree = 0.000) for 3110 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.1823 (Rfree = 0.000) for 3098 atoms. TimeTaking 52.42