Sun 23 Dec 23:41:27 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-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vmf-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vmf-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vmf-3.8-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-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vmf-3.8-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 ============================================================ Sun 23 Dec 23:41:32 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-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vmf-3.8-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 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-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-3.8-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 3.800 Wilson plot Bfac: 69.06 4824 reflections ( 99.61 % complete ) and 0 restraints for refining 3870 atoms. Observations/parameters ratio is 0.31 ------------------------------------------------------ Starting model: R = 0.3132 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3116 (Rfree = 0.000) for 3870 atoms. Found 21 (21 requested) and removed 35 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.51 3.60 Search for helices and strands: 0 residues in 0 chains, 3927 seeds are put forward NCS extension: 0 residues added, 3927 seeds are put forward Round 1: 203 peptides, 39 chains. Longest chain 12 peptides. Score 0.351 Round 2: 248 peptides, 40 chains. Longest chain 17 peptides. Score 0.488 Round 3: 260 peptides, 36 chains. Longest chain 20 peptides. Score 0.574 Round 4: 271 peptides, 36 chains. Longest chain 30 peptides. Score 0.603 Round 5: 258 peptides, 35 chains. Longest chain 19 peptides. Score 0.580 Taking the results from Round 4 Chains 36, Residues 235, Estimated correctness of the model 0.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4824 reflections ( 99.61 % complete ) and 7146 restraints for refining 3148 atoms. 6242 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2325 (Rfree = 0.000) for 3148 atoms. Found 12 (17 requested) and removed 18 (8 requested) atoms. Cycle 2: After refmac, R = 0.2104 (Rfree = 0.000) for 3100 atoms. Found 5 (17 requested) and removed 19 (8 requested) atoms. Cycle 3: After refmac, R = 0.2080 (Rfree = 0.000) for 3071 atoms. Found 4 (16 requested) and removed 11 (8 requested) atoms. Cycle 4: After refmac, R = 0.1774 (Rfree = 0.000) for 3054 atoms. Found 2 (16 requested) and removed 10 (8 requested) atoms. Cycle 5: After refmac, R = 0.1767 (Rfree = 0.000) for 3040 atoms. Found 3 (16 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.46 3.55 Search for helices and strands: 0 residues in 0 chains, 3148 seeds are put forward NCS extension: 36 residues added (3 deleted due to clashes), 3184 seeds are put forward Round 1: 236 peptides, 41 chains. Longest chain 16 peptides. Score 0.436 Round 2: 250 peptides, 38 chains. Longest chain 14 peptides. Score 0.521 Round 3: 234 peptides, 35 chains. Longest chain 15 peptides. Score 0.512 Round 4: 235 peptides, 28 chains. Longest chain 27 peptides. Score 0.603 Round 5: 243 peptides, 34 chains. Longest chain 17 peptides. Score 0.551 Taking the results from Round 4 Chains 28, Residues 207, Estimated correctness of the model 0.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4824 reflections ( 99.61 % complete ) and 7215 restraints for refining 3147 atoms. 6415 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2099 (Rfree = 0.000) for 3147 atoms. Found 9 (17 requested) and removed 21 (8 requested) atoms. Cycle 7: After refmac, R = 0.2079 (Rfree = 0.000) for 3117 atoms. Found 13 (17 requested) and removed 19 (8 requested) atoms. Cycle 8: After refmac, R = 0.2004 (Rfree = 0.000) for 3104 atoms. Found 17 (17 requested) and removed 17 (8 requested) atoms. Cycle 9: After refmac, R = 0.1658 (Rfree = 0.000) for 3097 atoms. Found 7 (17 requested) and removed 13 (8 requested) atoms. Cycle 10: After refmac, R = 0.1581 (Rfree = 0.000) for 3088 atoms. Found 0 (16 requested) and removed 14 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.51 3.60 Search for helices and strands: 0 residues in 0 chains, 3203 seeds are put forward NCS extension: 29 residues added (1 deleted due to clashes), 3232 seeds are put forward Round 1: 214 peptides, 36 chains. Longest chain 11 peptides. Score 0.434 Round 2: 241 peptides, 30 chains. Longest chain 24 peptides. Score 0.595 Round 3: 235 peptides, 26 chains. Longest chain 24 peptides. Score 0.627 Round 4: 249 peptides, 25 chains. Longest chain 33 peptides. Score 0.671 Round 5: 231 peptides, 30 chains. Longest chain 27 peptides. Score 0.568 Taking the results from Round 4 Chains 25, Residues 224, Estimated correctness of the model 29.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4824 reflections ( 99.61 % complete ) and 7124 restraints for refining 3147 atoms. 6253 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2114 (Rfree = 0.000) for 3147 atoms. Found 16 (17 requested) and removed 18 (8 requested) atoms. Cycle 12: After refmac, R = 0.1954 (Rfree = 0.000) for 3134 atoms. Found 6 (17 requested) and removed 14 (8 requested) atoms. Cycle 13: After refmac, R = 0.1909 (Rfree = 0.000) for 3123 atoms. Found 2 (17 requested) and removed 9 (8 requested) atoms. Cycle 14: After refmac, R = 0.1860 (Rfree = 0.000) for 3116 atoms. Found 3 (17 requested) and removed 8 (8 requested) atoms. Cycle 15: After refmac, R = 0.1843 (Rfree = 0.000) for 3109 atoms. Found 1 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.50 3.59 Search for helices and strands: 0 residues in 0 chains, 3183 seeds are put forward NCS extension: 32 residues added (1 deleted due to clashes), 3215 seeds are put forward Round 1: 220 peptides, 37 chains. Longest chain 12 peptides. Score 0.440 Round 2: 226 peptides, 36 chains. Longest chain 18 peptides. Score 0.473 Round 3: 224 peptides, 34 chains. Longest chain 18 peptides. Score 0.495 Round 4: 230 peptides, 31 chains. Longest chain 19 peptides. Score 0.552 Round 5: 234 peptides, 31 chains. Longest chain 16 peptides. Score 0.564 Taking the results from Round 5 Chains 31, Residues 203, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 4824 reflections ( 99.61 % complete ) and 7229 restraints for refining 3148 atoms. 6429 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2121 (Rfree = 0.000) for 3148 atoms. Found 10 (17 requested) and removed 9 (8 requested) atoms. Cycle 17: After refmac, R = 0.1950 (Rfree = 0.000) for 3134 atoms. Found 2 (17 requested) and removed 8 (8 requested) atoms. Cycle 18: After refmac, R = 0.1910 (Rfree = 0.000) for 3119 atoms. Found 3 (17 requested) and removed 10 (8 requested) atoms. Cycle 19: After refmac, R = 0.1871 (Rfree = 0.000) for 3108 atoms. Found 6 (17 requested) and removed 8 (8 requested) atoms. Cycle 20: After refmac, R = 0.1862 (Rfree = 0.000) for 3104 atoms. Found 1 (17 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.53 3.63 Search for helices and strands: 0 residues in 0 chains, 3173 seeds are put forward NCS extension: 30 residues added (1 deleted due to clashes), 3203 seeds are put forward Round 1: 209 peptides, 40 chains. Longest chain 9 peptides. Score 0.357 Round 2: 216 peptides, 34 chains. Longest chain 15 peptides. Score 0.469 Round 3: 224 peptides, 33 chains. Longest chain 24 peptides. Score 0.508 Round 4: 229 peptides, 32 chains. Longest chain 17 peptides. Score 0.536 Round 5: 228 peptides, 35 chains. Longest chain 13 peptides. Score 0.493 Taking the results from Round 4 Chains 32, Residues 197, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4824 reflections ( 99.61 % complete ) and 7381 restraints for refining 3147 atoms. 6625 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2298 (Rfree = 0.000) for 3147 atoms. Found 17 (17 requested) and removed 16 (8 requested) atoms. Cycle 22: After refmac, R = 0.2195 (Rfree = 0.000) for 3133 atoms. Found 14 (17 requested) and removed 14 (8 requested) atoms. Cycle 23: After refmac, R = 0.1847 (Rfree = 0.000) for 3127 atoms. Found 1 (17 requested) and removed 12 (8 requested) atoms. Cycle 24: After refmac, R = 0.1794 (Rfree = 0.000) for 3111 atoms. Found 2 (17 requested) and removed 11 (8 requested) atoms. Cycle 25: After refmac, R = 0.1761 (Rfree = 0.000) for 3101 atoms. Found 1 (17 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.51 3.60 Search for helices and strands: 0 residues in 0 chains, 3178 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 3198 seeds are put forward Round 1: 185 peptides, 34 chains. Longest chain 10 peptides. Score 0.363 Round 2: 191 peptides, 30 chains. Longest chain 17 peptides. Score 0.444 Round 3: 179 peptides, 27 chains. Longest chain 14 peptides. Score 0.448 Round 4: 195 peptides, 28 chains. Longest chain 19 peptides. Score 0.487 Round 5: 194 peptides, 25 chains. Longest chain 17 peptides. Score 0.526 Taking the results from Round 5 Chains 25, Residues 169, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4824 reflections ( 99.61 % complete ) and 7574 restraints for refining 3148 atoms. 6923 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2241 (Rfree = 0.000) for 3148 atoms. Found 17 (17 requested) and removed 16 (8 requested) atoms. Cycle 27: After refmac, R = 0.2146 (Rfree = 0.000) for 3129 atoms. Found 17 (17 requested) and removed 11 (8 requested) atoms. Cycle 28: After refmac, R = 0.2092 (Rfree = 0.000) for 3128 atoms. Found 14 (17 requested) and removed 13 (8 requested) atoms. Cycle 29: After refmac, R = 0.1767 (Rfree = 0.000) for 3121 atoms. Found 4 (17 requested) and removed 13 (8 requested) atoms. Cycle 30: After refmac, R = 0.1812 (Rfree = 0.000) for 3106 atoms. Found 8 (17 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.43 3.52 Search for helices and strands: 0 residues in 0 chains, 3198 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 3217 seeds are put forward Round 1: 147 peptides, 29 chains. Longest chain 8 peptides. Score 0.299 Round 2: 214 peptides, 34 chains. Longest chain 19 peptides. Score 0.463 Round 3: 208 peptides, 33 chains. Longest chain 11 peptides. Score 0.457 Round 4: 212 peptides, 31 chains. Longest chain 13 peptides. Score 0.498 Round 5: 214 peptides, 31 chains. Longest chain 18 peptides. Score 0.505 Taking the results from Round 5 Chains 31, Residues 183, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4824 reflections ( 99.61 % complete ) and 7391 restraints for refining 3144 atoms. 6690 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2118 (Rfree = 0.000) for 3144 atoms. Found 17 (17 requested) and removed 14 (8 requested) atoms. Cycle 32: After refmac, R = 0.2098 (Rfree = 0.000) for 3129 atoms. Found 17 (17 requested) and removed 14 (8 requested) atoms. Cycle 33: After refmac, R = 0.2077 (Rfree = 0.000) for 3121 atoms. Found 17 (17 requested) and removed 14 (8 requested) atoms. Cycle 34: After refmac, R = 0.1927 (Rfree = 0.000) for 3121 atoms. Found 17 (17 requested) and removed 13 (8 requested) atoms. Cycle 35: After refmac, R = 0.1833 (Rfree = 0.000) for 3121 atoms. Found 17 (17 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.52 3.62 Search for helices and strands: 0 residues in 0 chains, 3224 seeds are put forward NCS extension: 18 residues added (3 deleted due to clashes), 3242 seeds are put forward Round 1: 150 peptides, 33 chains. Longest chain 6 peptides. Score 0.243 Round 2: 185 peptides, 35 chains. Longest chain 13 peptides. Score 0.347 Round 3: 186 peptides, 33 chains. Longest chain 12 peptides. Score 0.382 Round 4: 199 peptides, 35 chains. Longest chain 11 peptides. Score 0.397 Round 5: 181 peptides, 32 chains. Longest chain 18 peptides. Score 0.379 Taking the results from Round 4 Chains 35, Residues 164, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4824 reflections ( 99.61 % complete ) and 7651 restraints for refining 3148 atoms. 7030 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2229 (Rfree = 0.000) for 3148 atoms. Found 17 (17 requested) and removed 9 (8 requested) atoms. Cycle 37: After refmac, R = 0.2202 (Rfree = 0.000) for 3139 atoms. Found 17 (17 requested) and removed 16 (8 requested) atoms. Cycle 38: After refmac, R = 0.1862 (Rfree = 0.000) for 3133 atoms. Found 17 (17 requested) and removed 14 (8 requested) atoms. Cycle 39: After refmac, R = 0.1501 (Rfree = 0.000) for 3130 atoms. Found 1 (17 requested) and removed 14 (8 requested) atoms. Cycle 40: After refmac, R = 0.1395 (Rfree = 0.000) for 3113 atoms. Found 5 (17 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.47 3.56 Search for helices and strands: 0 residues in 0 chains, 3199 seeds are put forward NCS extension: 0 residues added, 3199 seeds are put forward Round 1: 156 peptides, 34 chains. Longest chain 9 peptides. Score 0.251 Round 2: 160 peptides, 32 chains. Longest chain 8 peptides. Score 0.300 Round 3: 170 peptides, 31 chains. Longest chain 9 peptides. Score 0.354 Round 4: 165 peptides, 30 chains. Longest chain 9 peptides. Score 0.352 Round 5: 165 peptides, 29 chains. Longest chain 10 peptides. Score 0.368 Taking the results from Round 5 Chains 29, Residues 136, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4824 reflections ( 99.61 % complete ) and 7855 restraints for refining 3148 atoms. 7340 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2075 (Rfree = 0.000) for 3148 atoms. Found 15 (17 requested) and removed 14 (8 requested) atoms. Cycle 42: After refmac, R = 0.1988 (Rfree = 0.000) for 3132 atoms. Found 17 (17 requested) and removed 12 (8 requested) atoms. Cycle 43: After refmac, R = 0.1870 (Rfree = 0.000) for 3136 atoms. Found 17 (17 requested) and removed 12 (8 requested) atoms. Cycle 44: After refmac, R = 0.1788 (Rfree = 0.000) for 3134 atoms. Found 17 (17 requested) and removed 12 (8 requested) atoms. Cycle 45: After refmac, R = 0.1670 (Rfree = 0.000) for 3135 atoms. Found 13 (17 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.48 3.57 Search for helices and strands: 0 residues in 0 chains, 3224 seeds are put forward NCS extension: 0 residues added, 3224 seeds are put forward Round 1: 138 peptides, 29 chains. Longest chain 10 peptides. Score 0.262 Round 2: 155 peptides, 31 chains. Longest chain 10 peptides. Score 0.297 Round 3: 169 peptides, 30 chains. Longest chain 11 peptides. Score 0.367 Round 4: 156 peptides, 26 chains. Longest chain 11 peptides. Score 0.383 Round 5: 162 peptides, 29 chains. Longest chain 14 peptides. Score 0.357 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 26, 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-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4824 reflections ( 99.61 % complete ) and 7824 restraints for refining 3148 atoms. 7330 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2096 (Rfree = 0.000) for 3148 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.2130 (Rfree = 0.000) for 3134 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.1985 (Rfree = 0.000) for 3118 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.1551 (Rfree = 0.000) for 3106 atoms. TimeTaking 36.38