Sun 23 Dec 22:22:49 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-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vmf-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vmf-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vmf-3.8-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-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vmf-3.8-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 22:22:59 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-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vmf-3.8-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 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-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-3.8-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 3.800 Wilson plot Bfac: 69.06 4824 reflections ( 99.61 % complete ) and 0 restraints for refining 3848 atoms. Observations/parameters ratio is 0.31 ------------------------------------------------------ Starting model: R = 0.3149 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2978 (Rfree = 0.000) for 3848 atoms. Found 21 (21 requested) and removed 32 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.50 3.59 Search for helices and strands: 0 residues in 0 chains, 3907 seeds are put forward NCS extension: 0 residues added, 3907 seeds are put forward Round 1: 181 peptides, 34 chains. Longest chain 10 peptides. Score 0.348 Round 2: 228 peptides, 33 chains. Longest chain 16 peptides. Score 0.520 Round 3: 244 peptides, 34 chains. Longest chain 16 peptides. Score 0.554 Round 4: 267 peptides, 31 chains. Longest chain 21 peptides. Score 0.649 Round 5: 270 peptides, 33 chains. Longest chain 24 peptides. Score 0.634 Taking the results from Round 4 Chains 31, Residues 236, Estimated correctness of the model 20.4 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 4824 reflections ( 99.61 % complete ) and 6937 restraints for refining 3148 atoms. 5968 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2423 (Rfree = 0.000) for 3148 atoms. Found 12 (17 requested) and removed 27 (8 requested) atoms. Cycle 2: After refmac, R = 0.2375 (Rfree = 0.000) for 3086 atoms. Found 17 (17 requested) and removed 22 (8 requested) atoms. Cycle 3: After refmac, R = 0.2194 (Rfree = 0.000) for 3065 atoms. Found 10 (16 requested) and removed 31 (8 requested) atoms. Cycle 4: After refmac, R = 0.2060 (Rfree = 0.000) for 3030 atoms. Found 8 (16 requested) and removed 13 (8 requested) atoms. Cycle 5: After refmac, R = 0.2005 (Rfree = 0.000) for 3015 atoms. Found 5 (16 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.45 3.54 Search for helices and strands: 0 residues in 0 chains, 3106 seeds are put forward NCS extension: 22 residues added (4 deleted due to clashes), 3128 seeds are put forward Round 1: 220 peptides, 40 chains. Longest chain 13 peptides. Score 0.396 Round 2: 235 peptides, 33 chains. Longest chain 14 peptides. Score 0.541 Round 3: 252 peptides, 37 chains. Longest chain 14 peptides. Score 0.539 Round 4: 240 peptides, 32 chains. Longest chain 21 peptides. Score 0.568 Round 5: 231 peptides, 32 chains. Longest chain 16 peptides. Score 0.542 Taking the results from Round 4 Chains 34, Residues 208, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 4824 reflections ( 99.61 % complete ) and 7264 restraints for refining 3148 atoms. 6433 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2081 (Rfree = 0.000) for 3148 atoms. Found 12 (17 requested) and removed 21 (8 requested) atoms. Cycle 7: After refmac, R = 0.2009 (Rfree = 0.000) for 3128 atoms. Found 13 (17 requested) and removed 17 (8 requested) atoms. Cycle 8: After refmac, R = 0.1937 (Rfree = 0.000) for 3117 atoms. Found 13 (17 requested) and removed 15 (8 requested) atoms. Cycle 9: After refmac, R = 0.1804 (Rfree = 0.000) for 3113 atoms. Found 12 (17 requested) and removed 10 (8 requested) atoms. Cycle 10: After refmac, R = 0.1466 (Rfree = 0.000) for 3107 atoms. Found 5 (17 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.47 3.56 Search for helices and strands: 0 residues in 0 chains, 3206 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 3231 seeds are put forward Round 1: 201 peptides, 35 chains. Longest chain 14 peptides. Score 0.404 Round 2: 223 peptides, 31 chains. Longest chain 15 peptides. Score 0.532 Round 3: 224 peptides, 31 chains. Longest chain 17 peptides. Score 0.535 Round 4: 242 peptides, 30 chains. Longest chain 23 peptides. Score 0.598 Round 5: 247 peptides, 30 chains. Longest chain 26 peptides. Score 0.611 Taking the results from Round 5 Chains 30, Residues 217, Estimated correctness of the model 3.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4824 reflections ( 99.61 % complete ) and 7158 restraints for refining 3148 atoms. 6320 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1992 (Rfree = 0.000) for 3148 atoms. Found 12 (17 requested) and removed 10 (8 requested) atoms. Cycle 12: After refmac, R = 0.1786 (Rfree = 0.000) for 3128 atoms. Found 7 (17 requested) and removed 10 (8 requested) atoms. Cycle 13: After refmac, R = 0.1912 (Rfree = 0.000) for 3120 atoms. Found 10 (17 requested) and removed 10 (8 requested) atoms. Cycle 14: After refmac, R = 0.1876 (Rfree = 0.000) for 3112 atoms. Found 17 (17 requested) and removed 9 (8 requested) atoms. Cycle 15: After refmac, R = 0.1999 (Rfree = 0.000) for 3113 atoms. Found 17 (17 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.46 3.55 Search for helices and strands: 0 residues in 0 chains, 3233 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 3253 seeds are put forward Round 1: 183 peptides, 32 chains. Longest chain 16 peptides. Score 0.386 Round 2: 211 peptides, 30 chains. Longest chain 17 peptides. Score 0.509 Round 3: 215 peptides, 28 chains. Longest chain 18 peptides. Score 0.548 Round 4: 201 peptides, 28 chains. Longest chain 14 peptides. Score 0.506 Round 5: 212 peptides, 33 chains. Longest chain 16 peptides. Score 0.470 Taking the results from Round 3 Chains 28, Residues 187, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4824 reflections ( 99.61 % complete ) and 7330 restraints for refining 3148 atoms. 6610 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2103 (Rfree = 0.000) for 3148 atoms. Found 17 (17 requested) and removed 16 (8 requested) atoms. Cycle 17: After refmac, R = 0.1960 (Rfree = 0.000) for 3133 atoms. Found 17 (17 requested) and removed 14 (8 requested) atoms. Cycle 18: After refmac, R = 0.1944 (Rfree = 0.000) for 3126 atoms. Found 17 (17 requested) and removed 9 (8 requested) atoms. Cycle 19: After refmac, R = 0.1990 (Rfree = 0.000) for 3125 atoms. Found 17 (17 requested) and removed 12 (8 requested) atoms. Cycle 20: After refmac, R = 0.1790 (Rfree = 0.000) for 3124 atoms. Found 17 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.47 3.56 Search for helices and strands: 0 residues in 0 chains, 3243 seeds are put forward NCS extension: 25 residues added (3 deleted due to clashes), 3268 seeds are put forward Round 1: 191 peptides, 36 chains. Longest chain 15 peptides. Score 0.353 Round 2: 229 peptides, 35 chains. Longest chain 15 peptides. Score 0.496 Round 3: 216 peptides, 32 chains. Longest chain 12 peptides. Score 0.497 Round 4: 221 peptides, 33 chains. Longest chain 14 peptides. Score 0.499 Round 5: 226 peptides, 28 chains. Longest chain 20 peptides. Score 0.579 Taking the results from Round 5 Chains 28, Residues 198, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4824 reflections ( 99.61 % complete ) and 7268 restraints for refining 3148 atoms. 6504 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2140 (Rfree = 0.000) for 3148 atoms. Found 17 (17 requested) and removed 19 (8 requested) atoms. Cycle 22: After refmac, R = 0.1994 (Rfree = 0.000) for 3129 atoms. Found 17 (17 requested) and removed 15 (8 requested) atoms. Cycle 23: After refmac, R = 0.1682 (Rfree = 0.000) for 3123 atoms. Found 17 (17 requested) and removed 20 (8 requested) atoms. Cycle 24: After refmac, R = 0.1794 (Rfree = 0.000) for 3115 atoms. Found 17 (17 requested) and removed 14 (8 requested) atoms. Cycle 25: After refmac, R = 0.1660 (Rfree = 0.000) for 3114 atoms. Found 17 (17 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.43 3.52 Search for helices and strands: 0 residues in 0 chains, 3215 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 3230 seeds are put forward Round 1: 162 peptides, 32 chains. Longest chain 10 peptides. Score 0.308 Round 2: 195 peptides, 34 chains. Longest chain 13 peptides. Score 0.398 Round 3: 213 peptides, 30 chains. Longest chain 18 peptides. Score 0.515 Round 4: 213 peptides, 32 chains. Longest chain 15 peptides. Score 0.488 Round 5: 221 peptides, 34 chains. Longest chain 15 peptides. Score 0.485 Taking the results from Round 3 Chains 30, Residues 183, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4824 reflections ( 99.61 % complete ) and 7279 restraints for refining 3148 atoms. 6577 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2019 (Rfree = 0.000) for 3148 atoms. Found 10 (17 requested) and removed 18 (8 requested) atoms. Cycle 27: After refmac, R = 0.1821 (Rfree = 0.000) for 3125 atoms. Found 17 (17 requested) and removed 13 (8 requested) atoms. Cycle 28: After refmac, R = 0.1804 (Rfree = 0.000) for 3115 atoms. Found 17 (17 requested) and removed 14 (8 requested) atoms. Cycle 29: After refmac, R = 0.1744 (Rfree = 0.000) for 3111 atoms. Found 17 (17 requested) and removed 9 (8 requested) atoms. Cycle 30: After refmac, R = 0.1804 (Rfree = 0.000) for 3110 atoms. Found 17 (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, 3206 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 3221 seeds are put forward Round 1: 156 peptides, 33 chains. Longest chain 9 peptides. Score 0.268 Round 2: 186 peptides, 32 chains. Longest chain 12 peptides. Score 0.397 Round 3: 197 peptides, 31 chains. Longest chain 15 peptides. Score 0.450 Round 4: 199 peptides, 29 chains. Longest chain 15 peptides. Score 0.485 Round 5: 194 peptides, 32 chains. Longest chain 10 peptides. Score 0.425 Taking the results from Round 4 Chains 29, Residues 170, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 4824 reflections ( 99.61 % complete ) and 7310 restraints for refining 3147 atoms. 6630 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2104 (Rfree = 0.000) for 3147 atoms. Found 17 (17 requested) and removed 18 (8 requested) atoms. Cycle 32: After refmac, R = 0.2093 (Rfree = 0.000) for 3128 atoms. Found 17 (17 requested) and removed 34 (8 requested) atoms. Cycle 33: After refmac, R = 0.1870 (Rfree = 0.000) for 3101 atoms. Found 17 (17 requested) and removed 10 (8 requested) atoms. Cycle 34: After refmac, R = 0.1971 (Rfree = 0.000) for 3101 atoms. Found 17 (17 requested) and removed 22 (8 requested) atoms. Cycle 35: After refmac, R = 0.1766 (Rfree = 0.000) for 3090 atoms. Found 17 (17 requested) and removed 14 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.46 3.55 Search for helices and strands: 0 residues in 0 chains, 3191 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 3206 seeds are put forward Round 1: 141 peptides, 29 chains. Longest chain 10 peptides. Score 0.275 Round 2: 156 peptides, 27 chains. Longest chain 11 peptides. Score 0.367 Round 3: 167 peptides, 30 chains. Longest chain 12 peptides. Score 0.359 Round 4: 167 peptides, 28 chains. Longest chain 12 peptides. Score 0.391 Round 5: 171 peptides, 28 chains. Longest chain 13 peptides. Score 0.405 Taking the results from Round 5 Chains 28, Residues 143, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4824 reflections ( 99.61 % complete ) and 7519 restraints for refining 3148 atoms. 6975 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1983 (Rfree = 0.000) for 3148 atoms. Found 17 (17 requested) and removed 12 (8 requested) atoms. Cycle 37: After refmac, R = 0.1838 (Rfree = 0.000) for 3138 atoms. Found 15 (17 requested) and removed 11 (8 requested) atoms. Cycle 38: After refmac, R = 0.2119 (Rfree = 0.000) for 3133 atoms. Found 17 (17 requested) and removed 16 (8 requested) atoms. Cycle 39: After refmac, R = 0.1643 (Rfree = 0.000) for 3124 atoms. Found 15 (17 requested) and removed 9 (8 requested) atoms. Cycle 40: After refmac, R = 0.1958 (Rfree = 0.000) for 3121 atoms. Found 17 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.45 3.54 Search for helices and strands: 0 residues in 0 chains, 3217 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 3232 seeds are put forward Round 1: 131 peptides, 29 chains. Longest chain 10 peptides. Score 0.233 Round 2: 160 peptides, 33 chains. Longest chain 9 peptides. Score 0.284 Round 3: 173 peptides, 31 chains. Longest chain 10 peptides. Score 0.366 Round 4: 177 peptides, 29 chains. Longest chain 15 peptides. Score 0.411 Round 5: 160 peptides, 28 chains. Longest chain 12 peptides. Score 0.365 Taking the results from Round 4 Chains 29, Residues 148, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4824 reflections ( 99.61 % complete ) and 7658 restraints for refining 3148 atoms. 7095 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2437 (Rfree = 0.000) for 3148 atoms. Found 17 (17 requested) and removed 17 (8 requested) atoms. Cycle 42: After refmac, R = 0.2134 (Rfree = 0.000) for 3132 atoms. Found 17 (17 requested) and removed 12 (8 requested) atoms. Cycle 43: After refmac, R = 0.2186 (Rfree = 0.000) for 3120 atoms. Found 17 (17 requested) and removed 17 (8 requested) atoms. Cycle 44: After refmac, R = 0.1943 (Rfree = 0.000) for 3102 atoms. Found 17 (17 requested) and removed 15 (8 requested) atoms. Cycle 45: After refmac, R = 0.2055 (Rfree = 0.000) for 3096 atoms. Found 17 (17 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.44 3.53 Search for helices and strands: 0 residues in 0 chains, 3185 seeds are put forward NCS extension: 19 residues added (3 deleted due to clashes), 3204 seeds are put forward Round 1: 125 peptides, 28 chains. Longest chain 8 peptides. Score 0.225 Round 2: 151 peptides, 27 chains. Longest chain 12 peptides. Score 0.348 Round 3: 156 peptides, 25 chains. Longest chain 12 peptides. Score 0.399 Round 4: 165 peptides, 24 chains. Longest chain 15 peptides. Score 0.446 Round 5: 155 peptides, 28 chains. Longest chain 11 peptides. Score 0.347 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 24, Residues 141, 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 7579 restraints for refining 3147 atoms. 7039 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2210 (Rfree = 0.000) for 3147 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.2330 (Rfree = 0.000) for 3123 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.1936 (Rfree = 0.000) for 3107 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.1619 (Rfree = 0.000) for 3092 atoms. TimeTaking 53.5