Sun 23 Dec 22:23:01 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-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vmf-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vmf-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vmf-3.6-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-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vmf-3.6-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 22:23:11 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-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vmf-3.6-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 317 and 0 Target number of residues in the AU: 317 Target solvent content: 0.6226 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-3.6-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-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 3480 target number of atoms Had to go as low as 0.65 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 3.600 Wilson plot Bfac: 62.30 5624 reflections ( 99.66 % complete ) and 0 restraints for refining 3850 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Starting model: R = 0.3017 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2718 (Rfree = 0.000) for 3850 atoms. Found 24 (24 requested) and removed 23 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.35 3.44 Search for helices and strands: 0 residues in 0 chains, 3920 seeds are put forward NCS extension: 0 residues added, 3920 seeds are put forward Round 1: 201 peptides, 39 chains. Longest chain 9 peptides. Score 0.344 Round 2: 251 peptides, 37 chains. Longest chain 20 peptides. Score 0.536 Round 3: 269 peptides, 33 chains. Longest chain 28 peptides. Score 0.632 Round 4: 289 peptides, 33 chains. Longest chain 20 peptides. Score 0.678 Round 5: 296 peptides, 29 chains. Longest chain 33 peptides. Score 0.729 Taking the results from Round 5 Chains 30, Residues 267, Estimated correctness of the model 58.1 % 1 chains (23 residues) have been docked in sequence ------------------------------------------------------ 5624 reflections ( 99.66 % complete ) and 6478 restraints for refining 3152 atoms. 5343 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2403 (Rfree = 0.000) for 3152 atoms. Found 18 (20 requested) and removed 17 (10 requested) atoms. Failed to save intermediate PDB Cycle 2: After refmac, R = 0.2347 (Rfree = 0.000) for 3092 atoms. Found 11 (20 requested) and removed 14 (10 requested) atoms. Cycle 3: After refmac, R = 0.2318 (Rfree = 0.000) for 3064 atoms. Found 10 (18 requested) and removed 25 (9 requested) atoms. Cycle 4: After refmac, R = 0.2096 (Rfree = 0.000) for 3032 atoms. Found 12 (18 requested) and removed 11 (9 requested) atoms. Cycle 5: After refmac, R = 0.2201 (Rfree = 0.000) for 3028 atoms. Found 7 (17 requested) and removed 15 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.29 3.38 Search for helices and strands: 0 residues in 0 chains, 3108 seeds are put forward NCS extension: 19 residues added (12 deleted due to clashes), 3127 seeds are put forward Round 1: 237 peptides, 37 chains. Longest chain 17 peptides. Score 0.494 Round 2: 269 peptides, 31 chains. Longest chain 28 peptides. Score 0.653 Round 3: 272 peptides, 34 chains. Longest chain 31 peptides. Score 0.628 Round 4: 264 peptides, 34 chains. Longest chain 18 peptides. Score 0.608 Round 5: 282 peptides, 34 chains. Longest chain 31 peptides. Score 0.652 Taking the results from Round 2 Chains 31, Residues 238, Estimated correctness of the model 34.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5624 reflections ( 99.66 % complete ) and 7088 restraints for refining 3144 atoms. 6167 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2343 (Rfree = 0.000) for 3144 atoms. Found 16 (18 requested) and removed 53 (10 requested) atoms. Cycle 7: After refmac, R = 0.2188 (Rfree = 0.000) for 3092 atoms. Found 17 (17 requested) and removed 44 (9 requested) atoms. Cycle 8: After refmac, R = 0.2000 (Rfree = 0.000) for 3052 atoms. Found 12 (17 requested) and removed 20 (9 requested) atoms. Cycle 9: After refmac, R = 0.1961 (Rfree = 0.000) for 3041 atoms. Found 5 (17 requested) and removed 25 (9 requested) atoms. Cycle 10: After refmac, R = 0.1652 (Rfree = 0.000) for 3018 atoms. Found 4 (17 requested) and removed 16 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.33 3.42 Search for helices and strands: 0 residues in 0 chains, 3122 seeds are put forward NCS extension: 27 residues added (2 deleted due to clashes), 3149 seeds are put forward Round 1: 244 peptides, 44 chains. Longest chain 11 peptides. Score 0.420 Round 2: 253 peptides, 39 chains. Longest chain 12 peptides. Score 0.517 Round 3: 258 peptides, 39 chains. Longest chain 18 peptides. Score 0.531 Round 4: 266 peptides, 36 chains. Longest chain 14 peptides. Score 0.590 Round 5: 252 peptides, 35 chains. Longest chain 18 peptides. Score 0.564 Taking the results from Round 4 Chains 36, Residues 230, Estimated correctness of the model 10.7 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 5624 reflections ( 99.66 % complete ) and 7137 restraints for refining 3155 atoms. 6236 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2074 (Rfree = 0.000) for 3155 atoms. Found 12 (18 requested) and removed 20 (10 requested) atoms. Cycle 12: After refmac, R = 0.1907 (Rfree = 0.000) for 3142 atoms. Found 3 (18 requested) and removed 16 (10 requested) atoms. Cycle 13: After refmac, R = 0.1841 (Rfree = 0.000) for 3126 atoms. Found 4 (18 requested) and removed 11 (10 requested) atoms. Cycle 14: After refmac, R = 0.1820 (Rfree = 0.000) for 3117 atoms. Found 0 (18 requested) and removed 11 (10 requested) atoms. Cycle 15: After refmac, R = 0.1818 (Rfree = 0.000) for 3104 atoms. Found 4 (17 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.32 3.41 Search for helices and strands: 0 residues in 0 chains, 3182 seeds are put forward NCS extension: 10 residues added (4 deleted due to clashes), 3192 seeds are put forward Round 1: 221 peptides, 34 chains. Longest chain 15 peptides. Score 0.485 Round 2: 234 peptides, 31 chains. Longest chain 14 peptides. Score 0.564 Round 3: 223 peptides, 30 chains. Longest chain 18 peptides. Score 0.545 Round 4: 239 peptides, 28 chains. Longest chain 24 peptides. Score 0.614 Round 5: 240 peptides, 31 chains. Longest chain 24 peptides. Score 0.580 Taking the results from Round 4 Chains 30, Residues 211, Estimated correctness of the model 20.0 % 2 chains (41 residues) have been docked in sequence ------------------------------------------------------ 5624 reflections ( 99.66 % complete ) and 6663 restraints for refining 3155 atoms. 5652 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2207 (Rfree = 0.000) for 3155 atoms. Found 12 (18 requested) and removed 19 (10 requested) atoms. Cycle 17: After refmac, R = 0.2000 (Rfree = 0.000) for 3137 atoms. Found 5 (18 requested) and removed 14 (10 requested) atoms. Cycle 18: After refmac, R = 0.1948 (Rfree = 0.000) for 3123 atoms. Found 4 (18 requested) and removed 14 (10 requested) atoms. Cycle 19: After refmac, R = 0.1908 (Rfree = 0.000) for 3110 atoms. Found 2 (17 requested) and removed 9 (9 requested) atoms. Cycle 20: After refmac, R = 0.1897 (Rfree = 0.000) for 3103 atoms. Found 2 (17 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.31 3.40 Search for helices and strands: 0 residues in 0 chains, 3167 seeds are put forward NCS extension: 31 residues added (3 deleted due to clashes), 3198 seeds are put forward Round 1: 217 peptides, 34 chains. Longest chain 18 peptides. Score 0.472 Round 2: 227 peptides, 32 chains. Longest chain 21 peptides. Score 0.530 Round 3: 237 peptides, 31 chains. Longest chain 24 peptides. Score 0.572 Round 4: 232 peptides, 28 chains. Longest chain 28 peptides. Score 0.595 Round 5: 225 peptides, 28 chains. Longest chain 22 peptides. Score 0.576 Taking the results from Round 4 Chains 30, Residues 204, Estimated correctness of the model 12.7 % 1 chains (18 residues) have been docked in sequence ------------------------------------------------------ 5624 reflections ( 99.66 % complete ) and 7085 restraints for refining 3154 atoms. 6208 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2257 (Rfree = 0.000) for 3154 atoms. Found 14 (18 requested) and removed 24 (10 requested) atoms. Cycle 22: After refmac, R = 0.2021 (Rfree = 0.000) for 3130 atoms. Found 18 (18 requested) and removed 81 (10 requested) atoms. Cycle 23: After refmac, R = 0.1909 (Rfree = 0.000) for 3062 atoms. Found 17 (17 requested) and removed 12 (9 requested) atoms. Cycle 24: After refmac, R = 0.1786 (Rfree = 0.000) for 3064 atoms. Found 5 (17 requested) and removed 14 (9 requested) atoms. Cycle 25: After refmac, R = 0.1752 (Rfree = 0.000) for 3054 atoms. Found 6 (17 requested) and removed 14 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.32 3.41 Search for helices and strands: 0 residues in 0 chains, 3153 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 3171 seeds are put forward Round 1: 194 peptides, 34 chains. Longest chain 13 peptides. Score 0.395 Round 2: 233 peptides, 34 chains. Longest chain 19 peptides. Score 0.522 Round 3: 235 peptides, 27 chains. Longest chain 21 peptides. Score 0.615 Round 4: 231 peptides, 31 chains. Longest chain 19 peptides. Score 0.555 Round 5: 214 peptides, 27 chains. Longest chain 16 peptides. Score 0.558 Taking the results from Round 3 Chains 27, Residues 208, Estimated correctness of the model 20.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5624 reflections ( 99.66 % complete ) and 7102 restraints for refining 3155 atoms. 6297 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2050 (Rfree = 0.000) for 3155 atoms. Found 12 (18 requested) and removed 58 (10 requested) atoms. Cycle 27: After refmac, R = 0.1930 (Rfree = 0.000) for 3106 atoms. Found 7 (17 requested) and removed 26 (9 requested) atoms. Cycle 28: After refmac, R = 0.1872 (Rfree = 0.000) for 3086 atoms. Found 1 (17 requested) and removed 15 (9 requested) atoms. Cycle 29: After refmac, R = 0.1860 (Rfree = 0.000) for 3071 atoms. Found 2 (17 requested) and removed 14 (9 requested) atoms. Cycle 30: After refmac, R = 0.1877 (Rfree = 0.000) for 3056 atoms. Found 2 (17 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.34 3.43 Search for helices and strands: 0 residues in 0 chains, 3111 seeds are put forward NCS extension: 13 residues added (3 deleted due to clashes), 3124 seeds are put forward Round 1: 196 peptides, 38 chains. Longest chain 11 peptides. Score 0.341 Round 2: 196 peptides, 30 chains. Longest chain 17 peptides. Score 0.461 Round 3: 214 peptides, 32 chains. Longest chain 23 peptides. Score 0.491 Round 4: 197 peptides, 31 chains. Longest chain 16 peptides. Score 0.450 Round 5: 198 peptides, 29 chains. Longest chain 25 peptides. Score 0.482 Taking the results from Round 3 Chains 33, Residues 182, Estimated correctness of the model 0.0 % 2 chains (23 residues) have been docked in sequence ------------------------------------------------------ 5624 reflections ( 99.66 % complete ) and 7086 restraints for refining 3154 atoms. 6315 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2074 (Rfree = 0.000) for 3154 atoms. Found 12 (18 requested) and removed 38 (10 requested) atoms. Cycle 32: After refmac, R = 0.1908 (Rfree = 0.000) for 3116 atoms. Found 13 (18 requested) and removed 16 (10 requested) atoms. Cycle 33: After refmac, R = 0.1804 (Rfree = 0.000) for 3109 atoms. Found 10 (17 requested) and removed 12 (9 requested) atoms. Cycle 34: After refmac, R = 0.1727 (Rfree = 0.000) for 3106 atoms. Found 5 (17 requested) and removed 25 (9 requested) atoms. Cycle 35: After refmac, R = 0.1702 (Rfree = 0.000) for 3083 atoms. Found 7 (17 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.29 3.38 Search for helices and strands: 0 residues in 0 chains, 3162 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 3182 seeds are put forward Round 1: 201 peptides, 39 chains. Longest chain 11 peptides. Score 0.344 Round 2: 198 peptides, 30 chains. Longest chain 25 peptides. Score 0.468 Round 3: 190 peptides, 27 chains. Longest chain 29 peptides. Score 0.485 Round 4: 189 peptides, 25 chains. Longest chain 24 peptides. Score 0.510 Round 5: 185 peptides, 22 chains. Longest chain 20 peptides. Score 0.540 Taking the results from Round 5 Chains 22, Residues 163, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 5624 reflections ( 99.66 % complete ) and 7395 restraints for refining 3154 atoms. 6765 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1978 (Rfree = 0.000) for 3154 atoms. Found 17 (18 requested) and removed 14 (10 requested) atoms. Failed to save intermediate PDB Cycle 37: After refmac, R = 0.1815 (Rfree = 0.000) for 3152 atoms. Found 8 (18 requested) and removed 14 (10 requested) atoms. Cycle 38: After refmac, R = 0.2014 (Rfree = 0.000) for 3143 atoms. Found 18 (18 requested) and removed 20 (10 requested) atoms. Failed to save intermediate PDB Cycle 39: After refmac, R = 0.1904 (Rfree = 0.000) for 3139 atoms. Found 18 (18 requested) and removed 14 (10 requested) atoms. Cycle 40: After refmac, R = 0.1768 (Rfree = 0.000) for 3142 atoms. Found 10 (18 requested) and removed 14 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.31 3.40 Search for helices and strands: 0 residues in 0 chains, 3225 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 3243 seeds are put forward Round 1: 170 peptides, 33 chains. Longest chain 13 peptides. Score 0.322 Round 2: 187 peptides, 28 chains. Longest chain 14 peptides. Score 0.460 Round 3: 201 peptides, 29 chains. Longest chain 20 peptides. Score 0.492 Round 4: 201 peptides, 27 chains. Longest chain 22 peptides. Score 0.519 Round 5: 184 peptides, 26 chains. Longest chain 18 peptides. Score 0.480 Taking the results from Round 4 Chains 27, Residues 174, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5624 reflections ( 99.66 % complete ) and 7370 restraints for refining 3155 atoms. 6701 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2006 (Rfree = 0.000) for 3155 atoms. Found 11 (18 requested) and removed 11 (10 requested) atoms. Cycle 42: After refmac, R = 0.1882 (Rfree = 0.000) for 3150 atoms. Found 6 (18 requested) and removed 11 (10 requested) atoms. Cycle 43: After refmac, R = 0.1904 (Rfree = 0.000) for 3141 atoms. Found 5 (18 requested) and removed 11 (10 requested) atoms. Cycle 44: After refmac, R = 0.1905 (Rfree = 0.000) for 3127 atoms. Found 10 (18 requested) and removed 12 (10 requested) atoms. Cycle 45: After refmac, R = 0.1980 (Rfree = 0.000) for 3123 atoms. Found 11 (18 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.23 3.32 Search for helices and strands: 0 residues in 0 chains, 3197 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 3217 seeds are put forward Round 1: 156 peptides, 31 chains. Longest chain 14 peptides. Score 0.301 Round 2: 176 peptides, 28 chains. Longest chain 13 peptides. Score 0.423 Round 3: 183 peptides, 24 chains. Longest chain 16 peptides. Score 0.506 Round 4: 194 peptides, 26 chains. Longest chain 19 peptides. Score 0.512 Round 5: 186 peptides, 26 chains. Longest chain 23 peptides. Score 0.486 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 26, Residues 168, 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. 5624 reflections ( 99.66 % complete ) and 7304 restraints for refining 3155 atoms. 6658 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2253 (Rfree = 0.000) for 3155 atoms. Found 0 (18 requested) and removed 10 (10 requested) atoms. Cycle 47: After refmac, R = 0.2088 (Rfree = 0.000) for 3140 atoms. Found 0 (18 requested) and removed 10 (10 requested) atoms. Cycle 48: After refmac, R = 0.1989 (Rfree = 0.000) for 3127 atoms. Found 0 (18 requested) and removed 10 (10 requested) atoms. Cycle 49: After refmac, R = 0.1922 (Rfree = 0.000) for 3113 atoms. Found 0 (17 requested) and removed 9 (9 requested) atoms. Writing output files ... TimeTaking 52.82