null Mon 24 Dec 01:07:59 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 2prv-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2prv-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2prv-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2prv-3.4-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/2prv-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2prv-3.4-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 01:08:04 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/2prv-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2prv-3.4-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 204 and 0 Target number of residues in the AU: 204 Target solvent content: 0.6415 Checking the provided sequence file Detected sequence length: 153 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 306 Adjusted target solvent content: 0.46 Input MTZ file: 2prv-3.4-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: 1 Cell parameters: 40.107 45.170 48.067 84.512 67.558 73.075 Input sequence file: 2prv-3.4-parrot-mrncs.fasta_lf Building free atoms model in initial map for 2448 target number of atoms Had to go as low as 0.75 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: 44.420 3.401 Wilson plot Bfac: 71.97 4000 reflections ( 97.75 % complete ) and 0 restraints for refining 2727 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Starting model: R = 0.3805 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3286 (Rfree = 0.000) for 2727 atoms. Found 9 (20 requested) and removed 55 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.33 3.51 Search for helices and strands: 0 residues in 0 chains, 2708 seeds are put forward NCS extension: 0 residues added, 2708 seeds are put forward Round 1: 58 peptides, 12 chains. Longest chain 8 peptides. Score 0.242 Round 2: 72 peptides, 15 chains. Longest chain 7 peptides. Score 0.250 Round 3: 77 peptides, 15 chains. Longest chain 9 peptides. Score 0.282 Round 4: 81 peptides, 16 chains. Longest chain 9 peptides. Score 0.281 Round 5: 96 peptides, 18 chains. Longest chain 9 peptides. Score 0.319 Taking the results from Round 5 Chains 18, Residues 78, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4000 reflections ( 97.75 % complete ) and 5223 restraints for refining 2226 atoms. 4929 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2615 (Rfree = 0.000) for 2226 atoms. Found 9 (16 requested) and removed 12 (8 requested) atoms. Cycle 2: After refmac, R = 0.2561 (Rfree = 0.000) for 2207 atoms. Found 14 (16 requested) and removed 14 (8 requested) atoms. Cycle 3: After refmac, R = 0.2469 (Rfree = 0.000) for 2196 atoms. Found 6 (16 requested) and removed 9 (8 requested) atoms. Cycle 4: After refmac, R = 0.2298 (Rfree = 0.000) for 2187 atoms. Found 11 (16 requested) and removed 10 (8 requested) atoms. Cycle 5: After refmac, R = 0.2016 (Rfree = 0.000) for 2183 atoms. Found 1 (16 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.33 3.51 Search for helices and strands: 0 residues in 0 chains, 2228 seeds are put forward NCS extension: 0 residues added, 2228 seeds are put forward Round 1: 78 peptides, 17 chains. Longest chain 7 peptides. Score 0.235 Round 2: 105 peptides, 21 chains. Longest chain 8 peptides. Score 0.297 Round 3: 103 peptides, 21 chains. Longest chain 8 peptides. Score 0.285 Round 4: 116 peptides, 22 chains. Longest chain 9 peptides. Score 0.336 Round 5: 117 peptides, 22 chains. Longest chain 8 peptides. Score 0.341 Taking the results from Round 5 Chains 22, Residues 95, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4000 reflections ( 97.75 % complete ) and 5107 restraints for refining 2226 atoms. 4726 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2172 (Rfree = 0.000) for 2226 atoms. Found 6 (16 requested) and removed 9 (8 requested) atoms. Cycle 7: After refmac, R = 0.2030 (Rfree = 0.000) for 2221 atoms. Found 6 (16 requested) and removed 9 (8 requested) atoms. Cycle 8: After refmac, R = 0.2017 (Rfree = 0.000) for 2212 atoms. Found 6 (16 requested) and removed 9 (8 requested) atoms. Cycle 9: After refmac, R = 0.2547 (Rfree = 0.000) for 2207 atoms. Found 15 (16 requested) and removed 8 (8 requested) atoms. Cycle 10: After refmac, R = 0.2065 (Rfree = 0.000) for 2211 atoms. Found 4 (16 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.35 3.53 Search for helices and strands: 0 residues in 0 chains, 2251 seeds are put forward NCS extension: 0 residues added, 2251 seeds are put forward Round 1: 103 peptides, 22 chains. Longest chain 8 peptides. Score 0.261 Round 2: 126 peptides, 25 chains. Longest chain 8 peptides. Score 0.321 Round 3: 123 peptides, 23 chains. Longest chain 8 peptides. Score 0.351 Round 4: 142 peptides, 25 chains. Longest chain 14 peptides. Score 0.406 Round 5: 140 peptides, 25 chains. Longest chain 11 peptides. Score 0.396 Taking the results from Round 4 Chains 25, Residues 117, Estimated correctness of the model 0.0 % 2 chains (10 residues) have been docked in sequence ------------------------------------------------------ 4000 reflections ( 97.75 % complete ) and 5041 restraints for refining 2226 atoms. 4576 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2171 (Rfree = 0.000) for 2226 atoms. Found 7 (16 requested) and removed 10 (8 requested) atoms. Cycle 12: After refmac, R = 0.2190 (Rfree = 0.000) for 2222 atoms. Found 5 (16 requested) and removed 11 (8 requested) atoms. Cycle 13: After refmac, R = 0.1988 (Rfree = 0.000) for 2212 atoms. Found 5 (16 requested) and removed 12 (8 requested) atoms. Cycle 14: After refmac, R = 0.1987 (Rfree = 0.000) for 2204 atoms. Found 8 (16 requested) and removed 8 (8 requested) atoms. Cycle 15: After refmac, R = 0.1917 (Rfree = 0.000) for 2201 atoms. Found 9 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.34 3.52 Search for helices and strands: 0 residues in 0 chains, 2242 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 2266 seeds are put forward Round 1: 108 peptides, 23 chains. Longest chain 10 peptides. Score 0.266 Round 2: 119 peptides, 23 chains. Longest chain 9 peptides. Score 0.329 Round 3: 127 peptides, 23 chains. Longest chain 14 peptides. Score 0.373 Round 4: 121 peptides, 22 chains. Longest chain 8 peptides. Score 0.363 Round 5: 133 peptides, 23 chains. Longest chain 14 peptides. Score 0.404 Taking the results from Round 5 Chains 24, Residues 110, Estimated correctness of the model 0.0 % 2 chains (19 residues) have been docked in sequence ------------------------------------------------------ 4000 reflections ( 97.75 % complete ) and 4872 restraints for refining 2226 atoms. 4390 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2175 (Rfree = 0.000) for 2226 atoms. Found 14 (16 requested) and removed 11 (8 requested) atoms. Cycle 17: After refmac, R = 0.2026 (Rfree = 0.000) for 2225 atoms. Found 12 (16 requested) and removed 8 (8 requested) atoms. Cycle 18: After refmac, R = 0.2041 (Rfree = 0.000) for 2224 atoms. Found 14 (16 requested) and removed 10 (8 requested) atoms. Cycle 19: After refmac, R = 0.1969 (Rfree = 0.000) for 2225 atoms. Found 6 (16 requested) and removed 8 (8 requested) atoms. Cycle 20: After refmac, R = 0.2023 (Rfree = 0.000) for 2222 atoms. Found 11 (16 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.35 3.53 Search for helices and strands: 0 residues in 0 chains, 2259 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 2275 seeds are put forward Round 1: 115 peptides, 22 chains. Longest chain 8 peptides. Score 0.330 Round 2: 119 peptides, 22 chains. Longest chain 12 peptides. Score 0.352 Round 3: 127 peptides, 24 chains. Longest chain 11 peptides. Score 0.350 Round 4: 114 peptides, 22 chains. Longest chain 9 peptides. Score 0.325 Round 5: 124 peptides, 22 chains. Longest chain 12 peptides. Score 0.379 Taking the results from Round 5 Chains 22, Residues 102, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 4000 reflections ( 97.75 % complete ) and 5136 restraints for refining 2226 atoms. 4735 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2232 (Rfree = 0.000) for 2226 atoms. Found 13 (16 requested) and removed 13 (8 requested) atoms. Cycle 22: After refmac, R = 0.2112 (Rfree = 0.000) for 2221 atoms. Found 4 (16 requested) and removed 8 (8 requested) atoms. Cycle 23: After refmac, R = 0.1980 (Rfree = 0.000) for 2215 atoms. Found 1 (16 requested) and removed 8 (8 requested) atoms. Cycle 24: After refmac, R = 0.1947 (Rfree = 0.000) for 2207 atoms. Found 4 (16 requested) and removed 8 (8 requested) atoms. Cycle 25: After refmac, R = 0.1946 (Rfree = 0.000) for 2203 atoms. Found 2 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.34 3.52 Search for helices and strands: 0 residues in 0 chains, 2233 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 2246 seeds are put forward Round 1: 110 peptides, 23 chains. Longest chain 7 peptides. Score 0.277 Round 2: 121 peptides, 23 chains. Longest chain 7 peptides. Score 0.340 Round 3: 118 peptides, 23 chains. Longest chain 14 peptides. Score 0.323 Round 4: 117 peptides, 21 chains. Longest chain 10 peptides. Score 0.365 Round 5: 125 peptides, 21 chains. Longest chain 13 peptides. Score 0.407 Taking the results from Round 5 Chains 21, Residues 104, Estimated correctness of the model 0.0 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 4000 reflections ( 97.75 % complete ) and 4825 restraints for refining 2226 atoms. 4387 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2200 (Rfree = 0.000) for 2226 atoms. Found 5 (16 requested) and removed 9 (8 requested) atoms. Cycle 27: After refmac, R = 0.2236 (Rfree = 0.000) for 2219 atoms. Found 8 (16 requested) and removed 8 (8 requested) atoms. Cycle 28: After refmac, R = 0.2174 (Rfree = 0.000) for 2214 atoms. Found 5 (16 requested) and removed 8 (8 requested) atoms. Cycle 29: After refmac, R = 0.2141 (Rfree = 0.000) for 2208 atoms. Found 9 (16 requested) and removed 8 (8 requested) atoms. Cycle 30: After refmac, R = 0.1968 (Rfree = 0.000) for 2205 atoms. Found 1 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.35 3.53 Search for helices and strands: 0 residues in 0 chains, 2229 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 2246 seeds are put forward Round 1: 107 peptides, 23 chains. Longest chain 7 peptides. Score 0.260 Round 2: 119 peptides, 24 chains. Longest chain 8 peptides. Score 0.305 Round 3: 123 peptides, 23 chains. Longest chain 13 peptides. Score 0.351 Round 4: 121 peptides, 22 chains. Longest chain 17 peptides. Score 0.363 Round 5: 111 peptides, 22 chains. Longest chain 8 peptides. Score 0.308 Taking the results from Round 4 Chains 22, Residues 99, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4000 reflections ( 97.75 % complete ) and 5177 restraints for refining 2226 atoms. 4803 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2085 (Rfree = 0.000) for 2226 atoms. Found 16 (16 requested) and removed 10 (8 requested) atoms. Cycle 32: After refmac, R = 0.1854 (Rfree = 0.000) for 2229 atoms. Found 5 (16 requested) and removed 9 (8 requested) atoms. Cycle 33: After refmac, R = 0.1760 (Rfree = 0.000) for 2222 atoms. Found 3 (16 requested) and removed 8 (8 requested) atoms. Cycle 34: After refmac, R = 0.1695 (Rfree = 0.000) for 2214 atoms. Found 6 (16 requested) and removed 8 (8 requested) atoms. Cycle 35: After refmac, R = 0.1661 (Rfree = 0.000) for 2209 atoms. Found 2 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.35 3.53 Search for helices and strands: 0 residues in 0 chains, 2224 seeds are put forward NCS extension: 0 residues added, 2224 seeds are put forward Round 1: 91 peptides, 19 chains. Longest chain 8 peptides. Score 0.264 Round 2: 103 peptides, 19 chains. Longest chain 9 peptides. Score 0.335 Round 3: 92 peptides, 19 chains. Longest chain 8 peptides. Score 0.270 Round 4: 111 peptides, 21 chains. Longest chain 10 peptides. Score 0.332 Round 5: 113 peptides, 23 chains. Longest chain 9 peptides. Score 0.295 Taking the results from Round 2 Chains 19, Residues 84, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 4000 reflections ( 97.75 % complete ) and 5067 restraints for refining 2226 atoms. 4713 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1823 (Rfree = 0.000) for 2226 atoms. Found 3 (16 requested) and removed 8 (8 requested) atoms. Cycle 37: After refmac, R = 0.1953 (Rfree = 0.000) for 2215 atoms. Found 9 (16 requested) and removed 11 (8 requested) atoms. Cycle 38: After refmac, R = 0.1921 (Rfree = 0.000) for 2210 atoms. Found 10 (16 requested) and removed 8 (8 requested) atoms. Cycle 39: After refmac, R = 0.1634 (Rfree = 0.000) for 2212 atoms. Found 3 (16 requested) and removed 8 (8 requested) atoms. Cycle 40: After refmac, R = 0.1884 (Rfree = 0.000) for 2205 atoms. Found 10 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.35 3.53 Search for helices and strands: 0 residues in 0 chains, 2227 seeds are put forward NCS extension: 0 residues added, 2227 seeds are put forward Round 1: 96 peptides, 20 chains. Longest chain 11 peptides. Score 0.269 Round 2: 107 peptides, 21 chains. Longest chain 8 peptides. Score 0.309 Round 3: 100 peptides, 20 chains. Longest chain 9 peptides. Score 0.293 Round 4: 92 peptides, 17 chains. Longest chain 15 peptides. Score 0.321 Round 5: 103 peptides, 19 chains. Longest chain 11 peptides. Score 0.335 Taking the results from Round 5 Chains 19, Residues 84, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4000 reflections ( 97.75 % complete ) and 5103 restraints for refining 2225 atoms. 4786 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2012 (Rfree = 0.000) for 2225 atoms. Found 6 (16 requested) and removed 8 (8 requested) atoms. Cycle 42: After refmac, R = 0.1884 (Rfree = 0.000) for 2222 atoms. Found 11 (16 requested) and removed 8 (8 requested) atoms. Cycle 43: After refmac, R = 0.1730 (Rfree = 0.000) for 2221 atoms. Found 4 (16 requested) and removed 8 (8 requested) atoms. Cycle 44: After refmac, R = 0.1702 (Rfree = 0.000) for 2217 atoms. Found 2 (16 requested) and removed 8 (8 requested) atoms. Cycle 45: After refmac, R = 0.1653 (Rfree = 0.000) for 2208 atoms. Found 4 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.36 3.54 Search for helices and strands: 0 residues in 0 chains, 2234 seeds are put forward NCS extension: 0 residues added, 2234 seeds are put forward Round 1: 78 peptides, 17 chains. Longest chain 12 peptides. Score 0.235 Round 2: 93 peptides, 17 chains. Longest chain 12 peptides. Score 0.327 Round 3: 102 peptides, 20 chains. Longest chain 11 peptides. Score 0.304 Round 4: 101 peptides, 20 chains. Longest chain 8 peptides. Score 0.299 Round 5: 109 peptides, 19 chains. Longest chain 9 peptides. Score 0.368 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 19, Residues 90, 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 2prv-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4000 reflections ( 97.75 % complete ) and 5114 restraints for refining 2226 atoms. 4773 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1752 (Rfree = 0.000) for 2226 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.1763 (Rfree = 0.000) for 2216 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.1808 (Rfree = 0.000) for 2208 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.1611 (Rfree = 0.000) for 2197 atoms. Found 0 (16 requested) and removed 5 (8 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:34:36 GMT 2018 Job finished. TimeTaking 26.61 Used memory is bytes: 15433136