null Sun 23 Dec 23:44:03 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-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2prv-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2prv-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2prv-3.2-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-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2prv-3.2-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 23:44:08 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-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2prv-3.2-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 210 and 0 Target number of residues in the AU: 210 Target solvent content: 0.6309 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-3.2-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-3.2-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 3.200 Wilson plot Bfac: 66.67 4810 reflections ( 97.72 % complete ) and 0 restraints for refining 2702 atoms. Observations/parameters ratio is 0.45 ------------------------------------------------------ Starting model: R = 0.3850 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3303 (Rfree = 0.000) for 2702 atoms. Found 14 (24 requested) and removed 46 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.17 3.34 Search for helices and strands: 0 residues in 0 chains, 2700 seeds are put forward NCS extension: 0 residues added, 2700 seeds are put forward Round 1: 77 peptides, 19 chains. Longest chain 5 peptides. Score 0.173 Round 2: 102 peptides, 22 chains. Longest chain 7 peptides. Score 0.255 Round 3: 128 peptides, 25 chains. Longest chain 11 peptides. Score 0.332 Round 4: 118 peptides, 24 chains. Longest chain 8 peptides. Score 0.299 Round 5: 125 peptides, 23 chains. Longest chain 10 peptides. Score 0.362 Taking the results from Round 5 Chains 23, Residues 102, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4810 reflections ( 97.72 % complete ) and 5213 restraints for refining 2235 atoms. 4828 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2698 (Rfree = 0.000) for 2235 atoms. Found 12 (20 requested) and removed 16 (10 requested) atoms. Cycle 2: After refmac, R = 0.2519 (Rfree = 0.000) for 2214 atoms. Found 7 (20 requested) and removed 11 (10 requested) atoms. Cycle 3: After refmac, R = 0.2504 (Rfree = 0.000) for 2207 atoms. Found 2 (19 requested) and removed 13 (9 requested) atoms. Cycle 4: After refmac, R = 0.2461 (Rfree = 0.000) for 2196 atoms. Found 4 (19 requested) and removed 11 (9 requested) atoms. Cycle 5: After refmac, R = 0.2445 (Rfree = 0.000) for 2187 atoms. Found 5 (19 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.12 3.29 Search for helices and strands: 0 residues in 0 chains, 2232 seeds are put forward NCS extension: 0 residues added, 2232 seeds are put forward Round 1: 118 peptides, 24 chains. Longest chain 7 peptides. Score 0.299 Round 2: 125 peptides, 22 chains. Longest chain 13 peptides. Score 0.385 Round 3: 114 peptides, 19 chains. Longest chain 14 peptides. Score 0.395 Round 4: 131 peptides, 22 chains. Longest chain 14 peptides. Score 0.416 Round 5: 140 peptides, 21 chains. Longest chain 23 peptides. Score 0.482 Taking the results from Round 5 Chains 21, Residues 119, Estimated correctness of the model 5.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4810 reflections ( 97.72 % complete ) and 5090 restraints for refining 2235 atoms. 4635 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2473 (Rfree = 0.000) for 2235 atoms. Found 12 (20 requested) and removed 12 (10 requested) atoms. Cycle 7: After refmac, R = 0.2471 (Rfree = 0.000) for 2229 atoms. Found 5 (20 requested) and removed 10 (10 requested) atoms. Cycle 8: After refmac, R = 0.2456 (Rfree = 0.000) for 2223 atoms. Found 5 (19 requested) and removed 9 (9 requested) atoms. Cycle 9: After refmac, R = 0.2410 (Rfree = 0.000) for 2219 atoms. Found 6 (19 requested) and removed 9 (9 requested) atoms. Cycle 10: After refmac, R = 0.2451 (Rfree = 0.000) for 2216 atoms. Found 7 (19 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.11 3.28 Search for helices and strands: 0 residues in 0 chains, 2259 seeds are put forward NCS extension: 21 residues added (2 deleted due to clashes), 2280 seeds are put forward Round 1: 114 peptides, 22 chains. Longest chain 12 peptides. Score 0.325 Round 2: 119 peptides, 22 chains. Longest chain 11 peptides. Score 0.352 Round 3: 114 peptides, 20 chains. Longest chain 12 peptides. Score 0.372 Round 4: 120 peptides, 20 chains. Longest chain 11 peptides. Score 0.404 Round 5: 120 peptides, 21 chains. Longest chain 14 peptides. Score 0.381 Taking the results from Round 4 Chains 20, Residues 100, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 4810 reflections ( 97.72 % complete ) and 5052 restraints for refining 2235 atoms. 4656 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2409 (Rfree = 0.000) for 2235 atoms. Found 11 (20 requested) and removed 13 (10 requested) atoms. Cycle 12: After refmac, R = 0.2287 (Rfree = 0.000) for 2230 atoms. Found 8 (20 requested) and removed 12 (10 requested) atoms. Cycle 13: After refmac, R = 0.2297 (Rfree = 0.000) for 2220 atoms. Found 9 (19 requested) and removed 9 (9 requested) atoms. Cycle 14: After refmac, R = 0.2195 (Rfree = 0.000) for 2214 atoms. Found 4 (19 requested) and removed 10 (9 requested) atoms. Cycle 15: After refmac, R = 0.2203 (Rfree = 0.000) for 2206 atoms. Found 10 (19 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.17 3.34 Search for helices and strands: 0 residues in 0 chains, 2247 seeds are put forward NCS extension: 6 residues added (0 deleted due to clashes), 2253 seeds are put forward Round 1: 122 peptides, 27 chains. Longest chain 9 peptides. Score 0.251 Round 2: 143 peptides, 28 chains. Longest chain 10 peptides. Score 0.345 Round 3: 148 peptides, 27 chains. Longest chain 13 peptides. Score 0.393 Round 4: 154 peptides, 28 chains. Longest chain 10 peptides. Score 0.402 Round 5: 148 peptides, 24 chains. Longest chain 16 peptides. Score 0.458 Taking the results from Round 5 Chains 24, Residues 124, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 4810 reflections ( 97.72 % complete ) and 4831 restraints for refining 2235 atoms. 4345 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2156 (Rfree = 0.000) for 2235 atoms. Found 12 (20 requested) and removed 11 (10 requested) atoms. Cycle 17: After refmac, R = 0.2043 (Rfree = 0.000) for 2233 atoms. Found 6 (20 requested) and removed 11 (10 requested) atoms. Cycle 18: After refmac, R = 0.2049 (Rfree = 0.000) for 2224 atoms. Found 4 (19 requested) and removed 9 (9 requested) atoms. Cycle 19: After refmac, R = 0.2056 (Rfree = 0.000) for 2216 atoms. Found 9 (19 requested) and removed 9 (9 requested) atoms. Cycle 20: After refmac, R = 0.2048 (Rfree = 0.000) for 2215 atoms. Found 6 (19 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.14 3.31 Search for helices and strands: 0 residues in 0 chains, 2248 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 2273 seeds are put forward Round 1: 121 peptides, 25 chains. Longest chain 10 peptides. Score 0.293 Round 2: 135 peptides, 25 chains. Longest chain 9 peptides. Score 0.370 Round 3: 138 peptides, 24 chains. Longest chain 11 peptides. Score 0.408 Round 4: 131 peptides, 21 chains. Longest chain 10 peptides. Score 0.438 Round 5: 137 peptides, 23 chains. Longest chain 12 peptides. Score 0.425 Taking the results from Round 4 Chains 21, Residues 110, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 4810 reflections ( 97.72 % complete ) and 4929 restraints for refining 2235 atoms. 4494 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2105 (Rfree = 0.000) for 2235 atoms. Found 16 (20 requested) and removed 11 (10 requested) atoms. Cycle 22: After refmac, R = 0.2012 (Rfree = 0.000) for 2235 atoms. Found 6 (20 requested) and removed 11 (10 requested) atoms. Cycle 23: After refmac, R = 0.2035 (Rfree = 0.000) for 2227 atoms. Found 9 (20 requested) and removed 10 (10 requested) atoms. Cycle 24: After refmac, R = 0.2146 (Rfree = 0.000) for 2220 atoms. Found 15 (19 requested) and removed 11 (9 requested) atoms. Cycle 25: After refmac, R = 0.1938 (Rfree = 0.000) for 2222 atoms. Found 3 (19 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.09 3.26 Search for helices and strands: 0 residues in 0 chains, 2247 seeds are put forward NCS extension: 0 residues added, 2247 seeds are put forward Round 1: 121 peptides, 24 chains. Longest chain 12 peptides. Score 0.317 Round 2: 126 peptides, 24 chains. Longest chain 9 peptides. Score 0.344 Round 3: 123 peptides, 23 chains. Longest chain 9 peptides. Score 0.351 Round 4: 119 peptides, 20 chains. Longest chain 11 peptides. Score 0.399 Round 5: 131 peptides, 23 chains. Longest chain 8 peptides. Score 0.394 Taking the results from Round 4 Chains 20, Residues 99, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4810 reflections ( 97.72 % complete ) and 5008 restraints for refining 2235 atoms. 4632 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2002 (Rfree = 0.000) for 2235 atoms. Found 13 (20 requested) and removed 11 (10 requested) atoms. Cycle 27: After refmac, R = 0.1964 (Rfree = 0.000) for 2235 atoms. Found 12 (20 requested) and removed 10 (10 requested) atoms. Cycle 28: After refmac, R = 0.1863 (Rfree = 0.000) for 2234 atoms. Found 8 (20 requested) and removed 11 (10 requested) atoms. Cycle 29: After refmac, R = 0.2230 (Rfree = 0.000) for 2226 atoms. Found 20 (20 requested) and removed 11 (10 requested) atoms. Cycle 30: After refmac, R = 0.1759 (Rfree = 0.000) for 2232 atoms. Found 10 (20 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.12 3.29 Search for helices and strands: 0 residues in 0 chains, 2262 seeds are put forward NCS extension: 0 residues added, 2262 seeds are put forward Round 1: 103 peptides, 23 chains. Longest chain 8 peptides. Score 0.236 Round 2: 120 peptides, 22 chains. Longest chain 9 peptides. Score 0.358 Round 3: 118 peptides, 22 chains. Longest chain 11 peptides. Score 0.347 Round 4: 119 peptides, 19 chains. Longest chain 13 peptides. Score 0.422 Round 5: 118 peptides, 22 chains. Longest chain 9 peptides. Score 0.347 Taking the results from Round 4 Chains 19, Residues 100, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4810 reflections ( 97.72 % complete ) and 4848 restraints for refining 2235 atoms. 4448 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1971 (Rfree = 0.000) for 2235 atoms. Found 15 (20 requested) and removed 10 (10 requested) atoms. Cycle 32: After refmac, R = 0.2289 (Rfree = 0.000) for 2236 atoms. Found 20 (20 requested) and removed 12 (10 requested) atoms. Cycle 33: After refmac, R = 0.1883 (Rfree = 0.000) for 2242 atoms. Found 17 (20 requested) and removed 10 (10 requested) atoms. Cycle 34: After refmac, R = 0.2056 (Rfree = 0.000) for 2247 atoms. Found 19 (20 requested) and removed 11 (10 requested) atoms. Cycle 35: After refmac, R = 0.1658 (Rfree = 0.000) for 2254 atoms. Found 6 (20 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.12 3.29 Search for helices and strands: 0 residues in 0 chains, 2269 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 2288 seeds are put forward Round 1: 96 peptides, 21 chains. Longest chain 8 peptides. Score 0.243 Round 2: 105 peptides, 18 chains. Longest chain 9 peptides. Score 0.370 Round 3: 109 peptides, 20 chains. Longest chain 9 peptides. Score 0.344 Round 4: 114 peptides, 19 chains. Longest chain 16 peptides. Score 0.395 Round 5: 108 peptides, 19 chains. Longest chain 10 peptides. Score 0.363 Taking the results from Round 4 Chains 19, Residues 95, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4810 reflections ( 97.72 % complete ) and 4859 restraints for refining 2235 atoms. 4498 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2227 (Rfree = 0.000) for 2235 atoms. Found 20 (20 requested) and removed 12 (10 requested) atoms. Cycle 37: After refmac, R = 0.2278 (Rfree = 0.000) for 2237 atoms. Found 20 (20 requested) and removed 11 (10 requested) atoms. Cycle 38: After refmac, R = 0.2164 (Rfree = 0.000) for 2242 atoms. Found 20 (20 requested) and removed 13 (10 requested) atoms. Cycle 39: After refmac, R = 0.1679 (Rfree = 0.000) for 2248 atoms. Found 10 (20 requested) and removed 10 (10 requested) atoms. Cycle 40: After refmac, R = 0.1671 (Rfree = 0.000) for 2247 atoms. Found 14 (20 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.14 3.31 Search for helices and strands: 0 residues in 0 chains, 2278 seeds are put forward NCS extension: 0 residues added, 2278 seeds are put forward Round 1: 86 peptides, 19 chains. Longest chain 6 peptides. Score 0.233 Round 2: 98 peptides, 19 chains. Longest chain 13 peptides. Score 0.306 Round 3: 107 peptides, 20 chains. Longest chain 11 peptides. Score 0.333 Round 4: 110 peptides, 20 chains. Longest chain 11 peptides. Score 0.350 Round 5: 106 peptides, 20 chains. Longest chain 10 peptides. Score 0.327 Taking the results from Round 4 Chains 20, Residues 90, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 4810 reflections ( 97.72 % complete ) and 4846 restraints for refining 2235 atoms. 4493 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1692 (Rfree = 0.000) for 2235 atoms. Found 19 (20 requested) and removed 10 (10 requested) atoms. Cycle 42: After refmac, R = 0.1703 (Rfree = 0.000) for 2239 atoms. Found 17 (20 requested) and removed 10 (10 requested) atoms. Cycle 43: After refmac, R = 0.1691 (Rfree = 0.000) for 2242 atoms. Found 11 (20 requested) and removed 10 (10 requested) atoms. Cycle 44: After refmac, R = 0.1681 (Rfree = 0.000) for 2238 atoms. Found 15 (20 requested) and removed 11 (10 requested) atoms. Cycle 45: After refmac, R = 0.1975 (Rfree = 0.000) for 2238 atoms. Found 20 (20 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.10 3.27 Search for helices and strands: 0 residues in 0 chains, 2276 seeds are put forward NCS extension: 0 residues added, 2276 seeds are put forward Round 1: 82 peptides, 18 chains. Longest chain 7 peptides. Score 0.234 Round 2: 88 peptides, 18 chains. Longest chain 8 peptides. Score 0.271 Round 3: 91 peptides, 18 chains. Longest chain 9 peptides. Score 0.290 Round 4: 89 peptides, 17 chains. Longest chain 9 peptides. Score 0.303 Round 5: 90 peptides, 18 chains. Longest chain 7 peptides. Score 0.283 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 17, Residues 72, 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. 4810 reflections ( 97.72 % complete ) and 5055 restraints for refining 2235 atoms. 4784 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1852 (Rfree = 0.000) for 2235 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 47: After refmac, R = 0.1799 (Rfree = 0.000) for 2222 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 48: After refmac, R = 0.2333 (Rfree = 0.000) for 2213 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 49: After refmac, R = 0.1914 (Rfree = 0.000) for 2203 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 00:15:17 GMT 2018 Job finished. TimeTaking 31.23 Used memory is bytes: 19528936