null Mon 24 Dec 01:13:47 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-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2prv-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2prv-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2prv-3.6-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-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2prv-3.6-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 01:13:52 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-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2prv-3.6-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 199 and 0 Target number of residues in the AU: 199 Target solvent content: 0.6503 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-3.6-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-3.6-parrot-mrncs.fasta_lf Building free atoms model in initial map for 2448 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: 44.420 3.600 Wilson plot Bfac: 77.51 3382 reflections ( 97.72 % complete ) and 0 restraints for refining 2713 atoms. Observations/parameters ratio is 0.31 ------------------------------------------------------ Starting model: R = 0.3784 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3421 (Rfree = 0.000) for 2713 atoms. Found 15 (17 requested) and removed 72 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.46 3.65 Search for helices and strands: 0 residues in 0 chains, 2680 seeds are put forward NCS extension: 0 residues added, 2680 seeds are put forward Round 1: 73 peptides, 17 chains. Longest chain 6 peptides. Score 0.201 Round 2: 89 peptides, 20 chains. Longest chain 7 peptides. Score 0.225 Round 3: 89 peptides, 19 chains. Longest chain 8 peptides. Score 0.251 Round 4: 98 peptides, 21 chains. Longest chain 7 peptides. Score 0.256 Round 5: 110 peptides, 21 chains. Longest chain 8 peptides. Score 0.326 Taking the results from Round 5 Chains 21, Residues 89, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3382 reflections ( 97.72 % complete ) and 5278 restraints for refining 2219 atoms. 4943 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2758 (Rfree = 0.000) for 2219 atoms. Found 10 (14 requested) and removed 18 (7 requested) atoms. Cycle 2: After refmac, R = 0.2478 (Rfree = 0.000) for 2191 atoms. Found 6 (14 requested) and removed 11 (7 requested) atoms. Cycle 3: After refmac, R = 0.2097 (Rfree = 0.000) for 2177 atoms. Found 1 (14 requested) and removed 9 (7 requested) atoms. Cycle 4: After refmac, R = 0.1981 (Rfree = 0.000) for 2160 atoms. Found 1 (13 requested) and removed 9 (6 requested) atoms. Cycle 5: After refmac, R = 0.2507 (Rfree = 0.000) for 2145 atoms. Found 13 (13 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.39 3.58 Search for helices and strands: 0 residues in 0 chains, 2202 seeds are put forward NCS extension: 0 residues added, 2202 seeds are put forward Round 1: 100 peptides, 23 chains. Longest chain 6 peptides. Score 0.217 Round 2: 118 peptides, 25 chains. Longest chain 7 peptides. Score 0.276 Round 3: 118 peptides, 21 chains. Longest chain 11 peptides. Score 0.370 Round 4: 130 peptides, 24 chains. Longest chain 9 peptides. Score 0.366 Round 5: 115 peptides, 22 chains. Longest chain 7 peptides. Score 0.330 Taking the results from Round 3 Chains 21, Residues 97, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3382 reflections ( 97.72 % complete ) and 5127 restraints for refining 2215 atoms. 4760 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2543 (Rfree = 0.000) for 2215 atoms. Found 11 (14 requested) and removed 17 (7 requested) atoms. Cycle 7: After refmac, R = 0.2194 (Rfree = 0.000) for 2190 atoms. Found 9 (14 requested) and removed 14 (7 requested) atoms. Cycle 8: After refmac, R = 0.2103 (Rfree = 0.000) for 2171 atoms. Found 10 (14 requested) and removed 7 (7 requested) atoms. Cycle 9: After refmac, R = 0.1705 (Rfree = 0.000) for 2163 atoms. Found 4 (13 requested) and removed 57 (6 requested) atoms. Cycle 10: After refmac, R = 0.1986 (Rfree = 0.000) for 2107 atoms. Found 9 (13 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.42 3.61 Search for helices and strands: 0 residues in 0 chains, 2144 seeds are put forward NCS extension: 11 residues added (0 deleted due to clashes), 2155 seeds are put forward Round 1: 89 peptides, 20 chains. Longest chain 6 peptides. Score 0.225 Round 2: 109 peptides, 21 chains. Longest chain 10 peptides. Score 0.320 Round 3: 119 peptides, 23 chains. Longest chain 11 peptides. Score 0.329 Round 4: 122 peptides, 25 chains. Longest chain 8 peptides. Score 0.298 Round 5: 111 peptides, 21 chains. Longest chain 12 peptides. Score 0.332 Taking the results from Round 5 Chains 21, Residues 90, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3382 reflections ( 97.72 % complete ) and 4846 restraints for refining 2112 atoms. 4507 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2154 (Rfree = 0.000) for 2112 atoms. Found 8 (13 requested) and removed 16 (6 requested) atoms. Cycle 12: After refmac, R = 0.2105 (Rfree = 0.000) for 2094 atoms. Found 13 (13 requested) and removed 13 (6 requested) atoms. Cycle 13: After refmac, R = 0.1912 (Rfree = 0.000) for 2086 atoms. Found 12 (13 requested) and removed 10 (6 requested) atoms. Cycle 14: After refmac, R = 0.1504 (Rfree = 0.000) for 2087 atoms. Found 7 (13 requested) and removed 8 (6 requested) atoms. Cycle 15: After refmac, R = 0.1605 (Rfree = 0.000) for 2084 atoms. Found 7 (13 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.39 3.58 Search for helices and strands: 0 residues in 0 chains, 2143 seeds are put forward NCS extension: 0 residues added, 2143 seeds are put forward Round 1: 95 peptides, 22 chains. Longest chain 6 peptides. Score 0.212 Round 2: 113 peptides, 22 chains. Longest chain 9 peptides. Score 0.319 Round 3: 110 peptides, 21 chains. Longest chain 9 peptides. Score 0.326 Round 4: 124 peptides, 24 chains. Longest chain 8 peptides. Score 0.333 Round 5: 112 peptides, 21 chains. Longest chain 13 peptides. Score 0.337 Taking the results from Round 5 Chains 21, Residues 91, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3382 reflections ( 97.72 % complete ) and 5016 restraints for refining 2183 atoms. 4673 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2082 (Rfree = 0.000) for 2183 atoms. Found 10 (14 requested) and removed 22 (7 requested) atoms. Cycle 17: After refmac, R = 0.2194 (Rfree = 0.000) for 2164 atoms. Found 10 (13 requested) and removed 12 (6 requested) atoms. Cycle 18: After refmac, R = 0.2189 (Rfree = 0.000) for 2157 atoms. Found 13 (13 requested) and removed 13 (6 requested) atoms. Cycle 19: After refmac, R = 0.2007 (Rfree = 0.000) for 2154 atoms. Found 8 (13 requested) and removed 9 (6 requested) atoms. Cycle 20: After refmac, R = 0.2011 (Rfree = 0.000) for 2147 atoms. Found 12 (13 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.37 3.55 Search for helices and strands: 0 residues in 0 chains, 2201 seeds are put forward NCS extension: 0 residues added, 2201 seeds are put forward Round 1: 104 peptides, 24 chains. Longest chain 6 peptides. Score 0.217 Round 2: 113 peptides, 23 chains. Longest chain 8 peptides. Score 0.295 Round 3: 119 peptides, 22 chains. Longest chain 13 peptides. Score 0.352 Round 4: 116 peptides, 20 chains. Longest chain 9 peptides. Score 0.383 Round 5: 109 peptides, 20 chains. Longest chain 9 peptides. Score 0.344 Taking the results from Round 4 Chains 20, Residues 96, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3382 reflections ( 97.72 % complete ) and 5039 restraints for refining 2219 atoms. 4675 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1922 (Rfree = 0.000) for 2219 atoms. Found 9 (14 requested) and removed 11 (7 requested) atoms. Cycle 22: After refmac, R = 0.1702 (Rfree = 0.000) for 2210 atoms. Found 7 (14 requested) and removed 11 (7 requested) atoms. Cycle 23: After refmac, R = 0.1469 (Rfree = 0.000) for 2203 atoms. Found 3 (14 requested) and removed 7 (7 requested) atoms. Cycle 24: After refmac, R = 0.1387 (Rfree = 0.000) for 2197 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 25: After refmac, R = 0.1566 (Rfree = 0.000) for 2190 atoms. Found 4 (14 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.39 3.58 Search for helices and strands: 0 residues in 0 chains, 2223 seeds are put forward NCS extension: 0 residues added, 2223 seeds are put forward Round 1: 104 peptides, 22 chains. Longest chain 7 peptides. Score 0.267 Round 2: 116 peptides, 23 chains. Longest chain 8 peptides. Score 0.312 Round 3: 110 peptides, 23 chains. Longest chain 9 peptides. Score 0.277 Round 4: 104 peptides, 20 chains. Longest chain 8 peptides. Score 0.316 Round 5: 119 peptides, 24 chains. Longest chain 8 peptides. Score 0.305 Taking the results from Round 4 Chains 20, Residues 84, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 3382 reflections ( 97.72 % complete ) and 5162 restraints for refining 2219 atoms. 4835 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1767 (Rfree = 0.000) for 2219 atoms. Found 9 (14 requested) and removed 12 (7 requested) atoms. Cycle 27: After refmac, R = 0.1614 (Rfree = 0.000) for 2211 atoms. Found 4 (14 requested) and removed 7 (7 requested) atoms. Cycle 28: After refmac, R = 0.1611 (Rfree = 0.000) for 2206 atoms. Found 3 (14 requested) and removed 7 (7 requested) atoms. Cycle 29: After refmac, R = 0.2666 (Rfree = 0.000) for 2200 atoms. Found 14 (14 requested) and removed 15 (7 requested) atoms. Cycle 30: After refmac, R = 0.1694 (Rfree = 0.000) for 2189 atoms. Found 6 (14 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.38 3.57 Search for helices and strands: 0 residues in 0 chains, 2218 seeds are put forward NCS extension: 0 residues added, 2218 seeds are put forward Round 1: 96 peptides, 22 chains. Longest chain 6 peptides. Score 0.218 Round 2: 99 peptides, 20 chains. Longest chain 9 peptides. Score 0.287 Round 3: 99 peptides, 20 chains. Longest chain 7 peptides. Score 0.287 Round 4: 97 peptides, 19 chains. Longest chain 9 peptides. Score 0.300 Round 5: 101 peptides, 19 chains. Longest chain 9 peptides. Score 0.323 Taking the results from Round 5 Chains 19, Residues 82, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3382 reflections ( 97.72 % complete ) and 5154 restraints for refining 2219 atoms. 4845 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1771 (Rfree = 0.000) for 2219 atoms. Found 7 (14 requested) and removed 7 (7 requested) atoms. Cycle 32: After refmac, R = 0.1840 (Rfree = 0.000) for 2212 atoms. Found 14 (14 requested) and removed 8 (7 requested) atoms. Cycle 33: After refmac, R = 0.1871 (Rfree = 0.000) for 2214 atoms. Found 14 (14 requested) and removed 7 (7 requested) atoms. Cycle 34: After refmac, R = 0.1823 (Rfree = 0.000) for 2216 atoms. Found 13 (14 requested) and removed 8 (7 requested) atoms. Cycle 35: After refmac, R = 0.1730 (Rfree = 0.000) for 2220 atoms. Found 10 (14 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.41 3.60 Search for helices and strands: 0 residues in 0 chains, 2268 seeds are put forward NCS extension: 0 residues added, 2268 seeds are put forward Round 1: 96 peptides, 22 chains. Longest chain 6 peptides. Score 0.218 Round 2: 101 peptides, 21 chains. Longest chain 8 peptides. Score 0.274 Round 3: 111 peptides, 22 chains. Longest chain 9 peptides. Score 0.308 Round 4: 101 peptides, 20 chains. Longest chain 11 peptides. Score 0.299 Round 5: 99 peptides, 19 chains. Longest chain 10 peptides. Score 0.312 Taking the results from Round 5 Chains 19, Residues 80, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3382 reflections ( 97.72 % complete ) and 5134 restraints for refining 2219 atoms. 4833 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1712 (Rfree = 0.000) for 2219 atoms. Found 12 (14 requested) and removed 9 (7 requested) atoms. Cycle 37: After refmac, R = 0.1672 (Rfree = 0.000) for 2215 atoms. Found 12 (14 requested) and removed 7 (7 requested) atoms. Cycle 38: After refmac, R = 0.1522 (Rfree = 0.000) for 2215 atoms. Found 5 (14 requested) and removed 7 (7 requested) atoms. Cycle 39: After refmac, R = 0.1870 (Rfree = 0.000) for 2211 atoms. Found 14 (14 requested) and removed 9 (7 requested) atoms. Cycle 40: After refmac, R = 0.1404 (Rfree = 0.000) for 2212 atoms. Found 6 (14 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.40 3.59 Search for helices and strands: 0 residues in 0 chains, 2238 seeds are put forward NCS extension: 0 residues added, 2238 seeds are put forward Round 1: 84 peptides, 18 chains. Longest chain 7 peptides. Score 0.246 Round 2: 95 peptides, 19 chains. Longest chain 8 peptides. Score 0.288 Round 3: 101 peptides, 19 chains. Longest chain 9 peptides. Score 0.323 Round 4: 111 peptides, 20 chains. Longest chain 8 peptides. Score 0.355 Round 5: 110 peptides, 19 chains. Longest chain 11 peptides. Score 0.374 Taking the results from Round 5 Chains 19, Residues 91, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 3382 reflections ( 97.72 % complete ) and 5076 restraints for refining 2219 atoms. 4716 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1870 (Rfree = 0.000) for 2219 atoms. Found 6 (14 requested) and removed 8 (7 requested) atoms. Cycle 42: After refmac, R = 0.1511 (Rfree = 0.000) for 2211 atoms. Found 9 (14 requested) and removed 7 (7 requested) atoms. Cycle 43: After refmac, R = 0.1545 (Rfree = 0.000) for 2211 atoms. Found 14 (14 requested) and removed 11 (7 requested) atoms. Cycle 44: After refmac, R = 0.1545 (Rfree = 0.000) for 2214 atoms. Found 8 (14 requested) and removed 7 (7 requested) atoms. Cycle 45: After refmac, R = 0.1075 (Rfree = 0.000) for 2214 atoms. Found 5 (14 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.42 3.61 Search for helices and strands: 0 residues in 0 chains, 2241 seeds are put forward NCS extension: 0 residues added, 2241 seeds are put forward Round 1: 76 peptides, 17 chains. Longest chain 6 peptides. Score 0.221 Round 2: 81 peptides, 16 chains. Longest chain 9 peptides. Score 0.281 Round 3: 80 peptides, 16 chains. Longest chain 8 peptides. Score 0.274 Round 4: 89 peptides, 17 chains. Longest chain 9 peptides. Score 0.303 Round 5: 84 peptides, 17 chains. Longest chain 9 peptides. Score 0.273 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. 3382 reflections ( 97.72 % complete ) and 5159 restraints for refining 2219 atoms. 4888 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1375 (Rfree = 0.000) for 2219 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.1584 (Rfree = 0.000) for 2211 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.1369 (Rfree = 0.000) for 2201 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.1191 (Rfree = 0.000) for 2193 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:44:44 GMT 2018 Job finished. TimeTaking 30.95 Used memory is bytes: 14252480