null Mon 24 Dec 07:40:55 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2prx-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2prx-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2prx-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2prx-3.6-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2prx-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2prx-3.6-parrot-noncs ############### 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 07:40:59 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/noncs/ArpWArp/wArpResults/WorkingDir/2prx-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2prx-3.6-parrot-noncs/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 216 and 0 Target number of residues in the AU: 216 Target solvent content: 0.6024 Checking the provided sequence file Detected sequence length: 160 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 320 Adjusted target solvent content: 0.41 Input MTZ file: 2prx-3.6-parrot-noncs.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: 144 Cell parameters: 38.520 38.520 171.590 90.000 90.000 120.000 Input sequence file: 2prx-3.6-parrot-noncs.fasta_lf Building free atoms model in initial map for 2560 target number of atoms Had to go as low as 0.50 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: 28.816 3.600 Wilson plot Bfac: 53.52 3298 reflections ( 99.61 % complete ) and 0 restraints for refining 2835 atoms. Observations/parameters ratio is 0.29 ------------------------------------------------------ Starting model: R = 0.3167 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2877 (Rfree = 0.000) for 2835 atoms. Found 18 (18 requested) and removed 99 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.24 3.66 Search for helices and strands: 0 residues in 0 chains, 2776 seeds are put forward NCS extension: 0 residues added, 2776 seeds are put forward Round 1: 61 peptides, 13 chains. Longest chain 8 peptides. Score 0.235 Round 2: 84 peptides, 16 chains. Longest chain 9 peptides. Score 0.303 Round 3: 90 peptides, 17 chains. Longest chain 11 peptides. Score 0.314 Round 4: 97 peptides, 18 chains. Longest chain 12 peptides. Score 0.330 Round 5: 109 peptides, 19 chains. Longest chain 12 peptides. Score 0.375 Taking the results from Round 5 Chains 20, Residues 90, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 3298 reflections ( 99.61 % complete ) and 5734 restraints for refining 2321 atoms. 5364 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2220 (Rfree = 0.000) for 2321 atoms. Found 14 (14 requested) and removed 42 (7 requested) atoms. Cycle 2: After refmac, R = 0.2176 (Rfree = 0.000) for 2273 atoms. Found 13 (14 requested) and removed 35 (7 requested) atoms. Cycle 3: After refmac, R = 0.2068 (Rfree = 0.000) for 2248 atoms. Found 14 (14 requested) and removed 22 (7 requested) atoms. Cycle 4: After refmac, R = 0.1641 (Rfree = 0.000) for 2235 atoms. Found 3 (14 requested) and removed 10 (7 requested) atoms. Cycle 5: After refmac, R = 0.2276 (Rfree = 0.000) for 2225 atoms. Found 14 (14 requested) and removed 25 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.20 3.61 Search for helices and strands: 0 residues in 0 chains, 2261 seeds are put forward NCS extension: 0 residues added, 2261 seeds are put forward Round 1: 88 peptides, 19 chains. Longest chain 10 peptides. Score 0.248 Round 2: 119 peptides, 22 chains. Longest chain 13 peptides. Score 0.359 Round 3: 123 peptides, 20 chains. Longest chain 15 peptides. Score 0.428 Round 4: 121 peptides, 22 chains. Longest chain 11 peptides. Score 0.370 Round 5: 119 peptides, 22 chains. Longest chain 14 peptides. Score 0.359 Taking the results from Round 3 Chains 20, Residues 103, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3298 reflections ( 99.61 % complete ) and 5256 restraints for refining 2160 atoms. 4864 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1828 (Rfree = 0.000) for 2160 atoms. Found 12 (13 requested) and removed 15 (6 requested) atoms. Cycle 7: After refmac, R = 0.1721 (Rfree = 0.000) for 2146 atoms. Found 6 (13 requested) and removed 13 (6 requested) atoms. Cycle 8: After refmac, R = 0.1697 (Rfree = 0.000) for 2131 atoms. Found 5 (13 requested) and removed 10 (6 requested) atoms. Cycle 9: After refmac, R = 0.1639 (Rfree = 0.000) for 2124 atoms. Found 2 (13 requested) and removed 8 (6 requested) atoms. Cycle 10: After refmac, R = 0.1688 (Rfree = 0.000) for 2113 atoms. Found 5 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.19 3.60 Search for helices and strands: 0 residues in 0 chains, 2166 seeds are put forward NCS extension: 0 residues added, 2166 seeds are put forward Round 1: 90 peptides, 19 chains. Longest chain 7 peptides. Score 0.261 Round 2: 124 peptides, 23 chains. Longest chain 12 peptides. Score 0.363 Round 3: 109 peptides, 18 chains. Longest chain 12 peptides. Score 0.400 Round 4: 100 peptides, 18 chains. Longest chain 11 peptides. Score 0.348 Round 5: 106 peptides, 16 chains. Longest chain 14 peptides. Score 0.432 Taking the results from Round 5 Chains 16, Residues 90, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3298 reflections ( 99.61 % complete ) and 5054 restraints for refining 2124 atoms. 4710 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1697 (Rfree = 0.000) for 2124 atoms. Found 13 (13 requested) and removed 25 (6 requested) atoms. Cycle 12: After refmac, R = 0.1796 (Rfree = 0.000) for 2108 atoms. Found 13 (13 requested) and removed 11 (6 requested) atoms. Cycle 13: After refmac, R = 0.1649 (Rfree = 0.000) for 2105 atoms. Found 13 (13 requested) and removed 16 (6 requested) atoms. Cycle 14: After refmac, R = 0.1845 (Rfree = 0.000) for 2097 atoms. Found 13 (13 requested) and removed 12 (6 requested) atoms. Cycle 15: After refmac, R = 0.1744 (Rfree = 0.000) for 2091 atoms. Found 13 (13 requested) and removed 12 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.17 3.58 Search for helices and strands: 0 residues in 0 chains, 2132 seeds are put forward NCS extension: 0 residues added, 2132 seeds are put forward Round 1: 101 peptides, 23 chains. Longest chain 10 peptides. Score 0.225 Round 2: 99 peptides, 19 chains. Longest chain 13 peptides. Score 0.317 Round 3: 107 peptides, 20 chains. Longest chain 16 peptides. Score 0.339 Round 4: 110 peptides, 19 chains. Longest chain 14 peptides. Score 0.381 Round 5: 125 peptides, 21 chains. Longest chain 15 peptides. Score 0.416 Taking the results from Round 5 Chains 21, Residues 104, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 3298 reflections ( 99.61 % complete ) and 4951 restraints for refining 2114 atoms. 4540 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1584 (Rfree = 0.000) for 2114 atoms. Found 9 (13 requested) and removed 21 (6 requested) atoms. Cycle 17: After refmac, R = 0.1420 (Rfree = 0.000) for 2092 atoms. Found 5 (13 requested) and removed 12 (6 requested) atoms. Cycle 18: After refmac, R = 0.1657 (Rfree = 0.000) for 2083 atoms. Found 13 (13 requested) and removed 12 (6 requested) atoms. Cycle 19: After refmac, R = 0.1213 (Rfree = 0.000) for 2079 atoms. Found 4 (13 requested) and removed 8 (6 requested) atoms. Cycle 20: After refmac, R = 0.1244 (Rfree = 0.000) for 2074 atoms. Found 4 (13 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.20 3.61 Search for helices and strands: 0 residues in 0 chains, 2111 seeds are put forward NCS extension: 0 residues added, 2111 seeds are put forward Round 1: 107 peptides, 25 chains. Longest chain 5 peptides. Score 0.212 Round 2: 110 peptides, 22 chains. Longest chain 8 peptides. Score 0.307 Round 3: 117 peptides, 19 chains. Longest chain 13 peptides. Score 0.419 Round 4: 114 peptides, 19 chains. Longest chain 12 peptides. Score 0.403 Round 5: 103 peptides, 18 chains. Longest chain 9 peptides. Score 0.366 Taking the results from Round 3 Chains 19, Residues 98, Estimated correctness of the model 0.0 % 2 chains (11 residues) have been docked in sequence ------------------------------------------------------ 3298 reflections ( 99.61 % complete ) and 4835 restraints for refining 2141 atoms. 4431 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1609 (Rfree = 0.000) for 2141 atoms. Found 13 (13 requested) and removed 18 (6 requested) atoms. Cycle 22: After refmac, R = 0.1656 (Rfree = 0.000) for 2134 atoms. Found 8 (13 requested) and removed 14 (6 requested) atoms. Cycle 23: After refmac, R = 0.2241 (Rfree = 0.000) for 2123 atoms. Found 13 (13 requested) and removed 23 (6 requested) atoms. Cycle 24: After refmac, R = 0.1385 (Rfree = 0.000) for 2110 atoms. Found 7 (13 requested) and removed 9 (6 requested) atoms. Cycle 25: After refmac, R = 0.1209 (Rfree = 0.000) for 2105 atoms. Found 1 (13 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.19 3.60 Search for helices and strands: 0 residues in 0 chains, 2143 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 2160 seeds are put forward Round 1: 99 peptides, 22 chains. Longest chain 7 peptides. Score 0.239 Round 2: 115 peptides, 21 chains. Longest chain 13 peptides. Score 0.360 Round 3: 133 peptides, 24 chains. Longest chain 11 peptides. Score 0.389 Round 4: 131 peptides, 23 chains. Longest chain 13 peptides. Score 0.402 Round 5: 128 peptides, 23 chains. Longest chain 16 peptides. Score 0.385 Taking the results from Round 4 Chains 23, Residues 108, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 3298 reflections ( 99.61 % complete ) and 5022 restraints for refining 2144 atoms. 4597 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1537 (Rfree = 0.000) for 2144 atoms. Found 13 (13 requested) and removed 13 (6 requested) atoms. Cycle 27: After refmac, R = 0.1392 (Rfree = 0.000) for 2141 atoms. Found 6 (13 requested) and removed 13 (6 requested) atoms. Cycle 28: After refmac, R = 0.1352 (Rfree = 0.000) for 2133 atoms. Found 4 (13 requested) and removed 10 (6 requested) atoms. Cycle 29: After refmac, R = 0.1307 (Rfree = 0.000) for 2126 atoms. Found 2 (13 requested) and removed 7 (6 requested) atoms. Cycle 30: After refmac, R = 0.1338 (Rfree = 0.000) for 2121 atoms. Found 5 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.19 3.60 Search for helices and strands: 0 residues in 0 chains, 2151 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 2164 seeds are put forward Round 1: 96 peptides, 21 chains. Longest chain 9 peptides. Score 0.246 Round 2: 114 peptides, 22 chains. Longest chain 10 peptides. Score 0.330 Round 3: 110 peptides, 21 chains. Longest chain 8 peptides. Score 0.332 Round 4: 106 peptides, 19 chains. Longest chain 11 peptides. Score 0.358 Round 5: 102 peptides, 18 chains. Longest chain 9 peptides. Score 0.360 Taking the results from Round 5 Chains 18, Residues 84, Estimated correctness of the model 0.0 % 2 chains (10 residues) have been docked in sequence ------------------------------------------------------ 3298 reflections ( 99.61 % complete ) and 5305 restraints for refining 2221 atoms. 4959 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1385 (Rfree = 0.000) for 2221 atoms. Found 9 (14 requested) and removed 21 (7 requested) atoms. Cycle 32: After refmac, R = 0.1205 (Rfree = 0.000) for 2205 atoms. Found 3 (14 requested) and removed 9 (7 requested) atoms. Cycle 33: After refmac, R = 0.1206 (Rfree = 0.000) for 2193 atoms. Found 4 (14 requested) and removed 12 (7 requested) atoms. Cycle 34: After refmac, R = 0.1145 (Rfree = 0.000) for 2181 atoms. Found 1 (14 requested) and removed 9 (7 requested) atoms. Cycle 35: After refmac, R = 0.1704 (Rfree = 0.000) for 2170 atoms. Found 13 (13 requested) and removed 14 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.16 3.57 Search for helices and strands: 0 residues in 0 chains, 2193 seeds are put forward NCS extension: 0 residues added, 2193 seeds are put forward Round 1: 80 peptides, 16 chains. Longest chain 8 peptides. Score 0.278 Round 2: 93 peptides, 17 chains. Longest chain 11 peptides. Score 0.332 Round 3: 97 peptides, 19 chains. Longest chain 8 peptides. Score 0.304 Round 4: 103 peptides, 18 chains. Longest chain 11 peptides. Score 0.366 Round 5: 114 peptides, 20 chains. Longest chain 9 peptides. Score 0.379 Taking the results from Round 5 Chains 20, Residues 94, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3298 reflections ( 99.61 % complete ) and 5340 restraints for refining 2220 atoms. 4984 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1492 (Rfree = 0.000) for 2220 atoms. Found 14 (14 requested) and removed 23 (7 requested) atoms. Cycle 37: After refmac, R = 0.1521 (Rfree = 0.000) for 2203 atoms. Found 14 (14 requested) and removed 9 (7 requested) atoms. Cycle 38: After refmac, R = 0.1562 (Rfree = 0.000) for 2205 atoms. Found 14 (14 requested) and removed 14 (7 requested) atoms. Cycle 39: After refmac, R = 0.1082 (Rfree = 0.000) for 2200 atoms. Found 5 (14 requested) and removed 8 (7 requested) atoms. Cycle 40: After refmac, R = 0.0951 (Rfree = 0.000) for 2194 atoms. Found 3 (14 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.21 3.62 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: 102 peptides, 23 chains. Longest chain 7 peptides. Score 0.232 Round 2: 116 peptides, 21 chains. Longest chain 11 peptides. Score 0.366 Round 3: 115 peptides, 20 chains. Longest chain 12 peptides. Score 0.385 Round 4: 108 peptides, 18 chains. Longest chain 10 peptides. Score 0.394 Round 5: 110 peptides, 20 chains. Longest chain 10 peptides. Score 0.356 Taking the results from Round 4 Chains 18, Residues 90, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 3298 reflections ( 99.61 % complete ) and 5407 restraints for refining 2248 atoms. 5049 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1519 (Rfree = 0.000) for 2248 atoms. Found 14 (14 requested) and removed 16 (7 requested) atoms. Cycle 42: After refmac, R = 0.1465 (Rfree = 0.000) for 2239 atoms. Found 14 (14 requested) and removed 11 (7 requested) atoms. Cycle 43: After refmac, R = 0.1468 (Rfree = 0.000) for 2235 atoms. Found 14 (14 requested) and removed 10 (7 requested) atoms. Cycle 44: After refmac, R = 0.1306 (Rfree = 0.000) for 2237 atoms. Found 14 (14 requested) and removed 18 (7 requested) atoms. Cycle 45: After refmac, R = 0.1305 (Rfree = 0.000) for 2230 atoms. Found 14 (14 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.18 3.59 Search for helices and strands: 0 residues in 0 chains, 2286 seeds are put forward NCS extension: 9 residues added (3 deleted due to clashes), 2295 seeds are put forward Round 1: 83 peptides, 19 chains. Longest chain 6 peptides. Score 0.215 Round 2: 97 peptides, 19 chains. Longest chain 8 peptides. Score 0.304 Round 3: 84 peptides, 16 chains. Longest chain 9 peptides. Score 0.303 Round 4: 82 peptides, 16 chains. Longest chain 9 peptides. Score 0.291 Round 5: 84 peptides, 15 chains. Longest chain 9 peptides. Score 0.330 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 15, Residues 69, 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 2prx-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3298 reflections ( 99.61 % complete ) and 5791 restraints for refining 2320 atoms. 5530 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1384 (Rfree = 0.000) for 2320 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.1047 (Rfree = 0.000) for 2309 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.0979 (Rfree = 0.000) for 2296 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.0951 (Rfree = 0.000) for 2289 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:09:30 GMT 2018 Job finished. TimeTaking 28.6 Used memory is bytes: 11723672