Mon 24 Dec 00:20:30 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 2prx-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2prx-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2prx-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2prx-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/2prx-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2prx-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 00:20:35 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/2prx-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2prx-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 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-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: 144 Cell parameters: 38.520 38.520 171.590 90.000 90.000 120.000 Input sequence file: 2prx-3.6-parrot-mrncs.fasta_lf Building free atoms model in initial map for 2560 target number of atoms Had to go as low as 0.55 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 2819 atoms. Observations/parameters ratio is 0.29 ------------------------------------------------------ Starting model: R = 0.3198 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2861 (Rfree = 0.000) for 2819 atoms. Found 18 (18 requested) and removed 62 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.19 3.60 Search for helices and strands: 0 residues in 0 chains, 2803 seeds are put forward NCS extension: 0 residues added, 2803 seeds are put forward Round 1: 75 peptides, 17 chains. Longest chain 5 peptides. Score 0.216 Round 2: 96 peptides, 19 chains. Longest chain 9 peptides. Score 0.298 Round 3: 111 peptides, 22 chains. Longest chain 10 peptides. Score 0.312 Round 4: 112 peptides, 24 chains. Longest chain 7 peptides. Score 0.268 Round 5: 103 peptides, 19 chains. Longest chain 8 peptides. Score 0.341 Taking the results from Round 5 Chains 19, Residues 84, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 3298 reflections ( 99.61 % complete ) and 5881 restraints for refining 2321 atoms. 5556 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2406 (Rfree = 0.000) for 2321 atoms. Found 14 (14 requested) and removed 20 (7 requested) atoms. Cycle 2: After refmac, R = 0.2205 (Rfree = 0.000) for 2297 atoms. Found 14 (14 requested) and removed 16 (7 requested) atoms. Cycle 3: After refmac, R = 0.2193 (Rfree = 0.000) for 2283 atoms. Found 14 (14 requested) and removed 16 (7 requested) atoms. Cycle 4: After refmac, R = 0.1697 (Rfree = 0.000) for 2272 atoms. Found 6 (14 requested) and removed 12 (7 requested) atoms. Cycle 5: After refmac, R = 0.1596 (Rfree = 0.000) for 2259 atoms. Found 4 (14 requested) and removed 16 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.04 3.43 Search for helices and strands: 0 residues in 0 chains, 2290 seeds are put forward NCS extension: 0 residues added, 2290 seeds are put forward Round 1: 82 peptides, 18 chains. Longest chain 9 peptides. Score 0.236 Round 2: 104 peptides, 20 chains. Longest chain 9 peptides. Score 0.321 Round 3: 107 peptides, 20 chains. Longest chain 10 peptides. Score 0.339 Round 4: 110 peptides, 21 chains. Longest chain 11 peptides. Score 0.332 Round 5: 105 peptides, 21 chains. Longest chain 8 peptides. Score 0.302 Taking the results from Round 3 Chains 20, Residues 87, Estimated correctness of the model 0.0 % 2 chains (14 residues) have been docked in sequence ------------------------------------------------------ 3298 reflections ( 99.61 % complete ) and 4898 restraints for refining 2112 atoms. 4534 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1765 (Rfree = 0.000) for 2112 atoms. Found 11 (13 requested) and removed 18 (6 requested) atoms. Cycle 7: After refmac, R = 0.1790 (Rfree = 0.000) for 2073 atoms. Found 13 (13 requested) and removed 13 (6 requested) atoms. Cycle 8: After refmac, R = 0.1828 (Rfree = 0.000) for 2063 atoms. Found 13 (13 requested) and removed 12 (6 requested) atoms. Cycle 9: After refmac, R = 0.1768 (Rfree = 0.000) for 2056 atoms. Found 13 (13 requested) and removed 9 (6 requested) atoms. Cycle 10: After refmac, R = 0.1734 (Rfree = 0.000) for 2056 atoms. Found 11 (13 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.07 3.47 Search for helices and strands: 0 residues in 0 chains, 2102 seeds are put forward NCS extension: 0 residues added, 2102 seeds are put forward Round 1: 107 peptides, 22 chains. Longest chain 9 peptides. Score 0.288 Round 2: 114 peptides, 19 chains. Longest chain 15 peptides. Score 0.403 Round 3: 124 peptides, 22 chains. Longest chain 13 peptides. Score 0.387 Round 4: 119 peptides, 19 chains. Longest chain 13 peptides. Score 0.430 Round 5: 114 peptides, 17 chains. Longest chain 14 peptides. Score 0.450 Taking the results from Round 5 Chains 17, Residues 97, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3298 reflections ( 99.61 % complete ) and 5158 restraints for refining 2154 atoms. 4787 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1798 (Rfree = 0.000) for 2154 atoms. Found 13 (13 requested) and removed 16 (6 requested) atoms. Cycle 12: After refmac, R = 0.1730 (Rfree = 0.000) for 2145 atoms. Found 10 (13 requested) and removed 8 (6 requested) atoms. Cycle 13: After refmac, R = 0.1714 (Rfree = 0.000) for 2144 atoms. Found 7 (13 requested) and removed 8 (6 requested) atoms. Cycle 14: After refmac, R = 0.1755 (Rfree = 0.000) for 2141 atoms. Found 5 (13 requested) and removed 16 (6 requested) atoms. Cycle 15: After refmac, R = 0.1730 (Rfree = 0.000) for 2129 atoms. Found 7 (13 requested) and removed 11 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.17 3.58 Search for helices and strands: 0 residues in 0 chains, 2189 seeds are put forward NCS extension: 0 residues added, 2189 seeds are put forward Round 1: 98 peptides, 20 chains. Longest chain 10 peptides. Score 0.285 Round 2: 116 peptides, 18 chains. Longest chain 16 peptides. Score 0.438 Round 3: 106 peptides, 18 chains. Longest chain 15 peptides. Score 0.383 Round 4: 101 peptides, 18 chains. Longest chain 9 peptides. Score 0.354 Round 5: 112 peptides, 20 chains. Longest chain 10 peptides. Score 0.368 Taking the results from Round 2 Chains 18, Residues 98, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3298 reflections ( 99.61 % complete ) and 4936 restraints for refining 2147 atoms. 4562 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1766 (Rfree = 0.000) for 2147 atoms. Found 7 (13 requested) and removed 14 (6 requested) atoms. Cycle 17: After refmac, R = 0.1689 (Rfree = 0.000) for 2135 atoms. Found 5 (13 requested) and removed 12 (6 requested) atoms. Cycle 18: After refmac, R = 0.1668 (Rfree = 0.000) for 2125 atoms. Found 2 (13 requested) and removed 7 (6 requested) atoms. Cycle 19: After refmac, R = 0.1628 (Rfree = 0.000) for 2118 atoms. Found 0 (13 requested) and removed 10 (6 requested) atoms. Cycle 20: After refmac, R = 0.1660 (Rfree = 0.000) for 2105 atoms. Found 5 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.19 3.60 Search for helices and strands: 0 residues in 0 chains, 2146 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 2169 seeds are put forward Round 1: 107 peptides, 23 chains. Longest chain 7 peptides. Score 0.263 Round 2: 109 peptides, 20 chains. Longest chain 13 peptides. Score 0.351 Round 3: 112 peptides, 20 chains. Longest chain 9 peptides. Score 0.368 Round 4: 115 peptides, 20 chains. Longest chain 11 peptides. Score 0.385 Round 5: 117 peptides, 20 chains. Longest chain 14 peptides. Score 0.396 Taking the results from Round 5 Chains 20, Residues 97, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3298 reflections ( 99.61 % complete ) and 5310 restraints for refining 2202 atoms. 4942 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1837 (Rfree = 0.000) for 2202 atoms. Found 13 (14 requested) and removed 16 (7 requested) atoms. Cycle 22: After refmac, R = 0.1680 (Rfree = 0.000) for 2193 atoms. Found 8 (14 requested) and removed 13 (7 requested) atoms. Cycle 23: After refmac, R = 0.1634 (Rfree = 0.000) for 2184 atoms. Found 3 (14 requested) and removed 14 (7 requested) atoms. Cycle 24: After refmac, R = 0.1601 (Rfree = 0.000) for 2171 atoms. Found 2 (13 requested) and removed 8 (6 requested) atoms. Cycle 25: After refmac, R = 0.1567 (Rfree = 0.000) for 2164 atoms. Found 2 (13 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.17 3.58 Search for helices and strands: 0 residues in 0 chains, 2192 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 2214 seeds are put forward Round 1: 103 peptides, 22 chains. Longest chain 13 peptides. Score 0.264 Round 2: 121 peptides, 22 chains. Longest chain 13 peptides. Score 0.370 Round 3: 120 peptides, 23 chains. Longest chain 10 peptides. Score 0.340 Round 4: 105 peptides, 19 chains. Longest chain 15 peptides. Score 0.352 Round 5: 109 peptides, 19 chains. Longest chain 13 peptides. Score 0.375 Taking the results from Round 5 Chains 19, Residues 90, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 3298 reflections ( 99.61 % complete ) and 5373 restraints for refining 2225 atoms. 5013 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1777 (Rfree = 0.000) for 2225 atoms. Found 11 (14 requested) and removed 17 (7 requested) atoms. Cycle 27: After refmac, R = 0.1639 (Rfree = 0.000) for 2214 atoms. Found 2 (14 requested) and removed 11 (7 requested) atoms. Cycle 28: After refmac, R = 0.1627 (Rfree = 0.000) for 2203 atoms. Found 8 (14 requested) and removed 8 (7 requested) atoms. Cycle 29: After refmac, R = 0.1527 (Rfree = 0.000) for 2200 atoms. Found 5 (14 requested) and removed 8 (7 requested) atoms. Cycle 30: After refmac, R = 0.1561 (Rfree = 0.000) for 2192 atoms. Found 4 (14 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.13 3.53 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: 93 peptides, 21 chains. Longest chain 7 peptides. Score 0.227 Round 2: 118 peptides, 23 chains. Longest chain 9 peptides. Score 0.329 Round 3: 125 peptides, 23 chains. Longest chain 11 peptides. Score 0.369 Round 4: 116 peptides, 21 chains. Longest chain 11 peptides. Score 0.366 Round 5: 107 peptides, 17 chains. Longest chain 12 peptides. Score 0.413 Taking the results from Round 5 Chains 17, Residues 90, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 3298 reflections ( 99.61 % complete ) and 5204 restraints for refining 2228 atoms. 4834 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1658 (Rfree = 0.000) for 2228 atoms. Found 10 (14 requested) and removed 19 (7 requested) atoms. Cycle 32: After refmac, R = 0.1540 (Rfree = 0.000) for 2214 atoms. Found 6 (14 requested) and removed 12 (7 requested) atoms. Cycle 33: After refmac, R = 0.1491 (Rfree = 0.000) for 2207 atoms. Found 2 (14 requested) and removed 9 (7 requested) atoms. Cycle 34: After refmac, R = 0.1512 (Rfree = 0.000) for 2196 atoms. Found 3 (14 requested) and removed 10 (7 requested) atoms. Cycle 35: After refmac, R = 0.1555 (Rfree = 0.000) for 2189 atoms. Found 1 (14 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.12 3.52 Search for helices and strands: 0 residues in 0 chains, 2231 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 2246 seeds are put forward Round 1: 78 peptides, 17 chains. Longest chain 8 peptides. Score 0.237 Round 2: 101 peptides, 19 chains. Longest chain 9 peptides. Score 0.329 Round 3: 103 peptides, 18 chains. Longest chain 10 peptides. Score 0.366 Round 4: 105 peptides, 22 chains. Longest chain 8 peptides. Score 0.276 Round 5: 118 peptides, 20 chains. Longest chain 14 peptides. Score 0.401 Taking the results from Round 5 Chains 20, Residues 98, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 3298 reflections ( 99.61 % complete ) and 5150 restraints for refining 2216 atoms. 4769 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1987 (Rfree = 0.000) for 2216 atoms. Found 14 (14 requested) and removed 22 (7 requested) atoms. Cycle 37: After refmac, R = 0.1478 (Rfree = 0.000) for 2198 atoms. Found 6 (14 requested) and removed 12 (7 requested) atoms. Cycle 38: After refmac, R = 0.1368 (Rfree = 0.000) for 2187 atoms. Found 7 (14 requested) and removed 10 (7 requested) atoms. Cycle 39: After refmac, R = 0.1439 (Rfree = 0.000) for 2181 atoms. Found 10 (14 requested) and removed 14 (7 requested) atoms. Cycle 40: After refmac, R = 0.1263 (Rfree = 0.000) for 2176 atoms. Found 1 (13 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.10 3.50 Search for helices and strands: 0 residues in 0 chains, 2218 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 2234 seeds are put forward Round 1: 71 peptides, 14 chains. Longest chain 10 peptides. Score 0.275 Round 2: 95 peptides, 19 chains. Longest chain 10 peptides. Score 0.292 Round 3: 92 peptides, 16 chains. Longest chain 13 peptides. Score 0.352 Round 4: 90 peptides, 16 chains. Longest chain 14 peptides. Score 0.340 Round 5: 92 peptides, 14 chains. Longest chain 15 peptides. Score 0.404 Taking the results from Round 5 Chains 14, Residues 78, Estimated correctness of the model 0.0 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 3298 reflections ( 99.61 % complete ) and 5247 restraints for refining 2225 atoms. 4880 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1622 (Rfree = 0.000) for 2225 atoms. Found 11 (14 requested) and removed 16 (7 requested) atoms. Cycle 42: After refmac, R = 0.1637 (Rfree = 0.000) for 2214 atoms. Found 10 (14 requested) and removed 9 (7 requested) atoms. Cycle 43: After refmac, R = 0.1782 (Rfree = 0.000) for 2205 atoms. Found 5 (14 requested) and removed 17 (7 requested) atoms. Cycle 44: After refmac, R = 0.1544 (Rfree = 0.000) for 2186 atoms. Found 8 (14 requested) and removed 10 (7 requested) atoms. Cycle 45: After refmac, R = 0.1492 (Rfree = 0.000) for 2182 atoms. Found 6 (14 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.10 3.50 Search for helices and strands: 0 residues in 0 chains, 2223 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 2245 seeds are put forward Round 1: 86 peptides, 20 chains. Longest chain 5 peptides. Score 0.208 Round 2: 81 peptides, 16 chains. Longest chain 11 peptides. Score 0.284 Round 3: 93 peptides, 18 chains. Longest chain 11 peptides. Score 0.306 Round 4: 84 peptides, 15 chains. Longest chain 11 peptides. Score 0.330 Round 5: 83 peptides, 12 chains. Longest chain 13 peptides. Score 0.404 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 13, Residues 71, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence Sequence coverage is 12 % 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 5216 restraints for refining 2171 atoms. 4916 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1526 (Rfree = 0.000) for 2171 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.1624 (Rfree = 0.000) for 2163 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.2190 (Rfree = 0.000) for 2154 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.1510 (Rfree = 0.000) for 2145 atoms. TimeTaking 32.57