null Mon 24 Dec 00:33:31 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 2fzt-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2fzt-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2fzt-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fzt-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/2fzt-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fzt-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 00:33:36 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/2fzt-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fzt-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 120 and 0 Target number of residues in the AU: 120 Target solvent content: 0.6262 Checking the provided sequence file Detected sequence length: 79 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 158 Adjusted target solvent content: 0.51 Input MTZ file: 2fzt-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: 4 Cell parameters: 49.630 27.430 65.380 90.000 102.600 90.000 Input sequence file: 2fzt-3.6-parrot-mrncs.fasta_lf Building free atoms model in initial map for 1264 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: 63.805 3.600 Wilson plot Bfac: 63.14 2138 reflections ( 99.44 % complete ) and 0 restraints for refining 1390 atoms. Observations/parameters ratio is 0.38 ------------------------------------------------------ Starting model: R = 0.3667 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3556 (Rfree = 0.000) for 1390 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.38 3.34 Search for helices and strands: 0 residues in 0 chains, 1438 seeds are put forward NCS extension: 0 residues added, 1438 seeds are put forward Round 1: 51 peptides, 11 chains. Longest chain 6 peptides. Score 0.247 Round 2: 63 peptides, 12 chains. Longest chain 8 peptides. Score 0.328 Round 3: 69 peptides, 10 chains. Longest chain 11 peptides. Score 0.466 Round 4: 72 peptides, 10 chains. Longest chain 18 peptides. Score 0.491 Round 5: 70 peptides, 10 chains. Longest chain 13 peptides. Score 0.474 Taking the results from Round 4 Chains 10, Residues 62, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2138 reflections ( 99.44 % complete ) and 2755 restraints for refining 1145 atoms. 2517 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2985 (Rfree = 0.000) for 1145 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. Cycle 2: After refmac, R = 0.2824 (Rfree = 0.000) for 1124 atoms. Found 6 (7 requested) and removed 8 (3 requested) atoms. Cycle 3: After refmac, R = 0.2678 (Rfree = 0.000) for 1113 atoms. Found 1 (7 requested) and removed 7 (3 requested) atoms. Cycle 4: After refmac, R = 0.2505 (Rfree = 0.000) for 1098 atoms. Found 2 (7 requested) and removed 4 (3 requested) atoms. Cycle 5: After refmac, R = 0.2445 (Rfree = 0.000) for 1089 atoms. Found 2 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.21 3.17 Search for helices and strands: 0 residues in 0 chains, 1151 seeds are put forward NCS extension: 0 residues added, 1151 seeds are put forward Round 1: 70 peptides, 12 chains. Longest chain 12 peptides. Score 0.396 Round 2: 74 peptides, 12 chains. Longest chain 20 peptides. Score 0.432 Round 3: 70 peptides, 12 chains. Longest chain 11 peptides. Score 0.396 Round 4: 77 peptides, 11 chains. Longest chain 18 peptides. Score 0.496 Round 5: 82 peptides, 13 chains. Longest chain 11 peptides. Score 0.464 Taking the results from Round 4 Chains 11, Residues 66, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2138 reflections ( 99.44 % complete ) and 2454 restraints for refining 1073 atoms. 2201 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2482 (Rfree = 0.000) for 1073 atoms. Found 4 (6 requested) and removed 8 (3 requested) atoms. Cycle 7: After refmac, R = 0.2503 (Rfree = 0.000) for 1056 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Cycle 8: After refmac, R = 0.2177 (Rfree = 0.000) for 1051 atoms. Found 1 (6 requested) and removed 5 (3 requested) atoms. Cycle 9: After refmac, R = 0.2310 (Rfree = 0.000) for 1041 atoms. Found 5 (6 requested) and removed 3 (3 requested) atoms. Cycle 10: After refmac, R = 0.2356 (Rfree = 0.000) for 1035 atoms. Found 6 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.25 3.21 Search for helices and strands: 0 residues in 0 chains, 1115 seeds are put forward NCS extension: 0 residues added, 1115 seeds are put forward Round 1: 62 peptides, 12 chains. Longest chain 8 peptides. Score 0.318 Round 2: 79 peptides, 10 chains. Longest chain 18 peptides. Score 0.547 Round 3: 86 peptides, 12 chains. Longest chain 13 peptides. Score 0.532 Round 4: 80 peptides, 10 chains. Longest chain 19 peptides. Score 0.555 Round 5: 74 peptides, 8 chains. Longest chain 18 peptides. Score 0.579 Taking the results from Round 5 Chains 8, Residues 66, Estimated correctness of the model 6.3 % 1 chains (17 residues) have been docked in sequence ------------------------------------------------------ 2138 reflections ( 99.44 % complete ) and 2261 restraints for refining 1124 atoms. 1931 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2562 (Rfree = 0.000) for 1124 atoms. Found 5 (7 requested) and removed 11 (3 requested) atoms. Cycle 12: After refmac, R = 0.2367 (Rfree = 0.000) for 1104 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. Cycle 13: After refmac, R = 0.2346 (Rfree = 0.000) for 1103 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 14: After refmac, R = 0.2292 (Rfree = 0.000) for 1098 atoms. Found 4 (7 requested) and removed 4 (3 requested) atoms. Cycle 15: After refmac, R = 0.2308 (Rfree = 0.000) for 1097 atoms. Found 5 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.29 3.25 Search for helices and strands: 0 residues in 0 chains, 1168 seeds are put forward NCS extension: 26 residues added (2 deleted due to clashes), 1194 seeds are put forward Round 1: 63 peptides, 12 chains. Longest chain 9 peptides. Score 0.328 Round 2: 77 peptides, 12 chains. Longest chain 12 peptides. Score 0.458 Round 3: 67 peptides, 9 chains. Longest chain 17 peptides. Score 0.487 Round 4: 74 peptides, 12 chains. Longest chain 12 peptides. Score 0.432 Round 5: 80 peptides, 12 chains. Longest chain 12 peptides. Score 0.484 Taking the results from Round 3 Chains 9, Residues 58, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2138 reflections ( 99.44 % complete ) and 2578 restraints for refining 1146 atoms. 2355 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2878 (Rfree = 0.000) for 1146 atoms. Found 7 (7 requested) and removed 13 (3 requested) atoms. Cycle 17: After refmac, R = 0.2613 (Rfree = 0.000) for 1129 atoms. Found 7 (7 requested) and removed 3 (3 requested) atoms. Cycle 18: After refmac, R = 0.2431 (Rfree = 0.000) for 1122 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 19: After refmac, R = 0.2533 (Rfree = 0.000) for 1123 atoms. Found 6 (7 requested) and removed 5 (3 requested) atoms. Cycle 20: After refmac, R = 0.2352 (Rfree = 0.000) for 1117 atoms. Found 4 (7 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.34 3.30 Search for helices and strands: 0 residues in 0 chains, 1187 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 1207 seeds are put forward Round 1: 57 peptides, 13 chains. Longest chain 5 peptides. Score 0.222 Round 2: 65 peptides, 11 chains. Longest chain 10 peptides. Score 0.390 Round 3: 69 peptides, 11 chains. Longest chain 10 peptides. Score 0.427 Round 4: 76 peptides, 11 chains. Longest chain 12 peptides. Score 0.487 Round 5: 77 peptides, 12 chains. Longest chain 9 peptides. Score 0.458 Taking the results from Round 4 Chains 11, Residues 65, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2138 reflections ( 99.44 % complete ) and 2451 restraints for refining 1114 atoms. 2202 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2739 (Rfree = 0.000) for 1114 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 22: After refmac, R = 0.2600 (Rfree = 0.000) for 1109 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 23: After refmac, R = 0.2601 (Rfree = 0.000) for 1109 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. Cycle 24: After refmac, R = 0.2500 (Rfree = 0.000) for 1108 atoms. Found 6 (7 requested) and removed 3 (3 requested) atoms. Cycle 25: After refmac, R = 0.2467 (Rfree = 0.000) for 1106 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.28 3.24 Search for helices and strands: 0 residues in 0 chains, 1176 seeds are put forward NCS extension: 0 residues added, 1176 seeds are put forward Round 1: 61 peptides, 13 chains. Longest chain 7 peptides. Score 0.265 Round 2: 73 peptides, 14 chains. Longest chain 8 peptides. Score 0.343 Round 3: 73 peptides, 11 chains. Longest chain 13 peptides. Score 0.462 Round 4: 73 peptides, 11 chains. Longest chain 16 peptides. Score 0.462 Round 5: 81 peptides, 13 chains. Longest chain 11 peptides. Score 0.455 Taking the results from Round 4 Chains 11, Residues 62, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2138 reflections ( 99.44 % complete ) and 2477 restraints for refining 1114 atoms. 2240 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2599 (Rfree = 0.000) for 1114 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 27: After refmac, R = 0.2204 (Rfree = 0.000) for 1113 atoms. Found 5 (7 requested) and removed 6 (3 requested) atoms. Cycle 28: After refmac, R = 0.2280 (Rfree = 0.000) for 1112 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 29: After refmac, R = 0.1986 (Rfree = 0.000) for 1112 atoms. Found 3 (7 requested) and removed 3 (3 requested) atoms. Cycle 30: After refmac, R = 0.2297 (Rfree = 0.000) for 1106 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.30 3.26 Search for helices and strands: 0 residues in 0 chains, 1175 seeds are put forward NCS extension: 0 residues added, 1175 seeds are put forward Round 1: 61 peptides, 11 chains. Longest chain 12 peptides. Score 0.351 Round 2: 76 peptides, 12 chains. Longest chain 11 peptides. Score 0.450 Round 3: 69 peptides, 10 chains. Longest chain 12 peptides. Score 0.466 Round 4: 72 peptides, 10 chains. Longest chain 11 peptides. Score 0.491 Round 5: 78 peptides, 10 chains. Longest chain 15 peptides. Score 0.540 Taking the results from Round 5 Chains 10, Residues 68, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2138 reflections ( 99.44 % complete ) and 2406 restraints for refining 1116 atoms. 2144 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2896 (Rfree = 0.000) for 1116 atoms. Found 7 (7 requested) and removed 9 (3 requested) atoms. Cycle 32: After refmac, R = 0.2532 (Rfree = 0.000) for 1110 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. Cycle 33: After refmac, R = 0.2395 (Rfree = 0.000) for 1105 atoms. Found 6 (7 requested) and removed 4 (3 requested) atoms. Cycle 34: After refmac, R = 0.1976 (Rfree = 0.000) for 1104 atoms. Found 2 (7 requested) and removed 5 (3 requested) atoms. Cycle 35: After refmac, R = 0.1780 (Rfree = 0.000) for 1099 atoms. Found 1 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.32 3.28 Search for helices and strands: 0 residues in 0 chains, 1163 seeds are put forward NCS extension: 0 residues added, 1163 seeds are put forward Round 1: 66 peptides, 13 chains. Longest chain 7 peptides. Score 0.316 Round 2: 79 peptides, 14 chains. Longest chain 15 peptides. Score 0.400 Round 3: 74 peptides, 10 chains. Longest chain 20 peptides. Score 0.508 Round 4: 67 peptides, 10 chains. Longest chain 20 peptides. Score 0.448 Round 5: 69 peptides, 11 chains. Longest chain 11 peptides. Score 0.427 Taking the results from Round 3 Chains 12, Residues 64, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 2138 reflections ( 99.44 % complete ) and 2361 restraints for refining 1146 atoms. 2075 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2249 (Rfree = 0.000) for 1146 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 37: After refmac, R = 0.2176 (Rfree = 0.000) for 1141 atoms. Found 6 (7 requested) and removed 3 (3 requested) atoms. Cycle 38: After refmac, R = 0.2193 (Rfree = 0.000) for 1140 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 39: After refmac, R = 0.2179 (Rfree = 0.000) for 1137 atoms. Found 7 (7 requested) and removed 3 (3 requested) atoms. Cycle 40: After refmac, R = 0.1855 (Rfree = 0.000) for 1137 atoms. Found 3 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.26 3.22 Search for helices and strands: 0 residues in 0 chains, 1191 seeds are put forward NCS extension: 0 residues added, 1191 seeds are put forward Round 1: 53 peptides, 11 chains. Longest chain 6 peptides. Score 0.269 Round 2: 60 peptides, 11 chains. Longest chain 12 peptides. Score 0.341 Round 3: 58 peptides, 11 chains. Longest chain 7 peptides. Score 0.321 Round 4: 60 peptides, 10 chains. Longest chain 11 peptides. Score 0.384 Round 5: 67 peptides, 11 chains. Longest chain 11 peptides. Score 0.408 Taking the results from Round 5 Chains 11, Residues 56, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2138 reflections ( 99.44 % complete ) and 2521 restraints for refining 1127 atoms. 2308 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2254 (Rfree = 0.000) for 1127 atoms. Found 5 (7 requested) and removed 8 (3 requested) atoms. Cycle 42: After refmac, R = 0.2488 (Rfree = 0.000) for 1122 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. Cycle 43: After refmac, R = 0.2192 (Rfree = 0.000) for 1114 atoms. Found 3 (7 requested) and removed 4 (3 requested) atoms. Cycle 44: After refmac, R = 0.2172 (Rfree = 0.000) for 1110 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 45: After refmac, R = 0.2245 (Rfree = 0.000) for 1112 atoms. Found 7 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.22 3.18 Search for helices and strands: 0 residues in 0 chains, 1184 seeds are put forward NCS extension: 0 residues added, 1184 seeds are put forward Round 1: 50 peptides, 11 chains. Longest chain 5 peptides. Score 0.236 Round 2: 55 peptides, 9 chains. Longest chain 16 peptides. Score 0.378 Round 3: 47 peptides, 10 chains. Longest chain 7 peptides. Score 0.249 Round 4: 42 peptides, 8 chains. Longest chain 7 peptides. Score 0.288 Round 5: 44 peptides, 7 chains. Longest chain 13 peptides. Score 0.357 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 9, Residues 46, 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 2fzt-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2138 reflections ( 99.44 % complete ) and 2438 restraints for refining 1093 atoms. 2263 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2357 (Rfree = 0.000) for 1093 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.2202 (Rfree = 0.000) for 1085 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.1842 (Rfree = 0.000) for 1081 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.1874 (Rfree = 0.000) for 1077 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 00:53:11 GMT 2018 Job finished. TimeTaking 19.67 Used memory is bytes: 19573592