Sun 23 Dec 22:22:59 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2fcl-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2fcl-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2fcl-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fcl-3.8-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/2fcl-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fcl-3.8-parrot-hancs ############### 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 22:23:07 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/hancs/ArpWArp/wArpResults/WorkingDir/2fcl-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fcl-3.8-parrot-hancs/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 116 and 0 Target number of residues in the AU: 116 Target solvent content: 0.6418 Checking the provided sequence file Detected sequence length: 169 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 169 Adjusted target solvent content: 0.48 Input MTZ file: 2fcl-3.8-parrot-hancs.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: 32.560 36.210 39.280 74.110 86.380 79.700 Input sequence file: 2fcl-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 1352 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 Loops will be built when appropriate and at the last cycle Resolution range: 29.656 3.800 Wilson plot Bfac: 71.65 Failed to save intermediate PDB 1636 reflections ( 97.96 % complete ) and 0 restraints for refining 1500 atoms. Observations/parameters ratio is 0.27 ------------------------------------------------------ Starting model: R = 0.3177 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2560 (Rfree = 0.000) for 1500 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.52 3.62 Search for helices and strands: 0 residues in 0 chains, 1520 seeds are put forward Round 1: 51 peptides, 11 chains. Longest chain 7 peptides. Score 0.247 Round 2: 73 peptides, 13 chains. Longest chain 10 peptides. Score 0.383 Round 3: 81 peptides, 15 chains. Longest chain 8 peptides. Score 0.378 Round 4: 87 peptides, 12 chains. Longest chain 14 peptides. Score 0.538 Round 5: 91 peptides, 14 chains. Longest chain 13 peptides. Score 0.501 Taking the results from Round 4 Chains 12, Residues 75, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1636 reflections ( 97.96 % complete ) and 2895 restraints for refining 1222 atoms. 2607 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2249 (Rfree = 0.000) for 1222 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. Cycle 2: After refmac, R = 0.2175 (Rfree = 0.000) for 1208 atoms. Found 5 (6 requested) and removed 5 (3 requested) atoms. Cycle 3: After refmac, R = 0.2101 (Rfree = 0.000) for 1203 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Cycle 4: After refmac, R = 0.2333 (Rfree = 0.000) for 1199 atoms. Found 6 (6 requested) and removed 9 (3 requested) atoms. Cycle 5: After refmac, R = 0.1878 (Rfree = 0.000) for 1192 atoms. Found 5 (6 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.51 3.60 Search for helices and strands: 0 residues in 0 chains, 1241 seeds are put forward Round 1: 63 peptides, 12 chains. Longest chain 8 peptides. Score 0.328 Round 2: 74 peptides, 12 chains. Longest chain 10 peptides. Score 0.431 Round 3: 63 peptides, 10 chains. Longest chain 10 peptides. Score 0.411 Round 4: 75 peptides, 12 chains. Longest chain 12 peptides. Score 0.440 Round 5: 80 peptides, 12 chains. Longest chain 13 peptides. Score 0.482 Taking the results from Round 5 Chains 12, Residues 68, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1636 reflections ( 97.96 % complete ) and 2671 restraints for refining 1181 atoms. 2411 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2609 (Rfree = 0.000) for 1181 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. Cycle 7: After refmac, R = 0.2110 (Rfree = 0.000) for 1170 atoms. Found 0 (6 requested) and removed 4 (3 requested) atoms. Cycle 8: After refmac, R = 0.1835 (Rfree = 0.000) for 1163 atoms. Found 2 (6 requested) and removed 5 (3 requested) atoms. Cycle 9: After refmac, R = 0.1758 (Rfree = 0.000) for 1160 atoms. Found 1 (6 requested) and removed 6 (3 requested) atoms. Cycle 10: After refmac, R = 0.1746 (Rfree = 0.000) for 1154 atoms. Found 0 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.53 3.63 Search for helices and strands: 0 residues in 0 chains, 1205 seeds are put forward Round 1: 67 peptides, 12 chains. Longest chain 11 peptides. Score 0.367 Round 2: 77 peptides, 12 chains. Longest chain 11 peptides. Score 0.457 Round 3: 72 peptides, 11 chains. Longest chain 12 peptides. Score 0.452 Round 4: 73 peptides, 12 chains. Longest chain 13 peptides. Score 0.422 Round 5: 66 peptides, 10 chains. Longest chain 12 peptides. Score 0.438 Taking the results from Round 2 Chains 12, Residues 65, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1636 reflections ( 97.96 % complete ) and 2830 restraints for refining 1186 atoms. 2582 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2229 (Rfree = 0.000) for 1186 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. Cycle 12: After refmac, R = 0.2256 (Rfree = 0.000) for 1183 atoms. Found 6 (6 requested) and removed 10 (3 requested) atoms. Cycle 13: After refmac, R = 0.1971 (Rfree = 0.000) for 1177 atoms. Found 4 (6 requested) and removed 7 (3 requested) atoms. Cycle 14: After refmac, R = 0.2136 (Rfree = 0.000) for 1169 atoms. Found 5 (6 requested) and removed 6 (3 requested) atoms. Cycle 15: After refmac, R = 0.1638 (Rfree = 0.000) for 1166 atoms. Found 2 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.58 3.68 Search for helices and strands: 0 residues in 0 chains, 1214 seeds are put forward Round 1: 69 peptides, 14 chains. Longest chain 8 peptides. Score 0.304 Round 2: 79 peptides, 14 chains. Longest chain 11 peptides. Score 0.398 Round 3: 85 peptides, 13 chains. Longest chain 15 peptides. Score 0.487 Round 4: 86 peptides, 12 chains. Longest chain 14 peptides. Score 0.530 Round 5: 83 peptides, 15 chains. Longest chain 12 peptides. Score 0.396 Taking the results from Round 4 Chains 12, Residues 74, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1636 reflections ( 97.96 % complete ) and 2813 restraints for refining 1223 atoms. 2529 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2396 (Rfree = 0.000) for 1223 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. Cycle 17: After refmac, R = 0.2171 (Rfree = 0.000) for 1216 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Cycle 18: After refmac, R = 0.2170 (Rfree = 0.000) for 1213 atoms. Found 3 (6 requested) and removed 7 (3 requested) atoms. Cycle 19: After refmac, R = 0.1709 (Rfree = 0.000) for 1206 atoms. Found 4 (6 requested) and removed 5 (3 requested) atoms. Cycle 20: After refmac, R = 0.1615 (Rfree = 0.000) for 1202 atoms. Found 3 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.55 3.65 Search for helices and strands: 0 residues in 0 chains, 1238 seeds are put forward Round 1: 75 peptides, 13 chains. Longest chain 12 peptides. Score 0.401 Round 2: 78 peptides, 11 chains. Longest chain 15 peptides. Score 0.502 Round 3: 78 peptides, 10 chains. Longest chain 15 peptides. Score 0.538 Round 4: 81 peptides, 12 chains. Longest chain 15 peptides. Score 0.491 Round 5: 77 peptides, 10 chains. Longest chain 12 peptides. Score 0.530 Taking the results from Round 3 Chains 10, Residues 68, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1636 reflections ( 97.96 % complete ) and 2822 restraints for refining 1219 atoms. 2560 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2520 (Rfree = 0.000) for 1219 atoms. Found 3 (6 requested) and removed 6 (3 requested) atoms. Cycle 22: After refmac, R = 0.1986 (Rfree = 0.000) for 1214 atoms. Found 3 (6 requested) and removed 9 (3 requested) atoms. Cycle 23: After refmac, R = 0.2074 (Rfree = 0.000) for 1206 atoms. Found 4 (6 requested) and removed 7 (3 requested) atoms. Cycle 24: After refmac, R = 0.1833 (Rfree = 0.000) for 1202 atoms. Found 2 (6 requested) and removed 4 (3 requested) atoms. Cycle 25: After refmac, R = 0.2145 (Rfree = 0.000) for 1199 atoms. Found 5 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.49 3.58 Search for helices and strands: 0 residues in 0 chains, 1237 seeds are put forward Round 1: 68 peptides, 14 chains. Longest chain 8 peptides. Score 0.294 Round 2: 79 peptides, 13 chains. Longest chain 13 peptides. Score 0.437 Round 3: 81 peptides, 14 chains. Longest chain 16 peptides. Score 0.416 Round 4: 77 peptides, 11 chains. Longest chain 24 peptides. Score 0.494 Round 5: 88 peptides, 13 chains. Longest chain 24 peptides. Score 0.512 Taking the results from Round 5 Chains 13, Residues 75, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1636 reflections ( 97.96 % complete ) and 2781 restraints for refining 1223 atoms. 2494 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2305 (Rfree = 0.000) for 1223 atoms. Found 5 (6 requested) and removed 7 (3 requested) atoms. Cycle 27: After refmac, R = 0.2298 (Rfree = 0.000) for 1218 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. Cycle 28: After refmac, R = 0.1874 (Rfree = 0.000) for 1214 atoms. Found 2 (6 requested) and removed 4 (3 requested) atoms. Cycle 29: After refmac, R = 0.2200 (Rfree = 0.000) for 1207 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. Cycle 30: After refmac, R = 0.1943 (Rfree = 0.000) for 1206 atoms. Found 5 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.63 3.73 Search for helices and strands: 0 residues in 0 chains, 1239 seeds are put forward Round 1: 64 peptides, 12 chains. Longest chain 9 peptides. Score 0.338 Round 2: 60 peptides, 11 chains. Longest chain 9 peptides. Score 0.340 Round 3: 70 peptides, 11 chains. Longest chain 9 peptides. Score 0.434 Round 4: 72 peptides, 12 chains. Longest chain 10 peptides. Score 0.413 Round 5: 72 peptides, 11 chains. Longest chain 11 peptides. Score 0.452 Taking the results from Round 5 Chains 11, Residues 61, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1636 reflections ( 97.96 % complete ) and 2936 restraints for refining 1223 atoms. 2703 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2623 (Rfree = 0.000) for 1223 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. Cycle 32: After refmac, R = 0.2131 (Rfree = 0.000) for 1222 atoms. Found 4 (6 requested) and removed 6 (3 requested) atoms. Cycle 33: After refmac, R = 0.1940 (Rfree = 0.000) for 1220 atoms. Found 1 (6 requested) and removed 3 (3 requested) atoms. Cycle 34: After refmac, R = 0.1763 (Rfree = 0.000) for 1217 atoms. Found 3 (6 requested) and removed 4 (3 requested) atoms. Cycle 35: After refmac, R = 0.1563 (Rfree = 0.000) for 1216 atoms. Found 1 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.55 3.65 Search for helices and strands: 0 residues in 0 chains, 1244 seeds are put forward Round 1: 41 peptides, 8 chains. Longest chain 9 peptides. Score 0.277 Round 2: 60 peptides, 10 chains. Longest chain 12 peptides. Score 0.383 Round 3: 55 peptides, 9 chains. Longest chain 10 peptides. Score 0.377 Round 4: 59 peptides, 9 chains. Longest chain 10 peptides. Score 0.415 Round 5: 61 peptides, 11 chains. Longest chain 10 peptides. Score 0.350 Taking the results from Round 4 Chains 9, Residues 50, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1636 reflections ( 97.96 % complete ) and 2982 restraints for refining 1222 atoms. 2791 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2163 (Rfree = 0.000) for 1222 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Cycle 37: After refmac, R = 0.2023 (Rfree = 0.000) for 1218 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Cycle 38: After refmac, R = 0.1784 (Rfree = 0.000) for 1216 atoms. Found 3 (6 requested) and removed 4 (3 requested) atoms. Cycle 39: After refmac, R = 0.2167 (Rfree = 0.000) for 1215 atoms. Found 6 (6 requested) and removed 10 (3 requested) atoms. Cycle 40: After refmac, R = 0.1601 (Rfree = 0.000) for 1210 atoms. Found 4 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.52 3.62 Search for helices and strands: 0 residues in 0 chains, 1238 seeds are put forward Round 1: 54 peptides, 12 chains. Longest chain 8 peptides. Score 0.234 Round 2: 64 peptides, 13 chains. Longest chain 10 peptides. Score 0.295 Round 3: 63 peptides, 13 chains. Longest chain 8 peptides. Score 0.285 Round 4: 70 peptides, 14 chains. Longest chain 10 peptides. Score 0.313 Round 5: 63 peptides, 12 chains. Longest chain 9 peptides. Score 0.328 Taking the results from Round 5 Chains 12, Residues 51, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1636 reflections ( 97.96 % complete ) and 2936 restraints for refining 1223 atoms. 2744 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1929 (Rfree = 0.000) for 1223 atoms. Found 3 (6 requested) and removed 4 (3 requested) atoms. Cycle 42: After refmac, R = 0.1988 (Rfree = 0.000) for 1215 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. Cycle 43: After refmac, R = 0.1547 (Rfree = 0.000) for 1214 atoms. Found 1 (6 requested) and removed 3 (3 requested) atoms. Cycle 44: After refmac, R = 0.1620 (Rfree = 0.000) for 1210 atoms. Found 0 (6 requested) and removed 4 (3 requested) atoms. Cycle 45: After refmac, R = 0.1647 (Rfree = 0.000) for 1206 atoms. Found 0 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.48 3.57 Search for helices and strands: 0 residues in 0 chains, 1241 seeds are put forward Round 1: 42 peptides, 10 chains. Longest chain 5 peptides. Score 0.191 Round 2: 59 peptides, 12 chains. Longest chain 9 peptides. Score 0.287 Round 3: 54 peptides, 9 chains. Longest chain 9 peptides. Score 0.367 Round 4: 51 peptides, 10 chains. Longest chain 9 peptides. Score 0.292 Round 5: 56 peptides, 11 chains. Longest chain 9 peptides. Score 0.300 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 9, Residues 45, 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 2fcl-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 1636 reflections ( 97.96 % complete ) and 2964 restraints for refining 1222 atoms. 2793 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1827 (Rfree = 0.000) for 1222 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.1896 (Rfree = 0.000) for 1218 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.1646 (Rfree = 0.000) for 1214 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.1773 (Rfree = 0.000) for 1210 atoms. TimeTaking 24.58