Sun 23 Dec 22:22:41 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-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2fcl-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2fcl-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fcl-3.4-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-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fcl-3.4-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 22:22:50 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-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fcl-3.4-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 126 and 0 Target number of residues in the AU: 126 Target solvent content: 0.6109 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-3.4-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-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 1352 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 Loops will be built when appropriate and at the last cycle Resolution range: 29.656 3.401 Wilson plot Bfac: 56.34 2297 reflections ( 97.95 % complete ) and 0 restraints for refining 1500 atoms. Observations/parameters ratio is 0.38 ------------------------------------------------------ Starting model: R = 0.3090 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2616 (Rfree = 0.000) for 1500 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.05 3.13 Search for helices and strands: 0 residues in 0 chains, 1526 seeds are put forward Round 1: 52 peptides, 10 chains. Longest chain 9 peptides. Score 0.303 Round 2: 80 peptides, 14 chains. Longest chain 12 peptides. Score 0.408 Round 3: 88 peptides, 14 chains. Longest chain 14 peptides. Score 0.476 Round 4: 101 peptides, 15 chains. Longest chain 15 peptides. Score 0.544 Round 5: 103 peptides, 13 chains. Longest chain 23 peptides. Score 0.619 Taking the results from Round 5 Chains 13, Residues 90, Estimated correctness of the model 34.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2297 reflections ( 97.95 % complete ) and 2707 restraints for refining 1223 atoms. 2360 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2424 (Rfree = 0.000) for 1223 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. Cycle 2: After refmac, R = 0.2252 (Rfree = 0.000) for 1203 atoms. Found 9 (9 requested) and removed 5 (4 requested) atoms. Cycle 3: After refmac, R = 0.2110 (Rfree = 0.000) for 1203 atoms. Found 3 (9 requested) and removed 7 (4 requested) atoms. Cycle 4: After refmac, R = 0.2037 (Rfree = 0.000) for 1197 atoms. Found 3 (9 requested) and removed 4 (4 requested) atoms. Cycle 5: After refmac, R = 0.1998 (Rfree = 0.000) for 1194 atoms. Found 2 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.06 3.14 Search for helices and strands: 0 residues in 0 chains, 1228 seeds are put forward Round 1: 85 peptides, 14 chains. Longest chain 12 peptides. Score 0.451 Round 2: 85 peptides, 14 chains. Longest chain 12 peptides. Score 0.451 Round 3: 89 peptides, 14 chains. Longest chain 14 peptides. Score 0.485 Round 4: 97 peptides, 14 chains. Longest chain 16 peptides. Score 0.547 Round 5: 99 peptides, 14 chains. Longest chain 13 peptides. Score 0.561 Taking the results from Round 5 Chains 14, Residues 85, Estimated correctness of the model 15.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2297 reflections ( 97.95 % complete ) and 2658 restraints for refining 1206 atoms. 2332 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2254 (Rfree = 0.000) for 1206 atoms. Found 8 (9 requested) and removed 5 (4 requested) atoms. Cycle 7: After refmac, R = 0.2148 (Rfree = 0.000) for 1201 atoms. Found 7 (9 requested) and removed 10 (4 requested) atoms. Cycle 8: After refmac, R = 0.2584 (Rfree = 0.000) for 1195 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. Cycle 9: After refmac, R = 0.1881 (Rfree = 0.000) for 1187 atoms. Found 5 (8 requested) and removed 6 (4 requested) atoms. Cycle 10: After refmac, R = 0.1679 (Rfree = 0.000) for 1185 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.10 3.18 Search for helices and strands: 0 residues in 0 chains, 1224 seeds are put forward Round 1: 78 peptides, 16 chains. Longest chain 7 peptides. Score 0.310 Round 2: 87 peptides, 15 chains. Longest chain 14 peptides. Score 0.432 Round 3: 91 peptides, 13 chains. Longest chain 15 peptides. Score 0.535 Round 4: 86 peptides, 12 chains. Longest chain 16 peptides. Score 0.530 Round 5: 92 peptides, 13 chains. Longest chain 20 peptides. Score 0.542 Taking the results from Round 5 Chains 13, Residues 79, Estimated correctness of the model 8.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2297 reflections ( 97.95 % complete ) and 2720 restraints for refining 1210 atoms. 2417 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1996 (Rfree = 0.000) for 1210 atoms. Found 5 (9 requested) and removed 17 (4 requested) atoms. Cycle 12: After refmac, R = 0.1976 (Rfree = 0.000) for 1193 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. Cycle 13: After refmac, R = 0.1799 (Rfree = 0.000) for 1192 atoms. Found 8 (9 requested) and removed 7 (4 requested) atoms. Cycle 14: After refmac, R = 0.1892 (Rfree = 0.000) for 1191 atoms. Found 6 (9 requested) and removed 6 (4 requested) atoms. Cycle 15: After refmac, R = 0.1885 (Rfree = 0.000) for 1186 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.06 3.14 Search for helices and strands: 0 residues in 0 chains, 1218 seeds are put forward Round 1: 67 peptides, 12 chains. Longest chain 12 peptides. Score 0.367 Round 2: 76 peptides, 12 chains. Longest chain 15 peptides. Score 0.449 Round 3: 72 peptides, 13 chains. Longest chain 9 peptides. Score 0.373 Round 4: 76 peptides, 15 chains. Longest chain 8 peptides. Score 0.331 Round 5: 80 peptides, 15 chains. Longest chain 9 peptides. Score 0.369 Taking the results from Round 2 Chains 12, Residues 64, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2297 reflections ( 97.95 % complete ) and 2616 restraints for refining 1171 atoms. 2372 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1937 (Rfree = 0.000) for 1171 atoms. Found 3 (8 requested) and removed 6 (4 requested) atoms. Cycle 17: After refmac, R = 0.1778 (Rfree = 0.000) for 1167 atoms. Found 1 (8 requested) and removed 4 (4 requested) atoms. Cycle 18: After refmac, R = 0.1761 (Rfree = 0.000) for 1161 atoms. Found 2 (8 requested) and removed 5 (4 requested) atoms. Cycle 19: After refmac, R = 0.1767 (Rfree = 0.000) for 1158 atoms. Found 2 (8 requested) and removed 4 (4 requested) atoms. Cycle 20: After refmac, R = 0.2101 (Rfree = 0.000) for 1152 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.09 3.17 Search for helices and strands: 0 residues in 0 chains, 1185 seeds are put forward Round 1: 70 peptides, 13 chains. Longest chain 9 peptides. Score 0.354 Round 2: 76 peptides, 13 chains. Longest chain 12 peptides. Score 0.410 Round 3: 84 peptides, 13 chains. Longest chain 14 peptides. Score 0.479 Round 4: 81 peptides, 14 chains. Longest chain 15 peptides. Score 0.416 Round 5: 85 peptides, 15 chains. Longest chain 12 peptides. Score 0.414 Taking the results from Round 3 Chains 13, Residues 71, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2297 reflections ( 97.95 % complete ) and 2641 restraints for refining 1187 atoms. 2370 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1991 (Rfree = 0.000) for 1187 atoms. Found 2 (8 requested) and removed 7 (4 requested) atoms. Cycle 22: After refmac, R = 0.1801 (Rfree = 0.000) for 1179 atoms. Found 1 (8 requested) and removed 5 (4 requested) atoms. Cycle 23: After refmac, R = 0.1771 (Rfree = 0.000) for 1174 atoms. Found 2 (8 requested) and removed 5 (4 requested) atoms. Cycle 24: After refmac, R = 0.1874 (Rfree = 0.000) for 1170 atoms. Found 5 (8 requested) and removed 7 (4 requested) atoms. Cycle 25: After refmac, R = 0.1825 (Rfree = 0.000) for 1166 atoms. Found 6 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.08 3.16 Search for helices and strands: 0 residues in 0 chains, 1208 seeds are put forward Round 1: 67 peptides, 13 chains. Longest chain 10 peptides. Score 0.325 Round 2: 75 peptides, 11 chains. Longest chain 12 peptides. Score 0.478 Round 3: 77 peptides, 12 chains. Longest chain 11 peptides. Score 0.457 Round 4: 83 peptides, 13 chains. Longest chain 11 peptides. Score 0.471 Round 5: 88 peptides, 12 chains. Longest chain 16 peptides. Score 0.546 Taking the results from Round 5 Chains 12, Residues 76, Estimated correctness of the model 10.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2297 reflections ( 97.95 % complete ) and 2526 restraints for refining 1185 atoms. 2234 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2075 (Rfree = 0.000) for 1185 atoms. Found 6 (8 requested) and removed 11 (4 requested) atoms. Cycle 27: After refmac, R = 0.1864 (Rfree = 0.000) for 1177 atoms. Found 3 (8 requested) and removed 6 (4 requested) atoms. Cycle 28: After refmac, R = 0.1788 (Rfree = 0.000) for 1171 atoms. Found 5 (8 requested) and removed 6 (4 requested) atoms. Cycle 29: After refmac, R = 0.1737 (Rfree = 0.000) for 1167 atoms. Found 0 (8 requested) and removed 5 (4 requested) atoms. Cycle 30: After refmac, R = 0.1736 (Rfree = 0.000) for 1160 atoms. Found 1 (8 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.10 3.18 Search for helices and strands: 0 residues in 0 chains, 1188 seeds are put forward Round 1: 60 peptides, 13 chains. Longest chain 7 peptides. Score 0.254 Round 2: 73 peptides, 14 chains. Longest chain 9 peptides. Score 0.343 Round 3: 69 peptides, 14 chains. Longest chain 8 peptides. Score 0.304 Round 4: 74 peptides, 13 chains. Longest chain 9 peptides. Score 0.392 Round 5: 73 peptides, 11 chains. Longest chain 15 peptides. Score 0.461 Taking the results from Round 5 Chains 11, Residues 62, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2297 reflections ( 97.95 % complete ) and 2883 restraints for refining 1222 atoms. 2646 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1984 (Rfree = 0.000) for 1222 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Cycle 32: After refmac, R = 0.1829 (Rfree = 0.000) for 1218 atoms. Found 3 (9 requested) and removed 6 (4 requested) atoms. Cycle 33: After refmac, R = 0.1773 (Rfree = 0.000) for 1212 atoms. Found 1 (9 requested) and removed 4 (4 requested) atoms. Cycle 34: After refmac, R = 0.1766 (Rfree = 0.000) for 1208 atoms. Found 0 (9 requested) and removed 5 (4 requested) atoms. Cycle 35: After refmac, R = 0.1787 (Rfree = 0.000) for 1202 atoms. Found 4 (9 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.07 3.15 Search for helices and strands: 0 residues in 0 chains, 1232 seeds are put forward Round 1: 58 peptides, 12 chains. Longest chain 11 peptides. Score 0.277 Round 2: 70 peptides, 14 chains. Longest chain 7 peptides. Score 0.313 Round 3: 66 peptides, 11 chains. Longest chain 12 peptides. Score 0.398 Round 4: 75 peptides, 13 chains. Longest chain 12 peptides. Score 0.401 Round 5: 69 peptides, 11 chains. Longest chain 12 peptides. Score 0.425 Taking the results from Round 5 Chains 11, Residues 58, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2297 reflections ( 97.95 % complete ) and 2813 restraints for refining 1229 atoms. 2592 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1917 (Rfree = 0.000) for 1229 atoms. Found 7 (9 requested) and removed 4 (4 requested) atoms. Cycle 37: After refmac, R = 0.1754 (Rfree = 0.000) for 1230 atoms. Found 2 (9 requested) and removed 4 (4 requested) atoms. Cycle 38: After refmac, R = 0.1671 (Rfree = 0.000) for 1228 atoms. Found 1 (9 requested) and removed 4 (4 requested) atoms. Cycle 39: After refmac, R = 0.1645 (Rfree = 0.000) for 1224 atoms. Found 1 (9 requested) and removed 4 (4 requested) atoms. Cycle 40: After refmac, R = 0.1628 (Rfree = 0.000) for 1219 atoms. Found 1 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.12 3.20 Search for helices and strands: 0 residues in 0 chains, 1242 seeds are put forward Round 1: 62 peptides, 12 chains. Longest chain 10 peptides. Score 0.318 Round 2: 89 peptides, 14 chains. Longest chain 10 peptides. Score 0.485 Round 3: 82 peptides, 13 chains. Longest chain 13 peptides. Score 0.462 Round 4: 80 peptides, 12 chains. Longest chain 13 peptides. Score 0.482 Round 5: 73 peptides, 14 chains. Longest chain 10 peptides. Score 0.343 Taking the results from Round 2 Chains 14, Residues 75, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2297 reflections ( 97.95 % complete ) and 2728 restraints for refining 1223 atoms. 2442 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1788 (Rfree = 0.000) for 1223 atoms. Found 4 (9 requested) and removed 7 (4 requested) atoms. Cycle 42: After refmac, R = 0.1649 (Rfree = 0.000) for 1217 atoms. Found 3 (9 requested) and removed 4 (4 requested) atoms. Cycle 43: After refmac, R = 0.1594 (Rfree = 0.000) for 1213 atoms. Found 3 (9 requested) and removed 6 (4 requested) atoms. Cycle 44: After refmac, R = 0.1550 (Rfree = 0.000) for 1210 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 45: After refmac, R = 0.1594 (Rfree = 0.000) for 1203 atoms. Found 1 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.12 3.20 Search for helices and strands: 0 residues in 0 chains, 1231 seeds are put forward Round 1: 56 peptides, 12 chains. Longest chain 7 peptides. Score 0.256 Round 2: 66 peptides, 10 chains. Longest chain 12 peptides. Score 0.438 Round 3: 65 peptides, 9 chains. Longest chain 12 peptides. Score 0.469 Round 4: 60 peptides, 10 chains. Longest chain 10 peptides. Score 0.383 Round 5: 66 peptides, 11 chains. Longest chain 9 peptides. Score 0.398 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 9, Residues 56, 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. 2297 reflections ( 97.95 % complete ) and 2757 restraints for refining 1198 atoms. 2542 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1680 (Rfree = 0.000) for 1198 atoms. Found 0 (9 requested) and removed 2 (4 requested) atoms. Cycle 47: After refmac, R = 0.1600 (Rfree = 0.000) for 1195 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.1630 (Rfree = 0.000) for 1191 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.1596 (Rfree = 0.000) for 1185 atoms. TimeTaking 24.58