Sun 23 Dec 22:22:42 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-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2fcl-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2fcl-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fcl-3.6-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-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fcl-3.6-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 22:22:56 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-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fcl-3.6-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 121 and 0 Target number of residues in the AU: 121 Target solvent content: 0.6264 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-3.6-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-3.6-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 3.601 Wilson plot Bfac: 63.28 1919 reflections ( 98.11 % complete ) and 0 restraints for refining 1503 atoms. Observations/parameters ratio is 0.32 ------------------------------------------------------ Starting model: R = 0.3175 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2704 (Rfree = 0.000) for 1503 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.35 3.44 Search for helices and strands: 0 residues in 0 chains, 1527 seeds are put forward Round 1: 53 peptides, 11 chains. Longest chain 8 peptides. Score 0.268 Round 2: 57 peptides, 10 chains. Longest chain 10 peptides. Score 0.353 Round 3: 62 peptides, 10 chains. Longest chain 10 peptides. Score 0.402 Round 4: 74 peptides, 11 chains. Longest chain 13 peptides. Score 0.469 Round 5: 88 peptides, 14 chains. Longest chain 13 peptides. Score 0.476 Taking the results from Round 5 Chains 14, Residues 74, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1919 reflections ( 98.11 % complete ) and 2907 restraints for refining 1225 atoms. 2625 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2522 (Rfree = 0.000) for 1225 atoms. Found 6 (7 requested) and removed 8 (3 requested) atoms. Cycle 2: After refmac, R = 0.2437 (Rfree = 0.000) for 1202 atoms. Found 3 (7 requested) and removed 5 (3 requested) atoms. Cycle 3: After refmac, R = 0.2359 (Rfree = 0.000) for 1187 atoms. Found 4 (7 requested) and removed 5 (3 requested) atoms. Cycle 4: After refmac, R = 0.2364 (Rfree = 0.000) for 1178 atoms. Found 2 (7 requested) and removed 4 (3 requested) atoms. Cycle 5: After refmac, R = 0.2231 (Rfree = 0.000) for 1168 atoms. Found 6 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.40 3.49 Search for helices and strands: 0 residues in 0 chains, 1222 seeds are put forward Round 1: 77 peptides, 13 chains. Longest chain 9 peptides. Score 0.419 Round 2: 82 peptides, 13 chains. Longest chain 13 peptides. Score 0.462 Round 3: 96 peptides, 13 chains. Longest chain 26 peptides. Score 0.572 Round 4: 95 peptides, 13 chains. Longest chain 16 peptides. Score 0.564 Round 5: 90 peptides, 12 chains. Longest chain 22 peptides. Score 0.560 Taking the results from Round 3 Chains 13, Residues 83, Estimated correctness of the model 3.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1919 reflections ( 98.11 % complete ) and 2654 restraints for refining 1170 atoms. 2335 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2227 (Rfree = 0.000) for 1170 atoms. Found 7 (7 requested) and removed 11 (3 requested) atoms. Cycle 7: After refmac, R = 0.2117 (Rfree = 0.000) for 1162 atoms. Found 3 (7 requested) and removed 6 (3 requested) atoms. Cycle 8: After refmac, R = 0.2116 (Rfree = 0.000) for 1156 atoms. Found 3 (7 requested) and removed 8 (3 requested) atoms. Cycle 9: After refmac, R = 0.2013 (Rfree = 0.000) for 1148 atoms. Found 6 (7 requested) and removed 6 (3 requested) atoms. Cycle 10: After refmac, R = 0.1837 (Rfree = 0.000) for 1144 atoms. Found 5 (7 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.31 3.40 Search for helices and strands: 0 residues in 0 chains, 1191 seeds are put forward Round 1: 72 peptides, 13 chains. Longest chain 11 peptides. Score 0.373 Round 2: 79 peptides, 12 chains. Longest chain 13 peptides. Score 0.474 Round 3: 87 peptides, 13 chains. Longest chain 15 peptides. Score 0.504 Round 4: 89 peptides, 13 chains. Longest chain 18 peptides. Score 0.519 Round 5: 87 peptides, 13 chains. Longest chain 12 peptides. Score 0.504 Taking the results from Round 4 Chains 13, Residues 76, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1919 reflections ( 98.11 % complete ) and 2748 restraints for refining 1204 atoms. 2457 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2164 (Rfree = 0.000) for 1204 atoms. Found 7 (7 requested) and removed 11 (3 requested) atoms. Cycle 12: After refmac, R = 0.2033 (Rfree = 0.000) for 1193 atoms. Found 7 (7 requested) and removed 3 (3 requested) atoms. Cycle 13: After refmac, R = 0.1776 (Rfree = 0.000) for 1193 atoms. Found 4 (7 requested) and removed 6 (3 requested) atoms. Cycle 14: After refmac, R = 0.1489 (Rfree = 0.000) for 1188 atoms. Found 2 (7 requested) and removed 4 (3 requested) atoms. Cycle 15: After refmac, R = 0.1526 (Rfree = 0.000) for 1184 atoms. Found 2 (7 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.31 3.40 Search for helices and strands: 0 residues in 0 chains, 1223 seeds are put forward Round 1: 71 peptides, 13 chains. Longest chain 12 peptides. Score 0.364 Round 2: 76 peptides, 13 chains. Longest chain 9 peptides. Score 0.410 Round 3: 80 peptides, 13 chains. Longest chain 13 peptides. Score 0.445 Round 4: 75 peptides, 11 chains. Longest chain 15 peptides. Score 0.478 Round 5: 80 peptides, 12 chains. Longest chain 17 peptides. Score 0.482 Taking the results from Round 5 Chains 12, Residues 68, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 1919 reflections ( 98.11 % complete ) and 2665 restraints for refining 1188 atoms. 2379 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1964 (Rfree = 0.000) for 1188 atoms. Found 4 (7 requested) and removed 8 (3 requested) atoms. Cycle 17: After refmac, R = 0.1938 (Rfree = 0.000) for 1179 atoms. Found 6 (7 requested) and removed 6 (3 requested) atoms. Cycle 18: After refmac, R = 0.1871 (Rfree = 0.000) for 1173 atoms. Found 5 (7 requested) and removed 8 (3 requested) atoms. Cycle 19: After refmac, R = 0.1428 (Rfree = 0.000) for 1168 atoms. Found 3 (7 requested) and removed 3 (3 requested) atoms. Cycle 20: After refmac, R = 0.1477 (Rfree = 0.000) for 1167 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.29 3.38 Search for helices and strands: 0 residues in 0 chains, 1206 seeds are put forward Round 1: 77 peptides, 15 chains. Longest chain 10 peptides. Score 0.341 Round 2: 79 peptides, 13 chains. Longest chain 11 peptides. Score 0.437 Round 3: 80 peptides, 13 chains. Longest chain 13 peptides. Score 0.445 Round 4: 78 peptides, 12 chains. Longest chain 12 peptides. Score 0.466 Round 5: 75 peptides, 11 chains. Longest chain 14 peptides. Score 0.478 Taking the results from Round 5 Chains 11, Residues 64, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1919 reflections ( 98.11 % complete ) and 2800 restraints for refining 1210 atoms. 2555 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1853 (Rfree = 0.000) for 1210 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 22: After refmac, R = 0.1755 (Rfree = 0.000) for 1211 atoms. Found 2 (7 requested) and removed 4 (3 requested) atoms. Cycle 23: After refmac, R = 0.1657 (Rfree = 0.000) for 1207 atoms. Found 4 (7 requested) and removed 5 (3 requested) atoms. Cycle 24: After refmac, R = 0.1553 (Rfree = 0.000) for 1205 atoms. Found 1 (7 requested) and removed 3 (3 requested) atoms. Cycle 25: After refmac, R = 0.1533 (Rfree = 0.000) for 1201 atoms. Found 2 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.26 3.35 Search for helices and strands: 0 residues in 0 chains, 1237 seeds are put forward Round 1: 64 peptides, 13 chains. Longest chain 8 peptides. Score 0.295 Round 2: 69 peptides, 11 chains. Longest chain 13 peptides. Score 0.425 Round 3: 62 peptides, 11 chains. Longest chain 10 peptides. Score 0.360 Round 4: 64 peptides, 11 chains. Longest chain 11 peptides. Score 0.379 Round 5: 66 peptides, 11 chains. Longest chain 11 peptides. Score 0.398 Taking the results from Round 2 Chains 11, Residues 58, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1919 reflections ( 98.11 % complete ) and 2879 restraints for refining 1224 atoms. 2658 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1716 (Rfree = 0.000) for 1224 atoms. Found 2 (7 requested) and removed 4 (3 requested) atoms. Cycle 27: After refmac, R = 0.1655 (Rfree = 0.000) for 1217 atoms. Found 5 (7 requested) and removed 3 (3 requested) atoms. Cycle 28: After refmac, R = 0.1575 (Rfree = 0.000) for 1214 atoms. Found 3 (7 requested) and removed 3 (3 requested) atoms. Cycle 29: After refmac, R = 0.1401 (Rfree = 0.000) for 1212 atoms. Found 1 (7 requested) and removed 4 (3 requested) atoms. Cycle 30: After refmac, R = 0.1400 (Rfree = 0.000) for 1208 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.29 3.38 Search for helices and strands: 0 residues in 0 chains, 1232 seeds are put forward Round 1: 62 peptides, 12 chains. Longest chain 8 peptides. Score 0.318 Round 2: 67 peptides, 12 chains. Longest chain 10 peptides. Score 0.367 Round 3: 74 peptides, 13 chains. Longest chain 9 peptides. Score 0.392 Round 4: 71 peptides, 12 chains. Longest chain 10 peptides. Score 0.404 Round 5: 68 peptides, 11 chains. Longest chain 18 peptides. Score 0.416 Taking the results from Round 5 Chains 11, Residues 57, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1919 reflections ( 98.11 % complete ) and 2920 restraints for refining 1225 atoms. 2703 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1821 (Rfree = 0.000) for 1225 atoms. Found 3 (7 requested) and removed 4 (3 requested) atoms. Cycle 32: After refmac, R = 0.1765 (Rfree = 0.000) for 1216 atoms. Found 5 (7 requested) and removed 4 (3 requested) atoms. Cycle 33: After refmac, R = 0.1767 (Rfree = 0.000) for 1215 atoms. Found 4 (7 requested) and removed 3 (3 requested) atoms. Cycle 34: After refmac, R = 0.1724 (Rfree = 0.000) for 1215 atoms. Found 4 (7 requested) and removed 3 (3 requested) atoms. Cycle 35: After refmac, R = 0.1978 (Rfree = 0.000) for 1216 atoms. Found 7 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.24 3.33 Search for helices and strands: 0 residues in 0 chains, 1258 seeds are put forward Round 1: 58 peptides, 13 chains. Longest chain 6 peptides. Score 0.233 Round 2: 64 peptides, 13 chains. Longest chain 7 peptides. Score 0.295 Round 3: 67 peptides, 13 chains. Longest chain 8 peptides. Score 0.325 Round 4: 74 peptides, 13 chains. Longest chain 10 peptides. Score 0.392 Round 5: 64 peptides, 11 chains. Longest chain 10 peptides. Score 0.379 Taking the results from Round 4 Chains 13, Residues 61, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1919 reflections ( 98.11 % complete ) and 2730 restraints for refining 1225 atoms. 2499 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1706 (Rfree = 0.000) for 1225 atoms. Found 6 (7 requested) and removed 4 (3 requested) atoms. Cycle 37: After refmac, R = 0.1693 (Rfree = 0.000) for 1221 atoms. Found 3 (7 requested) and removed 5 (3 requested) atoms. Cycle 38: After refmac, R = 0.1685 (Rfree = 0.000) for 1213 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 39: After refmac, R = 0.1501 (Rfree = 0.000) for 1210 atoms. Found 1 (7 requested) and removed 4 (3 requested) atoms. Cycle 40: After refmac, R = 0.1542 (Rfree = 0.000) for 1206 atoms. Found 5 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.22 3.31 Search for helices and strands: 0 residues in 0 chains, 1235 seeds are put forward Round 1: 43 peptides, 10 chains. Longest chain 7 peptides. Score 0.203 Round 2: 46 peptides, 9 chains. Longest chain 9 peptides. Score 0.284 Round 3: 56 peptides, 10 chains. Longest chain 9 peptides. Score 0.343 Round 4: 50 peptides, 9 chains. Longest chain 10 peptides. Score 0.327 Round 5: 53 peptides, 9 chains. Longest chain 11 peptides. Score 0.357 Taking the results from Round 5 Chains 9, Residues 44, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1919 reflections ( 98.11 % complete ) and 2947 restraints for refining 1221 atoms. 2780 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1852 (Rfree = 0.000) for 1221 atoms. Found 6 (7 requested) and removed 5 (3 requested) atoms. Cycle 42: After refmac, R = 0.1714 (Rfree = 0.000) for 1218 atoms. Found 2 (7 requested) and removed 4 (3 requested) atoms. Cycle 43: After refmac, R = 0.1403 (Rfree = 0.000) for 1214 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 44: After refmac, R = 0.1304 (Rfree = 0.000) for 1210 atoms. Found 2 (7 requested) and removed 3 (3 requested) atoms. Cycle 45: After refmac, R = 0.1234 (Rfree = 0.000) for 1207 atoms. Found 1 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.20 3.29 Search for helices and strands: 0 residues in 0 chains, 1236 seeds are put forward Round 1: 49 peptides, 11 chains. Longest chain 6 peptides. Score 0.225 Round 2: 56 peptides, 10 chains. Longest chain 8 peptides. Score 0.343 Round 3: 54 peptides, 10 chains. Longest chain 8 peptides. Score 0.323 Round 4: 59 peptides, 12 chains. Longest chain 8 peptides. Score 0.287 Round 5: 59 peptides, 11 chains. Longest chain 8 peptides. Score 0.330 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 10, 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 2fcl-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 1919 reflections ( 98.11 % complete ) and 2689 restraints for refining 1169 atoms. 2515 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1577 (Rfree = 0.000) for 1169 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.1352 (Rfree = 0.000) for 1163 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.1644 (Rfree = 0.000) for 1160 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.1576 (Rfree = 0.000) for 1155 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Writing output files ... TimeTaking 55.35