null Sun 23 Dec 22:22:43 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-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2fcl-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2fcl-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fcl-4.0-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-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fcl-4.0-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 22:22:53 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-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fcl-4.0-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 111 and 0 Target number of residues in the AU: 111 Target solvent content: 0.6573 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-4.0-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-4.0-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 4.000 Wilson plot Bfac: 81.40 1404 reflections ( 98.11 % complete ) and 0 restraints for refining 1501 atoms. Observations/parameters ratio is 0.23 ------------------------------------------------------ Starting model: R = 0.3352 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2884 (Rfree = 0.000) for 1501 atoms. Found 7 (7 requested) and removed 19 (3 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.78 3.88 Search for helices and strands: 0 residues in 0 chains, 1517 seeds are put forward Round 1: 47 peptides, 9 chains. Longest chain 9 peptides. Score 0.295 Round 2: 65 peptides, 10 chains. Longest chain 16 peptides. Score 0.429 Round 3: 58 peptides, 8 chains. Longest chain 17 peptides. Score 0.447 Round 4: 66 peptides, 11 chains. Longest chain 12 peptides. Score 0.398 Round 5: 74 peptides, 11 chains. Longest chain 15 peptides. Score 0.469 Taking the results from Round 5 Chains 11, Residues 63, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1404 reflections ( 98.11 % complete ) and 3020 restraints for refining 1221 atoms. 2779 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2560 (Rfree = 0.000) for 1221 atoms. Found 3 (5 requested) and removed 5 (2 requested) atoms. Cycle 2: After refmac, R = 0.2248 (Rfree = 0.000) for 1204 atoms. Found 0 (5 requested) and removed 5 (2 requested) atoms. Cycle 3: After refmac, R = 0.2171 (Rfree = 0.000) for 1194 atoms. Found 1 (5 requested) and removed 4 (2 requested) atoms. Cycle 4: After refmac, R = 0.1997 (Rfree = 0.000) for 1186 atoms. Found 1 (5 requested) and removed 4 (2 requested) atoms. Cycle 5: After refmac, R = 0.2221 (Rfree = 0.000) for 1183 atoms. Found 3 (5 requested) and removed 6 (2 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.71 3.81 Search for helices and strands: 0 residues in 0 chains, 1233 seeds are put forward Round 1: 62 peptides, 11 chains. Longest chain 10 peptides. Score 0.360 Round 2: 84 peptides, 15 chains. Longest chain 11 peptides. Score 0.405 Round 3: 87 peptides, 15 chains. Longest chain 11 peptides. Score 0.432 Round 4: 88 peptides, 13 chains. Longest chain 12 peptides. Score 0.512 Round 5: 84 peptides, 12 chains. Longest chain 13 peptides. Score 0.515 Taking the results from Round 5 Chains 12, Residues 72, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1404 reflections ( 98.11 % complete ) and 2940 restraints for refining 1221 atoms. 2664 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2378 (Rfree = 0.000) for 1221 atoms. Found 5 (5 requested) and removed 10 (2 requested) atoms. Cycle 7: After refmac, R = 0.2018 (Rfree = 0.000) for 1209 atoms. Found 2 (5 requested) and removed 5 (2 requested) atoms. Cycle 8: After refmac, R = 0.1815 (Rfree = 0.000) for 1199 atoms. Found 2 (5 requested) and removed 4 (2 requested) atoms. Cycle 9: After refmac, R = 0.1717 (Rfree = 0.000) for 1196 atoms. Found 0 (5 requested) and removed 3 (2 requested) atoms. Cycle 10: After refmac, R = 0.1689 (Rfree = 0.000) for 1191 atoms. Found 0 (5 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.68 3.78 Search for helices and strands: 0 residues in 0 chains, 1233 seeds are put forward Round 1: 59 peptides, 12 chains. Longest chain 8 peptides. Score 0.287 Round 2: 70 peptides, 11 chains. Longest chain 11 peptides. Score 0.434 Round 3: 77 peptides, 12 chains. Longest chain 10 peptides. Score 0.457 Round 4: 74 peptides, 12 chains. Longest chain 12 peptides. Score 0.431 Round 5: 85 peptides, 11 chains. Longest chain 19 peptides. Score 0.557 Taking the results from Round 5 Chains 11, Residues 74, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1404 reflections ( 98.11 % complete ) and 2815 restraints for refining 1213 atoms. 2530 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2073 (Rfree = 0.000) for 1213 atoms. Found 2 (5 requested) and removed 9 (2 requested) atoms. Cycle 12: After refmac, R = 0.1883 (Rfree = 0.000) for 1199 atoms. Found 4 (5 requested) and removed 5 (2 requested) atoms. Cycle 13: After refmac, R = 0.1730 (Rfree = 0.000) for 1193 atoms. Found 0 (5 requested) and removed 4 (2 requested) atoms. Cycle 14: After refmac, R = 0.1648 (Rfree = 0.000) for 1183 atoms. Found 1 (5 requested) and removed 5 (2 requested) atoms. Cycle 15: After refmac, R = 0.1531 (Rfree = 0.000) for 1172 atoms. Found 1 (5 requested) and removed 5 (2 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.68 3.78 Search for helices and strands: 0 residues in 0 chains, 1209 seeds are put forward Round 1: 46 peptides, 11 chains. Longest chain 5 peptides. Score 0.190 Round 2: 58 peptides, 11 chains. Longest chain 8 peptides. Score 0.320 Round 3: 62 peptides, 11 chains. Longest chain 11 peptides. Score 0.360 Round 4: 65 peptides, 11 chains. Longest chain 8 peptides. Score 0.389 Round 5: 69 peptides, 10 chains. Longest chain 16 peptides. Score 0.464 Taking the results from Round 5 Chains 10, Residues 59, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1404 reflections ( 98.11 % complete ) and 2908 restraints for refining 1204 atoms. 2682 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1909 (Rfree = 0.000) for 1204 atoms. Found 2 (5 requested) and removed 7 (2 requested) atoms. Cycle 17: After refmac, R = 0.1674 (Rfree = 0.000) for 1197 atoms. Found 1 (5 requested) and removed 6 (2 requested) atoms. Cycle 18: After refmac, R = 0.1473 (Rfree = 0.000) for 1191 atoms. Found 2 (5 requested) and removed 4 (2 requested) atoms. Cycle 19: After refmac, R = 0.2130 (Rfree = 0.000) for 1189 atoms. Found 4 (5 requested) and removed 11 (2 requested) atoms. Cycle 20: After refmac, R = 0.1773 (Rfree = 0.000) for 1180 atoms. Found 1 (5 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.74 3.84 Search for helices and strands: 0 residues in 0 chains, 1216 seeds are put forward Round 1: 78 peptides, 16 chains. Longest chain 9 peptides. Score 0.310 Round 2: 76 peptides, 14 chains. Longest chain 9 peptides. Score 0.371 Round 3: 78 peptides, 13 chains. Longest chain 11 peptides. Score 0.428 Round 4: 73 peptides, 12 chains. Longest chain 11 peptides. Score 0.422 Round 5: 74 peptides, 10 chains. Longest chain 15 peptides. Score 0.506 Taking the results from Round 5 Chains 10, Residues 64, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1404 reflections ( 98.11 % complete ) and 2835 restraints for refining 1221 atoms. 2589 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1748 (Rfree = 0.000) for 1221 atoms. Found 2 (5 requested) and removed 6 (2 requested) atoms. Cycle 22: After refmac, R = 0.1651 (Rfree = 0.000) for 1210 atoms. Found 1 (5 requested) and removed 2 (2 requested) atoms. Cycle 23: After refmac, R = 0.1484 (Rfree = 0.000) for 1206 atoms. Found 1 (5 requested) and removed 2 (2 requested) atoms. Cycle 24: After refmac, R = 0.1355 (Rfree = 0.000) for 1204 atoms. Found 1 (5 requested) and removed 4 (2 requested) atoms. Cycle 25: After refmac, R = 0.1401 (Rfree = 0.000) for 1201 atoms. Found 0 (5 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.64 3.74 Search for helices and strands: 0 residues in 0 chains, 1234 seeds are put forward Round 1: 43 peptides, 9 chains. Longest chain 9 peptides. Score 0.251 Round 2: 46 peptides, 8 chains. Longest chain 10 peptides. Score 0.331 Round 3: 51 peptides, 10 chains. Longest chain 7 peptides. Score 0.292 Round 4: 50 peptides, 9 chains. Longest chain 9 peptides. Score 0.327 Round 5: 49 peptides, 10 chains. Longest chain 7 peptides. Score 0.271 Taking the results from Round 2 Chains 8, Residues 38, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1404 reflections ( 98.11 % complete ) and 3039 restraints for refining 1211 atoms. 2895 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1476 (Rfree = 0.000) for 1211 atoms. Found 0 (5 requested) and removed 3 (2 requested) atoms. Cycle 27: After refmac, R = 0.1516 (Rfree = 0.000) for 1206 atoms. Found 0 (5 requested) and removed 3 (2 requested) atoms. Cycle 28: After refmac, R = 0.1344 (Rfree = 0.000) for 1202 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 29: After refmac, R = 0.1590 (Rfree = 0.000) for 1200 atoms. Found 1 (5 requested) and removed 3 (2 requested) atoms. Cycle 30: After refmac, R = 0.1360 (Rfree = 0.000) for 1197 atoms. Found 0 (5 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.71 3.81 Search for helices and strands: 0 residues in 0 chains, 1212 seeds are put forward Round 1: 49 peptides, 9 chains. Longest chain 12 peptides. Score 0.316 Round 2: 54 peptides, 10 chains. Longest chain 11 peptides. Score 0.323 Round 3: 58 peptides, 10 chains. Longest chain 14 peptides. Score 0.363 Round 4: 58 peptides, 9 chains. Longest chain 14 peptides. Score 0.406 Round 5: 58 peptides, 11 chains. Longest chain 9 peptides. Score 0.320 Taking the results from Round 4 Chains 9, Residues 49, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1404 reflections ( 98.11 % complete ) and 2906 restraints for refining 1215 atoms. 2719 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1596 (Rfree = 0.000) for 1215 atoms. Found 4 (5 requested) and removed 3 (2 requested) atoms. Cycle 32: After refmac, R = 0.1569 (Rfree = 0.000) for 1216 atoms. Found 1 (5 requested) and removed 5 (2 requested) atoms. Cycle 33: After refmac, R = 0.1474 (Rfree = 0.000) for 1210 atoms. Found 0 (5 requested) and removed 3 (2 requested) atoms. Cycle 34: After refmac, R = 0.1514 (Rfree = 0.000) for 1207 atoms. Found 1 (5 requested) and removed 3 (2 requested) atoms. Cycle 35: After refmac, R = 0.1479 (Rfree = 0.000) for 1204 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.68 3.78 Search for helices and strands: 0 residues in 0 chains, 1227 seeds are put forward Round 1: 36 peptides, 8 chains. Longest chain 6 peptides. Score 0.218 Round 2: 54 peptides, 10 chains. Longest chain 9 peptides. Score 0.323 Round 3: 60 peptides, 11 chains. Longest chain 9 peptides. Score 0.340 Round 4: 50 peptides, 8 chains. Longest chain 16 peptides. Score 0.372 Round 5: 53 peptides, 8 chains. Longest chain 15 peptides. Score 0.401 Taking the results from Round 5 Chains 8, Residues 45, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1404 reflections ( 98.11 % complete ) and 3044 restraints for refining 1221 atoms. 2872 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1585 (Rfree = 0.000) for 1221 atoms. Found 1 (5 requested) and removed 4 (2 requested) atoms. Cycle 37: After refmac, R = 0.1603 (Rfree = 0.000) for 1215 atoms. Found 1 (5 requested) and removed 4 (2 requested) atoms. Cycle 38: After refmac, R = 0.1455 (Rfree = 0.000) for 1212 atoms. Found 2 (5 requested) and removed 3 (2 requested) atoms. Cycle 39: After refmac, R = 0.1444 (Rfree = 0.000) for 1211 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 40: After refmac, R = 0.1574 (Rfree = 0.000) for 1207 atoms. Found 3 (5 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.71 3.81 Search for helices and strands: 0 residues in 0 chains, 1222 seeds are put forward Round 1: 39 peptides, 9 chains. Longest chain 6 peptides. Score 0.204 Round 2: 47 peptides, 7 chains. Longest chain 16 peptides. Score 0.387 Round 3: 48 peptides, 9 chains. Longest chain 10 peptides. Score 0.306 Round 4: 43 peptides, 8 chains. Longest chain 8 peptides. Score 0.299 Round 5: 46 peptides, 9 chains. Longest chain 7 peptides. Score 0.284 Taking the results from Round 2 Chains 7, Residues 40, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1404 reflections ( 98.11 % complete ) and 3016 restraints for refining 1205 atoms. 2863 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1630 (Rfree = 0.000) for 1205 atoms. Found 1 (5 requested) and removed 2 (2 requested) atoms. Cycle 42: After refmac, R = 0.1495 (Rfree = 0.000) for 1201 atoms. Found 1 (5 requested) and removed 3 (2 requested) atoms. Cycle 43: After refmac, R = 0.1391 (Rfree = 0.000) for 1199 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 44: After refmac, R = 0.1442 (Rfree = 0.000) for 1197 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 45: After refmac, R = 0.1328 (Rfree = 0.000) for 1194 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.70 3.80 Search for helices and strands: 0 residues in 0 chains, 1210 seeds are put forward Round 1: 41 peptides, 9 chains. Longest chain 7 peptides. Score 0.228 Round 2: 43 peptides, 7 chains. Longest chain 9 peptides. Score 0.346 Round 3: 44 peptides, 7 chains. Longest chain 10 peptides. Score 0.356 Round 4: 46 peptides, 8 chains. Longest chain 8 peptides. Score 0.331 Round 5: 46 peptides, 8 chains. Longest chain 8 peptides. Score 0.331 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 7, Residues 37, 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-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 1404 reflections ( 98.11 % complete ) and 3026 restraints for refining 1208 atoms. 2885 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1624 (Rfree = 0.000) for 1208 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 47: After refmac, R = 0.1650 (Rfree = 0.000) for 1203 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 48: After refmac, R = 0.1462 (Rfree = 0.000) for 1201 atoms. Found 0 (5 requested) and removed 1 (2 requested) atoms. Cycle 49: After refmac, R = 0.1277 (Rfree = 0.000) for 1199 atoms. Found 0 (5 requested) and removed 1 (2 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:46:37 GMT 2018 Job finished. TimeTaking 23.9 Used memory is bytes: 926440