Sun 23 Dec 22:23:01 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 2hh6-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2hh6-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2hh6-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hh6-4.0-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/2hh6-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hh6-4.0-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 22:23:11 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/2hh6-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hh6-4.0-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 178 and 0 Target number of residues in the AU: 178 Target solvent content: 0.6692 Checking the provided sequence file Detected sequence length: 113 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 226 Adjusted target solvent content: 0.58 Input MTZ file: 2hh6-4.0-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: 179 Cell parameters: 93.536 93.536 115.318 90.000 90.000 120.000 Input sequence file: 2hh6-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 1808 target number of atoms Had to go as low as 0.60 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: 81.005 4.001 Wilson plot Bfac: 91.57 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 2783 reflections ( 99.39 % complete ) and 0 restraints for refining 1987 atoms. Observations/parameters ratio is 0.35 ------------------------------------------------------ Starting model: R = 0.3707 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3574 (Rfree = 0.000) for 1987 atoms. Found 9 (9 requested) and removed 22 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.84 3.45 Search for helices and strands: 0 residues in 0 chains, 1997 seeds are put forward NCS extension: 0 residues added, 1997 seeds are put forward Round 1: 36 peptides, 7 chains. Longest chain 8 peptides. Score 0.243 Round 2: 60 peptides, 10 chains. Longest chain 11 peptides. Score 0.320 Round 3: 61 peptides, 11 chains. Longest chain 9 peptides. Score 0.296 Round 4: 66 peptides, 11 chains. Longest chain 12 peptides. Score 0.329 Round 5: 66 peptides, 13 chains. Longest chain 8 peptides. Score 0.271 Taking the results from Round 4 Chains 11, Residues 55, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2783 reflections ( 99.39 % complete ) and 3940 restraints for refining 1523 atoms. 3731 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3603 (Rfree = 0.000) for 1523 atoms. Found 7 (7 requested) and removed 50 (3 requested) atoms. Cycle 2: After refmac, R = 0.3122 (Rfree = 0.000) for 1438 atoms. Found 7 (7 requested) and removed 10 (3 requested) atoms. Cycle 3: After refmac, R = 0.3203 (Rfree = 0.000) for 1414 atoms. Found 6 (6 requested) and removed 17 (3 requested) atoms. Cycle 4: After refmac, R = 0.3031 (Rfree = 0.000) for 1385 atoms. Found 6 (6 requested) and removed 11 (3 requested) atoms. Cycle 5: After refmac, R = 0.3648 (Rfree = 0.000) for 1363 atoms. Found 6 (6 requested) and removed 15 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.82 3.43 Search for helices and strands: 0 residues in 0 chains, 1415 seeds are put forward NCS extension: 0 residues added, 1415 seeds are put forward Round 1: 50 peptides, 8 chains. Longest chain 9 peptides. Score 0.315 Round 2: 59 peptides, 10 chains. Longest chain 10 peptides. Score 0.313 Round 3: 67 peptides, 10 chains. Longest chain 17 peptides. Score 0.365 Round 4: 73 peptides, 11 chains. Longest chain 20 peptides. Score 0.373 Round 5: 65 peptides, 8 chains. Longest chain 19 peptides. Score 0.410 Taking the results from Round 5 Chains 8, Residues 57, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2783 reflections ( 99.39 % complete ) and 2856 restraints for refining 1233 atoms. 2636 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3148 (Rfree = 0.000) for 1233 atoms. Found 4 (5 requested) and removed 22 (2 requested) atoms. Cycle 7: After refmac, R = 0.3155 (Rfree = 0.000) for 1195 atoms. Found 5 (5 requested) and removed 15 (2 requested) atoms. Cycle 8: After refmac, R = 0.2918 (Rfree = 0.000) for 1172 atoms. Found 5 (5 requested) and removed 12 (2 requested) atoms. Cycle 9: After refmac, R = 0.2817 (Rfree = 0.000) for 1162 atoms. Found 5 (5 requested) and removed 21 (2 requested) atoms. Cycle 10: After refmac, R = 0.2843 (Rfree = 0.000) for 1141 atoms. Found 4 (5 requested) and removed 31 (2 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.87 3.48 Search for helices and strands: 0 residues in 0 chains, 1177 seeds are put forward NCS extension: 0 residues added, 1177 seeds are put forward Round 1: 54 peptides, 9 chains. Longest chain 10 peptides. Score 0.310 Round 2: 68 peptides, 11 chains. Longest chain 13 peptides. Score 0.342 Round 3: 77 peptides, 13 chains. Longest chain 11 peptides. Score 0.342 Round 4: 76 peptides, 13 chains. Longest chain 10 peptides. Score 0.336 Round 5: 75 peptides, 12 chains. Longest chain 11 peptides. Score 0.358 Taking the results from Round 5 Chains 12, Residues 63, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2783 reflections ( 99.39 % complete ) and 2974 restraints for refining 1252 atoms. 2734 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3547 (Rfree = 0.000) for 1252 atoms. Found 5 (5 requested) and removed 25 (2 requested) atoms. Cycle 12: After refmac, R = 0.3105 (Rfree = 0.000) for 1205 atoms. Found 5 (5 requested) and removed 11 (2 requested) atoms. Cycle 13: After refmac, R = 0.3025 (Rfree = 0.000) for 1189 atoms. Found 5 (5 requested) and removed 17 (2 requested) atoms. Cycle 14: After refmac, R = 0.2845 (Rfree = 0.000) for 1168 atoms. Found 5 (5 requested) and removed 9 (2 requested) atoms. Cycle 15: After refmac, R = 0.2933 (Rfree = 0.000) for 1159 atoms. Found 5 (5 requested) and removed 8 (2 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.73 3.35 Search for helices and strands: 0 residues in 0 chains, 1232 seeds are put forward NCS extension: 0 residues added, 1232 seeds are put forward Round 1: 65 peptides, 9 chains. Longest chain 19 peptides. Score 0.382 Round 2: 69 peptides, 11 chains. Longest chain 14 peptides. Score 0.349 Round 3: 76 peptides, 9 chains. Longest chain 14 peptides. Score 0.446 Round 4: 84 peptides, 9 chains. Longest chain 19 peptides. Score 0.489 Round 5: 81 peptides, 10 chains. Longest chain 13 peptides. Score 0.447 Taking the results from Round 4 Chains 9, Residues 75, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2783 reflections ( 99.39 % complete ) and 2562 restraints for refining 1189 atoms. 2271 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2884 (Rfree = 0.000) for 1189 atoms. Found 4 (5 requested) and removed 12 (2 requested) atoms. Cycle 17: After refmac, R = 0.2690 (Rfree = 0.000) for 1168 atoms. Found 2 (5 requested) and removed 9 (2 requested) atoms. Cycle 18: After refmac, R = 0.2741 (Rfree = 0.000) for 1154 atoms. Found 3 (5 requested) and removed 4 (2 requested) atoms. Cycle 19: After refmac, R = 0.2604 (Rfree = 0.000) for 1146 atoms. Found 0 (5 requested) and removed 6 (2 requested) atoms. Cycle 20: After refmac, R = 0.2572 (Rfree = 0.000) for 1134 atoms. Found 0 (5 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.72 3.34 Search for helices and strands: 0 residues in 0 chains, 1203 seeds are put forward NCS extension: 0 residues added, 1203 seeds are put forward Round 1: 76 peptides, 13 chains. Longest chain 12 peptides. Score 0.336 Round 2: 82 peptides, 14 chains. Longest chain 13 peptides. Score 0.346 Round 3: 77 peptides, 11 chains. Longest chain 13 peptides. Score 0.397 Round 4: 78 peptides, 10 chains. Longest chain 16 peptides. Score 0.430 Round 5: 76 peptides, 10 chains. Longest chain 15 peptides. Score 0.419 Taking the results from Round 4 Chains 10, Residues 68, Estimated correctness of the model 0.0 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 2783 reflections ( 99.39 % complete ) and 2731 restraints for refining 1310 atoms. 2398 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3015 (Rfree = 0.000) for 1310 atoms. Found 6 (6 requested) and removed 12 (3 requested) atoms. Cycle 22: After refmac, R = 0.2774 (Rfree = 0.000) for 1290 atoms. Found 3 (6 requested) and removed 5 (3 requested) atoms. Cycle 23: After refmac, R = 0.2715 (Rfree = 0.000) for 1286 atoms. Found 4 (6 requested) and removed 8 (3 requested) atoms. Cycle 24: After refmac, R = 0.2660 (Rfree = 0.000) for 1280 atoms. Found 2 (6 requested) and removed 6 (3 requested) atoms. Cycle 25: After refmac, R = 0.2632 (Rfree = 0.000) for 1272 atoms. Found 0 (6 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.86 3.47 Search for helices and strands: 0 residues in 0 chains, 1308 seeds are put forward NCS extension: 0 residues added, 1308 seeds are put forward Round 1: 60 peptides, 9 chains. Longest chain 9 peptides. Score 0.350 Round 2: 61 peptides, 10 chains. Longest chain 9 peptides. Score 0.327 Round 3: 66 peptides, 11 chains. Longest chain 8 peptides. Score 0.329 Round 4: 72 peptides, 9 chains. Longest chain 14 peptides. Score 0.423 Round 5: 66 peptides, 8 chains. Longest chain 16 peptides. Score 0.416 Taking the results from Round 4 Chains 9, Residues 63, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2783 reflections ( 99.39 % complete ) and 3180 restraints for refining 1356 atoms. 2937 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2863 (Rfree = 0.000) for 1356 atoms. Found 6 (6 requested) and removed 23 (3 requested) atoms. Cycle 27: After refmac, R = 0.3129 (Rfree = 0.000) for 1317 atoms. Found 6 (6 requested) and removed 19 (3 requested) atoms. Cycle 28: After refmac, R = 0.2495 (Rfree = 0.000) for 1289 atoms. Found 4 (6 requested) and removed 11 (3 requested) atoms. Cycle 29: After refmac, R = 0.2526 (Rfree = 0.000) for 1269 atoms. Found 3 (6 requested) and removed 7 (3 requested) atoms. Cycle 30: After refmac, R = 0.2511 (Rfree = 0.000) for 1247 atoms. Found 5 (5 requested) and removed 8 (2 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.75 3.37 Search for helices and strands: 0 residues in 0 chains, 1319 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 1340 seeds are put forward Round 1: 74 peptides, 14 chains. Longest chain 9 peptides. Score 0.295 Round 2: 81 peptides, 13 chains. Longest chain 11 peptides. Score 0.367 Round 3: 83 peptides, 12 chains. Longest chain 15 peptides. Score 0.405 Round 4: 84 peptides, 12 chains. Longest chain 18 peptides. Score 0.411 Round 5: 84 peptides, 13 chains. Longest chain 14 peptides. Score 0.385 Taking the results from Round 4 Chains 12, Residues 72, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2783 reflections ( 99.39 % complete ) and 2858 restraints for refining 1298 atoms. 2582 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2765 (Rfree = 0.000) for 1298 atoms. Found 6 (6 requested) and removed 16 (3 requested) atoms. Cycle 32: After refmac, R = 0.2547 (Rfree = 0.000) for 1272 atoms. Found 5 (6 requested) and removed 12 (3 requested) atoms. Cycle 33: After refmac, R = 0.2739 (Rfree = 0.000) for 1261 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. Cycle 34: After refmac, R = 0.2621 (Rfree = 0.000) for 1257 atoms. Found 5 (5 requested) and removed 9 (2 requested) atoms. Cycle 35: After refmac, R = 0.2485 (Rfree = 0.000) for 1248 atoms. Found 2 (5 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.81 3.42 Search for helices and strands: 0 residues in 0 chains, 1321 seeds are put forward NCS extension: 30 residues added (1 deleted due to clashes), 1351 seeds are put forward Round 1: 65 peptides, 11 chains. Longest chain 10 peptides. Score 0.323 Round 2: 78 peptides, 11 chains. Longest chain 12 peptides. Score 0.403 Round 3: 81 peptides, 9 chains. Longest chain 21 peptides. Score 0.473 Round 4: 75 peptides, 10 chains. Longest chain 13 peptides. Score 0.413 Round 5: 81 peptides, 10 chains. Longest chain 12 peptides. Score 0.447 Taking the results from Round 3 Chains 9, Residues 72, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2783 reflections ( 99.39 % complete ) and 2696 restraints for refining 1266 atoms. 2417 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2611 (Rfree = 0.000) for 1266 atoms. Found 6 (6 requested) and removed 17 (3 requested) atoms. Cycle 37: After refmac, R = 0.2550 (Rfree = 0.000) for 1238 atoms. Found 4 (5 requested) and removed 10 (2 requested) atoms. Cycle 38: After refmac, R = 0.2607 (Rfree = 0.000) for 1223 atoms. Found 5 (5 requested) and removed 12 (2 requested) atoms. Cycle 39: After refmac, R = 0.2379 (Rfree = 0.000) for 1213 atoms. Found 2 (5 requested) and removed 6 (2 requested) atoms. Cycle 40: After refmac, R = 0.2404 (Rfree = 0.000) for 1204 atoms. Found 3 (5 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.81 3.42 Search for helices and strands: 0 residues in 0 chains, 1262 seeds are put forward NCS extension: 29 residues added (0 deleted due to clashes), 1291 seeds are put forward Round 1: 69 peptides, 14 chains. Longest chain 8 peptides. Score 0.262 Round 2: 83 peptides, 15 chains. Longest chain 10 peptides. Score 0.325 Round 3: 87 peptides, 12 chains. Longest chain 14 peptides. Score 0.428 Round 4: 74 peptides, 12 chains. Longest chain 9 peptides. Score 0.352 Round 5: 77 peptides, 11 chains. Longest chain 17 peptides. Score 0.397 Taking the results from Round 3 Chains 12, Residues 75, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2783 reflections ( 99.39 % complete ) and 2564 restraints for refining 1236 atoms. 2276 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2688 (Rfree = 0.000) for 1236 atoms. Found 2 (5 requested) and removed 20 (2 requested) atoms. Cycle 42: After refmac, R = 0.2396 (Rfree = 0.000) for 1208 atoms. Found 2 (5 requested) and removed 4 (2 requested) atoms. Cycle 43: After refmac, R = 0.2427 (Rfree = 0.000) for 1199 atoms. Found 5 (5 requested) and removed 11 (2 requested) atoms. Cycle 44: After refmac, R = 0.2349 (Rfree = 0.000) for 1188 atoms. Found 1 (5 requested) and removed 6 (2 requested) atoms. Cycle 45: After refmac, R = 0.2329 (Rfree = 0.000) for 1181 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.77 3.39 Search for helices and strands: 0 residues in 0 chains, 1250 seeds are put forward NCS extension: 0 residues added, 1250 seeds are put forward Round 1: 67 peptides, 11 chains. Longest chain 11 peptides. Score 0.336 Round 2: 86 peptides, 15 chains. Longest chain 12 peptides. Score 0.343 Round 3: 86 peptides, 13 chains. Longest chain 15 peptides. Score 0.396 Round 4: 73 peptides, 10 chains. Longest chain 14 peptides. Score 0.401 Round 5: 74 peptides, 11 chains. Longest chain 11 peptides. Score 0.380 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 10, Residues 63, 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 2hh6-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2783 reflections ( 99.39 % complete ) and 2819 restraints for refining 1298 atoms. 2577 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3288 (Rfree = 0.000) for 1298 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.3419 (Rfree = 0.000) for 1285 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.3122 (Rfree = 0.000) for 1261 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.3660 (Rfree = 0.000) for 1250 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Writing output files ... TimeTaking 30.75