null Sun 23 Dec 22:23:02 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 2hh6-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2hh6-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2hh6-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hh6-3.8-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/2hh6-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hh6-3.8-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 22:23:11 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/2hh6-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hh6-3.8-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 183 and 0 Target number of residues in the AU: 183 Target solvent content: 0.6599 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: 2hh6-3.8-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: 179 Cell parameters: 93.536 93.536 115.318 90.000 90.000 120.000 Input sequence file: 2hh6-3.8-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 3.802 Wilson plot Bfac: 84.85 3225 reflections ( 99.48 % complete ) and 0 restraints for refining 1995 atoms. Observations/parameters ratio is 0.40 ------------------------------------------------------ Starting model: R = 0.3530 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3827 (Rfree = 0.000) for 1995 atoms. Found 10 (10 requested) and removed 33 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.61 3.24 Search for helices and strands: 0 residues in 0 chains, 2005 seeds are put forward NCS extension: 0 residues added, 2005 seeds are put forward Round 1: 49 peptides, 8 chains. Longest chain 10 peptides. Score 0.308 Round 2: 65 peptides, 10 chains. Longest chain 11 peptides. Score 0.352 Round 3: 82 peptides, 14 chains. Longest chain 10 peptides. Score 0.346 Round 4: 79 peptides, 12 chains. Longest chain 13 peptides. Score 0.382 Round 5: 77 peptides, 11 chains. Longest chain 14 peptides. Score 0.397 Taking the results from Round 5 Chains 11, Residues 66, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3225 reflections ( 99.48 % complete ) and 3892 restraints for refining 1526 atoms. 3639 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3373 (Rfree = 0.000) for 1526 atoms. Found 8 (8 requested) and removed 62 (4 requested) atoms. Cycle 2: After refmac, R = 0.3416 (Rfree = 0.000) for 1426 atoms. Found 8 (8 requested) and removed 20 (4 requested) atoms. Cycle 3: After refmac, R = 0.3340 (Rfree = 0.000) for 1391 atoms. Found 7 (7 requested) and removed 10 (3 requested) atoms. Cycle 4: After refmac, R = 0.3295 (Rfree = 0.000) for 1366 atoms. Found 7 (7 requested) and removed 18 (3 requested) atoms. Cycle 5: After refmac, R = 0.3431 (Rfree = 0.000) for 1344 atoms. Found 7 (7 requested) and removed 10 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.67 3.30 Search for helices and strands: 0 residues in 0 chains, 1394 seeds are put forward NCS extension: 0 residues added, 1394 seeds are put forward Round 1: 65 peptides, 15 chains. Longest chain 7 peptides. Score 0.204 Round 2: 84 peptides, 14 chains. Longest chain 12 peptides. Score 0.358 Round 3: 98 peptides, 17 chains. Longest chain 11 peptides. Score 0.363 Round 4: 91 peptides, 15 chains. Longest chain 13 peptides. Score 0.373 Round 5: 90 peptides, 13 chains. Longest chain 13 peptides. Score 0.419 Taking the results from Round 5 Chains 13, Residues 77, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3225 reflections ( 99.48 % complete ) and 2796 restraints for refining 1263 atoms. 2501 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3623 (Rfree = 0.000) for 1263 atoms. Found 6 (6 requested) and removed 20 (3 requested) atoms. Cycle 7: After refmac, R = 0.3214 (Rfree = 0.000) for 1221 atoms. Found 6 (6 requested) and removed 14 (3 requested) atoms. Cycle 8: After refmac, R = 0.3153 (Rfree = 0.000) for 1190 atoms. Found 6 (6 requested) and removed 14 (3 requested) atoms. Cycle 9: After refmac, R = 0.2912 (Rfree = 0.000) for 1176 atoms. Found 6 (6 requested) and removed 9 (3 requested) atoms. Cycle 10: After refmac, R = 0.2968 (Rfree = 0.000) for 1164 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.61 3.24 Search for helices and strands: 0 residues in 0 chains, 1225 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 1240 seeds are put forward Round 1: 81 peptides, 15 chains. Longest chain 11 peptides. Score 0.312 Round 2: 88 peptides, 15 chains. Longest chain 9 peptides. Score 0.356 Round 3: 88 peptides, 14 chains. Longest chain 12 peptides. Score 0.382 Round 4: 87 peptides, 13 chains. Longest chain 13 peptides. Score 0.402 Round 5: 90 peptides, 12 chains. Longest chain 16 peptides. Score 0.445 Taking the results from Round 5 Chains 12, Residues 78, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3225 reflections ( 99.48 % complete ) and 2784 restraints for refining 1233 atoms. 2484 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3055 (Rfree = 0.000) for 1233 atoms. Found 6 (6 requested) and removed 20 (3 requested) atoms. Cycle 12: After refmac, R = 0.3059 (Rfree = 0.000) for 1200 atoms. Found 6 (6 requested) and removed 23 (3 requested) atoms. Cycle 13: After refmac, R = 0.3052 (Rfree = 0.000) for 1168 atoms. Found 6 (6 requested) and removed 11 (3 requested) atoms. Cycle 14: After refmac, R = 0.3124 (Rfree = 0.000) for 1153 atoms. Found 6 (6 requested) and removed 12 (3 requested) atoms. Cycle 15: After refmac, R = 0.3101 (Rfree = 0.000) for 1134 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.55 3.19 Search for helices and strands: 0 residues in 0 chains, 1208 seeds are put forward NCS extension: 0 residues added, 1208 seeds are put forward Round 1: 76 peptides, 15 chains. Longest chain 10 peptides. Score 0.280 Round 2: 95 peptides, 15 chains. Longest chain 15 peptides. Score 0.397 Round 3: 87 peptides, 14 chains. Longest chain 13 peptides. Score 0.376 Round 4: 86 peptides, 12 chains. Longest chain 18 peptides. Score 0.423 Round 5: 84 peptides, 12 chains. Longest chain 13 peptides. Score 0.411 Taking the results from Round 4 Chains 13, Residues 74, Estimated correctness of the model 0.0 % 1 chains (16 residues) have been docked in sequence ------------------------------------------------------ 3225 reflections ( 99.48 % complete ) and 2613 restraints for refining 1233 atoms. 2253 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3055 (Rfree = 0.000) for 1233 atoms. Found 6 (6 requested) and removed 13 (3 requested) atoms. Cycle 17: After refmac, R = 0.3067 (Rfree = 0.000) for 1187 atoms. Found 6 (6 requested) and removed 8 (3 requested) atoms. Cycle 18: After refmac, R = 0.2806 (Rfree = 0.000) for 1169 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. Cycle 19: After refmac, R = 0.2730 (Rfree = 0.000) for 1158 atoms. Found 6 (6 requested) and removed 8 (3 requested) atoms. Cycle 20: After refmac, R = 0.2883 (Rfree = 0.000) for 1147 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.55 3.19 Search for helices and strands: 0 residues in 0 chains, 1225 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 1246 seeds are put forward Round 1: 77 peptides, 15 chains. Longest chain 10 peptides. Score 0.287 Round 2: 80 peptides, 14 chains. Longest chain 11 peptides. Score 0.334 Round 3: 87 peptides, 14 chains. Longest chain 15 peptides. Score 0.376 Round 4: 80 peptides, 11 chains. Longest chain 19 peptides. Score 0.415 Round 5: 84 peptides, 12 chains. Longest chain 19 peptides. Score 0.411 Taking the results from Round 4 Chains 11, Residues 69, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3225 reflections ( 99.48 % complete ) and 2673 restraints for refining 1190 atoms. 2408 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3047 (Rfree = 0.000) for 1190 atoms. Found 6 (6 requested) and removed 15 (3 requested) atoms. Cycle 22: After refmac, R = 0.3011 (Rfree = 0.000) for 1164 atoms. Found 6 (6 requested) and removed 13 (3 requested) atoms. Cycle 23: After refmac, R = 0.2579 (Rfree = 0.000) for 1150 atoms. Found 6 (6 requested) and removed 9 (3 requested) atoms. Cycle 24: After refmac, R = 0.2646 (Rfree = 0.000) for 1141 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. Cycle 25: After refmac, R = 0.2483 (Rfree = 0.000) for 1139 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.58 3.22 Search for helices and strands: 0 residues in 0 chains, 1211 seeds are put forward NCS extension: 11 residues added (0 deleted due to clashes), 1222 seeds are put forward Round 1: 91 peptides, 16 chains. Longest chain 15 peptides. Score 0.347 Round 2: 103 peptides, 14 chains. Longest chain 18 peptides. Score 0.465 Round 3: 104 peptides, 15 chains. Longest chain 17 peptides. Score 0.446 Round 4: 104 peptides, 14 chains. Longest chain 14 peptides. Score 0.470 Round 5: 114 peptides, 14 chains. Longest chain 25 peptides. Score 0.521 Taking the results from Round 5 Chains 16, Residues 100, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 3225 reflections ( 99.48 % complete ) and 2825 restraints for refining 1318 atoms. 2407 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2866 (Rfree = 0.000) for 1318 atoms. Found 7 (7 requested) and removed 20 (3 requested) atoms. Cycle 27: After refmac, R = 0.2698 (Rfree = 0.000) for 1278 atoms. Found 6 (7 requested) and removed 15 (3 requested) atoms. Cycle 28: After refmac, R = 0.2665 (Rfree = 0.000) for 1258 atoms. Found 6 (6 requested) and removed 8 (3 requested) atoms. Cycle 29: After refmac, R = 0.2766 (Rfree = 0.000) for 1244 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Cycle 30: After refmac, R = 0.2446 (Rfree = 0.000) for 1237 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.50 3.14 Search for helices and strands: 0 residues in 0 chains, 1290 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 1307 seeds are put forward Round 1: 68 peptides, 10 chains. Longest chain 14 peptides. Score 0.371 Round 2: 86 peptides, 14 chains. Longest chain 13 peptides. Score 0.370 Round 3: 89 peptides, 12 chains. Longest chain 15 peptides. Score 0.439 Round 4: 82 peptides, 12 chains. Longest chain 12 peptides. Score 0.400 Round 5: 82 peptides, 11 chains. Longest chain 14 peptides. Score 0.426 Taking the results from Round 3 Chains 12, Residues 77, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 3225 reflections ( 99.48 % complete ) and 2684 restraints for refining 1261 atoms. 2369 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3166 (Rfree = 0.000) for 1261 atoms. Found 6 (6 requested) and removed 14 (3 requested) atoms. Cycle 32: After refmac, R = 0.2998 (Rfree = 0.000) for 1234 atoms. Found 6 (6 requested) and removed 13 (3 requested) atoms. Cycle 33: After refmac, R = 0.2957 (Rfree = 0.000) for 1214 atoms. Found 6 (6 requested) and removed 13 (3 requested) atoms. Cycle 34: After refmac, R = 0.2873 (Rfree = 0.000) for 1198 atoms. Found 6 (6 requested) and removed 11 (3 requested) atoms. Cycle 35: After refmac, R = 0.2700 (Rfree = 0.000) for 1188 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.69 3.31 Search for helices and strands: 0 residues in 0 chains, 1230 seeds are put forward NCS extension: 0 residues added, 1230 seeds are put forward Round 1: 63 peptides, 12 chains. Longest chain 11 peptides. Score 0.280 Round 2: 62 peptides, 10 chains. Longest chain 10 peptides. Score 0.333 Round 3: 67 peptides, 9 chains. Longest chain 14 peptides. Score 0.394 Round 4: 69 peptides, 11 chains. Longest chain 10 peptides. Score 0.349 Round 5: 77 peptides, 13 chains. Longest chain 12 peptides. Score 0.342 Taking the results from Round 3 Chains 9, Residues 58, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3225 reflections ( 99.48 % complete ) and 2620 restraints for refining 1220 atoms. 2397 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2924 (Rfree = 0.000) for 1220 atoms. Found 6 (6 requested) and removed 18 (3 requested) atoms. Cycle 37: After refmac, R = 0.3106 (Rfree = 0.000) for 1187 atoms. Found 6 (6 requested) and removed 12 (3 requested) atoms. Cycle 38: After refmac, R = 0.2994 (Rfree = 0.000) for 1159 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. Cycle 39: After refmac, R = 0.2929 (Rfree = 0.000) for 1147 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. Cycle 40: After refmac, R = 0.3058 (Rfree = 0.000) for 1137 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.62 3.25 Search for helices and strands: 0 residues in 0 chains, 1211 seeds are put forward NCS extension: 0 residues added, 1211 seeds are put forward Round 1: 62 peptides, 12 chains. Longest chain 10 peptides. Score 0.273 Round 2: 72 peptides, 13 chains. Longest chain 11 peptides. Score 0.311 Round 3: 77 peptides, 14 chains. Longest chain 10 peptides. Score 0.315 Round 4: 83 peptides, 14 chains. Longest chain 9 peptides. Score 0.352 Round 5: 76 peptides, 14 chains. Longest chain 10 peptides. Score 0.308 Taking the results from Round 4 Chains 14, Residues 69, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3225 reflections ( 99.48 % complete ) and 2378 restraints for refining 1144 atoms. 2116 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3090 (Rfree = 0.000) for 1144 atoms. Found 6 (6 requested) and removed 19 (3 requested) atoms. Cycle 42: After refmac, R = 0.2931 (Rfree = 0.000) for 1120 atoms. Found 6 (6 requested) and removed 15 (3 requested) atoms. Cycle 43: After refmac, R = 0.2936 (Rfree = 0.000) for 1101 atoms. Found 6 (6 requested) and removed 8 (3 requested) atoms. Cycle 44: After refmac, R = 0.3023 (Rfree = 0.000) for 1092 atoms. Found 6 (6 requested) and removed 9 (3 requested) atoms. Cycle 45: After refmac, R = 0.2954 (Rfree = 0.000) for 1085 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.52 3.16 Search for helices and strands: 0 residues in 0 chains, 1183 seeds are put forward NCS extension: 0 residues added, 1183 seeds are put forward Round 1: 65 peptides, 12 chains. Longest chain 9 peptides. Score 0.293 Round 2: 73 peptides, 11 chains. Longest chain 12 peptides. Score 0.373 Round 3: 76 peptides, 11 chains. Longest chain 15 peptides. Score 0.391 Round 4: 68 peptides, 10 chains. Longest chain 13 peptides. Score 0.371 Round 5: 71 peptides, 10 chains. Longest chain 13 peptides. Score 0.389 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 11, Residues 65, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence Sequence coverage is 12 % Consider running further cycles of model building using 2hh6-3_warpNtrace.pdb as input Building loops using Loopy2018 11 chains (65 residues) following loop building 2 chains (8 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3225 reflections ( 99.48 % complete ) and 2391 restraints for refining 1160 atoms. 2119 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3016 (Rfree = 0.000) for 1160 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.2977 (Rfree = 0.000) for 1147 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.2318 (Rfree = 0.000) for 1130 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.2250 (Rfree = 0.000) for 1124 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:54:07 GMT 2018 Job finished. TimeTaking 31.09 Used memory is bytes: 18449136