null Sun 23 Dec 22:22:59 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 2fzt-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2fzt-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2fzt-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fzt-3.2-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/2fzt-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fzt-3.2-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 22:23:08 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/2fzt-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fzt-3.2-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 129 and 0 Target number of residues in the AU: 129 Target solvent content: 0.5981 Checking the provided sequence file Detected sequence length: 79 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 158 Adjusted target solvent content: 0.51 Input MTZ file: 2fzt-3.2-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: 4 Cell parameters: 49.630 27.430 65.380 90.000 102.600 90.000 Input sequence file: 2fzt-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 1264 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 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: 63.805 3.201 Wilson plot Bfac: 51.08 3015 reflections ( 99.60 % complete ) and 0 restraints for refining 1406 atoms. Observations/parameters ratio is 0.54 ------------------------------------------------------ Starting model: R = 0.3536 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3194 (Rfree = 0.000) for 1406 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.05 3.01 Search for helices and strands: 0 residues in 0 chains, 1460 seeds are put forward NCS extension: 0 residues added, 1460 seeds are put forward Round 1: 47 peptides, 11 chains. Longest chain 5 peptides. Score 0.202 Round 2: 76 peptides, 15 chains. Longest chain 8 peptides. Score 0.332 Round 3: 87 peptides, 15 chains. Longest chain 12 peptides. Score 0.433 Round 4: 103 peptides, 17 chains. Longest chain 13 peptides. Score 0.495 Round 5: 97 peptides, 11 chains. Longest chain 25 peptides. Score 0.641 Taking the results from Round 5 Chains 11, Residues 86, Estimated correctness of the model 51.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3015 reflections ( 99.60 % complete ) and 2469 restraints for refining 1154 atoms. 2136 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3165 (Rfree = 0.000) for 1154 atoms. Found 9 (10 requested) and removed 8 (5 requested) atoms. Cycle 2: After refmac, R = 0.3003 (Rfree = 0.000) for 1149 atoms. Found 7 (10 requested) and removed 6 (5 requested) atoms. Cycle 3: After refmac, R = 0.2889 (Rfree = 0.000) for 1142 atoms. Found 2 (10 requested) and removed 8 (5 requested) atoms. Cycle 4: After refmac, R = 0.2816 (Rfree = 0.000) for 1131 atoms. Found 4 (10 requested) and removed 6 (5 requested) atoms. Cycle 5: After refmac, R = 0.2732 (Rfree = 0.000) for 1123 atoms. Found 6 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.10 3.06 Search for helices and strands: 0 residues in 0 chains, 1208 seeds are put forward NCS extension: 35 residues added (3 deleted due to clashes), 1243 seeds are put forward Round 1: 91 peptides, 18 chains. Longest chain 9 peptides. Score 0.355 Round 2: 98 peptides, 16 chains. Longest chain 15 peptides. Score 0.489 Round 3: 104 peptides, 16 chains. Longest chain 11 peptides. Score 0.536 Round 4: 103 peptides, 16 chains. Longest chain 12 peptides. Score 0.528 Round 5: 96 peptides, 14 chains. Longest chain 13 peptides. Score 0.541 Taking the results from Round 5 Chains 14, Residues 82, Estimated correctness of the model 24.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3015 reflections ( 99.60 % complete ) and 2543 restraints for refining 1154 atoms. 2229 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3001 (Rfree = 0.000) for 1154 atoms. Found 9 (10 requested) and removed 6 (5 requested) atoms. Cycle 7: After refmac, R = 0.3010 (Rfree = 0.000) for 1147 atoms. Found 3 (10 requested) and removed 19 (5 requested) atoms. Cycle 8: After refmac, R = 0.2854 (Rfree = 0.000) for 1125 atoms. Found 8 (10 requested) and removed 7 (5 requested) atoms. Cycle 9: After refmac, R = 0.2648 (Rfree = 0.000) for 1122 atoms. Found 1 (10 requested) and removed 6 (5 requested) atoms. Cycle 10: After refmac, R = 0.2619 (Rfree = 0.000) for 1117 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.06 3.02 Search for helices and strands: 0 residues in 0 chains, 1194 seeds are put forward NCS extension: 0 residues added, 1194 seeds are put forward Round 1: 82 peptides, 17 chains. Longest chain 11 peptides. Score 0.309 Round 2: 87 peptides, 13 chains. Longest chain 13 peptides. Score 0.505 Round 3: 96 peptides, 15 chains. Longest chain 11 peptides. Score 0.507 Round 4: 89 peptides, 14 chains. Longest chain 11 peptides. Score 0.486 Round 5: 91 peptides, 12 chains. Longest chain 13 peptides. Score 0.569 Taking the results from Round 5 Chains 12, Residues 79, Estimated correctness of the model 32.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3015 reflections ( 99.60 % complete ) and 2539 restraints for refining 1154 atoms. 2235 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2959 (Rfree = 0.000) for 1154 atoms. Found 9 (10 requested) and removed 6 (5 requested) atoms. Cycle 12: After refmac, R = 0.2843 (Rfree = 0.000) for 1154 atoms. Found 5 (10 requested) and removed 7 (5 requested) atoms. Cycle 13: After refmac, R = 0.2676 (Rfree = 0.000) for 1149 atoms. Found 3 (10 requested) and removed 5 (5 requested) atoms. Cycle 14: After refmac, R = 0.2671 (Rfree = 0.000) for 1146 atoms. Found 0 (10 requested) and removed 6 (5 requested) atoms. Cycle 15: After refmac, R = 0.2626 (Rfree = 0.000) for 1140 atoms. Found 1 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.10 3.06 Search for helices and strands: 0 residues in 0 chains, 1233 seeds are put forward NCS extension: 5 residues added (0 deleted due to clashes), 1238 seeds are put forward Round 1: 66 peptides, 13 chains. Longest chain 8 peptides. Score 0.316 Round 2: 74 peptides, 12 chains. Longest chain 9 peptides. Score 0.432 Round 3: 84 peptides, 12 chains. Longest chain 9 peptides. Score 0.516 Round 4: 77 peptides, 11 chains. Longest chain 13 peptides. Score 0.496 Round 5: 82 peptides, 12 chains. Longest chain 12 peptides. Score 0.500 Taking the results from Round 3 Chains 12, Residues 72, Estimated correctness of the model 16.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3015 reflections ( 99.60 % complete ) and 2545 restraints for refining 1154 atoms. 2269 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3034 (Rfree = 0.000) for 1154 atoms. Found 8 (10 requested) and removed 9 (5 requested) atoms. Cycle 17: After refmac, R = 0.2632 (Rfree = 0.000) for 1148 atoms. Found 2 (10 requested) and removed 6 (5 requested) atoms. Cycle 18: After refmac, R = 0.2584 (Rfree = 0.000) for 1142 atoms. Found 3 (10 requested) and removed 7 (5 requested) atoms. Cycle 19: After refmac, R = 0.2537 (Rfree = 0.000) for 1136 atoms. Found 5 (10 requested) and removed 7 (5 requested) atoms. Cycle 20: After refmac, R = 0.2547 (Rfree = 0.000) for 1126 atoms. Found 5 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.11 3.07 Search for helices and strands: 0 residues in 0 chains, 1196 seeds are put forward NCS extension: 0 residues added, 1196 seeds are put forward Round 1: 64 peptides, 12 chains. Longest chain 9 peptides. Score 0.338 Round 2: 84 peptides, 13 chains. Longest chain 9 peptides. Score 0.481 Round 3: 80 peptides, 12 chains. Longest chain 11 peptides. Score 0.484 Round 4: 96 peptides, 14 chains. Longest chain 10 peptides. Score 0.541 Round 5: 90 peptides, 15 chains. Longest chain 10 peptides. Score 0.458 Taking the results from Round 4 Chains 14, Residues 82, Estimated correctness of the model 24.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3015 reflections ( 99.60 % complete ) and 2408 restraints for refining 1154 atoms. 2094 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3006 (Rfree = 0.000) for 1154 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Cycle 22: After refmac, R = 0.2646 (Rfree = 0.000) for 1152 atoms. Found 3 (10 requested) and removed 6 (5 requested) atoms. Cycle 23: After refmac, R = 0.2625 (Rfree = 0.000) for 1147 atoms. Found 4 (10 requested) and removed 6 (5 requested) atoms. Cycle 24: After refmac, R = 0.2468 (Rfree = 0.000) for 1141 atoms. Found 4 (10 requested) and removed 5 (5 requested) atoms. Cycle 25: After refmac, R = 0.2260 (Rfree = 0.000) for 1134 atoms. Found 3 (10 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.10 3.06 Search for helices and strands: 0 residues in 0 chains, 1199 seeds are put forward NCS extension: 0 residues added, 1199 seeds are put forward Round 1: 67 peptides, 14 chains. Longest chain 7 peptides. Score 0.284 Round 2: 77 peptides, 14 chains. Longest chain 9 peptides. Score 0.381 Round 3: 78 peptides, 14 chains. Longest chain 9 peptides. Score 0.390 Round 4: 81 peptides, 15 chains. Longest chain 9 peptides. Score 0.379 Round 5: 78 peptides, 13 chains. Longest chain 10 peptides. Score 0.429 Taking the results from Round 5 Chains 13, Residues 65, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3015 reflections ( 99.60 % complete ) and 2585 restraints for refining 1154 atoms. 2338 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2474 (Rfree = 0.000) for 1154 atoms. Found 10 (10 requested) and removed 5 (5 requested) atoms. Cycle 27: After refmac, R = 0.2351 (Rfree = 0.000) for 1154 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. Cycle 28: After refmac, R = 0.2369 (Rfree = 0.000) for 1155 atoms. Found 10 (10 requested) and removed 5 (5 requested) atoms. Cycle 29: After refmac, R = 0.2307 (Rfree = 0.000) for 1155 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. Cycle 30: After refmac, R = 0.2303 (Rfree = 0.000) for 1156 atoms. Found 8 (10 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.02 2.98 Search for helices and strands: 0 residues in 0 chains, 1234 seeds are put forward NCS extension: 0 residues added, 1234 seeds are put forward Round 1: 52 peptides, 12 chains. Longest chain 5 peptides. Score 0.212 Round 2: 59 peptides, 11 chains. Longest chain 8 peptides. Score 0.331 Round 3: 61 peptides, 11 chains. Longest chain 9 peptides. Score 0.351 Round 4: 61 peptides, 11 chains. Longest chain 9 peptides. Score 0.351 Round 5: 60 peptides, 11 chains. Longest chain 9 peptides. Score 0.341 Taking the results from Round 4 Chains 11, Residues 50, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3015 reflections ( 99.60 % complete ) and 2503 restraints for refining 1110 atoms. 2314 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2469 (Rfree = 0.000) for 1110 atoms. Found 9 (9 requested) and removed 5 (4 requested) atoms. Cycle 32: After refmac, R = 0.2387 (Rfree = 0.000) for 1112 atoms. Found 6 (9 requested) and removed 4 (4 requested) atoms. Cycle 33: After refmac, R = 0.2399 (Rfree = 0.000) for 1113 atoms. Found 9 (9 requested) and removed 5 (4 requested) atoms. Cycle 34: After refmac, R = 0.2339 (Rfree = 0.000) for 1115 atoms. Found 9 (10 requested) and removed 5 (5 requested) atoms. Cycle 35: After refmac, R = 0.2253 (Rfree = 0.000) for 1116 atoms. Found 5 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.98 2.94 Search for helices and strands: 0 residues in 0 chains, 1181 seeds are put forward NCS extension: 0 residues added, 1181 seeds are put forward Round 1: 55 peptides, 10 chains. Longest chain 9 peptides. Score 0.334 Round 2: 67 peptides, 10 chains. Longest chain 12 peptides. Score 0.448 Round 3: 68 peptides, 12 chains. Longest chain 10 peptides. Score 0.377 Round 4: 61 peptides, 10 chains. Longest chain 9 peptides. Score 0.393 Round 5: 69 peptides, 13 chains. Longest chain 10 peptides. Score 0.346 Taking the results from Round 2 Chains 10, Residues 57, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3015 reflections ( 99.60 % complete ) and 2288 restraints for refining 1074 atoms. 2070 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2424 (Rfree = 0.000) for 1074 atoms. Found 9 (9 requested) and removed 5 (4 requested) atoms. Cycle 37: After refmac, R = 0.2250 (Rfree = 0.000) for 1076 atoms. Found 3 (9 requested) and removed 4 (4 requested) atoms. Cycle 38: After refmac, R = 0.2366 (Rfree = 0.000) for 1071 atoms. Found 7 (9 requested) and removed 4 (4 requested) atoms. Cycle 39: After refmac, R = 0.2256 (Rfree = 0.000) for 1073 atoms. Found 2 (9 requested) and removed 4 (4 requested) atoms. Cycle 40: After refmac, R = 0.2119 (Rfree = 0.000) for 1069 atoms. Found 1 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.98 2.94 Search for helices and strands: 0 residues in 0 chains, 1137 seeds are put forward NCS extension: 0 residues added, 1137 seeds are put forward Round 1: 63 peptides, 13 chains. Longest chain 8 peptides. Score 0.286 Round 2: 77 peptides, 12 chains. Longest chain 13 peptides. Score 0.458 Round 3: 67 peptides, 12 chains. Longest chain 8 peptides. Score 0.368 Round 4: 72 peptides, 14 chains. Longest chain 8 peptides. Score 0.334 Round 5: 68 peptides, 12 chains. Longest chain 11 peptides. Score 0.377 Taking the results from Round 2 Chains 12, Residues 65, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3015 reflections ( 99.60 % complete ) and 2219 restraints for refining 1066 atoms. 1971 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2487 (Rfree = 0.000) for 1066 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. Cycle 42: After refmac, R = 0.2362 (Rfree = 0.000) for 1067 atoms. Found 9 (9 requested) and removed 5 (4 requested) atoms. Cycle 43: After refmac, R = 0.2274 (Rfree = 0.000) for 1070 atoms. Found 9 (9 requested) and removed 4 (4 requested) atoms. Cycle 44: After refmac, R = 0.2281 (Rfree = 0.000) for 1071 atoms. Found 7 (9 requested) and removed 5 (4 requested) atoms. Cycle 45: After refmac, R = 0.2303 (Rfree = 0.000) for 1070 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.98 2.94 Search for helices and strands: 0 residues in 0 chains, 1127 seeds are put forward NCS extension: 0 residues added, 1127 seeds are put forward Round 1: 49 peptides, 11 chains. Longest chain 6 peptides. Score 0.225 Round 2: 55 peptides, 10 chains. Longest chain 11 peptides. Score 0.334 Round 3: 57 peptides, 10 chains. Longest chain 10 peptides. Score 0.354 Round 4: 57 peptides, 9 chains. Longest chain 10 peptides. Score 0.397 Round 5: 64 peptides, 11 chains. Longest chain 10 peptides. Score 0.380 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 9, Residues 48, 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 2fzt-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3015 reflections ( 99.60 % complete ) and 2412 restraints for refining 1078 atoms. 2229 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2560 (Rfree = 0.000) for 1078 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.2541 (Rfree = 0.000) for 1069 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.2497 (Rfree = 0.000) for 1064 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.2453 (Rfree = 0.000) for 1058 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:47:31 GMT 2018 Job finished. TimeTaking 24.54 Used memory is bytes: 5579608