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-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2fzt-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2fzt-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fzt-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/2fzt-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fzt-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 22:23:08 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-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fzt-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 120 and 0 Target number of residues in the AU: 120 Target solvent content: 0.6262 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-3.6-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: 4 Cell parameters: 49.630 27.430 65.380 90.000 102.600 90.000 Input sequence file: 2fzt-3.6-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 3.600 Wilson plot Bfac: 63.14 2138 reflections ( 99.44 % complete ) and 0 restraints for refining 1411 atoms. Observations/parameters ratio is 0.38 ------------------------------------------------------ Starting model: R = 0.3597 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3575 (Rfree = 0.000) for 1411 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.36 3.32 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: 46 peptides, 10 chains. Longest chain 10 peptides. Score 0.238 Round 2: 62 peptides, 12 chains. Longest chain 9 peptides. Score 0.318 Round 3: 70 peptides, 12 chains. Longest chain 10 peptides. Score 0.396 Round 4: 70 peptides, 13 chains. Longest chain 8 peptides. Score 0.355 Round 5: 81 peptides, 14 chains. Longest chain 10 peptides. Score 0.418 Taking the results from Round 5 Chains 14, Residues 67, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2138 reflections ( 99.44 % complete ) and 2756 restraints for refining 1146 atoms. 2502 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2912 (Rfree = 0.000) for 1146 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 2: After refmac, R = 0.2813 (Rfree = 0.000) for 1122 atoms. Found 6 (7 requested) and removed 9 (3 requested) atoms. Cycle 3: After refmac, R = 0.2617 (Rfree = 0.000) for 1100 atoms. Found 5 (7 requested) and removed 5 (3 requested) atoms. Cycle 4: After refmac, R = 0.2561 (Rfree = 0.000) for 1091 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. Cycle 5: After refmac, R = 0.2449 (Rfree = 0.000) for 1084 atoms. Found 2 (6 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.23 3.19 Search for helices and strands: 0 residues in 0 chains, 1168 seeds are put forward NCS extension: 0 residues added, 1168 seeds are put forward Round 1: 72 peptides, 16 chains. Longest chain 8 peptides. Score 0.251 Round 2: 83 peptides, 16 chains. Longest chain 8 peptides. Score 0.358 Round 3: 85 peptides, 15 chains. Longest chain 14 peptides. Score 0.415 Round 4: 75 peptides, 13 chains. Longest chain 9 peptides. Score 0.402 Round 5: 76 peptides, 14 chains. Longest chain 10 peptides. Score 0.372 Taking the results from Round 3 Chains 15, Residues 70, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2138 reflections ( 99.44 % complete ) and 2563 restraints for refining 1110 atoms. 2298 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2686 (Rfree = 0.000) for 1110 atoms. Found 5 (7 requested) and removed 5 (3 requested) atoms. Cycle 7: After refmac, R = 0.2462 (Rfree = 0.000) for 1095 atoms. Found 5 (7 requested) and removed 6 (3 requested) atoms. Cycle 8: After refmac, R = 0.2214 (Rfree = 0.000) for 1091 atoms. Found 3 (7 requested) and removed 5 (3 requested) atoms. Cycle 9: After refmac, R = 0.2156 (Rfree = 0.000) for 1088 atoms. Found 2 (6 requested) and removed 3 (3 requested) atoms. Cycle 10: After refmac, R = 0.2079 (Rfree = 0.000) for 1085 atoms. Found 2 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.22 3.18 Search for helices and strands: 0 residues in 0 chains, 1160 seeds are put forward NCS extension: 0 residues added, 1160 seeds are put forward Round 1: 75 peptides, 16 chains. Longest chain 10 peptides. Score 0.281 Round 2: 81 peptides, 15 chains. Longest chain 9 peptides. Score 0.379 Round 3: 78 peptides, 15 chains. Longest chain 8 peptides. Score 0.351 Round 4: 72 peptides, 14 chains. Longest chain 7 peptides. Score 0.334 Round 5: 75 peptides, 14 chains. Longest chain 11 peptides. Score 0.362 Taking the results from Round 2 Chains 15, Residues 66, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2138 reflections ( 99.44 % complete ) and 2663 restraints for refining 1146 atoms. 2414 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2375 (Rfree = 0.000) for 1146 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. Cycle 12: After refmac, R = 0.2067 (Rfree = 0.000) for 1139 atoms. Found 6 (7 requested) and removed 4 (3 requested) atoms. Cycle 13: After refmac, R = 0.2031 (Rfree = 0.000) for 1137 atoms. Found 2 (7 requested) and removed 3 (3 requested) atoms. Cycle 14: After refmac, R = 0.1990 (Rfree = 0.000) for 1135 atoms. Found 2 (7 requested) and removed 4 (3 requested) atoms. Cycle 15: After refmac, R = 0.1970 (Rfree = 0.000) for 1131 atoms. Found 2 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.29 3.25 Search for helices and strands: 0 residues in 0 chains, 1182 seeds are put forward NCS extension: 0 residues added, 1182 seeds are put forward Round 1: 52 peptides, 11 chains. Longest chain 6 peptides. Score 0.258 Round 2: 80 peptides, 15 chains. Longest chain 7 peptides. Score 0.370 Round 3: 78 peptides, 14 chains. Longest chain 9 peptides. Score 0.390 Round 4: 82 peptides, 14 chains. Longest chain 14 peptides. Score 0.426 Round 5: 82 peptides, 14 chains. Longest chain 14 peptides. Score 0.426 Taking the results from Round 5 Chains 14, Residues 68, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2138 reflections ( 99.44 % complete ) and 2589 restraints for refining 1146 atoms. 2331 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2606 (Rfree = 0.000) for 1146 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 17: After refmac, R = 0.2272 (Rfree = 0.000) for 1138 atoms. Found 4 (7 requested) and removed 4 (3 requested) atoms. Cycle 18: After refmac, R = 0.2112 (Rfree = 0.000) for 1135 atoms. Found 6 (7 requested) and removed 5 (3 requested) atoms. Cycle 19: After refmac, R = 0.2008 (Rfree = 0.000) for 1135 atoms. Found 1 (7 requested) and removed 4 (3 requested) atoms. Cycle 20: After refmac, R = 0.2096 (Rfree = 0.000) for 1129 atoms. Found 5 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.32 3.28 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: 67 peptides, 15 chains. Longest chain 7 peptides. Score 0.242 Round 2: 73 peptides, 14 chains. Longest chain 8 peptides. Score 0.343 Round 3: 87 peptides, 16 chains. Longest chain 9 peptides. Score 0.395 Round 4: 78 peptides, 14 chains. Longest chain 9 peptides. Score 0.390 Round 5: 76 peptides, 13 chains. Longest chain 11 peptides. Score 0.411 Taking the results from Round 5 Chains 13, Residues 63, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2138 reflections ( 99.44 % complete ) and 2577 restraints for refining 1145 atoms. 2338 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2334 (Rfree = 0.000) for 1145 atoms. Found 5 (7 requested) and removed 4 (3 requested) atoms. Cycle 22: After refmac, R = 0.2248 (Rfree = 0.000) for 1139 atoms. Found 5 (7 requested) and removed 5 (3 requested) atoms. Cycle 23: After refmac, R = 0.2146 (Rfree = 0.000) for 1137 atoms. Found 6 (7 requested) and removed 5 (3 requested) atoms. Cycle 24: After refmac, R = 0.2059 (Rfree = 0.000) for 1133 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 25: After refmac, R = 0.1916 (Rfree = 0.000) for 1135 atoms. Found 0 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.23 3.19 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: 67 peptides, 15 chains. Longest chain 6 peptides. Score 0.242 Round 2: 64 peptides, 11 chains. Longest chain 9 peptides. Score 0.380 Round 3: 78 peptides, 15 chains. Longest chain 9 peptides. Score 0.351 Round 4: 71 peptides, 12 chains. Longest chain 9 peptides. Score 0.405 Round 5: 77 peptides, 14 chains. Longest chain 7 peptides. Score 0.381 Taking the results from Round 4 Chains 12, Residues 59, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2138 reflections ( 99.44 % complete ) and 2709 restraints for refining 1146 atoms. 2485 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2519 (Rfree = 0.000) for 1146 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 27: After refmac, R = 0.2358 (Rfree = 0.000) for 1142 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 28: After refmac, R = 0.2333 (Rfree = 0.000) for 1139 atoms. Found 4 (7 requested) and removed 5 (3 requested) atoms. Cycle 29: After refmac, R = 0.2406 (Rfree = 0.000) for 1134 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 30: After refmac, R = 0.2095 (Rfree = 0.000) for 1135 atoms. Found 3 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.28 3.24 Search for helices and strands: 0 residues in 0 chains, 1191 seeds are put forward NCS extension: 0 residues added, 1191 seeds are put forward Round 1: 45 peptides, 11 chains. Longest chain 5 peptides. Score 0.179 Round 2: 63 peptides, 12 chains. Longest chain 10 peptides. Score 0.328 Round 3: 74 peptides, 15 chains. Longest chain 8 peptides. Score 0.312 Round 4: 60 peptides, 11 chains. Longest chain 11 peptides. Score 0.341 Round 5: 59 peptides, 10 chains. Longest chain 10 peptides. Score 0.374 Taking the results from Round 5 Chains 10, Residues 49, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2138 reflections ( 99.44 % complete ) and 2764 restraints for refining 1146 atoms. 2578 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2518 (Rfree = 0.000) for 1146 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 32: After refmac, R = 0.2155 (Rfree = 0.000) for 1146 atoms. Found 1 (7 requested) and removed 3 (3 requested) atoms. Cycle 33: After refmac, R = 0.2200 (Rfree = 0.000) for 1140 atoms. Found 6 (7 requested) and removed 3 (3 requested) atoms. Failed to save intermediate PDB Cycle 34: After refmac, R = 0.1922 (Rfree = 0.000) for 1141 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 35: After refmac, R = 0.1863 (Rfree = 0.000) for 1134 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.28 3.24 Search for helices and strands: 0 residues in 0 chains, 1186 seeds are put forward NCS extension: 0 residues added, 1186 seeds are put forward Round 1: 47 peptides, 9 chains. Longest chain 6 peptides. Score 0.296 Round 2: 58 peptides, 11 chains. Longest chain 7 peptides. Score 0.321 Round 3: 61 peptides, 11 chains. Longest chain 8 peptides. Score 0.351 Round 4: 62 peptides, 12 chains. Longest chain 7 peptides. Score 0.318 Round 5: 62 peptides, 12 chains. Longest chain 9 peptides. Score 0.318 Taking the results from Round 3 Chains 11, Residues 50, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2138 reflections ( 99.44 % complete ) and 2621 restraints for refining 1136 atoms. 2432 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2246 (Rfree = 0.000) for 1136 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. Cycle 37: After refmac, R = 0.2397 (Rfree = 0.000) for 1136 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 38: After refmac, R = 0.2082 (Rfree = 0.000) for 1135 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 39: After refmac, R = 0.1893 (Rfree = 0.000) for 1136 atoms. Found 7 (7 requested) and removed 3 (3 requested) atoms. Cycle 40: After refmac, R = 0.1848 (Rfree = 0.000) for 1137 atoms. Found 7 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.28 3.24 Search for helices and strands: 0 residues in 0 chains, 1205 seeds are put forward NCS extension: 0 residues added, 1205 seeds are put forward Round 1: 37 peptides, 8 chains. Longest chain 7 peptides. Score 0.230 Round 2: 37 peptides, 9 chains. Longest chain 5 peptides. Score 0.179 Round 3: 43 peptides, 10 chains. Longest chain 6 peptides. Score 0.203 Round 4: 51 peptides, 11 chains. Longest chain 7 peptides. Score 0.247 Round 5: 54 peptides, 12 chains. Longest chain 7 peptides. Score 0.234 Taking the results from Round 4 Chains 11, Residues 40, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2138 reflections ( 99.44 % complete ) and 2774 restraints for refining 1146 atoms. 2625 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2296 (Rfree = 0.000) for 1146 atoms. Found 7 (7 requested) and removed 3 (3 requested) atoms. Cycle 42: After refmac, R = 0.1799 (Rfree = 0.000) for 1148 atoms. Found 7 (7 requested) and removed 3 (3 requested) atoms. Cycle 43: After refmac, R = 0.1614 (Rfree = 0.000) for 1149 atoms. Found 6 (7 requested) and removed 3 (3 requested) atoms. Cycle 44: After refmac, R = 0.1539 (Rfree = 0.000) for 1152 atoms. Found 3 (7 requested) and removed 3 (3 requested) atoms. Cycle 45: After refmac, R = 0.1555 (Rfree = 0.000) for 1152 atoms. Found 1 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.33 3.29 Search for helices and strands: 0 residues in 0 chains, 1190 seeds are put forward NCS extension: 0 residues added, 1190 seeds are put forward Round 1: 36 peptides, 8 chains. Longest chain 6 peptides. Score 0.218 Round 2: 37 peptides, 7 chains. Longest chain 7 peptides. Score 0.281 Round 3: 38 peptides, 7 chains. Longest chain 7 peptides. Score 0.292 Round 4: 43 peptides, 8 chains. Longest chain 9 peptides. Score 0.299 Round 5: 36 peptides, 6 chains. Longest chain 10 peptides. Score 0.320 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 6, Residues 30, 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. 2138 reflections ( 99.44 % complete ) and 2780 restraints for refining 1146 atoms. 2666 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2979 (Rfree = 0.000) for 1146 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.2334 (Rfree = 0.000) for 1138 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.2482 (Rfree = 0.000) for 1131 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.2241 (Rfree = 0.000) for 1122 atoms. TimeTaking 24.08