null Sun 23 Dec 22:22:56 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 2o2g-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2o2g-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2o2g-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o2g-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/2o2g-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o2g-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 22:23:05 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/2o2g-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o2g-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 126 and 0 Target number of residues in the AU: 126 Target solvent content: 0.6646 Checking the provided sequence file Detected sequence length: 223 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 223 Adjusted target solvent content: 0.41 Input MTZ file: 2o2g-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: 19 Cell parameters: 47.887 62.444 67.988 90.000 90.000 90.000 Input sequence file: 2o2g-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 1784 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 Loops will be built when appropriate and at the last cycle Resolution range: 45.990 4.000 Wilson plot Bfac: 87.23 1863 reflections ( 97.90 % complete ) and 0 restraints for refining 1963 atoms. Observations/parameters ratio is 0.24 ------------------------------------------------------ Starting model: R = 0.3755 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3412 (Rfree = 0.000) for 1963 atoms. Found 9 (9 requested) and removed 31 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.78 4.27 Search for helices and strands: 0 residues in 0 chains, 1967 seeds are put forward Round 1: 35 peptides, 8 chains. Longest chain 6 peptides. Score 0.202 Round 2: 53 peptides, 12 chains. Longest chain 7 peptides. Score 0.218 Round 3: 52 peptides, 11 chains. Longest chain 7 peptides. Score 0.249 Round 4: 53 peptides, 10 chains. Longest chain 9 peptides. Score 0.299 Round 5: 51 peptides, 10 chains. Longest chain 8 peptides. Score 0.280 Taking the results from Round 4 Chains 10, Residues 43, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1863 reflections ( 97.90 % complete ) and 4201 restraints for refining 1611 atoms. 4039 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3113 (Rfree = 0.000) for 1611 atoms. Found 3 (7 requested) and removed 11 (3 requested) atoms. Cycle 2: After refmac, R = 0.3331 (Rfree = 0.000) for 1580 atoms. Found 7 (7 requested) and removed 11 (3 requested) atoms. Cycle 3: After refmac, R = 0.3307 (Rfree = 0.000) for 1562 atoms. Found 4 (7 requested) and removed 6 (3 requested) atoms. Cycle 4: After refmac, R = 0.3108 (Rfree = 0.000) for 1540 atoms. Found 2 (7 requested) and removed 5 (3 requested) atoms. Cycle 5: After refmac, R = 0.3082 (Rfree = 0.000) for 1529 atoms. Found 6 (7 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.77 4.26 Search for helices and strands: 0 residues in 0 chains, 1561 seeds are put forward Round 1: 36 peptides, 8 chains. Longest chain 6 peptides. Score 0.213 Round 2: 38 peptides, 8 chains. Longest chain 6 peptides. Score 0.235 Round 3: 45 peptides, 9 chains. Longest chain 8 peptides. Score 0.263 Round 4: 39 peptides, 9 chains. Longest chain 6 peptides. Score 0.201 Round 5: 42 peptides, 8 chains. Longest chain 7 peptides. Score 0.277 Taking the results from Round 5 Chains 8, Residues 34, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1863 reflections ( 97.90 % complete ) and 3024 restraints for refining 1234 atoms. 2896 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2991 (Rfree = 0.000) for 1234 atoms. Found 5 (5 requested) and removed 8 (2 requested) atoms. Cycle 7: After refmac, R = 0.2953 (Rfree = 0.000) for 1226 atoms. Found 5 (5 requested) and removed 7 (2 requested) atoms. Cycle 8: After refmac, R = 0.2717 (Rfree = 0.000) for 1219 atoms. Found 1 (5 requested) and removed 2 (2 requested) atoms. Cycle 9: After refmac, R = 0.2791 (Rfree = 0.000) for 1210 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. Cycle 10: After refmac, R = 0.3034 (Rfree = 0.000) for 1207 atoms. Found 5 (5 requested) and removed 8 (2 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.68 4.15 Search for helices and strands: 0 residues in 0 chains, 1244 seeds are put forward Round 1: 32 peptides, 7 chains. Longest chain 8 peptides. Score 0.216 Round 2: 38 peptides, 8 chains. Longest chain 9 peptides. Score 0.235 Round 3: 48 peptides, 7 chains. Longest chain 9 peptides. Score 0.375 Round 4: 51 peptides, 11 chains. Longest chain 7 peptides. Score 0.239 Round 5: 45 peptides, 7 chains. Longest chain 9 peptides. Score 0.348 Taking the results from Round 3 Chains 7, Residues 41, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1863 reflections ( 97.90 % complete ) and 2102 restraints for refining 1007 atoms. 1945 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2575 (Rfree = 0.000) for 1007 atoms. Found 4 (4 requested) and removed 3 (2 requested) atoms. Cycle 12: After refmac, R = 0.2613 (Rfree = 0.000) for 1002 atoms. Found 4 (4 requested) and removed 9 (2 requested) atoms. Cycle 13: After refmac, R = 0.2505 (Rfree = 0.000) for 993 atoms. Found 4 (4 requested) and removed 3 (2 requested) atoms. Cycle 14: After refmac, R = 0.2428 (Rfree = 0.000) for 992 atoms. Found 4 (4 requested) and removed 5 (2 requested) atoms. Cycle 15: After refmac, R = 0.2538 (Rfree = 0.000) for 990 atoms. Found 4 (4 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.74 4.22 Search for helices and strands: 0 residues in 0 chains, 1037 seeds are put forward Round 1: 54 peptides, 10 chains. Longest chain 8 peptides. Score 0.308 Round 2: 61 peptides, 11 chains. Longest chain 11 peptides. Score 0.332 Round 3: 54 peptides, 11 chains. Longest chain 6 peptides. Score 0.268 Round 4: 62 peptides, 11 chains. Longest chain 9 peptides. Score 0.341 Round 5: 67 peptides, 13 chains. Longest chain 7 peptides. Score 0.309 Taking the results from Round 4 Chains 11, Residues 51, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1863 reflections ( 97.90 % complete ) and 2212 restraints for refining 1043 atoms. 2019 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2910 (Rfree = 0.000) for 1043 atoms. Found 4 (4 requested) and removed 7 (2 requested) atoms. Cycle 17: After refmac, R = 0.2784 (Rfree = 0.000) for 1034 atoms. Found 4 (4 requested) and removed 2 (2 requested) atoms. Cycle 18: After refmac, R = 0.2800 (Rfree = 0.000) for 1032 atoms. Found 4 (4 requested) and removed 4 (2 requested) atoms. Cycle 19: After refmac, R = 0.2619 (Rfree = 0.000) for 1027 atoms. Found 4 (4 requested) and removed 5 (2 requested) atoms. Cycle 20: After refmac, R = 0.2664 (Rfree = 0.000) for 1025 atoms. Found 4 (4 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.73 4.21 Search for helices and strands: 0 residues in 0 chains, 1084 seeds are put forward Round 1: 56 peptides, 12 chains. Longest chain 6 peptides. Score 0.247 Round 2: 58 peptides, 10 chains. Longest chain 10 peptides. Score 0.344 Round 3: 68 peptides, 12 chains. Longest chain 10 peptides. Score 0.355 Round 4: 72 peptides, 12 chains. Longest chain 9 peptides. Score 0.388 Round 5: 72 peptides, 11 chains. Longest chain 10 peptides. Score 0.423 Taking the results from Round 5 Chains 11, Residues 61, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1863 reflections ( 97.90 % complete ) and 2272 restraints for refining 1075 atoms. 2039 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2829 (Rfree = 0.000) for 1075 atoms. Found 5 (5 requested) and removed 7 (2 requested) atoms. Cycle 22: After refmac, R = 0.2711 (Rfree = 0.000) for 1061 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. Cycle 23: After refmac, R = 0.2606 (Rfree = 0.000) for 1056 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. Cycle 24: After refmac, R = 0.2146 (Rfree = 0.000) for 1055 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 25: After refmac, R = 0.2433 (Rfree = 0.000) for 1052 atoms. Found 4 (5 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.70 4.18 Search for helices and strands: 0 residues in 0 chains, 1116 seeds are put forward Round 1: 60 peptides, 13 chains. Longest chain 8 peptides. Score 0.245 Round 2: 73 peptides, 13 chains. Longest chain 8 peptides. Score 0.360 Round 3: 75 peptides, 14 chains. Longest chain 8 peptides. Score 0.341 Round 4: 80 peptides, 13 chains. Longest chain 9 peptides. Score 0.417 Round 5: 73 peptides, 13 chains. Longest chain 11 peptides. Score 0.360 Taking the results from Round 4 Chains 13, Residues 67, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1863 reflections ( 97.90 % complete ) and 2393 restraints for refining 1137 atoms. 2138 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2586 (Rfree = 0.000) for 1137 atoms. Found 1 (5 requested) and removed 3 (2 requested) atoms. Cycle 27: After refmac, R = 0.2339 (Rfree = 0.000) for 1126 atoms. Found 0 (5 requested) and removed 5 (2 requested) atoms. Cycle 28: After refmac, R = 0.2382 (Rfree = 0.000) for 1118 atoms. Found 3 (5 requested) and removed 3 (2 requested) atoms. Cycle 29: After refmac, R = 0.2430 (Rfree = 0.000) for 1115 atoms. Found 2 (5 requested) and removed 3 (2 requested) atoms. Cycle 30: After refmac, R = 0.2128 (Rfree = 0.000) for 1110 atoms. Found 0 (5 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.75 4.23 Search for helices and strands: 0 residues in 0 chains, 1154 seeds are put forward Round 1: 43 peptides, 8 chains. Longest chain 10 peptides. Score 0.287 Round 2: 57 peptides, 10 chains. Longest chain 8 peptides. Score 0.335 Round 3: 72 peptides, 12 chains. Longest chain 12 peptides. Score 0.388 Round 4: 78 peptides, 13 chains. Longest chain 12 peptides. Score 0.401 Round 5: 72 peptides, 12 chains. Longest chain 9 peptides. Score 0.388 Taking the results from Round 4 Chains 13, Residues 65, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1863 reflections ( 97.90 % complete ) and 2395 restraints for refining 1131 atoms. 2148 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2692 (Rfree = 0.000) for 1131 atoms. Found 5 (5 requested) and removed 6 (2 requested) atoms. Cycle 32: After refmac, R = 0.2283 (Rfree = 0.000) for 1127 atoms. Found 4 (5 requested) and removed 2 (2 requested) atoms. Cycle 33: After refmac, R = 0.2283 (Rfree = 0.000) for 1127 atoms. Found 2 (5 requested) and removed 4 (2 requested) atoms. Cycle 34: After refmac, R = 0.2140 (Rfree = 0.000) for 1124 atoms. Found 4 (5 requested) and removed 3 (2 requested) atoms. Cycle 35: After refmac, R = 0.1935 (Rfree = 0.000) for 1125 atoms. Found 0 (5 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.78 4.27 Search for helices and strands: 0 residues in 0 chains, 1168 seeds are put forward Round 1: 51 peptides, 11 chains. Longest chain 8 peptides. Score 0.239 Round 2: 54 peptides, 11 chains. Longest chain 8 peptides. Score 0.268 Round 3: 57 peptides, 11 chains. Longest chain 8 peptides. Score 0.296 Round 4: 58 peptides, 11 chains. Longest chain 8 peptides. Score 0.305 Round 5: 64 peptides, 11 chains. Longest chain 11 peptides. Score 0.358 Taking the results from Round 5 Chains 11, Residues 53, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1863 reflections ( 97.90 % complete ) and 2623 restraints for refining 1184 atoms. 2422 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2469 (Rfree = 0.000) for 1184 atoms. Found 5 (5 requested) and removed 7 (2 requested) atoms. Cycle 37: After refmac, R = 0.2537 (Rfree = 0.000) for 1180 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. Cycle 38: After refmac, R = 0.2444 (Rfree = 0.000) for 1175 atoms. Found 4 (5 requested) and removed 6 (2 requested) atoms. Cycle 39: After refmac, R = 0.2355 (Rfree = 0.000) for 1172 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. Cycle 40: After refmac, R = 0.2189 (Rfree = 0.000) for 1172 atoms. Found 3 (5 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.75 4.23 Search for helices and strands: 0 residues in 0 chains, 1216 seeds are put forward Round 1: 37 peptides, 9 chains. Longest chain 5 peptides. Score 0.178 Round 2: 60 peptides, 13 chains. Longest chain 7 peptides. Score 0.245 Round 3: 48 peptides, 9 chains. Longest chain 11 peptides. Score 0.293 Round 4: 40 peptides, 8 chains. Longest chain 7 peptides. Score 0.256 Round 5: 36 peptides, 7 chains. Longest chain 8 peptides. Score 0.260 Taking the results from Round 3 Chains 9, Residues 39, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 1863 reflections ( 97.90 % complete ) and 2766 restraints for refining 1207 atoms. 2608 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2982 (Rfree = 0.000) for 1207 atoms. Found 5 (5 requested) and removed 10 (2 requested) atoms. Cycle 42: After refmac, R = 0.2558 (Rfree = 0.000) for 1199 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. Cycle 43: After refmac, R = 0.2297 (Rfree = 0.000) for 1193 atoms. Found 3 (5 requested) and removed 5 (2 requested) atoms. Cycle 44: After refmac, R = 0.2196 (Rfree = 0.000) for 1191 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. Cycle 45: After refmac, R = 0.2170 (Rfree = 0.000) for 1191 atoms. Found 1 (5 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.80 4.29 Search for helices and strands: 0 residues in 0 chains, 1224 seeds are put forward Round 1: 46 peptides, 11 chains. Longest chain 5 peptides. Score 0.188 Round 2: 48 peptides, 9 chains. Longest chain 8 peptides. Score 0.293 Round 3: 47 peptides, 9 chains. Longest chain 7 peptides. Score 0.283 Round 4: 50 peptides, 8 chains. Longest chain 11 peptides. Score 0.352 Round 5: 46 peptides, 9 chains. Longest chain 7 peptides. Score 0.273 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 8, Residues 42, 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 2o2g-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 1863 reflections ( 97.90 % complete ) and 2924 restraints for refining 1239 atoms. 2764 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2262 (Rfree = 0.000) for 1239 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 47: After refmac, R = 0.2083 (Rfree = 0.000) for 1235 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 48: After refmac, R = 0.1963 (Rfree = 0.000) for 1232 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 49: After refmac, R = 0.2168 (Rfree = 0.000) for 1227 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:47:42 GMT 2018 Job finished. TimeTaking 24.77 Used memory is bytes: 16397976