Sun 23 Dec 22:23:14 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 2oh3-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2oh3-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2oh3-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2oh3-4.0-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/2oh3-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2oh3-4.0-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 22:23:22 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/2oh3-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2oh3-4.0-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 132 and 0 Target number of residues in the AU: 132 Target solvent content: 0.6716 Checking the provided sequence file Detected sequence length: 167 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 167 Adjusted target solvent content: 0.58 Input MTZ file: 2oh3-4.0-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: 23 Cell parameters: 64.360 75.280 89.790 90.000 90.000 90.000 Input sequence file: 2oh3-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 1336 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 Loops will be built when appropriate and at the last cycle Resolution range: 57.688 4.001 Wilson plot Bfac: 93.26 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 1947 reflections ( 97.30 % complete ) and 0 restraints for refining 1479 atoms. Observations/parameters ratio is 0.33 ------------------------------------------------------ Starting model: R = 0.3301 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2677 (Rfree = 0.000) for 1479 atoms. Found 7 (7 requested) and removed 87 (3 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.86 2.57 Search for helices and strands: 0 residues in 0 chains, 1399 seeds are put forward Round 1: 55 peptides, 11 chains. Longest chain 6 peptides. Score 0.272 Round 2: 79 peptides, 14 chains. Longest chain 10 peptides. Score 0.364 Round 3: 80 peptides, 12 chains. Longest chain 10 peptides. Score 0.438 Round 4: 80 peptides, 12 chains. Longest chain 11 peptides. Score 0.438 Round 5: 83 peptides, 12 chains. Longest chain 19 peptides. Score 0.459 Taking the results from Round 5 Chains 12, Residues 71, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1947 reflections ( 97.30 % complete ) and 2815 restraints for refining 1183 atoms. 2543 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3328 (Rfree = 0.000) for 1183 atoms. Found 5 (5 requested) and removed 47 (2 requested) atoms. Cycle 2: After refmac, R = 0.3111 (Rfree = 0.000) for 1137 atoms. Found 5 (5 requested) and removed 13 (2 requested) atoms. Cycle 3: After refmac, R = 0.2980 (Rfree = 0.000) for 1128 atoms. Found 3 (5 requested) and removed 17 (2 requested) atoms. Cycle 4: After refmac, R = 0.2960 (Rfree = 0.000) for 1113 atoms. Found 0 (5 requested) and removed 4 (2 requested) atoms. Cycle 5: After refmac, R = 0.2894 (Rfree = 0.000) for 1107 atoms. Found 1 (5 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.63 3.26 Search for helices and strands: 0 residues in 0 chains, 1153 seeds are put forward Round 1: 56 peptides, 11 chains. Longest chain 7 peptides. Score 0.281 Round 2: 87 peptides, 14 chains. Longest chain 11 peptides. Score 0.424 Round 3: 89 peptides, 15 chains. Longest chain 16 peptides. Score 0.407 Round 4: 98 peptides, 14 chains. Longest chain 10 peptides. Score 0.500 Round 5: 93 peptides, 15 chains. Longest chain 12 peptides. Score 0.436 Taking the results from Round 4 Chains 14, Residues 84, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1947 reflections ( 97.30 % complete ) and 2685 restraints for refining 1196 atoms. 2363 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3311 (Rfree = 0.000) for 1196 atoms. Found 5 (5 requested) and removed 22 (2 requested) atoms. Cycle 7: After refmac, R = 0.3085 (Rfree = 0.000) for 1176 atoms. Found 5 (5 requested) and removed 8 (2 requested) atoms. Cycle 8: After refmac, R = 0.2977 (Rfree = 0.000) for 1168 atoms. Found 5 (5 requested) and removed 6 (2 requested) atoms. Cycle 9: After refmac, R = 0.2866 (Rfree = 0.000) for 1167 atoms. Found 1 (5 requested) and removed 4 (2 requested) atoms. Cycle 10: After refmac, R = 0.2802 (Rfree = 0.000) for 1164 atoms. Found 0 (5 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.36 3.02 Search for helices and strands: 0 residues in 0 chains, 1187 seeds are put forward Round 1: 79 peptides, 14 chains. Longest chain 13 peptides. Score 0.364 Round 2: 94 peptides, 15 chains. Longest chain 15 peptides. Score 0.443 Round 3: 81 peptides, 11 chains. Longest chain 16 peptides. Score 0.477 Round 4: 81 peptides, 11 chains. Longest chain 13 peptides. Score 0.477 Round 5: 82 peptides, 11 chains. Longest chain 11 peptides. Score 0.483 Taking the results from Round 5 Chains 11, Residues 71, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 1947 reflections ( 97.30 % complete ) and 2658 restraints for refining 1206 atoms. 2350 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3134 (Rfree = 0.000) for 1206 atoms. Found 4 (5 requested) and removed 8 (2 requested) atoms. Cycle 12: After refmac, R = 0.2971 (Rfree = 0.000) for 1198 atoms. Found 1 (5 requested) and removed 2 (2 requested) atoms. Cycle 13: After refmac, R = 0.2797 (Rfree = 0.000) for 1193 atoms. Found 3 (5 requested) and removed 5 (2 requested) atoms. Cycle 14: After refmac, R = 0.2780 (Rfree = 0.000) for 1188 atoms. Found 1 (5 requested) and removed 3 (2 requested) atoms. Cycle 15: After refmac, R = 0.2773 (Rfree = 0.000) for 1186 atoms. Found 1 (5 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.45 3.10 Search for helices and strands: 0 residues in 0 chains, 1203 seeds are put forward Round 1: 71 peptides, 13 chains. Longest chain 11 peptides. Score 0.335 Round 2: 85 peptides, 14 chains. Longest chain 9 peptides. Score 0.410 Round 3: 81 peptides, 14 chains. Longest chain 10 peptides. Score 0.380 Round 4: 75 peptides, 12 chains. Longest chain 10 peptides. Score 0.401 Round 5: 83 peptides, 15 chains. Longest chain 9 peptides. Score 0.362 Taking the results from Round 2 Chains 14, Residues 71, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1947 reflections ( 97.30 % complete ) and 2776 restraints for refining 1206 atoms. 2506 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3039 (Rfree = 0.000) for 1206 atoms. Found 5 (5 requested) and removed 14 (2 requested) atoms. Cycle 17: After refmac, R = 0.2852 (Rfree = 0.000) for 1196 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. Cycle 18: After refmac, R = 0.2851 (Rfree = 0.000) for 1194 atoms. Found 3 (5 requested) and removed 2 (2 requested) atoms. Cycle 19: After refmac, R = 0.2869 (Rfree = 0.000) for 1194 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. Cycle 20: After refmac, R = 0.2757 (Rfree = 0.000) for 1194 atoms. Found 3 (5 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.13 2.81 Search for helices and strands: 0 residues in 0 chains, 1203 seeds are put forward Round 1: 73 peptides, 14 chains. Longest chain 9 peptides. Score 0.317 Round 2: 85 peptides, 16 chains. Longest chain 9 peptides. Score 0.345 Round 3: 80 peptides, 13 chains. Longest chain 13 peptides. Score 0.405 Round 4: 91 peptides, 16 chains. Longest chain 12 peptides. Score 0.390 Round 5: 81 peptides, 14 chains. Longest chain 11 peptides. Score 0.380 Taking the results from Round 3 Chains 13, Residues 67, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 1947 reflections ( 97.30 % complete ) and 2602 restraints for refining 1206 atoms. 2322 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3153 (Rfree = 0.000) for 1206 atoms. Found 5 (5 requested) and removed 10 (2 requested) atoms. Cycle 22: After refmac, R = 0.2967 (Rfree = 0.000) for 1197 atoms. Found 3 (5 requested) and removed 4 (2 requested) atoms. Cycle 23: After refmac, R = 0.2835 (Rfree = 0.000) for 1194 atoms. Found 3 (5 requested) and removed 4 (2 requested) atoms. Cycle 24: After refmac, R = 0.2822 (Rfree = 0.000) for 1191 atoms. Found 0 (5 requested) and removed 3 (2 requested) atoms. Cycle 25: After refmac, R = 0.2762 (Rfree = 0.000) for 1188 atoms. Found 2 (5 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.05 2.74 Search for helices and strands: 0 residues in 0 chains, 1198 seeds are put forward Round 1: 66 peptides, 11 chains. Longest chain 13 peptides. Score 0.365 Round 2: 76 peptides, 13 chains. Longest chain 11 peptides. Score 0.375 Round 3: 78 peptides, 13 chains. Longest chain 12 peptides. Score 0.390 Round 4: 82 peptides, 14 chains. Longest chain 11 peptides. Score 0.387 Round 5: 92 peptides, 12 chains. Longest chain 14 peptides. Score 0.520 Taking the results from Round 5 Chains 14, Residues 80, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 1947 reflections ( 97.30 % complete ) and 2539 restraints for refining 1206 atoms. 2195 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3330 (Rfree = 0.000) for 1206 atoms. Found 5 (5 requested) and removed 12 (2 requested) atoms. Cycle 27: After refmac, R = 0.3180 (Rfree = 0.000) for 1198 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. Cycle 28: After refmac, R = 0.3075 (Rfree = 0.000) for 1199 atoms. Found 1 (5 requested) and removed 3 (2 requested) atoms. Cycle 29: After refmac, R = 0.3026 (Rfree = 0.000) for 1195 atoms. Found 1 (5 requested) and removed 2 (2 requested) atoms. Cycle 30: After refmac, R = 0.2993 (Rfree = 0.000) for 1193 atoms. Found 1 (5 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.63 2.36 Search for helices and strands: 0 residues in 0 chains, 1217 seeds are put forward Round 1: 61 peptides, 12 chains. Longest chain 8 peptides. Score 0.288 Round 2: 73 peptides, 13 chains. Longest chain 11 peptides. Score 0.351 Round 3: 67 peptides, 11 chains. Longest chain 9 peptides. Score 0.373 Round 4: 72 peptides, 11 chains. Longest chain 11 peptides. Score 0.412 Round 5: 68 peptides, 10 chains. Longest chain 10 peptides. Score 0.415 Taking the results from Round 5 Chains 10, Residues 58, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 1947 reflections ( 97.30 % complete ) and 2697 restraints for refining 1205 atoms. 2450 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3405 (Rfree = 0.000) for 1205 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. Cycle 32: After refmac, R = 0.3247 (Rfree = 0.000) for 1204 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. Cycle 33: After refmac, R = 0.3176 (Rfree = 0.000) for 1205 atoms. Found 2 (5 requested) and removed 2 (2 requested) atoms. Cycle 34: After refmac, R = 0.3115 (Rfree = 0.000) for 1205 atoms. Found 1 (5 requested) and removed 2 (2 requested) atoms. Cycle 35: After refmac, R = 0.3044 (Rfree = 0.000) for 1203 atoms. Found 1 (5 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.57 2.31 Search for helices and strands: 0 residues in 0 chains, 1214 seeds are put forward Round 1: 72 peptides, 15 chains. Longest chain 8 peptides. Score 0.273 Round 2: 69 peptides, 11 chains. Longest chain 9 peptides. Score 0.389 Round 3: 78 peptides, 14 chains. Longest chain 9 peptides. Score 0.357 Round 4: 75 peptides, 13 chains. Longest chain 11 peptides. Score 0.367 Round 5: 83 peptides, 14 chains. Longest chain 11 peptides. Score 0.395 Taking the results from Round 5 Chains 14, Residues 69, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1947 reflections ( 97.30 % complete ) and 2818 restraints for refining 1206 atoms. 2556 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3323 (Rfree = 0.000) for 1206 atoms. Found 5 (5 requested) and removed 7 (2 requested) atoms. Cycle 37: After refmac, R = 0.3206 (Rfree = 0.000) for 1204 atoms. Found 5 (5 requested) and removed 2 (2 requested) atoms. Cycle 38: After refmac, R = 0.3071 (Rfree = 0.000) for 1206 atoms. Found 2 (5 requested) and removed 2 (2 requested) atoms. Cycle 39: After refmac, R = 0.3023 (Rfree = 0.000) for 1204 atoms. Found 3 (5 requested) and removed 2 (2 requested) atoms. Cycle 40: After refmac, R = 0.2941 (Rfree = 0.000) for 1205 atoms. Found 0 (5 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.50 2.25 Search for helices and strands: 0 residues in 0 chains, 1216 seeds are put forward Round 1: 71 peptides, 16 chains. Longest chain 8 peptides. Score 0.229 Round 2: 73 peptides, 14 chains. Longest chain 10 peptides. Score 0.317 Round 3: 73 peptides, 14 chains. Longest chain 8 peptides. Score 0.317 Round 4: 74 peptides, 13 chains. Longest chain 10 peptides. Score 0.359 Round 5: 71 peptides, 14 chains. Longest chain 9 peptides. Score 0.300 Taking the results from Round 4 Chains 13, Residues 61, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1947 reflections ( 97.30 % complete ) and 2832 restraints for refining 1206 atoms. 2601 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3316 (Rfree = 0.000) for 1206 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. Cycle 42: After refmac, R = 0.3197 (Rfree = 0.000) for 1208 atoms. Found 5 (5 requested) and removed 2 (2 requested) atoms. Cycle 43: After refmac, R = 0.3091 (Rfree = 0.000) for 1210 atoms. Found 4 (5 requested) and removed 2 (2 requested) atoms. Cycle 44: After refmac, R = 0.3021 (Rfree = 0.000) for 1212 atoms. Found 1 (5 requested) and removed 2 (2 requested) atoms. Cycle 45: After refmac, R = 0.2991 (Rfree = 0.000) for 1209 atoms. Found 2 (5 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.43 3.08 Search for helices and strands: 0 residues in 0 chains, 1246 seeds are put forward Round 1: 48 peptides, 9 chains. Longest chain 8 peptides. Score 0.287 Round 2: 66 peptides, 13 chains. Longest chain 8 peptides. Score 0.294 Round 3: 76 peptides, 14 chains. Longest chain 8 peptides. Score 0.341 Round 4: 71 peptides, 14 chains. Longest chain 8 peptides. Score 0.300 Round 5: 78 peptides, 15 chains. Longest chain 9 peptides. Score 0.323 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 14, Residues 62, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence Sequence coverage is 9 % Consider running further cycles of model building using 2oh3-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 1947 reflections ( 97.30 % complete ) and 2691 restraints for refining 1206 atoms. 2432 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3229 (Rfree = 0.000) for 1206 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 47: After refmac, R = 0.3148 (Rfree = 0.000) for 1202 atoms. Found 0 (5 requested) and removed 0 (2 requested) atoms. Cycle 48: After refmac, R = 0.3085 (Rfree = 0.000) for 1202 atoms. Found 0 (5 requested) and removed 1 (2 requested) atoms. Cycle 49: After refmac, R = 0.3044 (Rfree = 0.000) for 1201 atoms. TimeTaking 24.15