Sun 23 Dec 22:22:43 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 2i9w-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2i9w-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2i9w-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2i9w-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/2i9w-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2i9w-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 22:22:53 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/2i9w-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2i9w-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 120 and 0 Target number of residues in the AU: 120 Target solvent content: 0.6578 Checking the provided sequence file Detected sequence length: 184 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 184 Adjusted target solvent content: 0.48 Input MTZ file: 2i9w-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: 19 Cell parameters: 41.450 54.640 83.800 90.000 90.000 90.000 Input sequence file: 2i9w-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 1472 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: 45.770 3.801 Wilson plot Bfac: 81.97 2065 reflections ( 99.42 % complete ) and 0 restraints for refining 1628 atoms. Observations/parameters ratio is 0.32 ------------------------------------------------------ Starting model: R = 0.3621 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3776 (Rfree = 0.000) for 1628 atoms. Found 8 (8 requested) and removed 15 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.56 3.66 Search for helices and strands: 0 residues in 0 chains, 1641 seeds are put forward Round 1: 55 peptides, 13 chains. Longest chain 6 peptides. Score 0.198 Round 2: 70 peptides, 14 chains. Longest chain 9 peptides. Score 0.305 Round 3: 86 peptides, 15 chains. Longest chain 12 peptides. Score 0.407 Round 4: 91 peptides, 15 chains. Longest chain 11 peptides. Score 0.448 Round 5: 97 peptides, 15 chains. Longest chain 10 peptides. Score 0.494 Taking the results from Round 5 Chains 15, Residues 82, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2065 reflections ( 99.42 % complete ) and 3162 restraints for refining 1332 atoms. 2849 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2907 (Rfree = 0.000) for 1332 atoms. Found 7 (7 requested) and removed 13 (3 requested) atoms. Cycle 2: After refmac, R = 0.2909 (Rfree = 0.000) for 1304 atoms. Found 7 (7 requested) and removed 11 (3 requested) atoms. Cycle 3: After refmac, R = 0.3016 (Rfree = 0.000) for 1280 atoms. Found 7 (7 requested) and removed 12 (3 requested) atoms. Cycle 4: After refmac, R = 0.2975 (Rfree = 0.000) for 1262 atoms. Found 7 (7 requested) and removed 12 (3 requested) atoms. Cycle 5: After refmac, R = 0.2899 (Rfree = 0.000) for 1246 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.59 3.69 Search for helices and strands: 0 residues in 0 chains, 1286 seeds are put forward Round 1: 81 peptides, 15 chains. Longest chain 8 peptides. Score 0.365 Round 2: 98 peptides, 17 chains. Longest chain 11 peptides. Score 0.435 Round 3: 95 peptides, 15 chains. Longest chain 11 peptides. Score 0.479 Round 4: 87 peptides, 14 chains. Longest chain 16 peptides. Score 0.450 Round 5: 85 peptides, 14 chains. Longest chain 11 peptides. Score 0.434 Taking the results from Round 3 Chains 15, Residues 80, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2065 reflections ( 99.42 % complete ) and 2881 restraints for refining 1255 atoms. 2576 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3041 (Rfree = 0.000) for 1255 atoms. Found 6 (6 requested) and removed 14 (3 requested) atoms. Cycle 7: After refmac, R = 0.2735 (Rfree = 0.000) for 1230 atoms. Found 6 (6 requested) and removed 10 (3 requested) atoms. Cycle 8: After refmac, R = 0.3028 (Rfree = 0.000) for 1218 atoms. Found 6 (6 requested) and removed 11 (3 requested) atoms. Cycle 9: After refmac, R = 0.2812 (Rfree = 0.000) for 1205 atoms. Found 6 (6 requested) and removed 10 (3 requested) atoms. Cycle 10: After refmac, R = 0.2821 (Rfree = 0.000) for 1192 atoms. Found 6 (6 requested) and removed 13 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.53 3.63 Search for helices and strands: 0 residues in 0 chains, 1248 seeds are put forward Round 1: 75 peptides, 16 chains. Longest chain 8 peptides. Score 0.274 Round 2: 85 peptides, 14 chains. Longest chain 10 peptides. Score 0.434 Round 3: 74 peptides, 11 chains. Longest chain 14 peptides. Score 0.452 Round 4: 85 peptides, 14 chains. Longest chain 11 peptides. Score 0.434 Round 5: 80 peptides, 12 chains. Longest chain 10 peptides. Score 0.464 Taking the results from Round 5 Chains 12, Residues 68, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2065 reflections ( 99.42 % complete ) and 2807 restraints for refining 1228 atoms. 2547 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2927 (Rfree = 0.000) for 1228 atoms. Found 6 (6 requested) and removed 9 (3 requested) atoms. Cycle 12: After refmac, R = 0.2917 (Rfree = 0.000) for 1215 atoms. Found 6 (6 requested) and removed 15 (3 requested) atoms. Cycle 13: After refmac, R = 0.2937 (Rfree = 0.000) for 1201 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Cycle 14: After refmac, R = 0.2908 (Rfree = 0.000) for 1194 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. Cycle 15: After refmac, R = 0.2680 (Rfree = 0.000) for 1187 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.54 3.64 Search for helices and strands: 0 residues in 0 chains, 1251 seeds are put forward Round 1: 71 peptides, 14 chains. Longest chain 10 peptides. Score 0.314 Round 2: 83 peptides, 16 chains. Longest chain 10 peptides. Score 0.346 Round 3: 94 peptides, 16 chains. Longest chain 13 peptides. Score 0.438 Round 4: 94 peptides, 16 chains. Longest chain 13 peptides. Score 0.438 Round 5: 103 peptides, 15 chains. Longest chain 17 peptides. Score 0.537 Taking the results from Round 5 Chains 15, Residues 88, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2065 reflections ( 99.42 % complete ) and 2857 restraints for refining 1284 atoms. 2520 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2799 (Rfree = 0.000) for 1284 atoms. Found 7 (7 requested) and removed 12 (3 requested) atoms. Cycle 17: After refmac, R = 0.2934 (Rfree = 0.000) for 1267 atoms. Found 7 (7 requested) and removed 23 (3 requested) atoms. Cycle 18: After refmac, R = 0.3134 (Rfree = 0.000) for 1234 atoms. Found 6 (6 requested) and removed 11 (3 requested) atoms. Cycle 19: After refmac, R = 0.2921 (Rfree = 0.000) for 1223 atoms. Found 6 (6 requested) and removed 10 (3 requested) atoms. Cycle 20: After refmac, R = 0.3027 (Rfree = 0.000) for 1207 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.36 3.45 Search for helices and strands: 0 residues in 0 chains, 1289 seeds are put forward Round 1: 67 peptides, 13 chains. Longest chain 9 peptides. Score 0.316 Round 2: 69 peptides, 12 chains. Longest chain 12 peptides. Score 0.373 Round 3: 83 peptides, 14 chains. Longest chain 9 peptides. Score 0.418 Round 4: 82 peptides, 13 chains. Longest chain 15 peptides. Score 0.445 Round 5: 71 peptides, 11 chains. Longest chain 15 peptides. Score 0.427 Taking the results from Round 4 Chains 13, Residues 69, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2065 reflections ( 99.42 % complete ) and 2882 restraints for refining 1267 atoms. 2619 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3221 (Rfree = 0.000) for 1267 atoms. Found 6 (6 requested) and removed 15 (3 requested) atoms. Cycle 22: After refmac, R = 0.2937 (Rfree = 0.000) for 1240 atoms. Found 6 (6 requested) and removed 9 (3 requested) atoms. Cycle 23: After refmac, R = 0.2774 (Rfree = 0.000) for 1230 atoms. Found 6 (6 requested) and removed 9 (3 requested) atoms. Cycle 24: After refmac, R = 0.2978 (Rfree = 0.000) for 1223 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. Cycle 25: After refmac, R = 0.3028 (Rfree = 0.000) for 1217 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.44 3.53 Search for helices and strands: 0 residues in 0 chains, 1258 seeds are put forward Round 1: 50 peptides, 10 chains. Longest chain 8 peptides. Score 0.275 Round 2: 62 peptides, 12 chains. Longest chain 9 peptides. Score 0.309 Round 3: 60 peptides, 10 chains. Longest chain 11 peptides. Score 0.370 Round 4: 57 peptides, 8 chains. Longest chain 12 peptides. Score 0.423 Round 5: 64 peptides, 11 chains. Longest chain 9 peptides. Score 0.367 Taking the results from Round 4 Chains 8, Residues 49, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2065 reflections ( 99.42 % complete ) and 2865 restraints for refining 1222 atoms. 2677 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3195 (Rfree = 0.000) for 1222 atoms. Found 6 (6 requested) and removed 8 (3 requested) atoms. Cycle 27: After refmac, R = 0.3109 (Rfree = 0.000) for 1214 atoms. Found 6 (6 requested) and removed 11 (3 requested) atoms. Cycle 28: After refmac, R = 0.3052 (Rfree = 0.000) for 1203 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Cycle 29: After refmac, R = 0.2980 (Rfree = 0.000) for 1201 atoms. Found 6 (6 requested) and removed 8 (3 requested) atoms. Cycle 30: After refmac, R = 0.2966 (Rfree = 0.000) for 1194 atoms. Found 6 (6 requested) and removed 8 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.65 3.75 Search for helices and strands: 0 residues in 0 chains, 1228 seeds are put forward Round 1: 49 peptides, 8 chains. Longest chain 12 peptides. Score 0.351 Round 2: 66 peptides, 10 chains. Longest chain 21 peptides. Score 0.423 Round 3: 61 peptides, 8 chains. Longest chain 22 peptides. Score 0.457 Round 4: 63 peptides, 10 chains. Longest chain 14 peptides. Score 0.397 Round 5: 65 peptides, 10 chains. Longest chain 14 peptides. Score 0.414 Taking the results from Round 3 Chains 8, Residues 53, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2065 reflections ( 99.42 % complete ) and 2526 restraints for refining 1160 atoms. 2322 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2972 (Rfree = 0.000) for 1160 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. Cycle 32: After refmac, R = 0.2601 (Rfree = 0.000) for 1153 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Cycle 33: After refmac, R = 0.2727 (Rfree = 0.000) for 1152 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Cycle 34: After refmac, R = 0.2706 (Rfree = 0.000) for 1150 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Cycle 35: After refmac, R = 0.2745 (Rfree = 0.000) for 1150 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.50 3.59 Search for helices and strands: 0 residues in 0 chains, 1187 seeds are put forward Round 1: 43 peptides, 9 chains. Longest chain 9 peptides. Score 0.246 Round 2: 60 peptides, 11 chains. Longest chain 10 peptides. Score 0.330 Round 3: 65 peptides, 11 chains. Longest chain 10 peptides. Score 0.376 Round 4: 76 peptides, 14 chains. Longest chain 10 peptides. Score 0.359 Round 5: 68 peptides, 12 chains. Longest chain 10 peptides. Score 0.364 Taking the results from Round 3 Chains 11, Residues 54, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2065 reflections ( 99.42 % complete ) and 2408 restraints for refining 1119 atoms. 2203 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2836 (Rfree = 0.000) for 1119 atoms. Found 6 (6 requested) and removed 3 (3 requested) atoms. Cycle 37: After refmac, R = 0.2703 (Rfree = 0.000) for 1115 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Cycle 38: After refmac, R = 0.2282 (Rfree = 0.000) for 1106 atoms. Found 6 (6 requested) and removed 3 (3 requested) atoms. Cycle 39: After refmac, R = 0.2286 (Rfree = 0.000) for 1105 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. Cycle 40: After refmac, R = 0.2377 (Rfree = 0.000) for 1104 atoms. Found 6 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.54 3.64 Search for helices and strands: 0 residues in 0 chains, 1141 seeds are put forward Round 1: 54 peptides, 12 chains. Longest chain 9 peptides. Score 0.230 Round 2: 65 peptides, 14 chains. Longest chain 10 peptides. Score 0.257 Round 3: 60 peptides, 13 chains. Longest chain 7 peptides. Score 0.249 Round 4: 69 peptides, 13 chains. Longest chain 11 peptides. Score 0.334 Round 5: 77 peptides, 14 chains. Longest chain 11 peptides. Score 0.367 Taking the results from Round 5 Chains 14, Residues 63, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2065 reflections ( 99.42 % complete ) and 2308 restraints for refining 1083 atoms. 2070 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2609 (Rfree = 0.000) for 1083 atoms. Found 4 (5 requested) and removed 5 (2 requested) atoms. Cycle 42: After refmac, R = 0.2692 (Rfree = 0.000) for 1073 atoms. Found 5 (5 requested) and removed 6 (2 requested) atoms. Cycle 43: After refmac, R = 0.2551 (Rfree = 0.000) for 1070 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. Cycle 44: After refmac, R = 0.2804 (Rfree = 0.000) for 1072 atoms. Found 5 (5 requested) and removed 2 (2 requested) atoms. Cycle 45: After refmac, R = 0.2596 (Rfree = 0.000) for 1072 atoms. Found 5 (5 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.50 3.59 Search for helices and strands: 0 residues in 0 chains, 1105 seeds are put forward Round 1: 51 peptides, 11 chains. Longest chain 8 peptides. Score 0.242 Round 2: 59 peptides, 10 chains. Longest chain 10 peptides. Score 0.361 Round 3: 59 peptides, 10 chains. Longest chain 11 peptides. Score 0.361 Round 4: 51 peptides, 11 chains. Longest chain 7 peptides. Score 0.242 Round 5: 59 peptides, 10 chains. Longest chain 11 peptides. Score 0.361 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 10, Residues 49, 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 2i9w-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2065 reflections ( 99.42 % complete ) and 2332 restraints for refining 1073 atoms. 2146 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2890 (Rfree = 0.000) for 1073 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 47: After refmac, R = 0.2724 (Rfree = 0.000) for 1063 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 48: After refmac, R = 0.2844 (Rfree = 0.000) for 1053 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 49: After refmac, R = 0.2700 (Rfree = 0.000) for 1048 atoms. TimeTaking 25.32