Mon 24 Dec 00:50:57 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1o6a-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1o6a-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1o6a-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1o6a-3.8-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/1o6a-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1o6a-3.8-parrot-mrncs ############### 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 ============================================================ Mon 24 Dec 00:51:02 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/mrncs/ArpWArp/wArpResults/WorkingDir/1o6a-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1o6a-3.8-parrot-mrncs/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 135 and 0 Target number of residues in the AU: 135 Target solvent content: 0.6607 Checking the provided sequence file Detected sequence length: 96 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 192 Adjusted target solvent content: 0.52 Input MTZ file: 1o6a-3.8-parrot-mrncs.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: 92 Cell parameters: 61.652 61.652 113.295 90.000 90.000 90.000 Input sequence file: 1o6a-3.8-parrot-mrncs.fasta_lf Building free atoms model in initial map for 1536 target number of atoms Had to go as low as 0.70 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: 41.713 3.801 Wilson plot Bfac: 84.88 2409 reflections ( 99.83 % complete ) and 0 restraints for refining 1706 atoms. Observations/parameters ratio is 0.35 ------------------------------------------------------ Starting model: R = 0.4316 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.4329 (Rfree = 0.000) for 1706 atoms. Found 9 (9 requested) and removed 41 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.62 3.52 Search for helices and strands: 0 residues in 0 chains, 1697 seeds are put forward NCS extension: 0 residues added, 1697 seeds are put forward Round 1: 70 peptides, 15 chains. Longest chain 8 peptides. Score 0.257 Round 2: 89 peptides, 15 chains. Longest chain 11 peptides. Score 0.409 Round 3: 87 peptides, 14 chains. Longest chain 11 peptides. Score 0.426 Round 4: 96 peptides, 15 chains. Longest chain 13 peptides. Score 0.459 Round 5: 95 peptides, 14 chains. Longest chain 14 peptides. Score 0.483 Taking the results from Round 5 Chains 14, Residues 81, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2409 reflections ( 99.83 % complete ) and 3346 restraints for refining 1389 atoms. 3036 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3299 (Rfree = 0.000) for 1389 atoms. Found 5 (7 requested) and removed 18 (3 requested) atoms. Cycle 2: After refmac, R = 0.3049 (Rfree = 0.000) for 1342 atoms. Found 3 (7 requested) and removed 11 (3 requested) atoms. Cycle 3: After refmac, R = 0.2995 (Rfree = 0.000) for 1318 atoms. Found 0 (7 requested) and removed 8 (3 requested) atoms. Cycle 4: After refmac, R = 0.2982 (Rfree = 0.000) for 1305 atoms. Found 1 (7 requested) and removed 7 (3 requested) atoms. Cycle 5: After refmac, R = 0.2976 (Rfree = 0.000) for 1298 atoms. Found 1 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.61 3.52 Search for helices and strands: 0 residues in 0 chains, 1326 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 1346 seeds are put forward Round 1: 81 peptides, 16 chains. Longest chain 9 peptides. Score 0.314 Round 2: 91 peptides, 14 chains. Longest chain 17 peptides. Score 0.455 Round 3: 98 peptides, 13 chains. Longest chain 17 peptides. Score 0.532 Round 4: 95 peptides, 17 chains. Longest chain 12 peptides. Score 0.390 Round 5: 102 peptides, 16 chains. Longest chain 14 peptides. Score 0.471 Taking the results from Round 3 Chains 13, Residues 85, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2409 reflections ( 99.83 % complete ) and 2890 restraints for refining 1292 atoms. 2563 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2943 (Rfree = 0.000) for 1292 atoms. Found 0 (7 requested) and removed 16 (3 requested) atoms. Cycle 7: After refmac, R = 0.3034 (Rfree = 0.000) for 1268 atoms. Found 4 (7 requested) and removed 11 (3 requested) atoms. Cycle 8: After refmac, R = 0.3260 (Rfree = 0.000) for 1247 atoms. Found 6 (6 requested) and removed 13 (3 requested) atoms. Cycle 9: After refmac, R = 0.3126 (Rfree = 0.000) for 1233 atoms. Found 6 (6 requested) and removed 12 (3 requested) atoms. Cycle 10: After refmac, R = 0.2944 (Rfree = 0.000) for 1220 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.58 3.49 Search for helices and strands: 0 residues in 0 chains, 1282 seeds are put forward NCS extension: 24 residues added (3 deleted due to clashes), 1306 seeds are put forward Round 1: 88 peptides, 15 chains. Longest chain 12 peptides. Score 0.402 Round 2: 88 peptides, 15 chains. Longest chain 12 peptides. Score 0.402 Round 3: 104 peptides, 18 chains. Longest chain 12 peptides. Score 0.424 Round 4: 109 peptides, 18 chains. Longest chain 10 peptides. Score 0.459 Round 5: 97 peptides, 16 chains. Longest chain 9 peptides. Score 0.436 Taking the results from Round 4 Chains 18, Residues 91, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2409 reflections ( 99.83 % complete ) and 2925 restraints for refining 1314 atoms. 2579 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3017 (Rfree = 0.000) for 1314 atoms. Found 7 (7 requested) and removed 20 (3 requested) atoms. Cycle 12: After refmac, R = 0.2887 (Rfree = 0.000) for 1284 atoms. Found 0 (7 requested) and removed 7 (3 requested) atoms. Cycle 13: After refmac, R = 0.2957 (Rfree = 0.000) for 1264 atoms. Found 6 (7 requested) and removed 13 (3 requested) atoms. Cycle 14: After refmac, R = 0.2746 (Rfree = 0.000) for 1251 atoms. Found 2 (6 requested) and removed 6 (3 requested) atoms. Cycle 15: After refmac, R = 0.2691 (Rfree = 0.000) for 1242 atoms. Found 2 (6 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.62 3.52 Search for helices and strands: 0 residues in 0 chains, 1303 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 1314 seeds are put forward Round 1: 74 peptides, 13 chains. Longest chain 12 peptides. Score 0.361 Round 2: 96 peptides, 16 chains. Longest chain 14 peptides. Score 0.429 Round 3: 87 peptides, 12 chains. Longest chain 13 peptides. Score 0.489 Round 4: 84 peptides, 14 chains. Longest chain 10 peptides. Score 0.404 Round 5: 85 peptides, 14 chains. Longest chain 10 peptides. Score 0.412 Taking the results from Round 3 Chains 12, Residues 75, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2409 reflections ( 99.83 % complete ) and 2983 restraints for refining 1324 atoms. 2695 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3123 (Rfree = 0.000) for 1324 atoms. Found 7 (7 requested) and removed 20 (3 requested) atoms. Cycle 17: After refmac, R = 0.3063 (Rfree = 0.000) for 1301 atoms. Found 7 (7 requested) and removed 9 (3 requested) atoms. Cycle 18: After refmac, R = 0.3110 (Rfree = 0.000) for 1286 atoms. Found 7 (7 requested) and removed 10 (3 requested) atoms. Cycle 19: After refmac, R = 0.2896 (Rfree = 0.000) for 1275 atoms. Found 7 (7 requested) and removed 11 (3 requested) atoms. Cycle 20: After refmac, R = 0.3034 (Rfree = 0.000) for 1269 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.63 3.53 Search for helices and strands: 0 residues in 0 chains, 1324 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 1344 seeds are put forward Round 1: 75 peptides, 14 chains. Longest chain 10 peptides. Score 0.334 Round 2: 79 peptides, 12 chains. Longest chain 10 peptides. Score 0.432 Round 3: 81 peptides, 13 chains. Longest chain 12 peptides. Score 0.414 Round 4: 81 peptides, 10 chains. Longest chain 15 peptides. Score 0.510 Round 5: 83 peptides, 13 chains. Longest chain 15 peptides. Score 0.429 Taking the results from Round 4 Chains 10, Residues 71, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2409 reflections ( 99.83 % complete ) and 3084 restraints for refining 1349 atoms. 2810 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2981 (Rfree = 0.000) for 1349 atoms. Found 7 (7 requested) and removed 51 (3 requested) atoms. Cycle 22: After refmac, R = 0.3041 (Rfree = 0.000) for 1296 atoms. Found 7 (7 requested) and removed 17 (3 requested) atoms. Cycle 23: After refmac, R = 0.3166 (Rfree = 0.000) for 1274 atoms. Found 7 (7 requested) and removed 21 (3 requested) atoms. Cycle 24: After refmac, R = 0.3213 (Rfree = 0.000) for 1249 atoms. Found 6 (6 requested) and removed 16 (3 requested) atoms. Cycle 25: After refmac, R = 0.2955 (Rfree = 0.000) for 1236 atoms. Found 6 (6 requested) and removed 9 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.68 3.58 Search for helices and strands: 0 residues in 0 chains, 1280 seeds are put forward NCS extension: 21 residues added (2 deleted due to clashes), 1301 seeds are put forward Round 1: 52 peptides, 11 chains. Longest chain 6 peptides. Score 0.245 Round 2: 63 peptides, 12 chains. Longest chain 7 peptides. Score 0.306 Round 3: 73 peptides, 13 chains. Longest chain 8 peptides. Score 0.353 Round 4: 69 peptides, 11 chains. Longest chain 10 peptides. Score 0.390 Round 5: 71 peptides, 13 chains. Longest chain 8 peptides. Score 0.336 Taking the results from Round 4 Chains 11, Residues 58, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2409 reflections ( 99.83 % complete ) and 2893 restraints for refining 1256 atoms. 2672 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3135 (Rfree = 0.000) for 1256 atoms. Found 5 (6 requested) and removed 22 (3 requested) atoms. Cycle 27: After refmac, R = 0.2948 (Rfree = 0.000) for 1228 atoms. Found 3 (6 requested) and removed 13 (3 requested) atoms. Cycle 28: After refmac, R = 0.2917 (Rfree = 0.000) for 1215 atoms. Found 2 (6 requested) and removed 10 (3 requested) atoms. Cycle 29: After refmac, R = 0.2891 (Rfree = 0.000) for 1205 atoms. Found 1 (6 requested) and removed 7 (3 requested) atoms. Cycle 30: After refmac, R = 0.2891 (Rfree = 0.000) for 1198 atoms. Found 2 (6 requested) and removed 10 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.72 3.62 Search for helices and strands: 0 residues in 0 chains, 1212 seeds are put forward NCS extension: 0 residues added, 1212 seeds are put forward Round 1: 59 peptides, 12 chains. Longest chain 7 peptides. Score 0.271 Round 2: 57 peptides, 10 chains. Longest chain 7 peptides. Score 0.329 Round 3: 62 peptides, 10 chains. Longest chain 9 peptides. Score 0.370 Round 4: 71 peptides, 12 chains. Longest chain 10 peptides. Score 0.371 Round 5: 59 peptides, 10 chains. Longest chain 8 peptides. Score 0.345 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 ------------------------------------------------------ 2409 reflections ( 99.83 % complete ) and 2868 restraints for refining 1245 atoms. 2644 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3171 (Rfree = 0.000) for 1245 atoms. Found 1 (6 requested) and removed 20 (3 requested) atoms. Cycle 32: After refmac, R = 0.2960 (Rfree = 0.000) for 1222 atoms. Found 0 (6 requested) and removed 10 (3 requested) atoms. Cycle 33: After refmac, R = 0.3006 (Rfree = 0.000) for 1210 atoms. Found 1 (6 requested) and removed 4 (3 requested) atoms. Cycle 34: After refmac, R = 0.2943 (Rfree = 0.000) for 1206 atoms. Found 0 (6 requested) and removed 7 (3 requested) atoms. Cycle 35: After refmac, R = 0.2977 (Rfree = 0.000) for 1198 atoms. Found 2 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.72 3.62 Search for helices and strands: 0 residues in 0 chains, 1229 seeds are put forward NCS extension: 0 residues added, 1229 seeds are put forward Round 1: 55 peptides, 12 chains. Longest chain 7 peptides. Score 0.234 Round 2: 70 peptides, 12 chains. Longest chain 11 peptides. Score 0.363 Round 3: 78 peptides, 13 chains. Longest chain 11 peptides. Score 0.392 Round 4: 79 peptides, 14 chains. Longest chain 10 peptides. Score 0.366 Round 5: 83 peptides, 12 chains. Longest chain 15 peptides. Score 0.461 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 ------------------------------------------------------ 2409 reflections ( 99.83 % complete ) and 2832 restraints for refining 1268 atoms. 2560 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3302 (Rfree = 0.000) for 1268 atoms. Found 6 (6 requested) and removed 19 (3 requested) atoms. Cycle 37: After refmac, R = 0.3182 (Rfree = 0.000) for 1251 atoms. Found 2 (6 requested) and removed 8 (3 requested) atoms. Cycle 38: After refmac, R = 0.3060 (Rfree = 0.000) for 1244 atoms. Found 1 (6 requested) and removed 6 (3 requested) atoms. Cycle 39: After refmac, R = 0.2962 (Rfree = 0.000) for 1239 atoms. Found 0 (6 requested) and removed 8 (3 requested) atoms. Cycle 40: After refmac, R = 0.2954 (Rfree = 0.000) for 1229 atoms. Found 0 (6 requested) and removed 9 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.74 3.64 Search for helices and strands: 0 residues in 0 chains, 1239 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 1259 seeds are put forward Round 1: 55 peptides, 12 chains. Longest chain 6 peptides. Score 0.234 Round 2: 62 peptides, 11 chains. Longest chain 10 peptides. Score 0.334 Round 3: 69 peptides, 11 chains. Longest chain 11 peptides. Score 0.390 Round 4: 72 peptides, 13 chains. Longest chain 9 peptides. Score 0.345 Round 5: 61 peptides, 11 chains. Longest chain 9 peptides. Score 0.325 Taking the results from Round 3 Chains 11, Residues 58, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2409 reflections ( 99.83 % complete ) and 2819 restraints for refining 1240 atoms. 2598 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3061 (Rfree = 0.000) for 1240 atoms. Found 6 (6 requested) and removed 10 (3 requested) atoms. Cycle 42: After refmac, R = 0.2904 (Rfree = 0.000) for 1233 atoms. Found 2 (6 requested) and removed 5 (3 requested) atoms. Cycle 43: After refmac, R = 0.2891 (Rfree = 0.000) for 1226 atoms. Found 3 (6 requested) and removed 4 (3 requested) atoms. Cycle 44: After refmac, R = 0.2998 (Rfree = 0.000) for 1221 atoms. Found 1 (6 requested) and removed 6 (3 requested) atoms. Cycle 45: After refmac, R = 0.2964 (Rfree = 0.000) for 1215 atoms. Found 3 (6 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.71 3.61 Search for helices and strands: 0 residues in 0 chains, 1236 seeds are put forward NCS extension: 0 residues added, 1236 seeds are put forward Round 1: 59 peptides, 13 chains. Longest chain 6 peptides. Score 0.233 Round 2: 58 peptides, 12 chains. Longest chain 7 peptides. Score 0.262 Round 3: 57 peptides, 9 chains. Longest chain 10 peptides. Score 0.366 Round 4: 60 peptides, 9 chains. Longest chain 11 peptides. Score 0.390 Round 5: 63 peptides, 10 chains. Longest chain 10 peptides. Score 0.378 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 9, Residues 51, 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 1o6a-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2409 reflections ( 99.83 % complete ) and 2903 restraints for refining 1259 atoms. 2708 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3145 (Rfree = 0.000) for 1259 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.3075 (Rfree = 0.000) for 1249 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.3107 (Rfree = 0.000) for 1240 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.2982 (Rfree = 0.000) for 1234 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Writing output files ... TimeTaking 24.53