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 2hh6-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2hh6-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2hh6-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hh6-3.6-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/2hh6-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hh6-3.6-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/2hh6-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hh6-3.6-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 191 and 0 Target number of residues in the AU: 191 Target solvent content: 0.6451 Checking the provided sequence file Detected sequence length: 113 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 226 Adjusted target solvent content: 0.58 Input MTZ file: 2hh6-3.6-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: 179 Cell parameters: 93.536 93.536 115.318 90.000 90.000 120.000 Input sequence file: 2hh6-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 1808 target number of atoms Had to go as low as 0.65 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: 81.005 3.600 Wilson plot Bfac: 75.07 3758 reflections ( 99.55 % complete ) and 0 restraints for refining 1990 atoms. Observations/parameters ratio is 0.47 ------------------------------------------------------ Starting model: R = 0.3514 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3841 (Rfree = 0.000) for 1990 atoms. Found 12 (12 requested) and removed 52 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.55 3.19 Search for helices and strands: 0 residues in 0 chains, 1973 seeds are put forward NCS extension: 0 residues added, 1973 seeds are put forward Round 1: 59 peptides, 12 chains. Longest chain 7 peptides. Score 0.252 Round 2: 79 peptides, 14 chains. Longest chain 10 peptides. Score 0.327 Round 3: 76 peptides, 11 chains. Longest chain 13 peptides. Score 0.391 Round 4: 81 peptides, 11 chains. Longest chain 14 peptides. Score 0.420 Round 5: 86 peptides, 12 chains. Longest chain 15 peptides. Score 0.423 Taking the results from Round 5 Chains 12, Residues 74, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3758 reflections ( 99.55 % complete ) and 3651 restraints for refining 1495 atoms. 3367 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3465 (Rfree = 0.000) for 1495 atoms. Found 9 (9 requested) and removed 39 (4 requested) atoms. Cycle 2: After refmac, R = 0.3366 (Rfree = 0.000) for 1423 atoms. Found 9 (9 requested) and removed 21 (4 requested) atoms. Cycle 3: After refmac, R = 0.3538 (Rfree = 0.000) for 1392 atoms. Found 9 (9 requested) and removed 17 (4 requested) atoms. Cycle 4: After refmac, R = 0.3353 (Rfree = 0.000) for 1356 atoms. Found 8 (8 requested) and removed 18 (4 requested) atoms. Cycle 5: After refmac, R = 0.3218 (Rfree = 0.000) for 1337 atoms. Found 8 (8 requested) and removed 17 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 4.02 3.61 Search for helices and strands: 0 residues in 0 chains, 1391 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 1405 seeds are put forward Round 1: 75 peptides, 14 chains. Longest chain 8 peptides. Score 0.302 Round 2: 83 peptides, 13 chains. Longest chain 12 peptides. Score 0.379 Round 3: 94 peptides, 14 chains. Longest chain 15 peptides. Score 0.416 Round 4: 84 peptides, 13 chains. Longest chain 13 peptides. Score 0.385 Round 5: 88 peptides, 11 chains. Longest chain 18 peptides. Score 0.459 Taking the results from Round 5 Chains 11, Residues 77, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3758 reflections ( 99.55 % complete ) and 2957 restraints for refining 1304 atoms. 2660 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3108 (Rfree = 0.000) for 1304 atoms. Found 8 (8 requested) and removed 17 (4 requested) atoms. Cycle 7: After refmac, R = 0.3189 (Rfree = 0.000) for 1276 atoms. Found 8 (8 requested) and removed 16 (4 requested) atoms. Cycle 8: After refmac, R = 0.3098 (Rfree = 0.000) for 1260 atoms. Found 6 (8 requested) and removed 9 (4 requested) atoms. Cycle 9: After refmac, R = 0.3216 (Rfree = 0.000) for 1243 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. Cycle 10: After refmac, R = 0.3226 (Rfree = 0.000) for 1225 atoms. Found 7 (7 requested) and removed 15 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 4.51 4.05 Search for helices and strands: 0 residues in 0 chains, 1303 seeds are put forward NCS extension: 0 residues added, 1303 seeds are put forward Round 1: 86 peptides, 15 chains. Longest chain 10 peptides. Score 0.343 Round 2: 97 peptides, 16 chains. Longest chain 11 peptides. Score 0.383 Round 3: 100 peptides, 14 chains. Longest chain 14 peptides. Score 0.449 Round 4: 105 peptides, 15 chains. Longest chain 15 peptides. Score 0.452 Round 5: 108 peptides, 14 chains. Longest chain 22 peptides. Score 0.491 Taking the results from Round 5 Chains 14, Residues 94, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 3758 reflections ( 99.55 % complete ) and 2643 restraints for refining 1296 atoms. 2260 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3140 (Rfree = 0.000) for 1296 atoms. Found 8 (8 requested) and removed 33 (4 requested) atoms. Cycle 12: After refmac, R = 0.2962 (Rfree = 0.000) for 1257 atoms. Found 6 (8 requested) and removed 11 (4 requested) atoms. Cycle 13: After refmac, R = 0.2895 (Rfree = 0.000) for 1239 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 14: After refmac, R = 0.2869 (Rfree = 0.000) for 1231 atoms. Found 7 (7 requested) and removed 12 (3 requested) atoms. Cycle 15: After refmac, R = 0.2837 (Rfree = 0.000) for 1224 atoms. Found 7 (7 requested) and removed 11 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 4.31 3.87 Search for helices and strands: 0 residues in 0 chains, 1262 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 1282 seeds are put forward Round 1: 79 peptides, 16 chains. Longest chain 7 peptides. Score 0.272 Round 2: 82 peptides, 13 chains. Longest chain 10 peptides. Score 0.373 Round 3: 92 peptides, 13 chains. Longest chain 14 peptides. Score 0.430 Round 4: 87 peptides, 14 chains. Longest chain 9 peptides. Score 0.376 Round 5: 93 peptides, 14 chains. Longest chain 14 peptides. Score 0.411 Taking the results from Round 3 Chains 13, Residues 79, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3758 reflections ( 99.55 % complete ) and 2936 restraints for refining 1345 atoms. 2633 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3151 (Rfree = 0.000) for 1345 atoms. Found 8 (8 requested) and removed 32 (4 requested) atoms. Cycle 17: After refmac, R = 0.3069 (Rfree = 0.000) for 1301 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. Cycle 18: After refmac, R = 0.2968 (Rfree = 0.000) for 1284 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. Cycle 19: After refmac, R = 0.3123 (Rfree = 0.000) for 1277 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. Cycle 20: After refmac, R = 0.3079 (Rfree = 0.000) for 1262 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 4.33 3.89 Search for helices and strands: 0 residues in 0 chains, 1320 seeds are put forward NCS extension: 6 residues added (0 deleted due to clashes), 1326 seeds are put forward Round 1: 81 peptides, 15 chains. Longest chain 8 peptides. Score 0.312 Round 2: 85 peptides, 15 chains. Longest chain 11 peptides. Score 0.337 Round 3: 95 peptides, 14 chains. Longest chain 16 peptides. Score 0.422 Round 4: 78 peptides, 11 chains. Longest chain 12 peptides. Score 0.403 Round 5: 87 peptides, 12 chains. Longest chain 18 peptides. Score 0.428 Taking the results from Round 5 Chains 12, Residues 75, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3758 reflections ( 99.55 % complete ) and 3109 restraints for refining 1368 atoms. 2821 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3211 (Rfree = 0.000) for 1368 atoms. Found 8 (8 requested) and removed 24 (4 requested) atoms. Cycle 22: After refmac, R = 0.3103 (Rfree = 0.000) for 1327 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. Cycle 23: After refmac, R = 0.3006 (Rfree = 0.000) for 1310 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. Cycle 24: After refmac, R = 0.2976 (Rfree = 0.000) for 1297 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 25: After refmac, R = 0.2989 (Rfree = 0.000) for 1288 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.75 3.37 Search for helices and strands: 0 residues in 0 chains, 1370 seeds are put forward NCS extension: 35 residues added (1 deleted due to clashes), 1405 seeds are put forward Round 1: 72 peptides, 16 chains. Longest chain 6 peptides. Score 0.225 Round 2: 89 peptides, 16 chains. Longest chain 11 peptides. Score 0.335 Round 3: 90 peptides, 16 chains. Longest chain 9 peptides. Score 0.341 Round 4: 94 peptides, 15 chains. Longest chain 14 peptides. Score 0.391 Round 5: 98 peptides, 16 chains. Longest chain 11 peptides. Score 0.388 Taking the results from Round 4 Chains 15, Residues 79, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3758 reflections ( 99.55 % complete ) and 3242 restraints for refining 1406 atoms. 2941 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2990 (Rfree = 0.000) for 1406 atoms. Found 6 (9 requested) and removed 8 (4 requested) atoms. Cycle 27: After refmac, R = 0.3007 (Rfree = 0.000) for 1377 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Cycle 28: After refmac, R = 0.3099 (Rfree = 0.000) for 1364 atoms. Found 6 (8 requested) and removed 12 (4 requested) atoms. Cycle 29: After refmac, R = 0.3220 (Rfree = 0.000) for 1347 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. Cycle 30: After refmac, R = 0.3187 (Rfree = 0.000) for 1343 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.66 3.29 Search for helices and strands: 0 residues in 0 chains, 1383 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 1400 seeds are put forward Round 1: 76 peptides, 15 chains. Longest chain 12 peptides. Score 0.280 Round 2: 79 peptides, 14 chains. Longest chain 9 peptides. Score 0.327 Round 3: 95 peptides, 15 chains. Longest chain 12 peptides. Score 0.397 Round 4: 91 peptides, 11 chains. Longest chain 19 peptides. Score 0.475 Round 5: 85 peptides, 13 chains. Longest chain 12 peptides. Score 0.391 Taking the results from Round 4 Chains 11, Residues 80, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3758 reflections ( 99.55 % complete ) and 3169 restraints for refining 1403 atoms. 2860 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3357 (Rfree = 0.000) for 1403 atoms. Found 9 (9 requested) and removed 17 (4 requested) atoms. Cycle 32: After refmac, R = 0.3417 (Rfree = 0.000) for 1380 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 33: After refmac, R = 0.3075 (Rfree = 0.000) for 1357 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. Cycle 34: After refmac, R = 0.3264 (Rfree = 0.000) for 1350 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. Cycle 35: After refmac, R = 0.3347 (Rfree = 0.000) for 1342 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.57 3.21 Search for helices and strands: 0 residues in 0 chains, 1392 seeds are put forward NCS extension: 39 residues added (3 deleted due to clashes), 1431 seeds are put forward Round 1: 81 peptides, 17 chains. Longest chain 8 peptides. Score 0.257 Round 2: 86 peptides, 16 chains. Longest chain 10 peptides. Score 0.317 Round 3: 88 peptides, 15 chains. Longest chain 11 peptides. Score 0.356 Round 4: 86 peptides, 14 chains. Longest chain 9 peptides. Score 0.370 Round 5: 98 peptides, 17 chains. Longest chain 9 peptides. Score 0.363 Taking the results from Round 4 Chains 14, Residues 72, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3758 reflections ( 99.55 % complete ) and 3210 restraints for refining 1386 atoms. 2936 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3684 (Rfree = 0.000) for 1386 atoms. Found 8 (8 requested) and removed 39 (4 requested) atoms. Cycle 37: After refmac, R = 0.3330 (Rfree = 0.000) for 1338 atoms. Found 8 (8 requested) and removed 14 (4 requested) atoms. Cycle 38: After refmac, R = 0.3589 (Rfree = 0.000) for 1316 atoms. Found 8 (8 requested) and removed 17 (4 requested) atoms. Cycle 39: After refmac, R = 0.3513 (Rfree = 0.000) for 1296 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. Cycle 40: After refmac, R = 0.3478 (Rfree = 0.000) for 1280 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.57 3.21 Search for helices and strands: 0 residues in 0 chains, 1336 seeds are put forward NCS extension: 0 residues added, 1336 seeds are put forward Round 1: 84 peptides, 18 chains. Longest chain 8 peptides. Score 0.249 Round 2: 89 peptides, 17 chains. Longest chain 14 peptides. Score 0.309 Round 3: 96 peptides, 16 chains. Longest chain 16 peptides. Score 0.377 Round 4: 94 peptides, 16 chains. Longest chain 10 peptides. Score 0.365 Round 5: 94 peptides, 17 chains. Longest chain 10 peptides. Score 0.339 Taking the results from Round 3 Chains 18, Residues 80, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 3758 reflections ( 99.55 % complete ) and 2811 restraints for refining 1346 atoms. 2457 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3395 (Rfree = 0.000) for 1346 atoms. Found 8 (8 requested) and removed 16 (4 requested) atoms. Cycle 42: After refmac, R = 0.3475 (Rfree = 0.000) for 1322 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 43: After refmac, R = 0.3462 (Rfree = 0.000) for 1300 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. Cycle 44: After refmac, R = 0.3523 (Rfree = 0.000) for 1291 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. Cycle 45: After refmac, R = 0.3493 (Rfree = 0.000) for 1278 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.86 3.47 Search for helices and strands: 0 residues in 0 chains, 1331 seeds are put forward NCS extension: 8 residues added (0 deleted due to clashes), 1339 seeds are put forward Round 1: 62 peptides, 13 chains. Longest chain 7 peptides. Score 0.243 Round 2: 84 peptides, 11 chains. Longest chain 15 peptides. Score 0.437 Round 3: 86 peptides, 14 chains. Longest chain 12 peptides. Score 0.370 Round 4: 91 peptides, 16 chains. Longest chain 15 peptides. Score 0.347 Round 5: 83 peptides, 17 chains. Longest chain 11 peptides. Score 0.270 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 12, Residues 73, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence Sequence coverage is 14 % Consider running further cycles of model building using 2hh6-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3758 reflections ( 99.55 % complete ) and 2594 restraints for refining 1274 atoms. 2261 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3613 (Rfree = 0.000) for 1274 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.3531 (Rfree = 0.000) for 1259 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.3571 (Rfree = 0.000) for 1245 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.3609 (Rfree = 0.000) for 1233 atoms. TimeTaking 32.75