Starting phenix.real_space_refine on Mon Aug 25 13:22:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oor_17026/08_2025/8oor_17026.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oor_17026/08_2025/8oor_17026.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8oor_17026/08_2025/8oor_17026.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oor_17026/08_2025/8oor_17026.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8oor_17026/08_2025/8oor_17026.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oor_17026/08_2025/8oor_17026.map" } resolution = 2.87 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 15 5.49 5 Mg 1 5.21 5 S 133 5.16 5 C 17787 2.51 5 N 5035 2.21 5 O 5400 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28371 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 3432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3432 Classifications: {'peptide': 449} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 429} Chain: "B" Number of atoms: 3352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3352 Classifications: {'peptide': 438} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 419} Chain breaks: 1 Chain: "C" Number of atoms: 3511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3511 Classifications: {'peptide': 459} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 439} Chain: "D" Number of atoms: 3401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3401 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 14, 'TRANS': 426} Chain: "E" Number of atoms: 3414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3414 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 14, 'TRANS': 428} Chain breaks: 1 Chain: "F" Number of atoms: 3394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3394 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 14, 'TRANS': 424} Chain breaks: 1 Chain: "G" Number of atoms: 2935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2935 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 22, 'TRANS': 339} Chain breaks: 1 Chain: "H" Number of atoms: 283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 283 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 4, 'TRANS': 33} Chain: "I" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 873 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 8, 'TRANS': 100} Chain breaks: 1 Chain: "J" Number of atoms: 3582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3582 Classifications: {'peptide': 448} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 419} Chain breaks: 3 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.20, per 1000 atoms: 0.22 Number of scatterers: 28371 At special positions: 0 Unit cell: (132.342, 161.934, 175.908, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 133 16.00 P 15 15.00 Mg 1 11.99 O 5400 8.00 N 5035 7.00 C 17787 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.91 Conformation dependent library (CDL) restraints added in 858.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 7180 Ramachandran restraints generated. 3590 Oldfield, 0 Emsley, 3590 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6690 Finding SS restraints... Secondary structure from input PDB file: 168 helices and 32 sheets defined 46.8% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 43 through 59 Processing helix chain 'A' and resid 76 through 89 Processing helix chain 'A' and resid 100 through 103 removed outlier: 3.923A pdb=" N TYR A 103 " --> pdb=" O SER A 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 100 through 103' Processing helix chain 'A' and resid 108 through 120 removed outlier: 3.598A pdb=" N VAL A 112 " --> pdb=" O LYS A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 184 removed outlier: 3.550A pdb=" N ALA A 180 " --> pdb=" O SER A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 211 No H-bonds generated for 'chain 'A' and resid 209 through 211' Processing helix chain 'A' and resid 241 through 250 Processing helix chain 'A' and resid 256 through 263 Processing helix chain 'A' and resid 273 through 290 Processing helix chain 'A' and resid 304 through 308 Processing helix chain 'A' and resid 309 through 320 removed outlier: 3.653A pdb=" N LYS A 318 " --> pdb=" O THR A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 357 Processing helix chain 'A' and resid 368 through 384 Processing helix chain 'A' and resid 388 through 402 Processing helix chain 'A' and resid 403 through 410 Processing helix chain 'A' and resid 410 through 421 Processing helix chain 'A' and resid 427 through 438 removed outlier: 3.718A pdb=" N GLU A 436 " --> pdb=" O ALA A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 452 Processing helix chain 'A' and resid 453 through 454 No H-bonds generated for 'chain 'A' and resid 453 through 454' Processing helix chain 'A' and resid 455 through 459 removed outlier: 4.005A pdb=" N HIS A 458 " --> pdb=" O GLY A 455 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY A 459 " --> pdb=" O GLY A 456 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 455 through 459' Processing helix chain 'B' and resid 43 through 59 Processing helix chain 'B' and resid 76 through 88 Processing helix chain 'B' and resid 100 through 103 removed outlier: 3.661A pdb=" N TYR B 103 " --> pdb=" O SER B 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 100 through 103' Processing helix chain 'B' and resid 108 through 120 Processing helix chain 'B' and resid 174 through 184 Processing helix chain 'B' and resid 209 through 211 No H-bonds generated for 'chain 'B' and resid 209 through 211' Processing helix chain 'B' and resid 241 through 250 Processing helix chain 'B' and resid 252 through 256 Processing helix chain 'B' and resid 257 through 266 removed outlier: 6.761A pdb=" N GLN B 263 " --> pdb=" O MET B 260 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N LEU B 264 " --> pdb=" O MET B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 290 Processing helix chain 'B' and resid 304 through 308 Processing helix chain 'B' and resid 309 through 320 removed outlier: 3.650A pdb=" N LYS B 318 " --> pdb=" O THR B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 351 Processing helix chain 'B' and resid 352 through 357 Processing helix chain 'B' and resid 368 through 384 Processing helix chain 'B' and resid 388 through 402 removed outlier: 3.604A pdb=" N HIS B 398 " --> pdb=" O ARG B 394 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY B 399 " --> pdb=" O VAL B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 421 removed outlier: 3.674A pdb=" N GLN B 409 " --> pdb=" O ARG B 405 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU B 410 " --> pdb=" O TYR B 406 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU B 411 " --> pdb=" O CYS B 407 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ALA B 412 " --> pdb=" O LEU B 408 " (cutoff:3.500A) Proline residue: B 413 - end of helix Processing helix chain 'B' and resid 427 through 438 Processing helix chain 'B' and resid 440 through 452 Processing helix chain 'C' and resid 43 through 60 removed outlier: 3.557A pdb=" N HIS C 60 " --> pdb=" O LEU C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 89 Processing helix chain 'C' and resid 100 through 103 removed outlier: 3.556A pdb=" N TYR C 103 " --> pdb=" O SER C 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 100 through 103' Processing helix chain 'C' and resid 108 through 120 Processing helix chain 'C' and resid 174 through 176 No H-bonds generated for 'chain 'C' and resid 174 through 176' Processing helix chain 'C' and resid 177 through 185 Processing helix chain 'C' and resid 209 through 211 No H-bonds generated for 'chain 'C' and resid 209 through 211' Processing helix chain 'C' and resid 241 through 250 Processing helix chain 'C' and resid 256 through 265 Processing helix chain 'C' and resid 273 through 290 Processing helix chain 'C' and resid 304 through 308 Processing helix chain 'C' and resid 309 through 322 removed outlier: 3.913A pdb=" N LYS C 318 " --> pdb=" O THR C 314 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU C 321 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER C 322 " --> pdb=" O LYS C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 357 Processing helix chain 'C' and resid 368 through 384 Processing helix chain 'C' and resid 388 through 402 Processing helix chain 'C' and resid 403 through 410 Processing helix chain 'C' and resid 410 through 420 Processing helix chain 'C' and resid 427 through 438 removed outlier: 3.993A pdb=" N GLU C 436 " --> pdb=" O ALA C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 451 Processing helix chain 'C' and resid 452 through 454 No H-bonds generated for 'chain 'C' and resid 452 through 454' Processing helix chain 'D' and resid 49 through 66 Processing helix chain 'D' and resid 82 through 95 Processing helix chain 'D' and resid 106 through 109 removed outlier: 3.656A pdb=" N PHE D 109 " --> pdb=" O SER D 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 106 through 109' Processing helix chain 'D' and resid 114 through 126 removed outlier: 3.538A pdb=" N SER D 126 " --> pdb=" O ALA D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 184 Processing helix chain 'D' and resid 243 through 251 Processing helix chain 'D' and resid 257 through 262 Processing helix chain 'D' and resid 268 through 285 removed outlier: 3.661A pdb=" N ARG D 272 " --> pdb=" O ARG D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 303 Processing helix chain 'D' and resid 304 through 315 removed outlier: 4.190A pdb=" N ARG D 313 " --> pdb=" O SER D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 351 Processing helix chain 'D' and resid 362 through 377 Processing helix chain 'D' and resid 382 through 397 Processing helix chain 'D' and resid 397 through 415 removed outlier: 3.851A pdb=" N THR D 406 " --> pdb=" O SER D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 432 Processing helix chain 'D' and resid 434 through 444 Processing helix chain 'E' and resid 49 through 66 Processing helix chain 'E' and resid 82 through 95 Processing helix chain 'E' and resid 96 through 98 No H-bonds generated for 'chain 'E' and resid 96 through 98' Processing helix chain 'E' and resid 106 through 109 removed outlier: 3.619A pdb=" N PHE E 109 " --> pdb=" O SER E 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 106 through 109' Processing helix chain 'E' and resid 114 through 125 Processing helix chain 'E' and resid 174 through 184 Processing helix chain 'E' and resid 208 through 211 Processing helix chain 'E' and resid 243 through 250 Processing helix chain 'E' and resid 254 through 256 No H-bonds generated for 'chain 'E' and resid 254 through 256' Processing helix chain 'E' and resid 257 through 262 Processing helix chain 'E' and resid 268 through 285 removed outlier: 3.572A pdb=" N ARG E 272 " --> pdb=" O ARG E 268 " (cutoff:3.500A) Processing helix chain 'E' and resid 300 through 303 Processing helix chain 'E' and resid 304 through 315 removed outlier: 4.152A pdb=" N ARG E 313 " --> pdb=" O SER E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 346 through 351 Processing helix chain 'E' and resid 362 through 377 Processing helix chain 'E' and resid 382 through 397 Processing helix chain 'E' and resid 397 through 415 removed outlier: 4.036A pdb=" N THR E 406 " --> pdb=" O SER E 402 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR E 407 " --> pdb=" O ASN E 403 " (cutoff:3.500A) Processing helix chain 'E' and resid 421 through 432 Processing helix chain 'E' and resid 434 through 445 Processing helix chain 'F' and resid 49 through 66 Processing helix chain 'F' and resid 82 through 95 Processing helix chain 'F' and resid 106 through 109 Processing helix chain 'F' and resid 114 through 125 Processing helix chain 'F' and resid 174 through 184 Processing helix chain 'F' and resid 209 through 214 removed outlier: 4.406A pdb=" N ARG F 212 " --> pdb=" O ALA F 209 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N TYR F 214 " --> pdb=" O SER F 211 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 252 removed outlier: 4.242A pdb=" N ARG F 252 " --> pdb=" O VAL F 248 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 256 No H-bonds generated for 'chain 'F' and resid 254 through 256' Processing helix chain 'F' and resid 257 through 262 Processing helix chain 'F' and resid 268 through 285 removed outlier: 3.630A pdb=" N ARG F 272 " --> pdb=" O ARG F 268 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 303 Processing helix chain 'F' and resid 304 through 315 removed outlier: 3.778A pdb=" N ARG F 313 " --> pdb=" O SER F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 346 through 351 Processing helix chain 'F' and resid 362 through 377 Processing helix chain 'F' and resid 382 through 397 Processing helix chain 'F' and resid 397 through 415 removed outlier: 4.098A pdb=" N THR F 406 " --> pdb=" O SER F 402 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG F 415 " --> pdb=" O ILE F 411 " (cutoff:3.500A) Processing helix chain 'F' and resid 421 through 432 Processing helix chain 'F' and resid 434 through 445 Processing helix chain 'G' and resid 1223 through 1241 removed outlier: 3.725A pdb=" N GLN G1236 " --> pdb=" O SER G1232 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE G1237 " --> pdb=" O LEU G1233 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N SER G1238 " --> pdb=" O ARG G1234 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ILE G1239 " --> pdb=" O ASN G1235 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N MET G1240 " --> pdb=" O GLN G1236 " (cutoff:3.500A) Processing helix chain 'G' and resid 1257 through 1270 Processing helix chain 'G' and resid 1270 through 1275 removed outlier: 3.908A pdb=" N PHE G1274 " --> pdb=" O HIS G1270 " (cutoff:3.500A) Processing helix chain 'G' and resid 1316 through 1321 Processing helix chain 'G' and resid 1333 through 1345 removed outlier: 4.370A pdb=" N GLY G1337 " --> pdb=" O ASN G1333 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N PHE G1338 " --> pdb=" O LEU G1334 " (cutoff:3.500A) Processing helix chain 'G' and resid 1351 through 1356 Processing helix chain 'G' and resid 1357 through 1359 No H-bonds generated for 'chain 'G' and resid 1357 through 1359' Processing helix chain 'G' and resid 1365 through 1371 removed outlier: 3.709A pdb=" N ARG G1369 " --> pdb=" O THR G1366 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL G1371 " --> pdb=" O LEU G1368 " (cutoff:3.500A) Processing helix chain 'G' and resid 1374 through 1384 Processing helix chain 'G' and resid 1385 through 1393 Processing helix chain 'G' and resid 1394 through 1396 No H-bonds generated for 'chain 'G' and resid 1394 through 1396' Processing helix chain 'G' and resid 1398 through 1407 removed outlier: 3.646A pdb=" N ILE G1405 " --> pdb=" O GLY G1401 " (cutoff:3.500A) Processing helix chain 'G' and resid 1409 through 1413 Processing helix chain 'G' and resid 1417 through 1421 Processing helix chain 'G' and resid 1423 through 1428 Processing helix chain 'G' and resid 1429 through 1435 removed outlier: 4.394A pdb=" N VAL G1433 " --> pdb=" O ASN G1429 " (cutoff:3.500A) Processing helix chain 'G' and resid 1440 through 1446 Processing helix chain 'G' and resid 1447 through 1456 Processing helix chain 'G' and resid 1480 through 1492 removed outlier: 3.517A pdb=" N VAL G1484 " --> pdb=" O SER G1480 " (cutoff:3.500A) Processing helix chain 'G' and resid 1493 through 1502 Processing helix chain 'G' and resid 1504 through 1514 removed outlier: 3.523A pdb=" N GLY G1514 " --> pdb=" O GLU G1510 " (cutoff:3.500A) Processing helix chain 'G' and resid 1544 through 1551 Processing helix chain 'G' and resid 1552 through 1566 removed outlier: 3.714A pdb=" N GLU G1564 " --> pdb=" O GLU G1560 " (cutoff:3.500A) Processing helix chain 'G' and resid 1578 through 1593 removed outlier: 3.713A pdb=" N ILE G1582 " --> pdb=" O MET G1578 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASP G1583 " --> pdb=" O THR G1579 " (cutoff:3.500A) Processing helix chain 'H' and resid 468 through 475 removed outlier: 4.101A pdb=" N VAL H 473 " --> pdb=" O ALA H 470 " (cutoff:3.500A) Processing helix chain 'I' and resid 8 through 21 Processing helix chain 'I' and resid 37 through 41 removed outlier: 4.522A pdb=" N ASN I 41 " --> pdb=" O GLN I 38 " (cutoff:3.500A) Processing helix chain 'I' and resid 43 through 51 Processing helix chain 'I' and resid 190 through 199 Processing helix chain 'I' and resid 203 through 212 removed outlier: 3.624A pdb=" N ALA I 211 " --> pdb=" O GLN I 207 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG I 212 " --> pdb=" O PHE I 208 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 22 Processing helix chain 'J' and resid 42 through 52 removed outlier: 3.739A pdb=" N ARG J 46 " --> pdb=" O GLN J 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 103 through 106 Processing helix chain 'J' and resid 128 through 144 Processing helix chain 'J' and resid 165 through 179 Processing helix chain 'J' and resid 190 through 198 Processing helix chain 'J' and resid 225 through 228 Processing helix chain 'J' and resid 234 through 250 Processing helix chain 'J' and resid 259 through 271 removed outlier: 3.538A pdb=" N HIS J 265 " --> pdb=" O SER J 261 " (cutoff:3.500A) Processing helix chain 'J' and resid 276 through 281 Processing helix chain 'J' and resid 282 through 284 No H-bonds generated for 'chain 'J' and resid 282 through 284' Processing helix chain 'J' and resid 289 through 294 Processing helix chain 'J' and resid 603 through 606 Processing helix chain 'J' and resid 607 through 615 Processing helix chain 'J' and resid 623 through 628 Processing helix chain 'J' and resid 634 through 639 removed outlier: 3.616A pdb=" N VAL J 639 " --> pdb=" O GLU J 635 " (cutoff:3.500A) Processing helix chain 'J' and resid 640 through 643 Processing helix chain 'J' and resid 645 through 651 Processing helix chain 'J' and resid 656 through 667 Processing helix chain 'J' and resid 667 through 672 removed outlier: 3.603A pdb=" N SER J 671 " --> pdb=" O GLN J 667 " (cutoff:3.500A) Processing helix chain 'J' and resid 679 through 684 Processing helix chain 'J' and resid 690 through 694 Processing helix chain 'J' and resid 697 through 708 Processing helix chain 'J' and resid 726 through 737 removed outlier: 4.633A pdb=" N CYS J 737 " --> pdb=" O ALA J 733 " (cutoff:3.500A) Processing helix chain 'J' and resid 738 through 745 Processing helix chain 'J' and resid 748 through 755 Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 37 Processing sheet with id=AA2, first strand: chain 'A' and resid 94 through 98 removed outlier: 6.105A pdb=" N VAL A 67 " --> pdb=" O LEU A 330 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N SER A 332 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU A 69 " --> pdb=" O SER A 332 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N GLY A 66 " --> pdb=" O LEU A 360 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N ILE A 362 " --> pdb=" O GLY A 66 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU A 68 " --> pdb=" O ILE A 362 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 121 through 144 removed outlier: 6.730A pdb=" N VAL A 136 " --> pdb=" O LEU A 162 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU A 162 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLU A 138 " --> pdb=" O ILE A 160 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ILE A 160 " --> pdb=" O GLU A 138 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N THR A 140 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N LEU A 158 " --> pdb=" O THR A 140 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N GLU A 142 " --> pdb=" O SER A 156 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 168 through 173 current: chain 'A' and resid 200 through 207 removed outlier: 5.994A pdb=" N VAL A 222 " --> pdb=" O VAL A 204 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N ARG A 206 " --> pdb=" O VAL A 222 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 336 through 338 Processing sheet with id=AA5, first strand: chain 'B' and resid 36 through 37 Processing sheet with id=AA6, first strand: chain 'B' and resid 94 through 98 removed outlier: 6.307A pdb=" N CYS B 95 " --> pdb=" O PHE B 301 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ASP B 303 " --> pdb=" O CYS B 95 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ILE B 97 " --> pdb=" O ASP B 303 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N VAL B 67 " --> pdb=" O LEU B 330 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N SER B 332 " --> pdb=" O VAL B 67 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU B 69 " --> pdb=" O SER B 332 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 121 through 141 removed outlier: 6.050A pdb=" N GLY B 161 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N MET B 139 " --> pdb=" O LEU B 159 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LEU B 159 " --> pdb=" O MET B 139 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU B 158 " --> pdb=" O LEU B 173 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 167 through 173 current: chain 'B' and resid 200 through 207 removed outlier: 6.343A pdb=" N VAL B 222 " --> pdb=" O VAL B 204 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N ARG B 206 " --> pdb=" O VAL B 222 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 337 through 339 removed outlier: 5.748A pdb=" N LEU B 345 " --> pdb=" O ILE B 339 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 36 through 37 Processing sheet with id=AB1, first strand: chain 'C' and resid 94 through 98 removed outlier: 6.371A pdb=" N CYS C 95 " --> pdb=" O PHE C 301 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ASP C 303 " --> pdb=" O CYS C 95 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ILE C 97 " --> pdb=" O ASP C 303 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL C 67 " --> pdb=" O LEU C 330 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N SER C 332 " --> pdb=" O VAL C 67 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N LEU C 69 " --> pdb=" O SER C 332 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 121 through 143 removed outlier: 6.088A pdb=" N GLY C 161 " --> pdb=" O THR C 137 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N MET C 139 " --> pdb=" O LEU C 159 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU C 159 " --> pdb=" O MET C 139 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N THR C 157 " --> pdb=" O PRO C 141 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLU C 143 " --> pdb=" O ILE C 155 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ILE C 155 " --> pdb=" O GLU C 143 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 167 through 173 current: chain 'C' and resid 201 through 207 removed outlier: 6.613A pdb=" N VAL C 222 " --> pdb=" O VAL C 204 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N ARG C 206 " --> pdb=" O VAL C 222 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 221 through 222 current: chain 'D' and resid 156 through 163 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 168 through 173 current: chain 'D' and resid 201 through 206 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 201 through 206 current: chain 'H' and resid 456 through 461 Processing sheet with id=AB3, first strand: chain 'C' and resid 336 through 339 removed outlier: 5.900A pdb=" N LEU C 345 " --> pdb=" O ILE C 339 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 386 through 387 removed outlier: 6.856A pdb=" N GLN C 386 " --> pdb=" O VAL C 426 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'D' and resid 42 through 43 Processing sheet with id=AB6, first strand: chain 'D' and resid 100 through 104 removed outlier: 6.379A pdb=" N THR D 101 " --> pdb=" O PHE D 296 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N ASP D 298 " --> pdb=" O THR D 101 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LEU D 103 " --> pdb=" O ASP D 298 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 331 through 333 Processing sheet with id=AB8, first strand: chain 'E' and resid 42 through 43 Processing sheet with id=AB9, first strand: chain 'E' and resid 100 through 104 removed outlier: 6.874A pdb=" N ALA E 72 " --> pdb=" O VAL E 354 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N ILE E 356 " --> pdb=" O ALA E 72 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N LEU E 74 " --> pdb=" O ILE E 356 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 127 through 148 removed outlier: 5.358A pdb=" N VAL E 142 " --> pdb=" O LYS E 163 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LYS E 163 " --> pdb=" O VAL E 142 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 168 through 172 current: chain 'E' and resid 201 through 206 Processing sheet with id=AC2, first strand: chain 'E' and resid 331 through 333 Processing sheet with id=AC3, first strand: chain 'F' and resid 42 through 43 Processing sheet with id=AC4, first strand: chain 'F' and resid 100 through 104 removed outlier: 6.602A pdb=" N THR F 101 " --> pdb=" O PHE F 296 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ASP F 298 " --> pdb=" O THR F 101 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LEU F 103 " --> pdb=" O ASP F 298 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ALA F 72 " --> pdb=" O VAL F 354 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ILE F 356 " --> pdb=" O ALA F 72 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU F 74 " --> pdb=" O ILE F 356 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 127 through 147 removed outlier: 6.716A pdb=" N THR F 161 " --> pdb=" O VAL F 143 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ILE F 145 " --> pdb=" O LYS F 159 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LYS F 159 " --> pdb=" O ILE F 145 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY F 158 " --> pdb=" O MET F 173 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 168 through 173 current: chain 'F' and resid 200 through 207 removed outlier: 6.516A pdb=" N LEU F 224 " --> pdb=" O LEU F 204 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ARG F 206 " --> pdb=" O LEU F 224 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 331 through 333 Processing sheet with id=AC7, first strand: chain 'G' and resid 1283 through 1284 removed outlier: 6.314A pdb=" N PHE G1283 " --> pdb=" O SER G1470 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'G' and resid 1286 through 1287 Processing sheet with id=AC9, first strand: chain 'G' and resid 1312 through 1314 removed outlier: 6.300A pdb=" N TYR G1313 " --> pdb=" O VAL G1477 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'I' and resid 179 through 180 removed outlier: 3.706A pdb=" N TYR I 179 " --> pdb=" O TYR I 188 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 27 through 29 removed outlier: 6.446A pdb=" N TYR J 28 " --> pdb=" O GLN J 298 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 80 through 82 removed outlier: 4.355A pdb=" N ASN J 63 " --> pdb=" O THR J 159 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 97 through 101 Processing sheet with id=AD5, first strand: chain 'J' and resid 203 through 208 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 222 through 223 current: chain 'J' and resid 718 through 720 1173 hydrogen bonds defined for protein. 3339 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.28 Time building geometry restraints manager: 2.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8406 1.33 - 1.45: 4236 1.45 - 1.57: 15956 1.57 - 1.70: 19 1.70 - 1.82: 230 Bond restraints: 28847 Sorted by residual: bond pdb=" CB CYS B 407 " pdb=" SG CYS B 407 " ideal model delta sigma weight residual 1.808 1.702 0.106 3.30e-02 9.18e+02 1.04e+01 bond pdb=" CB THR D 337 " pdb=" CG2 THR D 337 " ideal model delta sigma weight residual 1.521 1.427 0.094 3.30e-02 9.18e+02 8.08e+00 bond pdb=" CB ARG G1339 " pdb=" CG ARG G1339 " ideal model delta sigma weight residual 1.520 1.446 0.074 3.00e-02 1.11e+03 6.01e+00 bond pdb=" CB ARG A 379 " pdb=" CG ARG A 379 " ideal model delta sigma weight residual 1.520 1.447 0.073 3.00e-02 1.11e+03 5.97e+00 bond pdb=" CG ARG A 118 " pdb=" CD ARG A 118 " ideal model delta sigma weight residual 1.520 1.450 0.070 3.00e-02 1.11e+03 5.41e+00 ... (remaining 28842 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.16: 38464 3.16 - 6.32: 481 6.32 - 9.48: 41 9.48 - 12.64: 5 12.64 - 15.79: 2 Bond angle restraints: 38993 Sorted by residual: angle pdb=" CA LEU B 88 " pdb=" CB LEU B 88 " pdb=" CG LEU B 88 " ideal model delta sigma weight residual 116.30 132.09 -15.79 3.50e+00 8.16e-02 2.04e+01 angle pdb=" CB ARG C 118 " pdb=" CG ARG C 118 " pdb=" CD ARG C 118 " ideal model delta sigma weight residual 111.30 121.09 -9.79 2.30e+00 1.89e-01 1.81e+01 angle pdb=" CA ARG A 334 " pdb=" CB ARG A 334 " pdb=" CG ARG A 334 " ideal model delta sigma weight residual 114.10 106.60 7.50 2.00e+00 2.50e-01 1.41e+01 angle pdb=" CA LEU B 158 " pdb=" CB LEU B 158 " pdb=" CG LEU B 158 " ideal model delta sigma weight residual 116.30 129.25 -12.95 3.50e+00 8.16e-02 1.37e+01 angle pdb=" C GLU B 87 " pdb=" N LEU B 88 " pdb=" CA LEU B 88 " ideal model delta sigma weight residual 121.18 128.14 -6.96 1.98e+00 2.55e-01 1.23e+01 ... (remaining 38988 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.57: 17375 35.57 - 71.15: 267 71.15 - 106.72: 38 106.72 - 142.29: 4 142.29 - 177.86: 3 Dihedral angle restraints: 17687 sinusoidal: 7292 harmonic: 10395 Sorted by residual: dihedral pdb=" O1B ADP A 501 " pdb=" O3A ADP A 501 " pdb=" PB ADP A 501 " pdb=" PA ADP A 501 " ideal model delta sinusoidal sigma weight residual 300.00 122.13 177.86 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O1B ADP D 501 " pdb=" O3A ADP D 501 " pdb=" PB ADP D 501 " pdb=" PA ADP D 501 " ideal model delta sinusoidal sigma weight residual 300.00 129.07 170.92 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" C5' ADP D 501 " pdb=" O5' ADP D 501 " pdb=" PA ADP D 501 " pdb=" O2A ADP D 501 " ideal model delta sinusoidal sigma weight residual 300.00 151.14 148.86 1 2.00e+01 2.50e-03 4.45e+01 ... (remaining 17684 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 2508 0.051 - 0.101: 1439 0.101 - 0.152: 405 0.152 - 0.202: 61 0.202 - 0.253: 6 Chirality restraints: 4419 Sorted by residual: chirality pdb=" CA GLU I 158 " pdb=" N GLU I 158 " pdb=" C GLU I 158 " pdb=" CB GLU I 158 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" C3' ADP F 501 " pdb=" C2' ADP F 501 " pdb=" C4' ADP F 501 " pdb=" O3' ADP F 501 " both_signs ideal model delta sigma weight residual False -2.51 -2.74 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CB ILE B 84 " pdb=" CA ILE B 84 " pdb=" CG1 ILE B 84 " pdb=" CG2 ILE B 84 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 4416 not shown) Planarity restraints: 5049 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 437 " 0.418 9.50e-02 1.11e+02 1.88e-01 2.57e+01 pdb=" NE ARG F 437 " -0.037 2.00e-02 2.50e+03 pdb=" CZ ARG F 437 " 0.031 2.00e-02 2.50e+03 pdb=" NH1 ARG F 437 " -0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG F 437 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 8 " 0.348 9.50e-02 1.11e+02 1.57e-01 1.75e+01 pdb=" NE ARG C 8 " -0.030 2.00e-02 2.50e+03 pdb=" CZ ARG C 8 " 0.024 2.00e-02 2.50e+03 pdb=" NH1 ARG C 8 " -0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG C 8 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 118 " -0.317 9.50e-02 1.11e+02 1.43e-01 1.59e+01 pdb=" NE ARG B 118 " 0.030 2.00e-02 2.50e+03 pdb=" CZ ARG B 118 " -0.029 2.00e-02 2.50e+03 pdb=" NH1 ARG B 118 " 0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG B 118 " -0.000 2.00e-02 2.50e+03 ... (remaining 5046 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 107 2.51 - 3.11: 21819 3.11 - 3.71: 43260 3.71 - 4.30: 66975 4.30 - 4.90: 109161 Nonbonded interactions: 241322 Sorted by model distance: nonbonded pdb=" O1B ATP J 801 " pdb="MG MG J 802 " model vdw 1.914 2.170 nonbonded pdb=" O1G ATP J 801 " pdb="MG MG J 802 " model vdw 2.088 2.170 nonbonded pdb=" OD2 ASP J 190 " pdb="MG MG J 802 " model vdw 2.098 2.170 nonbonded pdb=" OD1 ASP J 137 " pdb=" OH TYR J 180 " model vdw 2.139 3.040 nonbonded pdb=" O GLU E 168 " pdb=" OH TYR I 188 " model vdw 2.141 3.040 ... (remaining 241317 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 144 or resid 156 through 501)) selection = chain 'B' selection = (chain 'C' and (resid 14 through 144 or resid 156 through 501)) } ncs_group { reference = (chain 'D' and (resid 20 through 150 or resid 156 through 501)) selection = (chain 'E' and (resid 20 through 150 or resid 156 through 501)) selection = (chain 'F' and resid 20 through 501) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 23.780 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.106 28847 Z= 0.441 Angle : 0.960 15.794 38993 Z= 0.516 Chirality : 0.063 0.253 4419 Planarity : 0.012 0.188 5049 Dihedral : 14.051 177.863 10997 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.86 (0.13), residues: 3590 helix: -1.23 (0.11), residues: 1510 sheet: 0.36 (0.21), residues: 547 loop : 0.04 (0.15), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.036 0.003 ARG F 437 TYR 0.033 0.005 TYR I 179 PHE 0.041 0.004 PHE G1501 TRP 0.026 0.004 TRP G1367 HIS 0.020 0.003 HIS B 19 Details of bonding type rmsd covalent geometry : bond 0.01087 (28847) covalent geometry : angle 0.95983 (38993) hydrogen bonds : bond 0.20236 ( 1173) hydrogen bonds : angle 7.56334 ( 3339) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7180 Ramachandran restraints generated. 3590 Oldfield, 0 Emsley, 3590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7180 Ramachandran restraints generated. 3590 Oldfield, 0 Emsley, 3590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 592 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7733 (mm-30) REVERT: A 216 LEU cc_start: 0.8283 (mt) cc_final: 0.8042 (mt) REVERT: A 419 ARG cc_start: 0.7977 (ttm110) cc_final: 0.7675 (ttm170) REVERT: D 208 TYR cc_start: 0.8374 (p90) cc_final: 0.8165 (p90) REVERT: D 235 LYS cc_start: 0.8540 (tttt) cc_final: 0.8287 (ptmt) REVERT: D 237 VAL cc_start: 0.9089 (t) cc_final: 0.8879 (p) REVERT: D 299 GLU cc_start: 0.8617 (mt-10) cc_final: 0.8388 (mt-10) REVERT: F 193 SER cc_start: 0.9082 (p) cc_final: 0.8861 (m) REVERT: F 263 ASP cc_start: 0.7986 (t70) cc_final: 0.7712 (t0) REVERT: F 325 MET cc_start: 0.9042 (ptp) cc_final: 0.8835 (ptp) REVERT: F 364 ASP cc_start: 0.8240 (t0) cc_final: 0.7734 (t70) REVERT: G 1372 ASP cc_start: 0.8366 (t0) cc_final: 0.8137 (t0) REVERT: G 1479 ASP cc_start: 0.7695 (p0) cc_final: 0.7480 (p0) REVERT: G 1554 LYS cc_start: 0.9075 (mttt) cc_final: 0.7637 (tttp) REVERT: G 1557 LYS cc_start: 0.8825 (tptm) cc_final: 0.8496 (mtmt) REVERT: I 204 MET cc_start: 0.8484 (mmm) cc_final: 0.8276 (mmm) REVERT: J 174 GLU cc_start: 0.8335 (mt-10) cc_final: 0.8101 (mt-10) REVERT: J 751 TYR cc_start: 0.8421 (t80) cc_final: 0.8043 (t80) outliers start: 0 outliers final: 1 residues processed: 592 average time/residue: 0.8678 time to fit residues: 574.2264 Evaluate side-chains 312 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 311 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 130 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 0.5980 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 7.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 GLN A 248 ASN A 381 GLN A 409 GLN B 19 HIS B 263 GLN C 86 GLN C 230 HIS C 421 ASN D 24 HIS D 65 GLN D 239 HIS E 225 GLN E 359 HIS F 65 GLN F 357 ASN G1235 ASN G1345 HIS I 19 GLN I 23 HIS I 33 ASN I 202 GLN ** J 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 628 HIS J 696 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.081198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.065062 restraints weight = 54253.630| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 1.89 r_work: 0.2811 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2670 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 28847 Z= 0.134 Angle : 0.621 10.909 38993 Z= 0.317 Chirality : 0.044 0.188 4419 Planarity : 0.005 0.052 5049 Dihedral : 8.641 147.935 4060 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.69 % Allowed : 9.07 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.14), residues: 3590 helix: 0.56 (0.13), residues: 1545 sheet: 0.68 (0.20), residues: 578 loop : 0.45 (0.16), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 116 TYR 0.021 0.002 TYR A 193 PHE 0.017 0.001 PHE G1274 TRP 0.012 0.001 TRP J 129 HIS 0.007 0.001 HIS G1345 Details of bonding type rmsd covalent geometry : bond 0.00304 (28847) covalent geometry : angle 0.62143 (38993) hydrogen bonds : bond 0.04139 ( 1173) hydrogen bonds : angle 4.87380 ( 3339) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7180 Ramachandran restraints generated. 3590 Oldfield, 0 Emsley, 3590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7180 Ramachandran restraints generated. 3590 Oldfield, 0 Emsley, 3590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 409 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8396 (mttp) REVERT: A 419 ARG cc_start: 0.8150 (ttm110) cc_final: 0.7855 (ttm170) REVERT: A 442 ARG cc_start: 0.8119 (mmm-85) cc_final: 0.7914 (mtm-85) REVERT: B 60 HIS cc_start: 0.7950 (OUTLIER) cc_final: 0.7459 (m90) REVERT: B 114 MET cc_start: 0.8632 (tpt) cc_final: 0.8424 (tpp) REVERT: B 250 ARG cc_start: 0.7893 (ttt90) cc_final: 0.7449 (ttt90) REVERT: B 265 MET cc_start: 0.8812 (mmt) cc_final: 0.8401 (mmm) REVERT: B 269 MET cc_start: 0.8166 (mtm) cc_final: 0.7422 (mmt) REVERT: C 8 ARG cc_start: 0.7770 (tpm-80) cc_final: 0.7326 (tpm-80) REVERT: C 220 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.7237 (pt0) REVERT: C 433 GLU cc_start: 0.8056 (tp30) cc_final: 0.7815 (tp30) REVERT: D 61 GLU cc_start: 0.8676 (mm-30) cc_final: 0.8260 (mm-30) REVERT: D 65 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.7983 (mt0) REVERT: D 137 ILE cc_start: 0.9166 (pt) cc_final: 0.8600 (mp) REVERT: D 138 MET cc_start: 0.8010 (ttm) cc_final: 0.7748 (ttp) REVERT: D 304 ASP cc_start: 0.8101 (OUTLIER) cc_final: 0.7859 (p0) REVERT: E 135 SER cc_start: 0.8946 (OUTLIER) cc_final: 0.8719 (p) REVERT: E 148 ASP cc_start: 0.7836 (t70) cc_final: 0.7348 (p0) REVERT: E 195 ASP cc_start: 0.7600 (t0) cc_final: 0.7191 (t70) REVERT: E 217 MET cc_start: 0.8690 (mmm) cc_final: 0.8445 (mmm) REVERT: E 447 LYS cc_start: 0.8804 (mppt) cc_final: 0.8582 (mptm) REVERT: F 109 PHE cc_start: 0.8915 (m-80) cc_final: 0.8697 (m-80) REVERT: F 171 TYR cc_start: 0.9141 (m-80) cc_final: 0.8896 (m-80) REVERT: F 183 LYS cc_start: 0.9088 (mtpm) cc_final: 0.8825 (OUTLIER) REVERT: F 263 ASP cc_start: 0.8049 (t70) cc_final: 0.7760 (t0) REVERT: F 299 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8187 (mt-10) REVERT: J 94 MET cc_start: 0.8210 (mpm) cc_final: 0.8008 (mpm) REVERT: J 174 GLU cc_start: 0.8358 (mt-10) cc_final: 0.8140 (mt-10) outliers start: 51 outliers final: 6 residues processed: 443 average time/residue: 0.7695 time to fit residues: 386.3181 Evaluate side-chains 318 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 306 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain B residue 60 HIS Chi-restraints excluded: chain B residue 407 CYS Chi-restraints excluded: chain C residue 220 GLU Chi-restraints excluded: chain D residue 65 GLN Chi-restraints excluded: chain D residue 304 ASP Chi-restraints excluded: chain E residue 135 SER Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain F residue 299 GLU Chi-restraints excluded: chain J residue 288 THR Chi-restraints excluded: chain J residue 622 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 96 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 149 optimal weight: 8.9990 chunk 69 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 201 optimal weight: 0.8980 chunk 293 optimal weight: 2.9990 chunk 254 optimal weight: 0.6980 chunk 313 optimal weight: 6.9990 chunk 117 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN B 421 ASN C 168 GLN C 317 ASN D 65 GLN D 274 GLN E 65 GLN E 419 GLN F 96 GLN H 452 ASN I 19 GLN I 202 GLN J 114 HIS J 633 ASN J 722 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.080391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.064688 restraints weight = 54754.882| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 1.95 r_work: 0.2804 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28847 Z= 0.124 Angle : 0.588 15.052 38993 Z= 0.294 Chirality : 0.043 0.256 4419 Planarity : 0.004 0.052 5049 Dihedral : 8.090 137.556 4058 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.92 % Allowed : 11.23 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.14), residues: 3590 helix: 0.95 (0.13), residues: 1535 sheet: 0.74 (0.20), residues: 590 loop : 0.49 (0.16), residues: 1465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 748 TYR 0.019 0.001 TYR A 193 PHE 0.019 0.001 PHE G1274 TRP 0.010 0.001 TRP J 129 HIS 0.004 0.001 HIS B 242 Details of bonding type rmsd covalent geometry : bond 0.00285 (28847) covalent geometry : angle 0.58784 (38993) hydrogen bonds : bond 0.03823 ( 1173) hydrogen bonds : angle 4.59997 ( 3339) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7180 Ramachandran restraints generated. 3590 Oldfield, 0 Emsley, 3590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7180 Ramachandran restraints generated. 3590 Oldfield, 0 Emsley, 3590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 354 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 159 LEU cc_start: 0.9084 (tp) cc_final: 0.8771 (tp) REVERT: A 419 ARG cc_start: 0.8219 (ttm110) cc_final: 0.7938 (ttm170) REVERT: A 442 ARG cc_start: 0.8145 (mmm-85) cc_final: 0.7924 (mtm-85) REVERT: B 60 HIS cc_start: 0.7894 (OUTLIER) cc_final: 0.7412 (m90) REVERT: B 250 ARG cc_start: 0.7876 (ttt90) cc_final: 0.7382 (ttt90) REVERT: B 265 MET cc_start: 0.8847 (mmt) cc_final: 0.8494 (mmm) REVERT: B 269 MET cc_start: 0.8183 (mtm) cc_final: 0.7399 (mmt) REVERT: C 127 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7646 (mt-10) REVERT: C 433 GLU cc_start: 0.8078 (tp30) cc_final: 0.7800 (tp30) REVERT: D 61 GLU cc_start: 0.8645 (mm-30) cc_final: 0.8147 (mm-30) REVERT: D 65 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.8205 (mt0) REVERT: D 134 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7319 (tp30) REVERT: D 137 ILE cc_start: 0.9085 (pt) cc_final: 0.8576 (mp) REVERT: D 217 MET cc_start: 0.7661 (mtp) cc_final: 0.7389 (mtp) REVERT: D 234 ARG cc_start: 0.7864 (OUTLIER) cc_final: 0.7246 (mtp180) REVERT: D 304 ASP cc_start: 0.8126 (OUTLIER) cc_final: 0.7893 (p0) REVERT: E 148 ASP cc_start: 0.7826 (t70) cc_final: 0.7362 (p0) REVERT: E 183 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8149 (ttpt) REVERT: E 273 ASP cc_start: 0.8534 (OUTLIER) cc_final: 0.8246 (m-30) REVERT: E 418 LYS cc_start: 0.8624 (mmmt) cc_final: 0.8330 (tptt) REVERT: F 109 PHE cc_start: 0.8878 (m-80) cc_final: 0.8602 (m-80) REVERT: F 183 LYS cc_start: 0.9079 (mtpm) cc_final: 0.8826 (tttp) REVERT: F 263 ASP cc_start: 0.7974 (t70) cc_final: 0.7722 (t0) REVERT: G 1240 MET cc_start: 0.6687 (mpm) cc_final: 0.5572 (mtt) REVERT: I 14 GLN cc_start: 0.8830 (mm-40) cc_final: 0.7617 (mm-40) REVERT: J 174 GLU cc_start: 0.8387 (mt-10) cc_final: 0.8138 (mt-10) outliers start: 58 outliers final: 9 residues processed: 392 average time/residue: 0.7562 time to fit residues: 337.2064 Evaluate side-chains 314 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 298 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain B residue 60 HIS Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 407 CYS Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain D residue 65 GLN Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 234 ARG Chi-restraints excluded: chain D residue 304 ASP Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain E residue 273 ASP Chi-restraints excluded: chain E residue 294 VAL Chi-restraints excluded: chain G residue 1593 ASN Chi-restraints excluded: chain J residue 288 THR Chi-restraints excluded: chain J residue 622 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 313 optimal weight: 6.9990 chunk 218 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 199 optimal weight: 0.9980 chunk 203 optimal weight: 5.9990 chunk 266 optimal weight: 1.9990 chunk 210 optimal weight: 1.9990 chunk 183 optimal weight: 0.9980 chunk 325 optimal weight: 1.9990 chunk 314 optimal weight: 9.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN A 146 ASN A 421 ASN B 421 ASN C 168 GLN D 65 GLN D 328 ASN D 359 HIS E 24 HIS E 65 GLN F 394 GLN I 19 GLN I 202 GLN J 633 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.079309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.063783 restraints weight = 54268.303| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 1.87 r_work: 0.2774 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2635 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 28847 Z= 0.165 Angle : 0.616 16.367 38993 Z= 0.306 Chirality : 0.044 0.233 4419 Planarity : 0.004 0.047 5049 Dihedral : 8.068 132.406 4058 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.38 % Allowed : 12.52 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.14), residues: 3590 helix: 0.92 (0.13), residues: 1536 sheet: 0.69 (0.20), residues: 604 loop : 0.42 (0.16), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 602 TYR 0.020 0.002 TYR G1591 PHE 0.022 0.002 PHE G1274 TRP 0.011 0.001 TRP J 129 HIS 0.007 0.001 HIS D 359 Details of bonding type rmsd covalent geometry : bond 0.00395 (28847) covalent geometry : angle 0.61579 (38993) hydrogen bonds : bond 0.04039 ( 1173) hydrogen bonds : angle 4.59961 ( 3339) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7180 Ramachandran restraints generated. 3590 Oldfield, 0 Emsley, 3590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7180 Ramachandran restraints generated. 3590 Oldfield, 0 Emsley, 3590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 306 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 GLN cc_start: 0.8728 (OUTLIER) cc_final: 0.8453 (mt0) REVERT: A 159 LEU cc_start: 0.9071 (tp) cc_final: 0.8743 (tp) REVERT: A 419 ARG cc_start: 0.8160 (ttm110) cc_final: 0.7889 (ttm170) REVERT: A 442 ARG cc_start: 0.8213 (mmm-85) cc_final: 0.7948 (mtm-85) REVERT: B 60 HIS cc_start: 0.7981 (OUTLIER) cc_final: 0.7499 (m90) REVERT: B 265 MET cc_start: 0.8904 (mmt) cc_final: 0.8652 (mmm) REVERT: C 8 ARG cc_start: 0.7912 (mmm160) cc_final: 0.7643 (mmm160) REVERT: C 427 ASP cc_start: 0.8308 (t0) cc_final: 0.7935 (t70) REVERT: C 433 GLU cc_start: 0.8131 (tp30) cc_final: 0.7809 (tp30) REVERT: D 65 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.7975 (mt0) REVERT: D 134 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7427 (tp30) REVERT: D 137 ILE cc_start: 0.9085 (pt) cc_final: 0.8609 (mp) REVERT: D 217 MET cc_start: 0.7551 (mtp) cc_final: 0.7259 (mtp) REVERT: D 304 ASP cc_start: 0.8167 (OUTLIER) cc_final: 0.7896 (p0) REVERT: E 148 ASP cc_start: 0.7880 (t70) cc_final: 0.7374 (p0) REVERT: E 273 ASP cc_start: 0.8557 (OUTLIER) cc_final: 0.8265 (m-30) REVERT: E 418 LYS cc_start: 0.8601 (mmmt) cc_final: 0.8324 (tptt) REVERT: F 109 PHE cc_start: 0.8859 (m-80) cc_final: 0.8584 (m-80) REVERT: F 168 GLU cc_start: 0.8502 (tt0) cc_final: 0.8241 (tt0) REVERT: F 183 LYS cc_start: 0.9110 (OUTLIER) cc_final: 0.8839 (tttp) REVERT: F 263 ASP cc_start: 0.7925 (t70) cc_final: 0.7676 (t0) REVERT: G 1240 MET cc_start: 0.6836 (mpm) cc_final: 0.5820 (mtt) REVERT: J 174 GLU cc_start: 0.8385 (mt-10) cc_final: 0.8139 (mt-10) outliers start: 72 outliers final: 19 residues processed: 358 average time/residue: 0.7312 time to fit residues: 296.9378 Evaluate side-chains 312 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 286 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 GLN Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain B residue 60 HIS Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 407 CYS Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain D residue 65 GLN Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 304 ASP Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 273 ASP Chi-restraints excluded: chain E residue 294 VAL Chi-restraints excluded: chain E residue 407 THR Chi-restraints excluded: chain F residue 183 LYS Chi-restraints excluded: chain G residue 1593 ASN Chi-restraints excluded: chain I residue 18 GLU Chi-restraints excluded: chain I residue 166 MET Chi-restraints excluded: chain J residue 278 ASP Chi-restraints excluded: chain J residue 288 THR Chi-restraints excluded: chain J residue 622 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 172 optimal weight: 1.9990 chunk 276 optimal weight: 2.9990 chunk 161 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 chunk 287 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 36 optimal weight: 0.7980 chunk 84 optimal weight: 0.5980 chunk 249 optimal weight: 7.9990 chunk 334 optimal weight: 3.9990 chunk 341 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN A 421 ASN B 421 ASN C 237 GLN D 65 GLN D 359 HIS E 65 GLN F 301 HIS I 19 GLN I 202 GLN J 633 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.079671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.064524 restraints weight = 54094.339| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 1.75 r_work: 0.2783 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2645 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28847 Z= 0.141 Angle : 0.593 17.267 38993 Z= 0.294 Chirality : 0.043 0.243 4419 Planarity : 0.004 0.057 5049 Dihedral : 7.873 129.349 4058 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.15 % Allowed : 13.58 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.14), residues: 3590 helix: 0.98 (0.13), residues: 1544 sheet: 0.70 (0.21), residues: 601 loop : 0.36 (0.16), residues: 1445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG F 234 TYR 0.022 0.001 TYR G1591 PHE 0.024 0.001 PHE G1274 TRP 0.011 0.001 TRP J 129 HIS 0.006 0.001 HIS D 359 Details of bonding type rmsd covalent geometry : bond 0.00333 (28847) covalent geometry : angle 0.59288 (38993) hydrogen bonds : bond 0.03716 ( 1173) hydrogen bonds : angle 4.49066 ( 3339) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7180 Ramachandran restraints generated. 3590 Oldfield, 0 Emsley, 3590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7180 Ramachandran restraints generated. 3590 Oldfield, 0 Emsley, 3590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 321 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 GLN cc_start: 0.8678 (OUTLIER) cc_final: 0.8406 (mt0) REVERT: A 159 LEU cc_start: 0.9073 (tp) cc_final: 0.8734 (tp) REVERT: A 345 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8160 (tt) REVERT: A 419 ARG cc_start: 0.8115 (ttm110) cc_final: 0.7705 (ttp80) REVERT: B 60 HIS cc_start: 0.8032 (OUTLIER) cc_final: 0.7543 (m90) REVERT: B 429 GLN cc_start: 0.8685 (OUTLIER) cc_final: 0.8466 (pm20) REVERT: C 8 ARG cc_start: 0.7843 (mmm160) cc_final: 0.7604 (mmm160) REVERT: C 179 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7795 (tm-30) REVERT: C 304 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.8089 (mm-30) REVERT: C 409 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.8072 (mt0) REVERT: C 427 ASP cc_start: 0.8237 (t0) cc_final: 0.7428 (t0) REVERT: C 433 GLU cc_start: 0.8104 (tp30) cc_final: 0.7840 (tp30) REVERT: D 61 GLU cc_start: 0.8601 (mm-30) cc_final: 0.8197 (mm-30) REVERT: D 65 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.7576 (mt0) REVERT: D 134 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7575 (tp30) REVERT: D 137 ILE cc_start: 0.9064 (pt) cc_final: 0.8778 (mp) REVERT: D 217 MET cc_start: 0.7599 (mtp) cc_final: 0.7268 (mtp) REVERT: D 304 ASP cc_start: 0.8135 (OUTLIER) cc_final: 0.7893 (p0) REVERT: E 148 ASP cc_start: 0.7885 (t70) cc_final: 0.7392 (p0) REVERT: E 183 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8229 (ttpt) REVERT: E 273 ASP cc_start: 0.8510 (OUTLIER) cc_final: 0.8225 (m-30) REVERT: E 418 LYS cc_start: 0.8523 (mmmt) cc_final: 0.8273 (tptt) REVERT: F 28 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7394 (mtt90) REVERT: F 109 PHE cc_start: 0.8835 (m-80) cc_final: 0.8594 (m-80) REVERT: F 168 GLU cc_start: 0.8454 (tt0) cc_final: 0.8204 (tt0) REVERT: F 183 LYS cc_start: 0.9088 (OUTLIER) cc_final: 0.8831 (tttp) REVERT: G 1240 MET cc_start: 0.6960 (mpm) cc_final: 0.5945 (mtt) REVERT: G 1275 GLU cc_start: 0.8059 (tp30) cc_final: 0.7644 (tp30) REVERT: J 42 GLN cc_start: 0.7785 (OUTLIER) cc_final: 0.7290 (mm-40) REVERT: J 94 MET cc_start: 0.7583 (mpm) cc_final: 0.7356 (mpm) REVERT: J 174 GLU cc_start: 0.8399 (mt-10) cc_final: 0.8168 (mt-10) REVERT: J 667 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.7675 (mt0) outliers start: 65 outliers final: 21 residues processed: 371 average time/residue: 0.7165 time to fit residues: 302.8273 Evaluate side-chains 319 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 282 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 GLN Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain B residue 60 HIS Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 407 CYS Chi-restraints excluded: chain B residue 429 GLN Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain D residue 65 GLN Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 304 ASP Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain E residue 135 SER Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 273 ASP Chi-restraints excluded: chain E residue 294 VAL Chi-restraints excluded: chain E residue 407 THR Chi-restraints excluded: chain F residue 28 ARG Chi-restraints excluded: chain F residue 183 LYS Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain I residue 18 GLU Chi-restraints excluded: chain I residue 166 MET Chi-restraints excluded: chain J residue 42 GLN Chi-restraints excluded: chain J residue 288 THR Chi-restraints excluded: chain J residue 622 SER Chi-restraints excluded: chain J residue 667 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 227 optimal weight: 4.9990 chunk 167 optimal weight: 5.9990 chunk 188 optimal weight: 4.9990 chunk 270 optimal weight: 5.9990 chunk 115 optimal weight: 5.9990 chunk 104 optimal weight: 0.5980 chunk 168 optimal weight: 0.6980 chunk 243 optimal weight: 3.9990 chunk 330 optimal weight: 7.9990 chunk 140 optimal weight: 2.9990 chunk 294 optimal weight: 6.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN D 65 GLN D 359 HIS E 24 HIS E 65 GLN E 232 GLN ** G1404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 19 GLN J 633 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.077703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.061708 restraints weight = 54408.964| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 1.97 r_work: 0.2711 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2567 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 28847 Z= 0.240 Angle : 0.686 17.856 38993 Z= 0.343 Chirality : 0.047 0.290 4419 Planarity : 0.005 0.060 5049 Dihedral : 8.225 132.631 4058 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.42 % Allowed : 14.17 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.14), residues: 3590 helix: 0.74 (0.13), residues: 1535 sheet: 0.63 (0.21), residues: 601 loop : 0.16 (0.16), residues: 1454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 166 TYR 0.021 0.002 TYR G1591 PHE 0.028 0.002 PHE G1274 TRP 0.012 0.002 TRP G1367 HIS 0.007 0.001 HIS B 242 Details of bonding type rmsd covalent geometry : bond 0.00577 (28847) covalent geometry : angle 0.68615 (38993) hydrogen bonds : bond 0.04535 ( 1173) hydrogen bonds : angle 4.72812 ( 3339) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7180 Ramachandran restraints generated. 3590 Oldfield, 0 Emsley, 3590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7180 Ramachandran restraints generated. 3590 Oldfield, 0 Emsley, 3590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 296 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8592 (tp) REVERT: A 86 GLN cc_start: 0.8749 (OUTLIER) cc_final: 0.8483 (mt0) REVERT: A 159 LEU cc_start: 0.9095 (tp) cc_final: 0.8781 (tp) REVERT: A 345 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8179 (tt) REVERT: A 419 ARG cc_start: 0.8176 (ttm110) cc_final: 0.7736 (ttp80) REVERT: B 60 HIS cc_start: 0.8078 (OUTLIER) cc_final: 0.7651 (m90) REVERT: B 429 GLN cc_start: 0.8665 (OUTLIER) cc_final: 0.8434 (pm20) REVERT: C 8 ARG cc_start: 0.7900 (mmm160) cc_final: 0.7647 (mmm160) REVERT: C 179 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7838 (tm-30) REVERT: C 409 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.8042 (mt0) REVERT: C 427 ASP cc_start: 0.8404 (t0) cc_final: 0.7992 (t0) REVERT: C 433 GLU cc_start: 0.8225 (tp30) cc_final: 0.7937 (tp30) REVERT: D 65 GLN cc_start: 0.8233 (OUTLIER) cc_final: 0.7825 (mt0) REVERT: D 137 ILE cc_start: 0.9066 (pt) cc_final: 0.8754 (mp) REVERT: D 217 MET cc_start: 0.7541 (mtp) cc_final: 0.7167 (mtp) REVERT: E 148 ASP cc_start: 0.8061 (t70) cc_final: 0.7535 (p0) REVERT: E 183 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.8279 (ttpt) REVERT: E 273 ASP cc_start: 0.8600 (OUTLIER) cc_final: 0.8315 (m-30) REVERT: E 418 LYS cc_start: 0.8562 (mmmt) cc_final: 0.8294 (tptt) REVERT: F 28 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.7393 (mtt90) REVERT: F 144 GLU cc_start: 0.8239 (pp20) cc_final: 0.8022 (pp20) REVERT: F 378 GLU cc_start: 0.8145 (mp0) cc_final: 0.7919 (mp0) REVERT: G 1240 MET cc_start: 0.6955 (mpm) cc_final: 0.5887 (mtt) REVERT: G 1299 THR cc_start: 0.8766 (m) cc_final: 0.8501 (t) REVERT: J 42 GLN cc_start: 0.7759 (OUTLIER) cc_final: 0.7210 (mm-40) REVERT: J 94 MET cc_start: 0.7526 (mpm) cc_final: 0.7296 (mpm) REVERT: J 174 GLU cc_start: 0.8407 (mt-10) cc_final: 0.8183 (mt-10) outliers start: 73 outliers final: 24 residues processed: 347 average time/residue: 0.7619 time to fit residues: 299.9607 Evaluate side-chains 310 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 274 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 86 GLN Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain B residue 60 HIS Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 407 CYS Chi-restraints excluded: chain B residue 429 GLN Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain D residue 65 GLN Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain E residue 135 SER Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 273 ASP Chi-restraints excluded: chain E residue 294 VAL Chi-restraints excluded: chain E residue 407 THR Chi-restraints excluded: chain F residue 28 ARG Chi-restraints excluded: chain F residue 183 LYS Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain G residue 1256 THR Chi-restraints excluded: chain G residue 1306 SER Chi-restraints excluded: chain I residue 18 GLU Chi-restraints excluded: chain I residue 166 MET Chi-restraints excluded: chain I residue 210 GLU Chi-restraints excluded: chain J residue 42 GLN Chi-restraints excluded: chain J residue 278 ASP Chi-restraints excluded: chain J residue 288 THR Chi-restraints excluded: chain J residue 622 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 86 optimal weight: 0.0050 chunk 133 optimal weight: 4.9990 chunk 195 optimal weight: 6.9990 chunk 102 optimal weight: 5.9990 chunk 105 optimal weight: 0.7980 chunk 244 optimal weight: 0.9990 chunk 153 optimal weight: 6.9990 chunk 267 optimal weight: 0.2980 chunk 298 optimal weight: 4.9990 chunk 137 optimal weight: 0.9980 chunk 274 optimal weight: 0.9980 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN D 65 GLN D 359 HIS E 65 GLN E 254 GLN ** G1404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 19 GLN J 633 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.080357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.064525 restraints weight = 53952.572| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 1.77 r_work: 0.2812 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28847 Z= 0.111 Angle : 0.582 19.489 38993 Z= 0.286 Chirality : 0.043 0.298 4419 Planarity : 0.004 0.069 5049 Dihedral : 7.644 130.067 4058 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.52 % Allowed : 15.40 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.14), residues: 3590 helix: 1.04 (0.13), residues: 1548 sheet: 0.73 (0.21), residues: 596 loop : 0.23 (0.16), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG F 234 TYR 0.016 0.001 TYR E 310 PHE 0.026 0.001 PHE G1274 TRP 0.010 0.001 TRP G1367 HIS 0.005 0.001 HIS D 359 Details of bonding type rmsd covalent geometry : bond 0.00257 (28847) covalent geometry : angle 0.58201 (38993) hydrogen bonds : bond 0.03334 ( 1173) hydrogen bonds : angle 4.40978 ( 3339) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7180 Ramachandran restraints generated. 3590 Oldfield, 0 Emsley, 3590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7180 Ramachandran restraints generated. 3590 Oldfield, 0 Emsley, 3590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 314 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8467 (tp) REVERT: A 159 LEU cc_start: 0.9077 (tp) cc_final: 0.8758 (tp) REVERT: A 419 ARG cc_start: 0.8053 (ttm110) cc_final: 0.7825 (ttp80) REVERT: B 60 HIS cc_start: 0.7956 (OUTLIER) cc_final: 0.7516 (m90) REVERT: B 269 MET cc_start: 0.8135 (mtm) cc_final: 0.7206 (mmt) REVERT: B 429 GLN cc_start: 0.8634 (OUTLIER) cc_final: 0.8432 (pm20) REVERT: C 179 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7796 (tm-30) REVERT: C 427 ASP cc_start: 0.8203 (t0) cc_final: 0.7827 (t0) REVERT: C 433 GLU cc_start: 0.8100 (tp30) cc_final: 0.7842 (tp30) REVERT: D 61 GLU cc_start: 0.8571 (mm-30) cc_final: 0.8132 (mm-30) REVERT: D 137 ILE cc_start: 0.8989 (pt) cc_final: 0.8767 (mp) REVERT: D 217 MET cc_start: 0.7580 (mtp) cc_final: 0.7256 (mtp) REVERT: E 148 ASP cc_start: 0.7943 (t70) cc_final: 0.7476 (p0) REVERT: E 183 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.8144 (ttpt) REVERT: E 273 ASP cc_start: 0.8454 (OUTLIER) cc_final: 0.8164 (m-30) REVERT: F 28 ARG cc_start: 0.8234 (OUTLIER) cc_final: 0.7372 (mtt90) REVERT: F 109 PHE cc_start: 0.8707 (m-80) cc_final: 0.8394 (m-80) REVERT: F 168 GLU cc_start: 0.8459 (tt0) cc_final: 0.8208 (tt0) REVERT: F 183 LYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8787 (tttp) REVERT: F 263 ASP cc_start: 0.7670 (t70) cc_final: 0.7433 (t0) REVERT: G 1240 MET cc_start: 0.6978 (mpm) cc_final: 0.5943 (mtt) REVERT: G 1275 GLU cc_start: 0.8081 (tp30) cc_final: 0.7692 (tp30) REVERT: G 1299 THR cc_start: 0.8737 (m) cc_final: 0.8498 (t) REVERT: G 1562 LEU cc_start: 0.8950 (mp) cc_final: 0.8709 (pp) REVERT: J 42 GLN cc_start: 0.7816 (OUTLIER) cc_final: 0.7210 (mm-40) REVERT: J 94 MET cc_start: 0.7428 (mpm) cc_final: 0.7177 (mpm) REVERT: J 174 GLU cc_start: 0.8363 (mt-10) cc_final: 0.8113 (mt-10) outliers start: 46 outliers final: 19 residues processed: 347 average time/residue: 0.7436 time to fit residues: 294.1326 Evaluate side-chains 308 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 280 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain B residue 60 HIS Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 407 CYS Chi-restraints excluded: chain B residue 429 GLN Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain E residue 135 SER Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain E residue 273 ASP Chi-restraints excluded: chain E residue 294 VAL Chi-restraints excluded: chain F residue 28 ARG Chi-restraints excluded: chain F residue 138 MET Chi-restraints excluded: chain F residue 144 GLU Chi-restraints excluded: chain F residue 183 LYS Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain I residue 18 GLU Chi-restraints excluded: chain I residue 156 ASN Chi-restraints excluded: chain I residue 166 MET Chi-restraints excluded: chain J residue 42 GLN Chi-restraints excluded: chain J residue 278 ASP Chi-restraints excluded: chain J residue 288 THR Chi-restraints excluded: chain J residue 622 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 148 optimal weight: 10.0000 chunk 162 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 182 optimal weight: 6.9990 chunk 306 optimal weight: 8.9990 chunk 218 optimal weight: 3.9990 chunk 120 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 313 optimal weight: 4.9990 chunk 150 optimal weight: 4.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN C 19 HIS D 359 HIS D 375 GLN E 65 GLN F 452 ASN ** G1404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 237 HIS J 633 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.077334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.061728 restraints weight = 54538.941| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 1.85 r_work: 0.2706 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2564 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 28847 Z= 0.251 Angle : 0.704 17.635 38993 Z= 0.350 Chirality : 0.047 0.284 4419 Planarity : 0.005 0.069 5049 Dihedral : 8.221 132.043 4058 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.82 % Allowed : 15.89 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.14), residues: 3590 helix: 0.72 (0.13), residues: 1543 sheet: 0.57 (0.21), residues: 604 loop : 0.08 (0.16), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 234 TYR 0.018 0.002 TYR F 310 PHE 0.031 0.002 PHE G1274 TRP 0.013 0.002 TRP G1367 HIS 0.007 0.001 HIS B 242 Details of bonding type rmsd covalent geometry : bond 0.00603 (28847) covalent geometry : angle 0.70388 (38993) hydrogen bonds : bond 0.04616 ( 1173) hydrogen bonds : angle 4.74045 ( 3339) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7180 Ramachandran restraints generated. 3590 Oldfield, 0 Emsley, 3590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7180 Ramachandran restraints generated. 3590 Oldfield, 0 Emsley, 3590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 291 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8633 (tp) REVERT: A 86 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.8483 (mt0) REVERT: A 159 LEU cc_start: 0.9098 (tp) cc_final: 0.8781 (tp) REVERT: A 345 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8199 (tt) REVERT: A 419 ARG cc_start: 0.8249 (ttm110) cc_final: 0.8000 (ttm170) REVERT: B 60 HIS cc_start: 0.8078 (OUTLIER) cc_final: 0.7570 (m90) REVERT: B 429 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.8452 (pm20) REVERT: C 8 ARG cc_start: 0.7795 (mmm160) cc_final: 0.7442 (tpm-80) REVERT: C 179 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7817 (tm-30) REVERT: C 409 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.8064 (mt0) REVERT: C 427 ASP cc_start: 0.8376 (t0) cc_final: 0.7973 (t70) REVERT: C 433 GLU cc_start: 0.8243 (tp30) cc_final: 0.7980 (tp30) REVERT: D 137 ILE cc_start: 0.8981 (pt) cc_final: 0.8778 (mp) REVERT: D 163 LYS cc_start: 0.9426 (OUTLIER) cc_final: 0.9142 (ttpp) REVERT: D 217 MET cc_start: 0.7545 (mtp) cc_final: 0.7184 (mtp) REVERT: E 183 LYS cc_start: 0.8758 (OUTLIER) cc_final: 0.8289 (ttpt) REVERT: E 273 ASP cc_start: 0.8590 (OUTLIER) cc_final: 0.8311 (m-30) REVERT: F 28 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7360 (mtt90) REVERT: F 263 ASP cc_start: 0.8001 (t70) cc_final: 0.7697 (t0) REVERT: G 1240 MET cc_start: 0.6972 (mpm) cc_final: 0.5938 (mtt) REVERT: G 1299 THR cc_start: 0.8746 (m) cc_final: 0.8508 (t) REVERT: G 1578 MET cc_start: 0.8074 (OUTLIER) cc_final: 0.7334 (mtm) REVERT: J 42 GLN cc_start: 0.7808 (OUTLIER) cc_final: 0.7125 (mm-40) REVERT: J 174 GLU cc_start: 0.8431 (mt-10) cc_final: 0.8219 (mt-10) REVERT: J 667 GLN cc_start: 0.8286 (OUTLIER) cc_final: 0.8010 (mt0) outliers start: 55 outliers final: 22 residues processed: 330 average time/residue: 0.7863 time to fit residues: 294.3596 Evaluate side-chains 310 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 274 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 86 GLN Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain B residue 60 HIS Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 407 CYS Chi-restraints excluded: chain B residue 429 GLN Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain D residue 163 LYS Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain E residue 135 SER Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain E residue 273 ASP Chi-restraints excluded: chain F residue 28 ARG Chi-restraints excluded: chain F residue 144 GLU Chi-restraints excluded: chain F residue 183 LYS Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain G residue 1578 MET Chi-restraints excluded: chain I residue 166 MET Chi-restraints excluded: chain J residue 42 GLN Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain J residue 278 ASP Chi-restraints excluded: chain J residue 288 THR Chi-restraints excluded: chain J residue 622 SER Chi-restraints excluded: chain J residue 667 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 79 optimal weight: 0.9980 chunk 284 optimal weight: 6.9990 chunk 266 optimal weight: 0.6980 chunk 92 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 169 optimal weight: 2.9990 chunk 213 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 359 HIS E 65 GLN ** G1404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 633 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.079605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.064430 restraints weight = 54168.597| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 1.75 r_work: 0.2781 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2644 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28847 Z= 0.129 Angle : 0.610 10.170 38993 Z= 0.303 Chirality : 0.043 0.292 4419 Planarity : 0.004 0.051 5049 Dihedral : 7.707 130.064 4058 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.26 % Allowed : 16.66 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.14), residues: 3590 helix: 1.00 (0.13), residues: 1537 sheet: 0.58 (0.21), residues: 606 loop : 0.16 (0.16), residues: 1447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 166 TYR 0.016 0.001 TYR E 310 PHE 0.027 0.001 PHE G1274 TRP 0.010 0.001 TRP G1367 HIS 0.005 0.001 HIS D 359 Details of bonding type rmsd covalent geometry : bond 0.00303 (28847) covalent geometry : angle 0.60997 (38993) hydrogen bonds : bond 0.03505 ( 1173) hydrogen bonds : angle 4.47485 ( 3339) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7180 Ramachandran restraints generated. 3590 Oldfield, 0 Emsley, 3590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7180 Ramachandran restraints generated. 3590 Oldfield, 0 Emsley, 3590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 295 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8509 (tp) REVERT: A 159 LEU cc_start: 0.9086 (tp) cc_final: 0.8759 (tp) REVERT: A 345 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8179 (tt) REVERT: A 419 ARG cc_start: 0.8182 (ttm110) cc_final: 0.7951 (ttm170) REVERT: B 60 HIS cc_start: 0.7976 (OUTLIER) cc_final: 0.7600 (m90) REVERT: B 269 MET cc_start: 0.8166 (mtm) cc_final: 0.7259 (mmt) REVERT: B 423 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.8162 (mtm180) REVERT: C 179 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7785 (tm-30) REVERT: C 427 ASP cc_start: 0.8229 (t0) cc_final: 0.7839 (t0) REVERT: C 433 GLU cc_start: 0.8156 (tp30) cc_final: 0.7885 (tp30) REVERT: D 61 GLU cc_start: 0.8614 (mm-30) cc_final: 0.8188 (mm-30) REVERT: D 217 MET cc_start: 0.7547 (mtp) cc_final: 0.7176 (mtp) REVERT: E 148 ASP cc_start: 0.8057 (t70) cc_final: 0.7574 (p0) REVERT: E 183 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8236 (ttpt) REVERT: E 273 ASP cc_start: 0.8488 (OUTLIER) cc_final: 0.8212 (m-30) REVERT: F 28 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.7369 (mtt90) REVERT: F 168 GLU cc_start: 0.8497 (tt0) cc_final: 0.8235 (tt0) REVERT: F 263 ASP cc_start: 0.7789 (t70) cc_final: 0.7512 (t0) REVERT: G 1240 MET cc_start: 0.6934 (mpm) cc_final: 0.5920 (mtt) REVERT: G 1275 GLU cc_start: 0.8142 (tp30) cc_final: 0.7757 (tp30) REVERT: G 1299 THR cc_start: 0.8752 (m) cc_final: 0.8535 (t) REVERT: I 30 ARG cc_start: 0.8837 (mtp-110) cc_final: 0.8636 (mtp-110) REVERT: J 21 ARG cc_start: 0.8605 (mpp80) cc_final: 0.8405 (mpp80) REVERT: J 42 GLN cc_start: 0.7810 (OUTLIER) cc_final: 0.7432 (mp10) REVERT: J 94 MET cc_start: 0.7454 (mpm) cc_final: 0.7202 (mpm) REVERT: J 174 GLU cc_start: 0.8346 (mt-10) cc_final: 0.8111 (mt-10) REVERT: J 667 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.7965 (mt0) outliers start: 38 outliers final: 18 residues processed: 324 average time/residue: 0.7699 time to fit residues: 283.8884 Evaluate side-chains 313 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 285 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain B residue 60 HIS Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 407 CYS Chi-restraints excluded: chain B residue 423 ARG Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 222 LYS Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain E residue 135 SER Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain E residue 273 ASP Chi-restraints excluded: chain E residue 294 VAL Chi-restraints excluded: chain F residue 28 ARG Chi-restraints excluded: chain F residue 144 GLU Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain I residue 166 MET Chi-restraints excluded: chain J residue 42 GLN Chi-restraints excluded: chain J residue 288 THR Chi-restraints excluded: chain J residue 622 SER Chi-restraints excluded: chain J residue 667 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 23 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 202 optimal weight: 0.0470 chunk 340 optimal weight: 0.0770 chunk 25 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 349 optimal weight: 5.9990 chunk 244 optimal weight: 0.0070 chunk 18 optimal weight: 1.9990 chunk 338 optimal weight: 4.9990 overall best weight: 0.6056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 359 HIS E 65 GLN ** G1404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 31 ASN J 633 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.080297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.064301 restraints weight = 54278.558| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 1.84 r_work: 0.2803 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2666 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.3628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 28847 Z= 0.114 Angle : 0.602 11.904 38993 Z= 0.297 Chirality : 0.043 0.310 4419 Planarity : 0.004 0.076 5049 Dihedral : 7.449 126.920 4058 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.99 % Allowed : 17.32 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.14), residues: 3590 helix: 1.16 (0.13), residues: 1535 sheet: 0.64 (0.21), residues: 596 loop : 0.22 (0.16), residues: 1459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG J 602 TYR 0.016 0.001 TYR E 310 PHE 0.028 0.001 PHE G1274 TRP 0.011 0.001 TRP G1367 HIS 0.004 0.001 HIS D 359 Details of bonding type rmsd covalent geometry : bond 0.00267 (28847) covalent geometry : angle 0.60217 (38993) hydrogen bonds : bond 0.03278 ( 1173) hydrogen bonds : angle 4.36198 ( 3339) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7180 Ramachandran restraints generated. 3590 Oldfield, 0 Emsley, 3590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7180 Ramachandran restraints generated. 3590 Oldfield, 0 Emsley, 3590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 315 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8534 (tp) REVERT: A 159 LEU cc_start: 0.9077 (tp) cc_final: 0.8776 (tp) REVERT: A 334 ARG cc_start: 0.8704 (OUTLIER) cc_final: 0.8444 (mmt180) REVERT: A 419 ARG cc_start: 0.8181 (ttm110) cc_final: 0.7945 (ttm170) REVERT: B 269 MET cc_start: 0.8056 (mtm) cc_final: 0.7151 (mmt) REVERT: C 8 ARG cc_start: 0.7644 (mmm160) cc_final: 0.7431 (tpm-80) REVERT: C 166 ARG cc_start: 0.7836 (ttm110) cc_final: 0.7535 (ptm-80) REVERT: C 179 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7824 (tm-30) REVERT: C 427 ASP cc_start: 0.8245 (t0) cc_final: 0.7387 (t0) REVERT: C 433 GLU cc_start: 0.8174 (tp30) cc_final: 0.7870 (tp30) REVERT: D 61 GLU cc_start: 0.8613 (mm-30) cc_final: 0.8169 (mm-30) REVERT: D 217 MET cc_start: 0.7613 (mtp) cc_final: 0.7267 (mtp) REVERT: D 337 THR cc_start: 0.8428 (OUTLIER) cc_final: 0.8139 (p) REVERT: E 148 ASP cc_start: 0.8037 (t70) cc_final: 0.7544 (p0) REVERT: E 183 LYS cc_start: 0.8652 (OUTLIER) cc_final: 0.8199 (ttpt) REVERT: E 384 ASP cc_start: 0.8544 (m-30) cc_final: 0.8303 (p0) REVERT: F 28 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.7467 (mtt90) REVERT: F 168 GLU cc_start: 0.8486 (tt0) cc_final: 0.8228 (tt0) REVERT: F 183 LYS cc_start: 0.9045 (mtpm) cc_final: 0.8789 (tttp) REVERT: G 1240 MET cc_start: 0.6927 (mpm) cc_final: 0.5992 (mtt) REVERT: G 1275 GLU cc_start: 0.8100 (tp30) cc_final: 0.7695 (tp30) REVERT: G 1299 THR cc_start: 0.8724 (m) cc_final: 0.8490 (t) REVERT: G 1578 MET cc_start: 0.8001 (OUTLIER) cc_final: 0.7178 (mtm) REVERT: J 42 GLN cc_start: 0.7859 (OUTLIER) cc_final: 0.7508 (mp10) REVERT: J 94 MET cc_start: 0.7407 (mpm) cc_final: 0.7154 (mpm) REVERT: J 174 GLU cc_start: 0.8308 (mt-10) cc_final: 0.8092 (mt-10) outliers start: 30 outliers final: 11 residues processed: 338 average time/residue: 0.7160 time to fit residues: 276.2231 Evaluate side-chains 310 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 291 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 334 ARG Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 407 CYS Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain F residue 28 ARG Chi-restraints excluded: chain F residue 144 GLU Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain G residue 1408 ASP Chi-restraints excluded: chain G residue 1578 MET Chi-restraints excluded: chain I residue 156 ASN Chi-restraints excluded: chain J residue 42 GLN Chi-restraints excluded: chain J residue 288 THR Chi-restraints excluded: chain J residue 622 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 188 optimal weight: 3.9990 chunk 293 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 chunk 70 optimal weight: 0.9980 chunk 336 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 163 optimal weight: 0.0020 chunk 154 optimal weight: 0.7980 chunk 300 optimal weight: 0.0470 chunk 310 optimal weight: 0.5980 chunk 350 optimal weight: 5.9990 overall best weight: 0.4886 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 359 HIS E 65 GLN F 452 ASN ** G1404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 19 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.080941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.065524 restraints weight = 54341.378| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 1.88 r_work: 0.2830 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.3715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 28847 Z= 0.112 Angle : 0.601 12.563 38993 Z= 0.297 Chirality : 0.043 0.320 4419 Planarity : 0.004 0.066 5049 Dihedral : 7.336 125.694 4058 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.76 % Allowed : 18.01 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.03 (0.14), residues: 3590 helix: 1.23 (0.13), residues: 1535 sheet: 0.65 (0.21), residues: 596 loop : 0.26 (0.16), residues: 1459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG J 602 TYR 0.015 0.001 TYR E 310 PHE 0.028 0.001 PHE G1274 TRP 0.011 0.001 TRP G1367 HIS 0.004 0.001 HIS D 359 Details of bonding type rmsd covalent geometry : bond 0.00262 (28847) covalent geometry : angle 0.60147 (38993) hydrogen bonds : bond 0.03189 ( 1173) hydrogen bonds : angle 4.33285 ( 3339) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9491.43 seconds wall clock time: 162 minutes 12.55 seconds (9732.55 seconds total)