Starting phenix.real_space_refine on Mon May 26 12:47:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oor_17026/05_2025/8oor_17026.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oor_17026/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8oor_17026/05_2025/8oor_17026.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oor_17026/05_2025/8oor_17026.map" model { file = "/net/cci-nas-00/data/ceres_data/8oor_17026/05_2025/8oor_17026.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oor_17026/05_2025/8oor_17026.cif" } resolution = 2.87 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 16.01, per 1000 atoms: 0.56 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: 6.69 Conformation dependent library (CDL) restraints added in 3.7 seconds 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: 3.45 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: 10.89 Time building geometry restraints manager: 7.71 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 462 or resid 501)) selection = chain 'B' selection = (chain 'C' and (resid 14 through 144 or resid 156 through 462 or resid 501)) } ncs_group { reference = (chain 'D' and (resid 20 through 150 or resid 156 through 460 or resid 501)) selection = (chain 'E' and (resid 20 through 150 or resid 156 through 460 or resid 501)) selection = (chain 'F' and (resid 20 through 460 or resid 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.860 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: 1.140 Check model and map are aligned: 0.200 Set scattering table: 0.240 Process input model: 60.540 Find NCS groups from input model: 1.330 Set up NCS constraints: 0.120 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:12.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.150 ------------------------------------------------------------------------------- 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 : 2.74 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.026 0.004 TRP G1367 HIS 0.020 0.003 HIS B 19 PHE 0.041 0.004 PHE G1501 TYR 0.033 0.005 TYR I 179 ARG 0.036 0.003 ARG F 437 Details of bonding type rmsd hydrogen bonds : bond 0.20236 ( 1173) hydrogen bonds : angle 7.56334 ( 3339) covalent geometry : bond 0.01087 (28847) covalent geometry : angle 0.95983 (38993) *********************** 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 : 3.104 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: 1.9055 time to fit residues: 1262.6386 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 : 3.007 ------------------------------------------------------------------------------- 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 300 optimal weight: 4.9990 chunk 269 optimal weight: 4.9990 chunk 149 optimal weight: 6.9990 chunk 92 optimal weight: 0.8980 chunk 182 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 279 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 169 optimal weight: 0.9980 chunk 207 optimal weight: 0.9980 chunk 323 optimal weight: 0.9980 overall best weight: 0.9780 ------------------------------------------------------------------------------- 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 A 421 ASN 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 G1287 HIS G1345 HIS I 19 GLN I 23 HIS I 33 ASN I 202 GLN J 114 HIS J 628 HIS J 696 GLN J 722 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.080073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.064409 restraints weight = 54155.369| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 1.96 r_work: 0.2797 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 28847 Z= 0.139 Angle : 0.629 10.909 38993 Z= 0.322 Chirality : 0.044 0.182 4419 Planarity : 0.005 0.055 5049 Dihedral : 8.719 148.750 4060 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.69 % Allowed : 9.21 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.14), residues: 3590 helix: 0.52 (0.13), residues: 1542 sheet: 0.65 (0.20), residues: 570 loop : 0.41 (0.16), residues: 1478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 129 HIS 0.007 0.001 HIS G1345 PHE 0.017 0.002 PHE C 117 TYR 0.021 0.002 TYR A 193 ARG 0.008 0.001 ARG J 748 Details of bonding type rmsd hydrogen bonds : bond 0.04336 ( 1173) hydrogen bonds : angle 4.92169 ( 3339) covalent geometry : bond 0.00317 (28847) covalent geometry : angle 0.62925 (38993) *********************** 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 450 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 399 time to evaluate : 3.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 LYS cc_start: 0.8773 (OUTLIER) cc_final: 0.8416 (mttp) REVERT: A 419 ARG cc_start: 0.8176 (ttm110) cc_final: 0.7850 (ttm170) REVERT: B 60 HIS cc_start: 0.7995 (OUTLIER) cc_final: 0.7509 (m90) REVERT: B 114 MET cc_start: 0.8643 (tpt) cc_final: 0.8395 (tpp) REVERT: B 250 ARG cc_start: 0.7906 (ttt90) cc_final: 0.7463 (ttt90) REVERT: B 265 MET cc_start: 0.8842 (mmt) cc_final: 0.8446 (mmm) REVERT: B 269 MET cc_start: 0.8208 (mtm) cc_final: 0.7432 (mmt) REVERT: C 8 ARG cc_start: 0.7792 (tpm-80) cc_final: 0.7344 (tpm-80) REVERT: C 143 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7537 (mp0) REVERT: C 433 GLU cc_start: 0.8090 (tp30) cc_final: 0.7864 (tp30) REVERT: D 61 GLU cc_start: 0.8690 (mm-30) cc_final: 0.8246 (mm-30) REVERT: D 65 GLN cc_start: 0.8325 (OUTLIER) cc_final: 0.8054 (mt0) REVERT: D 217 MET cc_start: 0.7635 (mtp) cc_final: 0.7432 (mtp) REVERT: D 304 ASP cc_start: 0.8132 (OUTLIER) cc_final: 0.7893 (p0) REVERT: E 96 GLN cc_start: 0.8014 (tp40) cc_final: 0.7799 (tm-30) REVERT: E 148 ASP cc_start: 0.7870 (t70) cc_final: 0.7351 (p0) REVERT: E 195 ASP cc_start: 0.7615 (t0) cc_final: 0.7206 (t70) REVERT: E 217 MET cc_start: 0.8696 (mmm) cc_final: 0.8448 (mmm) REVERT: E 447 LYS cc_start: 0.8832 (mppt) cc_final: 0.8606 (mptm) REVERT: F 109 PHE cc_start: 0.8934 (m-80) cc_final: 0.8713 (m-80) REVERT: F 171 TYR cc_start: 0.9151 (m-80) cc_final: 0.8856 (m-80) REVERT: F 183 LYS cc_start: 0.9089 (mtpm) cc_final: 0.8821 (OUTLIER) REVERT: F 263 ASP cc_start: 0.8077 (t70) cc_final: 0.7791 (t0) REVERT: F 299 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8198 (mt-10) REVERT: J 174 GLU cc_start: 0.8374 (mt-10) cc_final: 0.8150 (mt-10) outliers start: 51 outliers final: 6 residues processed: 433 average time/residue: 1.7184 time to fit residues: 844.8175 Evaluate side-chains 318 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 307 time to evaluate : 3.456 ------------------------------------------------------------------------------- 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 143 GLU Chi-restraints excluded: chain D residue 65 GLN Chi-restraints excluded: chain D residue 304 ASP 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 338 optimal weight: 7.9990 chunk 25 optimal weight: 0.0970 chunk 334 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 189 optimal weight: 0.0030 chunk 257 optimal weight: 3.9990 chunk 163 optimal weight: 3.9990 chunk 280 optimal weight: 0.9980 chunk 301 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 265 optimal weight: 7.9990 overall best weight: 1.4192 ------------------------------------------------------------------------------- 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 274 GLN E 24 HIS E 65 GLN E 419 GLN F 96 GLN F 357 ASN H 452 ASN I 19 GLN I 202 GLN 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 = 0.3228 r_free = 0.3228 target = 0.079087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.062849 restraints weight = 54550.960| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 1.87 r_work: 0.2763 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2622 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 28847 Z= 0.160 Angle : 0.618 13.444 38993 Z= 0.310 Chirality : 0.044 0.197 4419 Planarity : 0.004 0.052 5049 Dihedral : 8.279 139.367 4058 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.09 % Allowed : 11.16 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.14), residues: 3590 helix: 0.81 (0.13), residues: 1541 sheet: 0.70 (0.20), residues: 596 loop : 0.40 (0.16), residues: 1453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 129 HIS 0.006 0.001 HIS B 242 PHE 0.020 0.002 PHE G1274 TYR 0.020 0.002 TYR A 193 ARG 0.006 0.001 ARG C 419 Details of bonding type rmsd hydrogen bonds : bond 0.04215 ( 1173) hydrogen bonds : angle 4.70004 ( 3339) covalent geometry : bond 0.00379 (28847) covalent geometry : angle 0.61816 (38993) *********************** 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 406 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 343 time to evaluate : 3.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.8457 (mt0) REVERT: A 159 LEU cc_start: 0.9075 (tp) cc_final: 0.8785 (tp) REVERT: A 419 ARG cc_start: 0.8228 (ttm110) cc_final: 0.7921 (ttm170) REVERT: B 60 HIS cc_start: 0.7980 (OUTLIER) cc_final: 0.7478 (m90) REVERT: B 114 MET cc_start: 0.8640 (tpt) cc_final: 0.8437 (tpp) REVERT: B 265 MET cc_start: 0.8903 (mmt) cc_final: 0.8634 (mmm) REVERT: C 127 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7619 (mt-10) REVERT: C 143 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7676 (mp0) REVERT: C 409 GLN cc_start: 0.8307 (OUTLIER) cc_final: 0.8097 (mt0) REVERT: C 433 GLU cc_start: 0.8090 (tp30) cc_final: 0.7803 (tp30) REVERT: D 134 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7098 (tp30) REVERT: D 137 ILE cc_start: 0.9088 (pt) cc_final: 0.8591 (mp) REVERT: D 217 MET cc_start: 0.7681 (mtp) cc_final: 0.7377 (mtt) REVERT: D 304 ASP cc_start: 0.8221 (OUTLIER) cc_final: 0.7969 (p0) REVERT: E 96 GLN cc_start: 0.8014 (tp40) cc_final: 0.7753 (tm-30) REVERT: E 148 ASP cc_start: 0.7906 (t70) cc_final: 0.7382 (p0) REVERT: E 418 LYS cc_start: 0.8644 (mmmt) cc_final: 0.8330 (tptt) REVERT: E 447 LYS cc_start: 0.8852 (mppt) cc_final: 0.8642 (mptm) REVERT: F 28 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.7566 (mtt180) REVERT: F 109 PHE cc_start: 0.8884 (m-80) cc_final: 0.8649 (m-80) REVERT: F 171 TYR cc_start: 0.9151 (m-80) cc_final: 0.8923 (m-80) REVERT: F 183 LYS cc_start: 0.9094 (mtpm) cc_final: 0.8821 (tttp) REVERT: F 263 ASP cc_start: 0.8084 (t70) cc_final: 0.7823 (t0) REVERT: G 1240 MET cc_start: 0.6627 (mpm) cc_final: 0.5598 (mtt) REVERT: I 14 GLN cc_start: 0.8739 (tp40) cc_final: 0.8085 (mm-40) REVERT: J 174 GLU cc_start: 0.8392 (mt-10) cc_final: 0.8135 (mt-10) outliers start: 63 outliers final: 13 residues processed: 387 average time/residue: 1.7466 time to fit residues: 766.0859 Evaluate side-chains 312 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 292 time to evaluate : 3.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 GLN 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 143 GLU Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 409 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 E residue 183 LYS Chi-restraints excluded: chain E residue 202 THR 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 138 MET 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 20 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 188 optimal weight: 3.9990 chunk 147 optimal weight: 0.7980 chunk 89 optimal weight: 6.9990 chunk 326 optimal weight: 0.0870 chunk 304 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 161 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 overall best weight: 1.5764 ------------------------------------------------------------------------------- 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 263 GLN A 421 ASN B 421 ASN D 65 GLN D 328 ASN E 65 GLN F 301 HIS F 357 ASN I 19 GLN I 202 GLN J 633 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.078627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.062375 restraints weight = 54942.888| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 1.87 r_work: 0.2753 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2613 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.2946 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= 0.164 Angle : 0.617 17.905 38993 Z= 0.306 Chirality : 0.044 0.228 4419 Planarity : 0.004 0.056 5049 Dihedral : 8.129 133.543 4058 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.32 % Allowed : 12.68 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.14), residues: 3590 helix: 0.87 (0.13), residues: 1536 sheet: 0.67 (0.20), residues: 604 loop : 0.37 (0.16), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 129 HIS 0.005 0.001 HIS B 242 PHE 0.022 0.002 PHE G1274 TYR 0.021 0.002 TYR G1591 ARG 0.013 0.001 ARG F 234 Details of bonding type rmsd hydrogen bonds : bond 0.04053 ( 1173) hydrogen bonds : angle 4.61211 ( 3339) covalent geometry : bond 0.00391 (28847) covalent geometry : angle 0.61669 (38993) *********************** 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 388 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 318 time to evaluate : 3.162 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 GLN cc_start: 0.8707 (OUTLIER) cc_final: 0.8436 (mt0) REVERT: A 159 LEU cc_start: 0.9081 (tp) cc_final: 0.8773 (tp) REVERT: A 419 ARG cc_start: 0.8194 (ttm110) cc_final: 0.7929 (ttm170) REVERT: B 60 HIS cc_start: 0.8021 (OUTLIER) cc_final: 0.7542 (m90) REVERT: B 114 MET cc_start: 0.8677 (tpt) cc_final: 0.8470 (tpp) REVERT: B 265 MET cc_start: 0.8920 (mmt) cc_final: 0.8691 (mmm) REVERT: B 269 MET cc_start: 0.8222 (mtm) cc_final: 0.7285 (mmt) REVERT: B 429 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.8444 (pm20) REVERT: C 8 ARG cc_start: 0.7883 (mmm160) cc_final: 0.7608 (mmm160) REVERT: C 127 GLU cc_start: 0.7897 (mt-10) cc_final: 0.7665 (mt-10) REVERT: C 143 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7709 (mp0) REVERT: C 409 GLN cc_start: 0.8333 (OUTLIER) cc_final: 0.8114 (mt0) REVERT: C 427 ASP cc_start: 0.8347 (t0) cc_final: 0.7931 (t0) REVERT: C 433 GLU cc_start: 0.8109 (tp30) cc_final: 0.7790 (tp30) REVERT: D 61 GLU cc_start: 0.8666 (mm-30) cc_final: 0.8249 (mm-30) REVERT: D 65 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.8080 (mt0) REVERT: D 137 ILE cc_start: 0.9077 (pt) cc_final: 0.8696 (mp) REVERT: D 217 MET cc_start: 0.7764 (mtp) cc_final: 0.7434 (mtt) REVERT: D 304 ASP cc_start: 0.8291 (OUTLIER) cc_final: 0.8034 (p0) REVERT: E 96 GLN cc_start: 0.7966 (tp40) cc_final: 0.7719 (tm-30) REVERT: E 148 ASP cc_start: 0.7930 (t70) cc_final: 0.7411 (p0) REVERT: E 418 LYS cc_start: 0.8578 (mmmt) cc_final: 0.8325 (tptt) REVERT: E 447 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8648 (mptm) REVERT: F 28 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.7579 (mtt180) REVERT: F 109 PHE cc_start: 0.8888 (m-80) cc_final: 0.8626 (m-80) REVERT: F 171 TYR cc_start: 0.9149 (m-80) cc_final: 0.8909 (m-80) REVERT: F 224 LEU cc_start: 0.8409 (mt) cc_final: 0.8195 (mp) REVERT: F 263 ASP cc_start: 0.8000 (t70) cc_final: 0.7759 (t0) REVERT: G 1240 MET cc_start: 0.6807 (mpm) cc_final: 0.5755 (mtt) outliers start: 70 outliers final: 19 residues processed: 365 average time/residue: 1.7335 time to fit residues: 723.2712 Evaluate side-chains 319 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 291 time to evaluate : 3.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 GLN 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 143 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 134 GLU Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 304 ASP 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 294 VAL Chi-restraints excluded: chain E residue 407 THR Chi-restraints excluded: chain E residue 447 LYS Chi-restraints excluded: chain F residue 28 ARG Chi-restraints excluded: chain F residue 138 MET Chi-restraints excluded: chain F residue 183 LYS Chi-restraints excluded: chain G residue 1362 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 232 optimal weight: 4.9990 chunk 210 optimal weight: 0.7980 chunk 182 optimal weight: 0.5980 chunk 266 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 86 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 333 optimal weight: 2.9990 chunk 225 optimal weight: 5.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 ASN B 421 ASN D 65 GLN E 65 GLN F 357 ASN 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 = 0.3234 r_free = 0.3234 target = 0.079357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.063121 restraints weight = 54592.078| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 1.87 r_work: 0.2770 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2630 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.3160 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= 0.129 Angle : 0.586 17.387 38993 Z= 0.289 Chirality : 0.043 0.250 4419 Planarity : 0.004 0.046 5049 Dihedral : 7.857 129.340 4058 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.79 % Allowed : 13.64 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.14), residues: 3590 helix: 1.01 (0.13), residues: 1547 sheet: 0.70 (0.21), residues: 601 loop : 0.33 (0.16), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 129 HIS 0.004 0.001 HIS B 242 PHE 0.023 0.001 PHE G1274 TYR 0.023 0.001 TYR G1591 ARG 0.010 0.000 ARG C 166 Details of bonding type rmsd hydrogen bonds : bond 0.03637 ( 1173) hydrogen bonds : angle 4.46925 ( 3339) covalent geometry : bond 0.00302 (28847) covalent geometry : angle 0.58580 (38993) *********************** 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 381 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 327 time to evaluate : 3.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8501 (tp) REVERT: A 159 LEU cc_start: 0.9095 (tp) cc_final: 0.8767 (tp) REVERT: A 345 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8173 (tt) REVERT: A 419 ARG cc_start: 0.8152 (ttm110) cc_final: 0.7774 (ttp80) REVERT: B 60 HIS cc_start: 0.8032 (OUTLIER) cc_final: 0.7562 (m90) REVERT: B 269 MET cc_start: 0.8164 (mtm) cc_final: 0.7243 (mmt) REVERT: B 429 GLN cc_start: 0.8697 (OUTLIER) cc_final: 0.8470 (pm20) REVERT: C 8 ARG cc_start: 0.7805 (mmm160) cc_final: 0.7562 (mmm160) REVERT: C 127 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7630 (mt-10) REVERT: C 179 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7800 (tm-30) REVERT: C 304 GLU cc_start: 0.8830 (OUTLIER) cc_final: 0.8408 (mm-30) REVERT: C 427 ASP cc_start: 0.8309 (t0) cc_final: 0.7898 (t0) REVERT: C 433 GLU cc_start: 0.8106 (tp30) cc_final: 0.7871 (tp30) REVERT: D 137 ILE cc_start: 0.9055 (pt) cc_final: 0.8752 (mp) REVERT: D 217 MET cc_start: 0.7784 (mtp) cc_final: 0.7447 (mtt) REVERT: E 96 GLN cc_start: 0.7879 (tp40) cc_final: 0.7643 (tm-30) REVERT: E 112 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.6788 (tm-30) REVERT: E 148 ASP cc_start: 0.7965 (t70) cc_final: 0.7422 (p0) REVERT: E 183 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8148 (ttpt) REVERT: E 418 LYS cc_start: 0.8540 (mmmt) cc_final: 0.8303 (tptt) REVERT: F 109 PHE cc_start: 0.8837 (m-80) cc_final: 0.8589 (m-80) REVERT: F 168 GLU cc_start: 0.8414 (tt0) cc_final: 0.8131 (tt0) REVERT: F 171 TYR cc_start: 0.9116 (m-80) cc_final: 0.8908 (m-80) REVERT: F 183 LYS cc_start: 0.9096 (OUTLIER) cc_final: 0.8836 (tttp) REVERT: G 1240 MET cc_start: 0.6893 (mpm) cc_final: 0.5907 (mtt) REVERT: G 1275 GLU cc_start: 0.8049 (tp30) cc_final: 0.7616 (tp30) REVERT: G 1429 ASN cc_start: 0.8317 (p0) cc_final: 0.8033 (p0) REVERT: G 1585 MET cc_start: 0.8910 (tpp) cc_final: 0.8707 (tpp) REVERT: J 42 GLN cc_start: 0.7792 (OUTLIER) cc_final: 0.7293 (mm-40) REVERT: J 94 MET cc_start: 0.7723 (mpm) cc_final: 0.7459 (mpm) REVERT: J 667 GLN cc_start: 0.8221 (OUTLIER) cc_final: 0.7697 (mt0) outliers start: 54 outliers final: 15 residues processed: 365 average time/residue: 1.6682 time to fit residues: 694.6781 Evaluate side-chains 316 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 290 time to evaluate : 3.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU 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 179 GLU Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 304 GLU 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 E residue 112 GLU Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 294 VAL Chi-restraints excluded: chain F residue 183 LYS Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain G residue 1346 MET Chi-restraints excluded: chain J residue 42 GLN Chi-restraints excluded: chain J residue 86 MET 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 262 optimal weight: 0.9990 chunk 253 optimal weight: 0.5980 chunk 65 optimal weight: 5.9990 chunk 243 optimal weight: 4.9990 chunk 67 optimal weight: 0.7980 chunk 171 optimal weight: 0.9980 chunk 336 optimal weight: 3.9990 chunk 250 optimal weight: 5.9990 chunk 130 optimal weight: 0.9990 chunk 107 optimal weight: 8.9990 chunk 141 optimal weight: 6.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 GLN E 24 HIS E 65 GLN F 357 ASN ** G1404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 19 GLN J 633 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.079767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.064102 restraints weight = 54523.077| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 1.92 r_work: 0.2767 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2625 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28847 Z= 0.122 Angle : 0.580 18.243 38993 Z= 0.286 Chirality : 0.043 0.283 4419 Planarity : 0.004 0.055 5049 Dihedral : 7.676 127.478 4058 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.72 % Allowed : 14.34 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.14), residues: 3590 helix: 1.15 (0.13), residues: 1534 sheet: 0.68 (0.21), residues: 604 loop : 0.35 (0.16), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G1415 HIS 0.004 0.001 HIS G1345 PHE 0.025 0.001 PHE G1274 TYR 0.016 0.001 TYR G1591 ARG 0.014 0.000 ARG F 234 Details of bonding type rmsd hydrogen bonds : bond 0.03494 ( 1173) hydrogen bonds : angle 4.40134 ( 3339) covalent geometry : bond 0.00285 (28847) covalent geometry : angle 0.57957 (38993) *********************** 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 384 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 332 time to evaluate : 3.040 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8503 (tp) REVERT: A 159 LEU cc_start: 0.9085 (tp) cc_final: 0.8762 (tp) REVERT: A 345 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8157 (tt) REVERT: A 419 ARG cc_start: 0.8168 (ttm110) cc_final: 0.7750 (ttp80) REVERT: B 60 HIS cc_start: 0.7986 (OUTLIER) cc_final: 0.7532 (m90) REVERT: B 269 MET cc_start: 0.8160 (mtm) cc_final: 0.7232 (mmt) REVERT: B 429 GLN cc_start: 0.8700 (OUTLIER) cc_final: 0.8451 (pm20) REVERT: B 430 ASP cc_start: 0.8444 (m-30) cc_final: 0.8237 (m-30) REVERT: C 127 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7661 (mt-10) REVERT: C 179 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7845 (tm-30) REVERT: C 427 ASP cc_start: 0.8295 (t0) cc_final: 0.7415 (t0) REVERT: C 433 GLU cc_start: 0.8170 (tp30) cc_final: 0.7900 (tp30) REVERT: D 65 GLN cc_start: 0.8262 (OUTLIER) cc_final: 0.7605 (mt0) REVERT: D 137 ILE cc_start: 0.9011 (pt) cc_final: 0.8750 (mp) REVERT: D 217 MET cc_start: 0.7829 (mtp) cc_final: 0.7483 (mtt) REVERT: D 304 ASP cc_start: 0.8150 (OUTLIER) cc_final: 0.7899 (p0) REVERT: E 96 GLN cc_start: 0.7896 (tp40) cc_final: 0.7663 (tm-30) REVERT: E 112 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.6929 (tm-30) REVERT: E 136 GLU cc_start: 0.8494 (mm-30) cc_final: 0.8265 (mt-10) REVERT: E 138 MET cc_start: 0.8901 (ttm) cc_final: 0.8661 (ttm) REVERT: E 148 ASP cc_start: 0.7976 (t70) cc_final: 0.7423 (p0) REVERT: E 183 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8152 (ttpt) REVERT: E 418 LYS cc_start: 0.8522 (mmmt) cc_final: 0.8281 (tptt) REVERT: F 109 PHE cc_start: 0.8793 (m-80) cc_final: 0.8512 (m-80) REVERT: F 168 GLU cc_start: 0.8450 (tt0) cc_final: 0.8170 (tt0) REVERT: F 183 LYS cc_start: 0.9077 (OUTLIER) cc_final: 0.8821 (tttp) REVERT: G 1240 MET cc_start: 0.6913 (mpm) cc_final: 0.5889 (mtt) REVERT: G 1275 GLU cc_start: 0.8126 (tp30) cc_final: 0.7669 (tp30) REVERT: J 42 GLN cc_start: 0.7742 (OUTLIER) cc_final: 0.7204 (mm-40) REVERT: J 667 GLN cc_start: 0.8248 (OUTLIER) cc_final: 0.7735 (mt0) outliers start: 52 outliers final: 17 residues processed: 366 average time/residue: 1.7324 time to fit residues: 728.5148 Evaluate side-chains 329 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 300 time to evaluate : 3.241 ------------------------------------------------------------------------------- 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 345 LEU 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 65 GLN 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 112 GLU Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 294 VAL Chi-restraints excluded: chain F residue 138 MET Chi-restraints excluded: chain F residue 183 LYS Chi-restraints excluded: chain G residue 1256 THR Chi-restraints excluded: chain G residue 1593 ASN Chi-restraints excluded: chain I residue 156 ASN Chi-restraints excluded: chain I residue 210 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 279 optimal weight: 0.9990 chunk 157 optimal weight: 0.8980 chunk 235 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 158 optimal weight: 0.6980 chunk 198 optimal weight: 3.9990 chunk 351 optimal weight: 8.9990 chunk 82 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 341 optimal weight: 4.9990 chunk 209 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 375 GLN E 65 GLN E 232 GLN F 357 ASN ** 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 = 0.3223 r_free = 0.3223 target = 0.078816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.062542 restraints weight = 54668.717| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 1.86 r_work: 0.2756 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2617 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 28847 Z= 0.160 Angle : 0.618 18.193 38993 Z= 0.304 Chirality : 0.044 0.305 4419 Planarity : 0.004 0.053 5049 Dihedral : 7.814 128.754 4058 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.99 % Allowed : 15.26 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.14), residues: 3590 helix: 1.06 (0.13), residues: 1538 sheet: 0.59 (0.21), residues: 606 loop : 0.27 (0.16), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G1415 HIS 0.005 0.001 HIS G1345 PHE 0.026 0.002 PHE G1274 TYR 0.017 0.001 TYR F 310 ARG 0.011 0.001 ARG C 166 Details of bonding type rmsd hydrogen bonds : bond 0.03807 ( 1173) hydrogen bonds : angle 4.47856 ( 3339) covalent geometry : bond 0.00382 (28847) covalent geometry : angle 0.61824 (38993) *********************** 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 372 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 312 time to evaluate : 3.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8520 (tp) REVERT: A 159 LEU cc_start: 0.9099 (tp) cc_final: 0.8775 (tp) REVERT: A 345 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8195 (tt) REVERT: A 419 ARG cc_start: 0.8101 (ttm110) cc_final: 0.7686 (ttp80) REVERT: B 60 HIS cc_start: 0.8017 (OUTLIER) cc_final: 0.7607 (m90) REVERT: B 429 GLN cc_start: 0.8703 (OUTLIER) cc_final: 0.8476 (pm20) REVERT: C 8 ARG cc_start: 0.7724 (OUTLIER) cc_final: 0.7497 (mmm160) REVERT: C 127 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7643 (mt-10) REVERT: C 179 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7801 (tm-30) REVERT: C 409 GLN cc_start: 0.8320 (OUTLIER) cc_final: 0.8097 (mt0) REVERT: C 427 ASP cc_start: 0.8289 (t0) cc_final: 0.7885 (t0) REVERT: C 433 GLU cc_start: 0.8161 (tp30) cc_final: 0.7901 (tp30) REVERT: D 65 GLN cc_start: 0.8200 (OUTLIER) cc_final: 0.7557 (mt0) REVERT: D 134 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7383 (tp30) REVERT: D 137 ILE cc_start: 0.9044 (pt) cc_final: 0.8764 (mp) REVERT: D 217 MET cc_start: 0.7792 (mtp) cc_final: 0.7431 (mtt) REVERT: D 304 ASP cc_start: 0.8258 (OUTLIER) cc_final: 0.8005 (p0) REVERT: E 96 GLN cc_start: 0.7892 (tp40) cc_final: 0.7664 (tm-30) REVERT: E 136 GLU cc_start: 0.8479 (mm-30) cc_final: 0.8263 (mt-10) REVERT: E 148 ASP cc_start: 0.8002 (t70) cc_final: 0.7460 (p0) REVERT: E 183 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8156 (ttpt) REVERT: E 273 ASP cc_start: 0.8534 (OUTLIER) cc_final: 0.8249 (m-30) REVERT: E 418 LYS cc_start: 0.8493 (mmmt) cc_final: 0.8263 (tptt) REVERT: F 28 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.7427 (mtt90) REVERT: F 109 PHE cc_start: 0.8766 (m-80) cc_final: 0.8499 (m-80) REVERT: F 168 GLU cc_start: 0.8426 (tt0) cc_final: 0.8148 (tt0) REVERT: F 183 LYS cc_start: 0.9084 (OUTLIER) cc_final: 0.8806 (tttp) REVERT: F 263 ASP cc_start: 0.7825 (t70) cc_final: 0.7524 (t0) REVERT: G 1240 MET cc_start: 0.6976 (mpm) cc_final: 0.5920 (mtt) REVERT: J 42 GLN cc_start: 0.7780 (OUTLIER) cc_final: 0.7135 (mm-40) REVERT: J 94 MET cc_start: 0.7512 (mpm) cc_final: 0.7230 (mpm) REVERT: J 106 TYR cc_start: 0.8052 (m-80) cc_final: 0.7476 (m-80) REVERT: J 667 GLN cc_start: 0.8219 (OUTLIER) cc_final: 0.8006 (mp10) outliers start: 60 outliers final: 24 residues processed: 358 average time/residue: 1.6622 time to fit residues: 678.3721 Evaluate side-chains 338 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 298 time to evaluate : 3.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU 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 345 LEU 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 8 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 C residue 409 GLN Chi-restraints excluded: chain C residue 419 ARG 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 202 THR 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 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 325 MET Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain G residue 1593 ASN Chi-restraints excluded: chain I residue 156 ASN Chi-restraints excluded: chain I residue 210 GLU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 214 optimal weight: 5.9990 chunk 208 optimal weight: 3.9990 chunk 337 optimal weight: 2.9990 chunk 170 optimal weight: 5.9990 chunk 219 optimal weight: 5.9990 chunk 351 optimal weight: 7.9990 chunk 120 optimal weight: 0.9980 chunk 195 optimal weight: 6.9990 chunk 233 optimal weight: 7.9990 chunk 105 optimal weight: 2.9990 chunk 226 optimal weight: 4.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN B 252 GLN C 19 HIS C 237 GLN D 65 GLN E 65 GLN ** 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 = 0.3184 r_free = 0.3184 target = 0.076908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.060788 restraints weight = 55246.286| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 1.83 r_work: 0.2708 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2568 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 28847 Z= 0.278 Angle : 0.722 16.603 38993 Z= 0.359 Chirality : 0.049 0.425 4419 Planarity : 0.005 0.076 5049 Dihedral : 8.304 132.706 4058 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.99 % Allowed : 15.66 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.14), residues: 3590 helix: 0.66 (0.13), residues: 1539 sheet: 0.51 (0.21), residues: 606 loop : 0.07 (0.16), residues: 1445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP G1367 HIS 0.007 0.001 HIS G1345 PHE 0.029 0.002 PHE G1274 TYR 0.019 0.002 TYR A 193 ARG 0.019 0.001 ARG F 234 Details of bonding type rmsd hydrogen bonds : bond 0.04769 ( 1173) hydrogen bonds : angle 4.78959 ( 3339) covalent geometry : bond 0.00670 (28847) covalent geometry : angle 0.72177 (38993) *********************** 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 357 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 297 time to evaluate : 3.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8593 (tp) REVERT: A 86 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.8338 (mt0) REVERT: A 159 LEU cc_start: 0.9091 (tp) cc_final: 0.8750 (tp) REVERT: A 345 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8228 (tt) REVERT: A 419 ARG cc_start: 0.8132 (ttm110) cc_final: 0.7906 (ttp80) REVERT: B 60 HIS cc_start: 0.8089 (OUTLIER) cc_final: 0.7542 (m90) REVERT: B 429 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.8452 (pm20) REVERT: C 127 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7588 (mt-10) REVERT: C 179 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7745 (tm-30) REVERT: C 409 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.8047 (mt0) REVERT: C 427 ASP cc_start: 0.8372 (t0) cc_final: 0.7946 (t70) REVERT: C 433 GLU cc_start: 0.8221 (tp30) cc_final: 0.7952 (tp30) REVERT: D 137 ILE cc_start: 0.9028 (pt) cc_final: 0.8723 (mp) REVERT: E 96 GLN cc_start: 0.7996 (tp40) cc_final: 0.7785 (tm-30) REVERT: E 137 ILE cc_start: 0.9209 (OUTLIER) cc_final: 0.8987 (tp) REVERT: E 183 LYS cc_start: 0.8747 (OUTLIER) cc_final: 0.8228 (ttpt) REVERT: E 273 ASP cc_start: 0.8562 (OUTLIER) cc_final: 0.8269 (m-30) REVERT: E 418 LYS cc_start: 0.8550 (mmmt) cc_final: 0.8274 (tptt) REVERT: F 28 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.7350 (mtt90) REVERT: F 263 ASP cc_start: 0.8012 (t70) cc_final: 0.7640 (t0) REVERT: G 1240 MET cc_start: 0.6882 (mpm) cc_final: 0.5906 (mtt) REVERT: G 1299 THR cc_start: 0.8740 (m) cc_final: 0.8487 (t) REVERT: J 42 GLN cc_start: 0.7762 (OUTLIER) cc_final: 0.7082 (mm-40) REVERT: J 94 MET cc_start: 0.7455 (mpm) cc_final: 0.7214 (mpm) REVERT: J 106 TYR cc_start: 0.8186 (m-80) cc_final: 0.7498 (m-80) outliers start: 60 outliers final: 28 residues processed: 344 average time/residue: 1.7503 time to fit residues: 687.1721 Evaluate side-chains 314 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 274 time to evaluate : 3.050 ------------------------------------------------------------------------------- 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 345 LEU 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 419 ARG Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain E residue 137 ILE 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 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 138 MET 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 1593 ASN Chi-restraints excluded: chain I residue 23 HIS Chi-restraints excluded: chain I residue 156 ASN Chi-restraints excluded: chain I residue 210 GLU Chi-restraints excluded: chain J residue 42 GLN Chi-restraints excluded: chain J residue 50 LEU 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 218 optimal weight: 3.9990 chunk 295 optimal weight: 7.9990 chunk 314 optimal weight: 0.0670 chunk 165 optimal weight: 3.9990 chunk 243 optimal weight: 0.7980 chunk 345 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 291 optimal weight: 3.9990 chunk 240 optimal weight: 0.8980 chunk 268 optimal weight: 3.9990 chunk 275 optimal weight: 3.9990 overall best weight: 1.1320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 65 GLN E 254 GLN F 357 ASN ** G1404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.078695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.062479 restraints weight = 54501.568| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 1.86 r_work: 0.2756 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2617 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28847 Z= 0.140 Angle : 0.627 18.859 38993 Z= 0.308 Chirality : 0.043 0.270 4419 Planarity : 0.004 0.066 5049 Dihedral : 7.845 129.806 4058 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.39 % Allowed : 16.49 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.14), residues: 3590 helix: 0.96 (0.13), residues: 1536 sheet: 0.55 (0.21), residues: 603 loop : 0.14 (0.16), residues: 1451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G1367 HIS 0.004 0.001 HIS G1345 PHE 0.027 0.001 PHE G1274 TYR 0.016 0.001 TYR E 310 ARG 0.018 0.001 ARG F 234 Details of bonding type rmsd hydrogen bonds : bond 0.03682 ( 1173) hydrogen bonds : angle 4.50753 ( 3339) covalent geometry : bond 0.00331 (28847) covalent geometry : angle 0.62704 (38993) *********************** 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 348 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 306 time to evaluate : 3.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8505 (tp) REVERT: A 159 LEU cc_start: 0.9081 (tp) cc_final: 0.8772 (tp) REVERT: A 345 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8212 (tt) REVERT: A 419 ARG cc_start: 0.8220 (ttm110) cc_final: 0.7975 (ttm170) REVERT: B 60 HIS cc_start: 0.7975 (OUTLIER) cc_final: 0.7546 (m90) REVERT: B 269 MET cc_start: 0.8126 (mtm) cc_final: 0.7189 (mmt) REVERT: B 423 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.8135 (mtm180) REVERT: C 8 ARG cc_start: 0.7713 (mmm160) cc_final: 0.7391 (tpm-80) REVERT: C 127 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7618 (mt-10) REVERT: C 179 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7799 (tm-30) REVERT: C 427 ASP cc_start: 0.8316 (t0) cc_final: 0.7915 (t70) REVERT: C 433 GLU cc_start: 0.8172 (tp30) cc_final: 0.7885 (tp30) REVERT: D 137 ILE cc_start: 0.9026 (pt) cc_final: 0.8765 (mp) REVERT: E 137 ILE cc_start: 0.9144 (OUTLIER) cc_final: 0.8901 (tp) REVERT: E 183 LYS cc_start: 0.8696 (OUTLIER) cc_final: 0.8140 (ttpt) REVERT: E 273 ASP cc_start: 0.8523 (OUTLIER) cc_final: 0.8240 (m-30) REVERT: E 418 LYS cc_start: 0.8562 (mmmt) cc_final: 0.8299 (tptt) REVERT: F 28 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7404 (mtt90) REVERT: F 109 PHE cc_start: 0.8752 (m-80) cc_final: 0.8492 (m-80) REVERT: F 263 ASP cc_start: 0.7903 (t70) cc_final: 0.7579 (t0) REVERT: G 1240 MET cc_start: 0.6903 (mpm) cc_final: 0.5855 (mtt) REVERT: G 1299 THR cc_start: 0.8767 (m) cc_final: 0.8527 (t) REVERT: J 42 GLN cc_start: 0.7776 (OUTLIER) cc_final: 0.7103 (mm-40) REVERT: J 106 TYR cc_start: 0.8160 (m-80) cc_final: 0.7482 (m-80) outliers start: 42 outliers final: 23 residues processed: 339 average time/residue: 1.6803 time to fit residues: 649.7166 Evaluate side-chains 328 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 295 time to evaluate : 3.350 ------------------------------------------------------------------------------- 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 A residue 428 VAL Chi-restraints excluded: chain B residue 60 HIS Chi-restraints excluded: chain B residue 345 LEU 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 420 VAL Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 222 LYS Chi-restraints excluded: chain E residue 137 ILE 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 F residue 28 ARG Chi-restraints excluded: chain F residue 138 MET 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 1256 THR Chi-restraints excluded: chain G residue 1593 ASN Chi-restraints excluded: chain I residue 23 HIS Chi-restraints excluded: chain I residue 156 ASN Chi-restraints excluded: chain I residue 210 GLU 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 274 optimal weight: 4.9990 chunk 300 optimal weight: 6.9990 chunk 193 optimal weight: 5.9990 chunk 225 optimal weight: 6.9990 chunk 246 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 336 optimal weight: 4.9990 chunk 141 optimal weight: 1.9990 chunk 204 optimal weight: 0.7980 chunk 341 optimal weight: 0.8980 chunk 292 optimal weight: 0.0870 overall best weight: 1.7562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 65 GLN ** G1404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 31 ASN J 633 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.078036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.061737 restraints weight = 54917.307| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 1.87 r_work: 0.2737 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2597 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 28847 Z= 0.178 Angle : 0.652 12.059 38993 Z= 0.323 Chirality : 0.045 0.320 4419 Planarity : 0.005 0.075 5049 Dihedral : 7.954 129.771 4058 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.39 % Allowed : 16.82 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.14), residues: 3590 helix: 0.92 (0.13), residues: 1531 sheet: 0.51 (0.21), residues: 606 loop : 0.09 (0.16), residues: 1453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G1367 HIS 0.006 0.001 HIS G1345 PHE 0.029 0.002 PHE G1274 TYR 0.017 0.002 TYR E 310 ARG 0.017 0.001 ARG F 234 Details of bonding type rmsd hydrogen bonds : bond 0.04000 ( 1173) hydrogen bonds : angle 4.56628 ( 3339) covalent geometry : bond 0.00428 (28847) covalent geometry : angle 0.65188 (38993) ********************** 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 338 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 296 time to evaluate : 3.240 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8541 (tp) REVERT: A 159 LEU cc_start: 0.9086 (tp) cc_final: 0.8792 (tp) REVERT: A 345 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8238 (tt) REVERT: A 419 ARG cc_start: 0.8254 (ttm110) cc_final: 0.8015 (ttm170) REVERT: B 60 HIS cc_start: 0.7990 (OUTLIER) cc_final: 0.7548 (m90) REVERT: B 269 MET cc_start: 0.8138 (mtm) cc_final: 0.7193 (mmt) REVERT: C 8 ARG cc_start: 0.7721 (mmm160) cc_final: 0.7384 (tpm-80) REVERT: C 127 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7648 (mt-10) REVERT: C 179 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7789 (tm-30) REVERT: C 409 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.8136 (mt0) REVERT: C 427 ASP cc_start: 0.8313 (t0) cc_final: 0.7903 (t70) REVERT: C 433 GLU cc_start: 0.8187 (tp30) cc_final: 0.7896 (tp30) REVERT: D 137 ILE cc_start: 0.9020 (pt) cc_final: 0.8764 (mp) REVERT: E 137 ILE cc_start: 0.9172 (OUTLIER) cc_final: 0.8932 (tp) REVERT: E 183 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.8196 (ttpt) REVERT: E 273 ASP cc_start: 0.8553 (OUTLIER) cc_final: 0.8268 (m-30) REVERT: E 418 LYS cc_start: 0.8569 (mmmt) cc_final: 0.8287 (tptt) REVERT: F 28 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.7397 (mtt90) REVERT: F 109 PHE cc_start: 0.8777 (m-80) cc_final: 0.8510 (m-80) REVERT: F 263 ASP cc_start: 0.7925 (t70) cc_final: 0.7582 (t0) REVERT: G 1240 MET cc_start: 0.6930 (mpm) cc_final: 0.5904 (mtt) REVERT: G 1299 THR cc_start: 0.8775 (m) cc_final: 0.8542 (t) REVERT: G 1578 MET cc_start: 0.8017 (OUTLIER) cc_final: 0.7192 (mtm) REVERT: J 42 GLN cc_start: 0.7813 (OUTLIER) cc_final: 0.7109 (mm-40) REVERT: J 94 MET cc_start: 0.7437 (mpm) cc_final: 0.7225 (mpm) REVERT: J 106 TYR cc_start: 0.8139 (m-80) cc_final: 0.7447 (m-80) outliers start: 42 outliers final: 25 residues processed: 325 average time/residue: 1.6837 time to fit residues: 623.8877 Evaluate side-chains 319 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 283 time to evaluate : 3.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU 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 345 LEU 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 C residue 409 GLN Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 222 LYS Chi-restraints excluded: chain E residue 62 MET Chi-restraints excluded: chain E residue 137 ILE 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 F residue 28 ARG Chi-restraints excluded: chain F residue 138 MET 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 1256 THR Chi-restraints excluded: chain G residue 1408 ASP Chi-restraints excluded: chain G residue 1578 MET Chi-restraints excluded: chain G residue 1593 ASN Chi-restraints excluded: chain I residue 156 ASN Chi-restraints excluded: chain I residue 210 GLU 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 212 optimal weight: 0.6980 chunk 225 optimal weight: 6.9990 chunk 313 optimal weight: 4.9990 chunk 331 optimal weight: 3.9990 chunk 307 optimal weight: 0.0470 chunk 201 optimal weight: 0.9980 chunk 238 optimal weight: 3.9990 chunk 325 optimal weight: 0.8980 chunk 210 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 190 optimal weight: 5.9990 overall best weight: 1.3280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 357 ASN ** G1404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 633 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.078408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.062193 restraints weight = 54897.921| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 1.86 r_work: 0.2749 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2609 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 28847 Z= 0.153 Angle : 0.648 20.125 38993 Z= 0.317 Chirality : 0.044 0.323 4419 Planarity : 0.005 0.077 5049 Dihedral : 7.865 128.295 4058 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.49 % Allowed : 16.99 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.14), residues: 3590 helix: 0.99 (0.13), residues: 1531 sheet: 0.52 (0.21), residues: 606 loop : 0.10 (0.16), residues: 1453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G1367 HIS 0.005 0.001 HIS G1345 PHE 0.029 0.001 PHE G1274 TYR 0.017 0.002 TYR G1521 ARG 0.017 0.001 ARG J 602 Details of bonding type rmsd hydrogen bonds : bond 0.03808 ( 1173) hydrogen bonds : angle 4.51699 ( 3339) covalent geometry : bond 0.00364 (28847) covalent geometry : angle 0.64799 (38993) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21357.68 seconds wall clock time: 368 minutes 52.04 seconds (22132.04 seconds total)