Starting phenix.real_space_refine on Mon May 26 12:39:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ooc_17010/05_2025/8ooc_17010.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ooc_17010/05_2025/8ooc_17010.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ooc_17010/05_2025/8ooc_17010.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ooc_17010/05_2025/8ooc_17010.map" model { file = "/net/cci-nas-00/data/ceres_data/8ooc_17010/05_2025/8ooc_17010.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ooc_17010/05_2025/8ooc_17010.cif" } resolution = 2.93 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= 0.030 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 Symmetric amino acids flipped. Time to flip 5 residue(s): 0.07s 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: {'PCIS': 2, 'PTRANS': 20, '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: 15.91, per 1000 atoms: 0.56 Number of scatterers: 28371 At special positions: 0 Unit cell: (133.164, 161.934, 176.73, 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: 7.61 Conformation dependent library (CDL) restraints added in 4.0 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: 156 helices and 31 sheets defined 45.5% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.62 Creating SS restraints... Processing helix chain 'A' and resid 43 through 59 Processing helix chain 'A' and resid 76 through 88 Processing helix chain 'A' and resid 100 through 102 No H-bonds generated for 'chain 'A' and resid 100 through 102' Processing helix chain 'A' and resid 108 through 120 Processing helix chain 'A' and resid 174 through 184 removed outlier: 3.597A pdb=" N ALA A 180 " --> pdb=" O SER A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 250 Processing helix chain 'A' and resid 256 through 265 removed outlier: 3.679A pdb=" N LEU A 264 " --> pdb=" O MET A 260 " (cutoff:3.500A) 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 321 removed outlier: 3.995A pdb=" N LYS A 318 " --> pdb=" O THR A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 357 removed outlier: 3.642A pdb=" N GLN A 357 " --> pdb=" O PRO A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 383 Processing helix chain 'A' and resid 388 through 396 Processing helix chain 'A' and resid 403 through 421 removed outlier: 3.703A pdb=" N CYS A 407 " --> pdb=" O SER A 403 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU A 411 " --> pdb=" O CYS A 407 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ALA A 412 " --> pdb=" O LEU A 408 " (cutoff:3.500A) Proline residue: A 413 - end of helix Processing helix chain 'A' and resid 427 through 438 removed outlier: 3.530A pdb=" N ILE A 431 " --> pdb=" O ASP A 427 " (cutoff:3.500A) removed outlier: 3.598A 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 'B' and resid 43 through 60 removed outlier: 3.527A pdb=" N HIS B 60 " --> pdb=" O LEU B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 88 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: 6.859A pdb=" N GLN B 263 " --> pdb=" O MET B 260 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N LEU B 264 " --> pdb=" O MET B 261 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS B 266 " --> pdb=" O GLN B 263 " (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: 3.768A pdb=" N LYS B 318 " --> pdb=" O THR B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 357 Processing helix chain 'B' and resid 368 through 383 Processing helix chain 'B' and resid 388 through 402 Processing helix chain 'B' and resid 403 through 421 removed outlier: 3.904A pdb=" N LEU B 411 " --> pdb=" O CYS B 407 " (cutoff:3.500A) removed outlier: 4.512A 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 removed outlier: 3.863A pdb=" N GLU B 436 " --> pdb=" O ALA B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 452 Processing helix chain 'C' and resid 43 through 59 Processing helix chain 'C' and resid 76 through 89 Processing helix 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 263 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 321 removed outlier: 3.817A pdb=" N LYS C 318 " --> pdb=" O THR C 314 " (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 421 removed outlier: 3.724A pdb=" N LEU C 411 " --> pdb=" O CYS C 407 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ALA C 412 " --> pdb=" O LEU C 408 " (cutoff:3.500A) Proline residue: C 413 - end of helix Processing helix chain 'C' and resid 427 through 438 removed outlier: 3.528A pdb=" N GLU C 433 " --> pdb=" O GLN C 429 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLU C 436 " --> pdb=" O ALA C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 452 Processing helix chain 'D' and resid 49 through 66 removed outlier: 3.619A pdb=" N GLY D 66 " --> pdb=" O MET D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 95 Processing helix chain 'D' and resid 106 through 109 removed outlier: 3.784A 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 125 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: 3.686A 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: 4.836A 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 396 Processing helix chain 'D' and resid 397 through 415 removed outlier: 3.616A pdb=" N ILE D 405 " --> pdb=" O ALA D 401 " (cutoff:3.500A) removed outlier: 3.866A 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: 3.615A 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 214 removed outlier: 5.013A pdb=" N ARG E 212 " --> pdb=" O ALA E 209 " (cutoff:3.500A) 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: 3.505A 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: 3.936A 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: 3.972A pdb=" N THR E 406 " --> pdb=" O SER E 402 " (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 126 removed outlier: 3.601A pdb=" N SER F 126 " --> pdb=" O ALA F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 184 Processing helix chain 'F' and resid 209 through 213 removed outlier: 4.178A pdb=" N ARG F 212 " --> pdb=" O ALA F 209 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 252 removed outlier: 4.281A 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: 3.583A 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: 3.950A 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: 4.081A pdb=" N THR F 406 " --> pdb=" O SER F 402 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR F 407 " --> pdb=" O ASN F 403 " (cutoff:3.500A) Processing helix chain 'F' and resid 421 through 432 Processing helix chain 'F' and resid 434 through 445 Processing helix chain 'F' and resid 446 through 449 Processing helix chain 'G' and resid 1223 through 1235 Processing helix chain 'G' and resid 1235 through 1240 removed outlier: 3.780A pdb=" N ILE G1239 " --> pdb=" O ASN G1235 " (cutoff:3.500A) Processing helix chain 'G' and resid 1257 through 1270 Processing helix chain 'G' and resid 1270 through 1275 removed outlier: 4.001A 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: 4.525A pdb=" N GLY G1337 " --> pdb=" O ASN G1333 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N PHE G1338 " --> pdb=" O LEU G1334 " (cutoff:3.500A) Processing helix chain 'G' and resid 1351 through 1357 removed outlier: 3.553A pdb=" N SER G1357 " --> pdb=" O GLU G1353 " (cutoff:3.500A) Processing helix chain 'G' and resid 1365 through 1370 removed outlier: 3.749A pdb=" N ARG G1369 " --> pdb=" O THR G1366 " (cutoff:3.500A) Processing helix chain 'G' and resid 1374 through 1384 Processing helix chain 'G' and resid 1385 through 1394 Processing helix chain 'G' and resid 1398 through 1407 removed outlier: 3.723A pdb=" N ILE G1405 " --> pdb=" O GLY G1401 " (cutoff:3.500A) 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: 4.060A pdb=" N VAL G1433 " --> pdb=" O ASN G1429 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU G1435 " --> pdb=" O LYS G1431 " (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: 3.668A 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 Processing helix chain 'G' and resid 1544 through 1551 Processing helix chain 'G' and resid 1552 through 1568 removed outlier: 3.791A pdb=" N GLU G1560 " --> pdb=" O ALA G1556 " (cutoff:3.500A) Processing helix chain 'G' and resid 1579 through 1593 removed outlier: 3.896A pdb=" N ASP G1583 " --> pdb=" O THR G1579 " (cutoff:3.500A) Processing helix chain 'H' and resid 468 through 475 removed outlier: 4.293A 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 43 through 51 Processing helix chain 'I' and resid 190 through 198 Processing helix chain 'I' and resid 203 through 212 removed outlier: 3.962A pdb=" N GLN I 207 " --> pdb=" O GLY I 203 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG I 212 " --> pdb=" O PHE I 208 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 21 Processing helix chain 'J' and resid 42 through 52 removed outlier: 3.852A pdb=" N ARG J 46 " --> pdb=" O GLN J 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 128 through 143 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: 3.873A pdb=" N HIS J 265 " --> pdb=" O SER J 261 " (cutoff:3.500A) Processing helix chain 'J' and resid 276 through 283 removed outlier: 3.934A pdb=" N GLY J 283 " --> pdb=" O ARG J 279 " (cutoff:3.500A) 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: 3.570A 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 668 Processing helix chain 'J' and resid 669 through 672 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 710 removed outlier: 3.636A pdb=" N ALA J 708 " --> pdb=" O GLN J 704 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU J 709 " --> pdb=" O GLY J 705 " (cutoff:3.500A) Processing helix chain 'J' and resid 726 through 736 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: 6.255A pdb=" N VAL A 67 " --> pdb=" O LEU A 330 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N SER A 332 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU A 69 " --> pdb=" O SER A 332 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N GLY A 66 " --> pdb=" O LEU A 360 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ILE A 362 " --> pdb=" O GLY A 66 " (cutoff:3.500A) removed outlier: 6.496A 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: 6.173A pdb=" N GLY A 161 " --> pdb=" O THR A 137 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N MET A 139 " --> pdb=" O LEU A 159 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU A 159 " --> pdb=" O MET A 139 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N THR A 157 " --> pdb=" O PRO A 141 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N GLU A 143 " --> pdb=" O ILE A 155 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE A 155 " --> pdb=" O GLU A 143 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 167 through 173 current: chain 'A' and resid 201 through 207 removed outlier: 5.975A pdb=" N VAL A 222 " --> pdb=" O VAL A 204 " (cutoff:3.500A) removed outlier: 5.917A 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 339 removed outlier: 5.666A pdb=" N LEU A 345 " --> pdb=" O ILE A 339 " (cutoff:3.500A) 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: 6.325A pdb=" N CYS B 95 " --> pdb=" O PHE B 301 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N ASP B 303 " --> pdb=" O CYS B 95 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE B 97 " --> pdb=" O ASP B 303 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N GLY B 66 " --> pdb=" O LEU B 360 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N ILE B 362 " --> pdb=" O GLY B 66 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU B 68 " --> pdb=" O ILE B 362 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 121 through 141 removed outlier: 6.083A pdb=" N GLY B 161 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N MET B 139 " --> pdb=" O LEU B 159 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU B 159 " --> pdb=" O MET B 139 " (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 201 through 207 removed outlier: 6.386A pdb=" N VAL B 222 " --> pdb=" O VAL B 204 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N ARG B 206 " --> pdb=" O VAL B 222 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 336 through 339 removed outlier: 5.869A 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: 6.223A pdb=" N VAL C 67 " --> pdb=" O LEU C 330 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N SER C 332 " --> pdb=" O VAL C 67 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LEU C 69 " --> pdb=" O SER C 332 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N GLY C 66 " --> pdb=" O LEU C 360 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ILE C 362 " --> pdb=" O GLY C 66 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LEU C 68 " --> pdb=" O ILE C 362 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N THR C 364 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ALA C 70 " --> pdb=" O THR C 364 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 121 through 143 removed outlier: 5.700A pdb=" N VAL C 136 " --> pdb=" O LYS C 163 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LYS C 163 " --> pdb=" O VAL C 136 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU C 138 " --> pdb=" O GLY C 161 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY C 167 " --> pdb=" O SER C 164 " (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: 6.491A pdb=" N VAL C 222 " --> pdb=" O VAL C 204 " (cutoff:3.500A) removed outlier: 5.848A 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 removed outlier: 3.729A pdb=" N GLY D 158 " --> pdb=" O MET D 173 " (cutoff:3.500A) 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: 6.016A pdb=" N LEU C 345 " --> pdb=" O ILE C 339 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 42 through 43 Processing sheet with id=AB5, first strand: chain 'D' and resid 100 through 104 Processing sheet with id=AB6, first strand: chain 'D' and resid 331 through 333 Processing sheet with id=AB7, first strand: chain 'E' and resid 42 through 43 Processing sheet with id=AB8, first strand: chain 'E' and resid 100 through 104 removed outlier: 6.583A pdb=" N THR E 101 " --> pdb=" O PHE E 296 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N ASP E 298 " --> pdb=" O THR E 101 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU E 103 " --> pdb=" O ASP E 298 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 127 through 147 removed outlier: 6.796A pdb=" N THR E 161 " --> pdb=" O VAL E 143 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ILE E 145 " --> pdb=" O LYS E 159 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LYS E 159 " --> pdb=" O ILE E 145 " (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=AC1, first strand: chain 'E' and resid 331 through 333 Processing sheet with id=AC2, first strand: chain 'F' and resid 42 through 43 Processing sheet with id=AC3, first strand: chain 'F' and resid 100 through 104 removed outlier: 6.648A pdb=" N THR F 101 " --> pdb=" O PHE F 296 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N ASP F 298 " --> pdb=" O THR F 101 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU F 103 " --> pdb=" O ASP F 298 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ALA F 72 " --> pdb=" O VAL F 354 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N ILE F 356 " --> pdb=" O ALA F 72 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N LEU F 74 " --> pdb=" O ILE F 356 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 127 through 148 removed outlier: 6.712A pdb=" N THR F 161 " --> pdb=" O VAL F 143 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ILE F 145 " --> pdb=" O LYS F 159 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LYS F 159 " --> pdb=" O ILE F 145 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N ILE F 147 " --> pdb=" O GLN F 157 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N GLN F 157 " --> pdb=" O ILE F 147 " (cutoff:3.500A) removed outlier: 3.600A 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 201 through 207 removed outlier: 6.643A pdb=" N LEU F 224 " --> pdb=" O LEU F 204 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ARG F 206 " --> pdb=" O LEU F 224 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 331 through 333 Processing sheet with id=AC6, first strand: chain 'G' and resid 1283 through 1284 removed outlier: 6.081A pdb=" N PHE G1283 " --> pdb=" O SER G1470 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'G' and resid 1286 through 1287 Processing sheet with id=AC8, first strand: chain 'G' and resid 1312 through 1314 removed outlier: 6.073A pdb=" N TYR G1313 " --> pdb=" O VAL G1477 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'I' and resid 179 through 180 removed outlier: 3.773A pdb=" N TYR I 179 " --> pdb=" O TYR I 188 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 27 through 29 Processing sheet with id=AD2, first strand: chain 'J' and resid 80 through 82 removed outlier: 4.676A pdb=" N ASN J 63 " --> pdb=" O THR J 159 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 97 through 101 Processing sheet with id=AD4, 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 1165 hydrogen bonds defined for protein. 3333 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: 10.53 Time building geometry restraints manager: 8.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9565 1.34 - 1.46: 3166 1.46 - 1.57: 15863 1.57 - 1.69: 23 1.69 - 1.81: 230 Bond restraints: 28847 Sorted by residual: bond pdb=" CB CYS C 407 " pdb=" SG CYS C 407 " ideal model delta sigma weight residual 1.808 1.743 0.065 3.30e-02 9.18e+02 3.93e+00 bond pdb=" CB CYS A 407 " pdb=" SG CYS A 407 " ideal model delta sigma weight residual 1.808 1.766 0.042 3.30e-02 9.18e+02 1.62e+00 bond pdb=" CA PRO G1522 " pdb=" CB PRO G1522 " ideal model delta sigma weight residual 1.533 1.556 -0.023 1.80e-02 3.09e+03 1.59e+00 bond pdb=" C4 ADP B 501 " pdb=" C5 ADP B 501 " ideal model delta sigma weight residual 1.490 1.466 0.024 2.00e-02 2.50e+03 1.42e+00 bond pdb=" CG1 ILE B 102 " pdb=" CD1 ILE B 102 " ideal model delta sigma weight residual 1.513 1.467 0.046 3.90e-02 6.57e+02 1.38e+00 ... (remaining 28842 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 38228 2.01 - 4.02: 665 4.02 - 6.03: 84 6.03 - 8.04: 8 8.04 - 10.05: 8 Bond angle restraints: 38993 Sorted by residual: angle pdb=" C1' ADP A 501 " pdb=" C2' ADP A 501 " pdb=" C3' ADP A 501 " ideal model delta sigma weight residual 111.00 100.95 10.05 3.00e+00 1.11e-01 1.12e+01 angle pdb=" CA PRO G1522 " pdb=" C PRO G1522 " pdb=" N PRO G1523 " ideal model delta sigma weight residual 117.10 126.25 -9.15 2.80e+00 1.28e-01 1.07e+01 angle pdb=" C1' ADP F 501 " pdb=" C2' ADP F 501 " pdb=" C3' ADP F 501 " ideal model delta sigma weight residual 111.00 101.27 9.73 3.00e+00 1.11e-01 1.05e+01 angle pdb=" C1' ADP D 501 " pdb=" C2' ADP D 501 " pdb=" C3' ADP D 501 " ideal model delta sigma weight residual 111.00 102.27 8.73 3.00e+00 1.11e-01 8.47e+00 angle pdb=" C1' ADP E 501 " pdb=" C2' ADP E 501 " pdb=" C3' ADP E 501 " ideal model delta sigma weight residual 111.00 102.41 8.59 3.00e+00 1.11e-01 8.20e+00 ... (remaining 38988 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.46: 17387 35.46 - 70.91: 263 70.91 - 106.36: 28 106.36 - 141.82: 3 141.82 - 177.27: 6 Dihedral angle restraints: 17687 sinusoidal: 7292 harmonic: 10395 Sorted by residual: 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 300.00 122.72 177.27 1 2.00e+01 2.50e-03 4.80e+01 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 -60.00 97.98 -157.99 1 2.00e+01 2.50e-03 4.63e+01 dihedral pdb=" C5' ADP A 501 " pdb=" O5' ADP A 501 " pdb=" PA ADP A 501 " pdb=" O2A ADP A 501 " ideal model delta sinusoidal sigma weight residual 300.00 148.52 151.49 1 2.00e+01 2.50e-03 4.51e+01 ... (remaining 17684 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 3278 0.048 - 0.096: 879 0.096 - 0.145: 242 0.145 - 0.193: 19 0.193 - 0.241: 1 Chirality restraints: 4419 Sorted by residual: chirality pdb=" CA THR D 81 " pdb=" N THR D 81 " pdb=" C THR D 81 " pdb=" CB THR D 81 " both_signs ideal model delta sigma weight residual False 2.53 2.29 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" C2' ADP D 501 " pdb=" C1' ADP D 501 " pdb=" C3' ADP D 501 " pdb=" O2' ADP D 501 " both_signs ideal model delta sigma weight residual False -2.51 -2.68 0.17 2.00e-01 2.50e+01 7.46e-01 chirality pdb=" CA ILE B 351 " pdb=" N ILE B 351 " pdb=" C ILE B 351 " pdb=" CB ILE B 351 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.33e-01 ... (remaining 4416 not shown) Planarity restraints: 5049 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 252 " 0.380 9.50e-02 1.11e+02 1.71e-01 2.10e+01 pdb=" NE ARG D 252 " -0.033 2.00e-02 2.50e+03 pdb=" CZ ARG D 252 " 0.027 2.00e-02 2.50e+03 pdb=" NH1 ARG D 252 " -0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG D 252 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 313 " -0.359 9.50e-02 1.11e+02 1.62e-01 2.08e+01 pdb=" NE ARG E 313 " 0.034 2.00e-02 2.50e+03 pdb=" CZ ARG E 313 " -0.035 2.00e-02 2.50e+03 pdb=" NH1 ARG E 313 " 0.016 2.00e-02 2.50e+03 pdb=" NH2 ARG E 313 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 437 " 0.351 9.50e-02 1.11e+02 1.58e-01 1.86e+01 pdb=" NE ARG F 437 " -0.032 2.00e-02 2.50e+03 pdb=" CZ ARG F 437 " 0.028 2.00e-02 2.50e+03 pdb=" NH1 ARG F 437 " -0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG F 437 " 0.002 2.00e-02 2.50e+03 ... (remaining 5046 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 325 2.64 - 3.20: 26583 3.20 - 3.77: 43501 3.77 - 4.33: 65066 4.33 - 4.90: 104124 Nonbonded interactions: 239599 Sorted by model distance: nonbonded pdb=" OD2 ASP J 190 " pdb="MG MG J 801 " model vdw 2.069 2.170 nonbonded pdb="MG MG J 801 " pdb=" O1G ATP J 802 " model vdw 2.096 2.170 nonbonded pdb="MG MG J 801 " pdb=" O1B ATP J 802 " model vdw 2.159 2.170 nonbonded pdb=" ND1 HIS J 197 " pdb=" OD2 ASP J 727 " model vdw 2.204 3.120 nonbonded pdb=" OH TYR E 400 " pdb=" O PHE E 432 " model vdw 2.208 3.040 ... (remaining 239594 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.440 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: 1.020 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 63.410 Find NCS groups from input model: 1.370 Set up NCS constraints: 0.130 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:12.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 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 : 0.003 0.065 28847 Z= 0.133 Angle : 0.695 10.048 38993 Z= 0.390 Chirality : 0.047 0.241 4419 Planarity : 0.011 0.171 5049 Dihedral : 14.059 177.274 10997 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % 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: -1.01 (0.13), residues: 3590 helix: -1.47 (0.11), residues: 1523 sheet: 0.59 (0.21), residues: 544 loop : -0.02 (0.15), residues: 1523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP H 450 HIS 0.007 0.001 HIS G1345 PHE 0.020 0.002 PHE G1501 TYR 0.032 0.005 TYR A 210 ARG 0.039 0.004 ARG E 313 Details of bonding type rmsd hydrogen bonds : bond 0.19071 ( 1165) hydrogen bonds : angle 7.48059 ( 3333) covalent geometry : bond 0.00289 (28847) covalent geometry : angle 0.69533 (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 707 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 707 time to evaluate : 3.195 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 373 ARG cc_start: 0.8139 (ttm110) cc_final: 0.7672 (ttp80) REVERT: B 181 ILE cc_start: 0.8499 (mm) cc_final: 0.8291 (mt) REVERT: B 265 MET cc_start: 0.8698 (mmt) cc_final: 0.8359 (mmt) REVERT: B 378 ILE cc_start: 0.8669 (mt) cc_final: 0.8307 (mp) REVERT: B 449 THR cc_start: 0.8041 (m) cc_final: 0.7763 (p) REVERT: C 6 GLU cc_start: 0.7028 (mt-10) cc_final: 0.6647 (mt-10) REVERT: C 103 TYR cc_start: 0.8282 (m-80) cc_final: 0.8002 (m-10) REVERT: C 106 GLU cc_start: 0.7902 (tt0) cc_final: 0.7596 (mt-10) REVERT: C 303 ASP cc_start: 0.7487 (t0) cc_final: 0.6616 (t0) REVERT: C 307 MET cc_start: 0.8592 (mmp) cc_final: 0.8201 (mmt) REVERT: C 368 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7688 (mm-30) REVERT: D 134 GLU cc_start: 0.7432 (tt0) cc_final: 0.6774 (tt0) REVERT: D 167 MET cc_start: 0.8664 (mtp) cc_final: 0.8325 (ttm) REVERT: D 184 GLU cc_start: 0.8022 (tp30) cc_final: 0.7576 (tp30) REVERT: D 232 GLN cc_start: 0.8194 (mm-40) cc_final: 0.7666 (mm-40) REVERT: D 441 PHE cc_start: 0.8709 (t80) cc_final: 0.8452 (t80) REVERT: F 167 MET cc_start: 0.7945 (mtp) cc_final: 0.7675 (ttm) REVERT: F 183 LYS cc_start: 0.8573 (mmmm) cc_final: 0.8191 (tptp) REVERT: G 1479 ASP cc_start: 0.7077 (p0) cc_final: 0.6724 (p0) REVERT: G 1538 THR cc_start: 0.8402 (p) cc_final: 0.8188 (t) REVERT: G 1545 MET cc_start: 0.7764 (mmt) cc_final: 0.7407 (mmt) REVERT: I 166 MET cc_start: 0.8411 (ptp) cc_final: 0.8204 (ptp) REVERT: J 142 LYS cc_start: 0.8243 (mmtt) cc_final: 0.8034 (mptp) REVERT: J 168 SER cc_start: 0.8875 (m) cc_final: 0.8494 (p) REVERT: J 751 TYR cc_start: 0.8618 (t80) cc_final: 0.8036 (t80) outliers start: 0 outliers final: 0 residues processed: 707 average time/residue: 1.8916 time to fit residues: 1501.0681 Evaluate side-chains 361 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 361 time to evaluate : 3.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 300 optimal weight: 0.2980 chunk 269 optimal weight: 5.9990 chunk 149 optimal weight: 0.6980 chunk 92 optimal weight: 0.5980 chunk 182 optimal weight: 1.9990 chunk 144 optimal weight: 0.9990 chunk 279 optimal weight: 5.9990 chunk 107 optimal weight: 7.9990 chunk 169 optimal weight: 0.9980 chunk 207 optimal weight: 3.9990 chunk 323 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 60 HIS B 421 ASN B 446 ASN C 237 GLN D 225 GLN D 328 ASN E 312 ASN E 419 GLN F 96 GLN F 394 GLN G1345 HIS G1423 GLN J 697 ASN J 722 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.086857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.070657 restraints weight = 52740.141| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 1.94 r_work: 0.2912 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 28847 Z= 0.139 Angle : 0.641 9.293 38993 Z= 0.329 Chirality : 0.044 0.257 4419 Planarity : 0.005 0.057 5049 Dihedral : 9.406 177.915 4058 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 2.48 % Allowed : 10.93 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % 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: 0.41 (0.14), residues: 3590 helix: 0.24 (0.13), residues: 1547 sheet: 0.49 (0.21), residues: 548 loop : 0.48 (0.16), residues: 1495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP J 19 HIS 0.009 0.001 HIS B 60 PHE 0.020 0.002 PHE D 223 TYR 0.015 0.002 TYR D 310 ARG 0.010 0.001 ARG J 21 Details of bonding type rmsd hydrogen bonds : bond 0.04452 ( 1165) hydrogen bonds : angle 5.14326 ( 3333) covalent geometry : bond 0.00308 (28847) covalent geometry : angle 0.64107 (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 470 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 395 time to evaluate : 3.260 Fit side-chains revert: symmetry clash REVERT: A 373 ARG cc_start: 0.8321 (ttm110) cc_final: 0.7866 (ttp80) REVERT: B 62 MET cc_start: 0.8385 (OUTLIER) cc_final: 0.8038 (mpp) REVERT: B 265 MET cc_start: 0.8668 (mmt) cc_final: 0.8438 (mmt) REVERT: B 449 THR cc_start: 0.7959 (m) cc_final: 0.7735 (p) REVERT: C 106 GLU cc_start: 0.8163 (tt0) cc_final: 0.7765 (mt-10) REVERT: C 307 MET cc_start: 0.8631 (mmp) cc_final: 0.8313 (mmt) REVERT: C 368 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7563 (mm-30) REVERT: D 184 GLU cc_start: 0.8336 (tp30) cc_final: 0.8129 (mm-30) REVERT: D 232 GLN cc_start: 0.8316 (mm-40) cc_final: 0.7909 (mm110) REVERT: D 460 TYR cc_start: 0.7928 (t80) cc_final: 0.7564 (t80) REVERT: E 159 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8296 (tttm) REVERT: F 62 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.8339 (mtp) REVERT: F 133 GLU cc_start: 0.6127 (tt0) cc_final: 0.5903 (pp20) REVERT: F 183 LYS cc_start: 0.8666 (mmmm) cc_final: 0.8336 (tptp) REVERT: G 1377 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6976 (mm-30) REVERT: G 1397 GLN cc_start: 0.8208 (OUTLIER) cc_final: 0.7474 (mm-40) REVERT: G 1538 THR cc_start: 0.8497 (p) cc_final: 0.8286 (t) REVERT: H 455 MET cc_start: 0.8495 (mmp) cc_final: 0.7974 (mpp) REVERT: I 30 ARG cc_start: 0.8071 (ttm-80) cc_final: 0.7625 (tpt90) REVERT: I 167 LYS cc_start: 0.8379 (OUTLIER) cc_final: 0.8065 (mttm) REVERT: J 86 MET cc_start: 0.8022 (OUTLIER) cc_final: 0.7812 (ptt) REVERT: J 168 SER cc_start: 0.8814 (m) cc_final: 0.8426 (p) REVERT: J 174 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7185 (mp0) REVERT: J 222 LYS cc_start: 0.8301 (OUTLIER) cc_final: 0.7672 (ttmm) outliers start: 75 outliers final: 24 residues processed: 443 average time/residue: 1.7155 time to fit residues: 862.8983 Evaluate side-chains 351 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 318 time to evaluate : 3.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 386 GLN Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain D residue 306 GLU Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 187 MET Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain F residue 62 MET Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain G residue 1377 GLU Chi-restraints excluded: chain G residue 1397 GLN Chi-restraints excluded: chain G residue 1544 SER Chi-restraints excluded: chain H residue 461 VAL Chi-restraints excluded: chain I residue 163 LEU Chi-restraints excluded: chain I residue 167 LYS Chi-restraints excluded: chain J residue 52 GLN Chi-restraints excluded: chain J residue 86 MET Chi-restraints excluded: chain J residue 128 ASN Chi-restraints excluded: chain J residue 174 GLU Chi-restraints excluded: chain J residue 222 LYS Chi-restraints excluded: chain J residue 288 THR Chi-restraints excluded: chain J residue 297 VAL Chi-restraints excluded: chain J residue 623 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: 0.5980 chunk 334 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 chunk 189 optimal weight: 0.8980 chunk 257 optimal weight: 5.9990 chunk 163 optimal weight: 3.9990 chunk 280 optimal weight: 0.6980 chunk 301 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 265 optimal weight: 6.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 421 ASN B 446 ASN C 230 HIS D 24 HIS D 328 ASN E 312 ASN J 259 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.084277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.067823 restraints weight = 53128.221| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 1.95 r_work: 0.2853 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2713 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 28847 Z= 0.190 Angle : 0.645 10.063 38993 Z= 0.326 Chirality : 0.046 0.177 4419 Planarity : 0.005 0.063 5049 Dihedral : 8.935 171.896 4058 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.05 % Allowed : 12.09 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % 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: 0.45 (0.14), residues: 3590 helix: 0.43 (0.13), residues: 1541 sheet: 0.42 (0.21), residues: 542 loop : 0.33 (0.16), residues: 1507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP J 129 HIS 0.008 0.002 HIS B 21 PHE 0.020 0.002 PHE G1501 TYR 0.019 0.002 TYR D 310 ARG 0.009 0.001 ARG D 234 Details of bonding type rmsd hydrogen bonds : bond 0.04576 ( 1165) hydrogen bonds : angle 4.94659 ( 3333) covalent geometry : bond 0.00452 (28847) covalent geometry : angle 0.64478 (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 430 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 338 time to evaluate : 3.116 Fit side-chains revert: symmetry clash REVERT: A 157 THR cc_start: 0.8637 (t) cc_final: 0.8318 (m) REVERT: A 373 ARG cc_start: 0.8359 (ttm110) cc_final: 0.7900 (ttp80) REVERT: B 62 MET cc_start: 0.8419 (OUTLIER) cc_final: 0.8042 (mpp) REVERT: B 386 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.7909 (mp10) REVERT: B 449 THR cc_start: 0.8063 (m) cc_final: 0.7817 (p) REVERT: C 106 GLU cc_start: 0.8168 (tt0) cc_final: 0.7791 (mt-10) REVERT: C 307 MET cc_start: 0.8685 (mmp) cc_final: 0.8212 (mmt) REVERT: C 368 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7708 (mm-30) REVERT: D 184 GLU cc_start: 0.8308 (tp30) cc_final: 0.7925 (tp30) REVERT: D 220 ASP cc_start: 0.7659 (OUTLIER) cc_final: 0.7411 (m-30) REVERT: E 159 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.8318 (tttm) REVERT: F 183 LYS cc_start: 0.8592 (mmmm) cc_final: 0.8262 (tptp) REVERT: G 1392 ASP cc_start: 0.7820 (OUTLIER) cc_final: 0.7443 (m-30) REVERT: G 1397 GLN cc_start: 0.8199 (OUTLIER) cc_final: 0.7499 (mm-40) REVERT: H 463 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.7184 (pm20) REVERT: I 30 ARG cc_start: 0.8131 (ttm-80) cc_final: 0.7893 (ttt-90) REVERT: I 167 LYS cc_start: 0.8411 (OUTLIER) cc_final: 0.8198 (mttm) REVERT: J 34 ARG cc_start: 0.7479 (ptp-110) cc_final: 0.7279 (ptp90) REVERT: J 154 MET cc_start: 0.7801 (tpp) cc_final: 0.6972 (mtt) REVERT: J 168 SER cc_start: 0.8832 (m) cc_final: 0.8494 (p) REVERT: J 174 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7390 (mp0) REVERT: J 222 LYS cc_start: 0.8414 (OUTLIER) cc_final: 0.7783 (ttmm) REVERT: J 295 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.6539 (mtm-85) outliers start: 92 outliers final: 37 residues processed: 399 average time/residue: 1.7328 time to fit residues: 791.0557 Evaluate side-chains 348 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 300 time to evaluate : 3.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 386 GLN Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain D residue 220 ASP Chi-restraints excluded: chain D residue 306 GLU Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 187 MET Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 305 ILE Chi-restraints excluded: chain E residue 407 THR Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 273 ASP Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain G residue 1233 LEU Chi-restraints excluded: chain G residue 1268 CYS Chi-restraints excluded: chain G residue 1377 GLU Chi-restraints excluded: chain G residue 1392 ASP Chi-restraints excluded: chain G residue 1397 GLN Chi-restraints excluded: chain G residue 1544 SER Chi-restraints excluded: chain H residue 447 MET Chi-restraints excluded: chain H residue 463 GLU Chi-restraints excluded: chain I residue 21 ASP Chi-restraints excluded: chain I residue 167 LYS Chi-restraints excluded: chain J residue 52 GLN Chi-restraints excluded: chain J residue 128 ASN Chi-restraints excluded: chain J residue 174 GLU Chi-restraints excluded: chain J residue 222 LYS Chi-restraints excluded: chain J residue 288 THR Chi-restraints excluded: chain J residue 295 ARG Chi-restraints excluded: chain J residue 623 SER Chi-restraints excluded: chain J residue 630 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 20 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 188 optimal weight: 0.1980 chunk 147 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 326 optimal weight: 8.9990 chunk 304 optimal weight: 0.0370 chunk 155 optimal weight: 0.0470 chunk 161 optimal weight: 5.9990 chunk 101 optimal weight: 0.0170 chunk 17 optimal weight: 0.8980 overall best weight: 0.2394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 446 ASN D 328 ASN E 394 GLN F 96 GLN J 259 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.087078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.070888 restraints weight = 53414.726| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 1.92 r_work: 0.2925 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 28847 Z= 0.103 Angle : 0.553 9.235 38993 Z= 0.277 Chirality : 0.042 0.214 4419 Planarity : 0.004 0.046 5049 Dihedral : 8.091 153.106 4058 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.19 % Allowed : 13.44 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % 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: 0.83 (0.14), residues: 3590 helix: 0.87 (0.13), residues: 1547 sheet: 0.45 (0.21), residues: 552 loop : 0.46 (0.16), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 129 HIS 0.004 0.001 HIS J 134 PHE 0.017 0.001 PHE J 35 TYR 0.026 0.001 TYR J 751 ARG 0.008 0.000 ARG G1296 Details of bonding type rmsd hydrogen bonds : bond 0.03412 ( 1165) hydrogen bonds : angle 4.58262 ( 3333) covalent geometry : bond 0.00220 (28847) covalent geometry : angle 0.55280 (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 429 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 363 time to evaluate : 3.408 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 157 THR cc_start: 0.8607 (t) cc_final: 0.8327 (m) REVERT: A 373 ARG cc_start: 0.8315 (ttm110) cc_final: 0.7912 (ttp80) REVERT: A 419 ARG cc_start: 0.8252 (ttp80) cc_final: 0.8017 (ttm110) REVERT: B 35 LYS cc_start: 0.7633 (ptmm) cc_final: 0.7379 (tmtt) REVERT: B 62 MET cc_start: 0.8388 (OUTLIER) cc_final: 0.8011 (mpp) REVERT: B 421 ASN cc_start: 0.7775 (m-40) cc_final: 0.7479 (m110) REVERT: C 106 GLU cc_start: 0.8093 (tt0) cc_final: 0.7728 (mt-10) REVERT: C 184 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7450 (mp0) REVERT: C 307 MET cc_start: 0.8593 (mmp) cc_final: 0.8061 (mmt) REVERT: D 184 GLU cc_start: 0.8278 (tp30) cc_final: 0.7914 (tp30) REVERT: E 312 ASN cc_start: 0.8685 (m-40) cc_final: 0.8366 (m110) REVERT: F 162 ILE cc_start: 0.8619 (mt) cc_final: 0.8284 (mt) REVERT: F 183 LYS cc_start: 0.8548 (mmmm) cc_final: 0.8235 (tptp) REVERT: G 1265 ARG cc_start: 0.7919 (ttp80) cc_final: 0.7651 (ttm110) REVERT: H 455 MET cc_start: 0.8491 (mmm) cc_final: 0.8070 (mpp) REVERT: I 30 ARG cc_start: 0.8160 (ttm-80) cc_final: 0.7958 (ttt-90) REVERT: J 154 MET cc_start: 0.7717 (tpp) cc_final: 0.7044 (mtt) REVERT: J 168 SER cc_start: 0.8790 (m) cc_final: 0.8418 (p) REVERT: J 174 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7420 (mp0) outliers start: 66 outliers final: 22 residues processed: 403 average time/residue: 1.6736 time to fit residues: 768.7159 Evaluate side-chains 330 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 305 time to evaluate : 3.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain D residue 406 THR Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain G residue 1268 CYS Chi-restraints excluded: chain G residue 1544 SER Chi-restraints excluded: chain H residue 447 MET Chi-restraints excluded: chain H residue 461 VAL Chi-restraints excluded: chain I residue 163 LEU Chi-restraints excluded: chain J residue 52 GLN Chi-restraints excluded: chain J residue 174 GLU Chi-restraints excluded: chain J residue 288 THR Chi-restraints excluded: chain J residue 297 VAL Chi-restraints excluded: chain J residue 623 SER Chi-restraints excluded: chain J residue 630 VAL 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: 4.9990 chunk 182 optimal weight: 4.9990 chunk 266 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 86 optimal weight: 10.0000 chunk 36 optimal weight: 0.8980 chunk 333 optimal weight: 6.9990 chunk 225 optimal weight: 6.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 255 GLN B 285 GLN B 446 ASN C 19 HIS D 328 ASN E 24 HIS F 96 GLN J 134 HIS J 237 HIS J 259 ASN J 265 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.082339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.065926 restraints weight = 53488.447| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 1.94 r_work: 0.2802 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 28847 Z= 0.301 Angle : 0.730 10.718 38993 Z= 0.367 Chirality : 0.050 0.312 4419 Planarity : 0.006 0.091 5049 Dihedral : 8.901 159.824 4058 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.41 % Allowed : 13.94 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % 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: 0.35 (0.14), residues: 3590 helix: 0.46 (0.13), residues: 1527 sheet: 0.35 (0.21), residues: 571 loop : 0.15 (0.16), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G1367 HIS 0.011 0.002 HIS B 21 PHE 0.024 0.003 PHE J 612 TYR 0.039 0.003 TYR J 751 ARG 0.013 0.001 ARG J 21 Details of bonding type rmsd hydrogen bonds : bond 0.04991 ( 1165) hydrogen bonds : angle 5.03024 ( 3333) covalent geometry : bond 0.00726 (28847) covalent geometry : angle 0.73040 (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 417 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 314 time to evaluate : 3.383 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 126 ARG cc_start: 0.8080 (tpp80) cc_final: 0.7650 (mmm-85) REVERT: A 373 ARG cc_start: 0.8419 (ttm110) cc_final: 0.7937 (ttp80) REVERT: A 401 ARG cc_start: 0.7599 (OUTLIER) cc_final: 0.7316 (mtm180) REVERT: B 62 MET cc_start: 0.8443 (OUTLIER) cc_final: 0.8090 (mpp) REVERT: B 421 ASN cc_start: 0.7844 (m-40) cc_final: 0.7610 (m110) REVERT: C 307 MET cc_start: 0.8679 (mmp) cc_final: 0.8152 (mmt) REVERT: E 28 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.7746 (tpp-160) REVERT: E 159 LYS cc_start: 0.8837 (OUTLIER) cc_final: 0.8363 (tttm) REVERT: E 183 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8559 (ttmm) REVERT: E 312 ASN cc_start: 0.8802 (m-40) cc_final: 0.8442 (m110) REVERT: F 183 LYS cc_start: 0.8645 (mmmm) cc_final: 0.8340 (tptp) REVERT: F 222 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.8131 (pttm) REVERT: G 1265 ARG cc_start: 0.7933 (ttp80) cc_final: 0.7718 (ttm110) REVERT: G 1392 ASP cc_start: 0.7820 (OUTLIER) cc_final: 0.7433 (m-30) REVERT: H 455 MET cc_start: 0.8565 (mmm) cc_final: 0.8217 (mpp) REVERT: I 167 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.8055 (mttm) REVERT: J 154 MET cc_start: 0.7763 (tpp) cc_final: 0.6957 (mtt) REVERT: J 168 SER cc_start: 0.8825 (m) cc_final: 0.8517 (p) REVERT: J 174 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7551 (mp0) REVERT: J 222 LYS cc_start: 0.8415 (OUTLIER) cc_final: 0.7780 (ttmm) REVERT: J 295 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.6570 (mtm-85) REVERT: J 760 LYS cc_start: 0.7351 (OUTLIER) cc_final: 0.7137 (mmtp) outliers start: 103 outliers final: 45 residues processed: 390 average time/residue: 1.7328 time to fit residues: 767.6386 Evaluate side-chains 339 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 282 time to evaluate : 3.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 401 ARG Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 373 ARG Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 306 GLU Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 406 THR Chi-restraints excluded: chain E residue 28 ARG Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 132 LYS Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain E residue 407 THR Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 162 ILE Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 222 LYS Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 352 ARG Chi-restraints excluded: chain G residue 1229 MET Chi-restraints excluded: chain G residue 1301 VAL Chi-restraints excluded: chain G residue 1377 GLU Chi-restraints excluded: chain G residue 1392 ASP Chi-restraints excluded: chain G residue 1438 THR Chi-restraints excluded: chain G residue 1538 THR Chi-restraints excluded: chain G residue 1544 SER Chi-restraints excluded: chain H residue 461 VAL Chi-restraints excluded: chain H residue 473 VAL Chi-restraints excluded: chain I residue 167 LYS Chi-restraints excluded: chain I residue 204 MET Chi-restraints excluded: chain J residue 52 GLN Chi-restraints excluded: chain J residue 127 SER Chi-restraints excluded: chain J residue 174 GLU Chi-restraints excluded: chain J residue 222 LYS Chi-restraints excluded: chain J residue 295 ARG Chi-restraints excluded: chain J residue 297 VAL Chi-restraints excluded: chain J residue 630 VAL Chi-restraints excluded: chain J residue 760 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 262 optimal weight: 0.7980 chunk 253 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 243 optimal weight: 0.3980 chunk 67 optimal weight: 1.9990 chunk 171 optimal weight: 1.9990 chunk 336 optimal weight: 0.9980 chunk 250 optimal weight: 0.9980 chunk 130 optimal weight: 0.8980 chunk 107 optimal weight: 5.9990 chunk 141 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 255 GLN B 263 GLN B 446 ASN F 96 GLN ** J 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 259 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.084758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.067848 restraints weight = 53085.276| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 1.89 r_work: 0.2862 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.3503 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= 0.128 Angle : 0.586 11.366 38993 Z= 0.292 Chirality : 0.043 0.375 4419 Planarity : 0.004 0.056 5049 Dihedral : 8.317 152.259 4058 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.28 % Allowed : 15.63 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % 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: 0.79 (0.13), residues: 1539 sheet: 0.36 (0.21), residues: 560 loop : 0.21 (0.16), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G1367 HIS 0.004 0.001 HIS B 242 PHE 0.027 0.002 PHE J 98 TYR 0.039 0.001 TYR J 751 ARG 0.010 0.000 ARG J 21 Details of bonding type rmsd hydrogen bonds : bond 0.03741 ( 1165) hydrogen bonds : angle 4.70352 ( 3333) covalent geometry : bond 0.00290 (28847) covalent geometry : angle 0.58578 (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 381 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 312 time to evaluate : 3.100 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 126 ARG cc_start: 0.8043 (tpp80) cc_final: 0.7616 (mmm-85) REVERT: A 373 ARG cc_start: 0.8392 (ttm110) cc_final: 0.7967 (ttp80) REVERT: B 62 MET cc_start: 0.8427 (OUTLIER) cc_final: 0.8058 (mpp) REVERT: B 421 ASN cc_start: 0.7839 (m-40) cc_final: 0.7569 (m110) REVERT: C 184 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7417 (mp0) REVERT: C 307 MET cc_start: 0.8662 (mmp) cc_final: 0.8025 (mmt) REVERT: E 159 LYS cc_start: 0.8773 (OUTLIER) cc_final: 0.8349 (tttm) REVERT: E 183 LYS cc_start: 0.8741 (OUTLIER) cc_final: 0.8518 (ttmm) REVERT: E 263 ASP cc_start: 0.7462 (t70) cc_final: 0.6962 (t0) REVERT: E 312 ASN cc_start: 0.8717 (m-40) cc_final: 0.8442 (m110) REVERT: F 162 ILE cc_start: 0.8683 (mt) cc_final: 0.8343 (mt) REVERT: F 183 LYS cc_start: 0.8583 (mmmm) cc_final: 0.8286 (tptp) REVERT: F 222 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.8058 (pttm) REVERT: F 266 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7590 (mt-10) REVERT: G 1265 ARG cc_start: 0.7926 (ttp80) cc_final: 0.7713 (ttm110) REVERT: G 1392 ASP cc_start: 0.7762 (OUTLIER) cc_final: 0.7375 (m-30) REVERT: H 455 MET cc_start: 0.8493 (mmm) cc_final: 0.8144 (mpp) REVERT: I 23 HIS cc_start: 0.7373 (OUTLIER) cc_final: 0.6775 (m170) REVERT: J 154 MET cc_start: 0.7753 (tpp) cc_final: 0.6993 (mtt) REVERT: J 168 SER cc_start: 0.8812 (m) cc_final: 0.8483 (p) REVERT: J 222 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.7755 (ttmm) REVERT: J 266 MET cc_start: 0.8803 (OUTLIER) cc_final: 0.8573 (mtp) outliers start: 69 outliers final: 30 residues processed: 357 average time/residue: 1.6997 time to fit residues: 691.2979 Evaluate side-chains 329 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 289 time to evaluate : 3.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain D residue 406 THR Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 132 LYS Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 222 LYS Chi-restraints excluded: chain F residue 266 GLU Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 352 ARG Chi-restraints excluded: chain G residue 1301 VAL Chi-restraints excluded: chain G residue 1341 LYS Chi-restraints excluded: chain G residue 1377 GLU Chi-restraints excluded: chain G residue 1392 ASP Chi-restraints excluded: chain G residue 1438 THR Chi-restraints excluded: chain G residue 1504 THR Chi-restraints excluded: chain G residue 1538 THR Chi-restraints excluded: chain G residue 1544 SER Chi-restraints excluded: chain H residue 447 MET Chi-restraints excluded: chain I residue 23 HIS Chi-restraints excluded: chain J residue 52 GLN Chi-restraints excluded: chain J residue 127 SER Chi-restraints excluded: chain J residue 174 GLU Chi-restraints excluded: chain J residue 222 LYS Chi-restraints excluded: chain J residue 266 MET Chi-restraints excluded: chain J residue 297 VAL Chi-restraints excluded: chain J residue 630 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 279 optimal weight: 0.8980 chunk 157 optimal weight: 0.9990 chunk 235 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 158 optimal weight: 0.8980 chunk 198 optimal weight: 6.9990 chunk 351 optimal weight: 0.3980 chunk 82 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 341 optimal weight: 3.9990 chunk 209 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 GLN B 446 ASN D 328 ASN ** G1263 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 = 0.3325 r_free = 0.3325 target = 0.085350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.069031 restraints weight = 53107.723| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 1.95 r_work: 0.2875 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.3656 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 : 0.574 10.476 38993 Z= 0.285 Chirality : 0.043 0.372 4419 Planarity : 0.004 0.062 5049 Dihedral : 7.985 141.970 4058 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.19 % Allowed : 16.69 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % 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: 0.78 (0.14), residues: 3590 helix: 1.00 (0.13), residues: 1533 sheet: 0.43 (0.22), residues: 555 loop : 0.22 (0.16), residues: 1502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 19 HIS 0.003 0.001 HIS B 242 PHE 0.019 0.001 PHE J 98 TYR 0.037 0.001 TYR J 751 ARG 0.017 0.000 ARG J 21 Details of bonding type rmsd hydrogen bonds : bond 0.03516 ( 1165) hydrogen bonds : angle 4.58406 ( 3333) covalent geometry : bond 0.00281 (28847) covalent geometry : angle 0.57362 (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 385 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 319 time to evaluate : 3.098 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 126 ARG cc_start: 0.7907 (tpp80) cc_final: 0.7586 (mmm-85) REVERT: A 373 ARG cc_start: 0.8398 (ttm110) cc_final: 0.7971 (ttp80) REVERT: B 62 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.8082 (mpp) REVERT: B 378 ILE cc_start: 0.8803 (mt) cc_final: 0.8450 (mp) REVERT: B 421 ASN cc_start: 0.7846 (m-40) cc_final: 0.7581 (m110) REVERT: C 307 MET cc_start: 0.8623 (mmp) cc_final: 0.7926 (mmt) REVERT: E 112 GLU cc_start: 0.7737 (tt0) cc_final: 0.7527 (tt0) REVERT: E 159 LYS cc_start: 0.8758 (OUTLIER) cc_final: 0.8350 (tttm) REVERT: E 183 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8517 (ttmm) REVERT: E 263 ASP cc_start: 0.7463 (t70) cc_final: 0.6956 (t0) REVERT: E 312 ASN cc_start: 0.8646 (m-40) cc_final: 0.8421 (m110) REVERT: F 162 ILE cc_start: 0.8682 (mt) cc_final: 0.8346 (mt) REVERT: F 183 LYS cc_start: 0.8590 (mmmm) cc_final: 0.8290 (tptp) REVERT: F 222 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.8008 (pttm) REVERT: F 266 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7536 (mt-10) REVERT: G 1392 ASP cc_start: 0.7782 (OUTLIER) cc_final: 0.7388 (m-30) REVERT: I 23 HIS cc_start: 0.7305 (OUTLIER) cc_final: 0.6671 (m170) REVERT: J 154 MET cc_start: 0.7743 (tpp) cc_final: 0.7028 (mtt) REVERT: J 168 SER cc_start: 0.8827 (m) cc_final: 0.8509 (p) outliers start: 66 outliers final: 34 residues processed: 362 average time/residue: 1.6612 time to fit residues: 685.9164 Evaluate side-chains 332 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 291 time to evaluate : 3.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 132 LYS Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 222 LYS Chi-restraints excluded: chain F residue 266 GLU Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 352 ARG Chi-restraints excluded: chain G residue 1301 VAL Chi-restraints excluded: chain G residue 1341 LYS Chi-restraints excluded: chain G residue 1392 ASP Chi-restraints excluded: chain G residue 1438 THR Chi-restraints excluded: chain G residue 1504 THR Chi-restraints excluded: chain G residue 1538 THR Chi-restraints excluded: chain G residue 1544 SER Chi-restraints excluded: chain I residue 23 HIS Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 174 GLU Chi-restraints excluded: chain J residue 297 VAL Chi-restraints excluded: chain J residue 630 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 214 optimal weight: 4.9990 chunk 208 optimal weight: 4.9990 chunk 337 optimal weight: 6.9990 chunk 170 optimal weight: 3.9990 chunk 219 optimal weight: 4.9990 chunk 351 optimal weight: 0.6980 chunk 120 optimal weight: 7.9990 chunk 195 optimal weight: 0.5980 chunk 233 optimal weight: 2.9990 chunk 105 optimal weight: 0.6980 chunk 226 optimal weight: 3.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 446 ASN J 259 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.083755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.066837 restraints weight = 53237.596| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 1.89 r_work: 0.2840 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 28847 Z= 0.183 Angle : 0.630 11.136 38993 Z= 0.314 Chirality : 0.045 0.345 4419 Planarity : 0.005 0.066 5049 Dihedral : 8.233 142.024 4058 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.42 % Allowed : 17.05 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % 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: 0.61 (0.14), residues: 3590 helix: 0.83 (0.13), residues: 1537 sheet: 0.34 (0.21), residues: 569 loop : 0.15 (0.16), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 19 HIS 0.005 0.001 HIS B 21 PHE 0.018 0.002 PHE J 612 TYR 0.021 0.002 TYR E 339 ARG 0.015 0.001 ARG J 21 Details of bonding type rmsd hydrogen bonds : bond 0.04056 ( 1165) hydrogen bonds : angle 4.74590 ( 3333) covalent geometry : bond 0.00438 (28847) covalent geometry : angle 0.62953 (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 373 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 300 time to evaluate : 3.375 Fit side-chains revert: symmetry clash REVERT: A 126 ARG cc_start: 0.8026 (tpp80) cc_final: 0.7664 (mmm-85) REVERT: A 373 ARG cc_start: 0.8403 (ttm110) cc_final: 0.7969 (ttp80) REVERT: B 62 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.8057 (mpp) REVERT: B 421 ASN cc_start: 0.7853 (m-40) cc_final: 0.7599 (m110) REVERT: C 62 MET cc_start: 0.6030 (OUTLIER) cc_final: 0.5618 (ppp) REVERT: C 184 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7423 (mp0) REVERT: C 307 MET cc_start: 0.8642 (mmp) cc_final: 0.7894 (mmt) REVERT: E 159 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8342 (tttm) REVERT: E 183 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8551 (ttmm) REVERT: E 263 ASP cc_start: 0.7586 (t70) cc_final: 0.7133 (t0) REVERT: E 378 GLU cc_start: 0.7502 (mm-30) cc_final: 0.7106 (mp0) REVERT: F 208 TYR cc_start: 0.8078 (OUTLIER) cc_final: 0.7875 (m-80) REVERT: F 222 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.8071 (pttm) REVERT: F 266 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7548 (mt-10) REVERT: G 1265 ARG cc_start: 0.7912 (ttm110) cc_final: 0.7536 (ptm-80) REVERT: G 1392 ASP cc_start: 0.7791 (OUTLIER) cc_final: 0.7420 (m-30) REVERT: I 23 HIS cc_start: 0.7282 (OUTLIER) cc_final: 0.6577 (m170) REVERT: I 27 LYS cc_start: 0.7031 (mttm) cc_final: 0.6525 (mtpt) REVERT: J 154 MET cc_start: 0.7728 (tpp) cc_final: 0.7055 (mtt) REVERT: J 168 SER cc_start: 0.8850 (m) cc_final: 0.8570 (p) REVERT: J 174 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.8016 (mp0) REVERT: J 222 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.7753 (ttmm) outliers start: 73 outliers final: 40 residues processed: 349 average time/residue: 1.7491 time to fit residues: 694.8527 Evaluate side-chains 339 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 287 time to evaluate : 3.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 306 GLU Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 132 LYS Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 162 ILE Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 208 TYR Chi-restraints excluded: chain F residue 222 LYS Chi-restraints excluded: chain F residue 266 GLU Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 352 ARG Chi-restraints excluded: chain G residue 1301 VAL Chi-restraints excluded: chain G residue 1341 LYS Chi-restraints excluded: chain G residue 1392 ASP Chi-restraints excluded: chain G residue 1438 THR Chi-restraints excluded: chain G residue 1504 THR Chi-restraints excluded: chain G residue 1544 SER Chi-restraints excluded: chain I residue 23 HIS Chi-restraints excluded: chain I residue 204 MET Chi-restraints excluded: chain J residue 52 GLN Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 174 GLU Chi-restraints excluded: chain J residue 222 LYS Chi-restraints excluded: chain J residue 292 ASP Chi-restraints excluded: chain J residue 297 VAL Chi-restraints excluded: chain J residue 630 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 218 optimal weight: 4.9990 chunk 295 optimal weight: 6.9990 chunk 314 optimal weight: 0.8980 chunk 165 optimal weight: 0.9990 chunk 243 optimal weight: 0.7980 chunk 345 optimal weight: 0.6980 chunk 110 optimal weight: 0.6980 chunk 291 optimal weight: 2.9990 chunk 240 optimal weight: 1.9990 chunk 268 optimal weight: 9.9990 chunk 275 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 446 ASN E 24 HIS E 312 ASN ** G1263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 19 GLN J 42 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.085175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.068839 restraints weight = 52990.252| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 1.95 r_work: 0.2876 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.3776 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= 0.121 Angle : 0.579 11.248 38993 Z= 0.287 Chirality : 0.043 0.330 4419 Planarity : 0.004 0.061 5049 Dihedral : 7.897 135.227 4058 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.95 % Allowed : 17.81 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % 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: 0.78 (0.14), residues: 3590 helix: 1.01 (0.13), residues: 1540 sheet: 0.39 (0.21), residues: 571 loop : 0.22 (0.16), residues: 1479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 129 HIS 0.004 0.001 HIS B 242 PHE 0.015 0.001 PHE C 117 TYR 0.021 0.001 TYR E 339 ARG 0.014 0.000 ARG J 21 Details of bonding type rmsd hydrogen bonds : bond 0.03500 ( 1165) hydrogen bonds : angle 4.61313 ( 3333) covalent geometry : bond 0.00281 (28847) covalent geometry : angle 0.57872 (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 370 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 311 time to evaluate : 3.028 Fit side-chains revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8306 (ttpt) cc_final: 0.8072 (tppp) REVERT: A 126 ARG cc_start: 0.7951 (tpp80) cc_final: 0.7635 (mmm-85) REVERT: A 373 ARG cc_start: 0.8389 (ttm110) cc_final: 0.7956 (ttp80) REVERT: B 62 MET cc_start: 0.8428 (OUTLIER) cc_final: 0.8057 (mpp) REVERT: B 378 ILE cc_start: 0.8801 (mt) cc_final: 0.8455 (mp) REVERT: B 421 ASN cc_start: 0.7855 (m-40) cc_final: 0.7581 (m110) REVERT: C 62 MET cc_start: 0.5859 (OUTLIER) cc_final: 0.5481 (ppp) REVERT: C 184 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7434 (mp0) REVERT: C 307 MET cc_start: 0.8605 (mmp) cc_final: 0.7877 (mmt) REVERT: D 184 GLU cc_start: 0.8203 (tp30) cc_final: 0.7847 (tm-30) REVERT: E 159 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8328 (tttm) REVERT: E 183 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8597 (ttmm) REVERT: E 187 MET cc_start: 0.8662 (ttm) cc_final: 0.8327 (ptp) REVERT: E 263 ASP cc_start: 0.7524 (t70) cc_final: 0.7068 (t0) REVERT: E 378 GLU cc_start: 0.7433 (mm-30) cc_final: 0.6928 (mm-30) REVERT: F 162 ILE cc_start: 0.8675 (OUTLIER) cc_final: 0.8351 (mt) REVERT: F 222 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.7972 (pttm) REVERT: F 266 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7544 (mt-10) REVERT: G 1265 ARG cc_start: 0.7913 (ttm110) cc_final: 0.7581 (ptm-80) REVERT: G 1274 PHE cc_start: 0.8622 (t80) cc_final: 0.8320 (t80) REVERT: G 1312 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.6847 (mp0) REVERT: G 1392 ASP cc_start: 0.7771 (OUTLIER) cc_final: 0.7391 (m-30) REVERT: I 23 HIS cc_start: 0.7178 (OUTLIER) cc_final: 0.6411 (m170) REVERT: I 27 LYS cc_start: 0.7061 (mttm) cc_final: 0.6558 (mtpt) REVERT: J 154 MET cc_start: 0.7703 (tpp) cc_final: 0.7058 (mtt) REVERT: J 168 SER cc_start: 0.8831 (m) cc_final: 0.8550 (p) REVERT: J 174 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.8012 (mp0) outliers start: 59 outliers final: 35 residues processed: 352 average time/residue: 1.6967 time to fit residues: 680.2559 Evaluate side-chains 335 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 288 time to evaluate : 2.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 132 LYS Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 162 ILE Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 222 LYS Chi-restraints excluded: chain F residue 266 GLU Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 352 ARG Chi-restraints excluded: chain G residue 1312 GLU Chi-restraints excluded: chain G residue 1341 LYS Chi-restraints excluded: chain G residue 1392 ASP Chi-restraints excluded: chain G residue 1429 ASN Chi-restraints excluded: chain G residue 1438 THR Chi-restraints excluded: chain G residue 1504 THR Chi-restraints excluded: chain G residue 1544 SER Chi-restraints excluded: chain I residue 23 HIS Chi-restraints excluded: chain J residue 52 GLN Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 174 GLU Chi-restraints excluded: chain J residue 297 VAL Chi-restraints excluded: chain J residue 630 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 274 optimal weight: 2.9990 chunk 300 optimal weight: 3.9990 chunk 193 optimal weight: 0.0980 chunk 225 optimal weight: 6.9990 chunk 246 optimal weight: 0.9990 chunk 22 optimal weight: 6.9990 chunk 336 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 204 optimal weight: 0.9990 chunk 341 optimal weight: 0.9990 chunk 292 optimal weight: 2.9990 overall best weight: 1.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 446 ASN E 96 GLN E 357 ASN ** G1263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 19 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.085036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.068661 restraints weight = 53218.929| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 1.92 r_work: 0.2869 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.3833 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= 0.134 Angle : 0.606 11.940 38993 Z= 0.300 Chirality : 0.043 0.341 4419 Planarity : 0.004 0.065 5049 Dihedral : 7.821 129.329 4058 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.85 % Allowed : 18.38 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % 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: 0.81 (0.14), residues: 3590 helix: 1.04 (0.13), residues: 1531 sheet: 0.39 (0.21), residues: 582 loop : 0.24 (0.16), residues: 1477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP J 129 HIS 0.004 0.001 HIS E 301 PHE 0.018 0.001 PHE E 308 TYR 0.024 0.001 TYR J 167 ARG 0.013 0.000 ARG J 21 Details of bonding type rmsd hydrogen bonds : bond 0.03595 ( 1165) hydrogen bonds : angle 4.61511 ( 3333) covalent geometry : bond 0.00315 (28847) covalent geometry : angle 0.60566 (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 353 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 297 time to evaluate : 3.001 Fit side-chains REVERT: A 35 LYS cc_start: 0.8319 (ttpt) cc_final: 0.8077 (tppp) REVERT: A 126 ARG cc_start: 0.7759 (tpp80) cc_final: 0.7489 (mmm-85) REVERT: A 373 ARG cc_start: 0.8390 (ttm110) cc_final: 0.7955 (ttp80) REVERT: B 62 MET cc_start: 0.8465 (OUTLIER) cc_final: 0.8089 (mpp) REVERT: B 378 ILE cc_start: 0.8815 (mt) cc_final: 0.8467 (mp) REVERT: B 421 ASN cc_start: 0.7869 (m-40) cc_final: 0.7606 (m110) REVERT: C 62 MET cc_start: 0.5934 (OUTLIER) cc_final: 0.5531 (ppp) REVERT: C 106 GLU cc_start: 0.8107 (tt0) cc_final: 0.7884 (mt-10) REVERT: C 184 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7466 (mp0) REVERT: C 307 MET cc_start: 0.8608 (mmp) cc_final: 0.7871 (mmt) REVERT: D 175 SER cc_start: 0.8296 (p) cc_final: 0.8072 (t) REVERT: D 184 GLU cc_start: 0.8117 (tp30) cc_final: 0.7896 (tm-30) REVERT: E 159 LYS cc_start: 0.8773 (OUTLIER) cc_final: 0.8347 (tttm) REVERT: E 183 LYS cc_start: 0.8802 (OUTLIER) cc_final: 0.8597 (ttmm) REVERT: E 187 MET cc_start: 0.8670 (ttm) cc_final: 0.8320 (ptp) REVERT: E 263 ASP cc_start: 0.7509 (t70) cc_final: 0.7089 (t0) REVERT: E 378 GLU cc_start: 0.7418 (mm-30) cc_final: 0.6981 (mm-30) REVERT: F 162 ILE cc_start: 0.8683 (OUTLIER) cc_final: 0.8363 (mt) REVERT: F 222 LYS cc_start: 0.8369 (OUTLIER) cc_final: 0.8006 (pttm) REVERT: F 266 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7468 (mt-10) REVERT: G 1265 ARG cc_start: 0.7958 (ttm110) cc_final: 0.7707 (ptm-80) REVERT: G 1274 PHE cc_start: 0.8636 (t80) cc_final: 0.8331 (t80) REVERT: G 1312 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.6863 (mp0) REVERT: G 1392 ASP cc_start: 0.7778 (OUTLIER) cc_final: 0.7399 (m-30) REVERT: I 23 HIS cc_start: 0.7192 (OUTLIER) cc_final: 0.6377 (m170) REVERT: I 27 LYS cc_start: 0.7051 (mttm) cc_final: 0.6564 (mtpt) REVERT: J 154 MET cc_start: 0.7673 (tpp) cc_final: 0.7072 (mtt) REVERT: J 168 SER cc_start: 0.8796 (m) cc_final: 0.8526 (p) REVERT: J 174 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.8067 (mp0) outliers start: 56 outliers final: 34 residues processed: 337 average time/residue: 1.6709 time to fit residues: 648.4023 Evaluate side-chains 332 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 286 time to evaluate : 3.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 132 LYS Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 162 ILE Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 222 LYS Chi-restraints excluded: chain F residue 266 GLU Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 352 ARG Chi-restraints excluded: chain G residue 1301 VAL Chi-restraints excluded: chain G residue 1312 GLU Chi-restraints excluded: chain G residue 1341 LYS Chi-restraints excluded: chain G residue 1392 ASP Chi-restraints excluded: chain G residue 1429 ASN Chi-restraints excluded: chain G residue 1438 THR Chi-restraints excluded: chain G residue 1504 THR Chi-restraints excluded: chain G residue 1544 SER Chi-restraints excluded: chain I residue 23 HIS Chi-restraints excluded: chain J residue 174 GLU Chi-restraints excluded: chain J residue 292 ASP Chi-restraints excluded: chain J residue 297 VAL Chi-restraints excluded: chain J residue 630 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 212 optimal weight: 1.9990 chunk 225 optimal weight: 0.1980 chunk 313 optimal weight: 3.9990 chunk 331 optimal weight: 0.9980 chunk 307 optimal weight: 4.9990 chunk 201 optimal weight: 0.8980 chunk 238 optimal weight: 0.7980 chunk 325 optimal weight: 0.9980 chunk 210 optimal weight: 0.3980 chunk 92 optimal weight: 1.9990 chunk 190 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 446 ASN E 357 ASN ** G1263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 19 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.086066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.069966 restraints weight = 53329.888| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 1.93 r_work: 0.2896 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.3941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 28847 Z= 0.114 Angle : 0.578 11.871 38993 Z= 0.285 Chirality : 0.043 0.339 4419 Planarity : 0.004 0.062 5049 Dihedral : 7.558 121.650 4058 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.52 % Allowed : 18.81 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % 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: 0.91 (0.14), residues: 3590 helix: 1.14 (0.13), residues: 1527 sheet: 0.44 (0.22), residues: 567 loop : 0.29 (0.16), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP J 129 HIS 0.003 0.001 HIS B 242 PHE 0.018 0.001 PHE E 308 TYR 0.023 0.001 TYR J 167 ARG 0.012 0.000 ARG J 21 Details of bonding type rmsd hydrogen bonds : bond 0.03313 ( 1165) hydrogen bonds : angle 4.51913 ( 3333) covalent geometry : bond 0.00262 (28847) covalent geometry : angle 0.57771 (38993) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23870.62 seconds wall clock time: 410 minutes 32.86 seconds (24632.86 seconds total)