Starting phenix.real_space_refine on Fri Jun 13 07:34:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6qi8_4552/06_2025/6qi8_4552.cif Found real_map, /net/cci-nas-00/data/ceres_data/6qi8_4552/06_2025/6qi8_4552.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6qi8_4552/06_2025/6qi8_4552.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6qi8_4552/06_2025/6qi8_4552.map" model { file = "/net/cci-nas-00/data/ceres_data/6qi8_4552/06_2025/6qi8_4552.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6qi8_4552/06_2025/6qi8_4552.cif" } resolution = 3.75 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= 0.000 sd= 0.003 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: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 69 5.16 5 C 9244 2.51 5 N 2584 2.21 5 O 2880 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 100 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 14789 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2423 Classifications: {'peptide': 317} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 306} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2369 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 10, 'TRANS': 299} Chain breaks: 2 Chain: "C" Number of atoms: 2401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2401 Classifications: {'peptide': 316} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 10, 'TRANS': 305} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 2287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2287 Classifications: {'peptide': 296} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 9, 'TRANS': 286} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 9 Chain: "E" Number of atoms: 2585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2585 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 10, 'TRANS': 324} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "F" Number of atoms: 2562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2562 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 10, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 18 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} Time building chain proxies: 10.27, per 1000 atoms: 0.69 Number of scatterers: 14789 At special positions: 0 Unit cell: (135.16, 128.62, 80.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 69 16.00 P 12 15.00 O 2880 8.00 N 2584 7.00 C 9244 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=9, symmetry=0 Number of additional bonds: simple=9, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.13 Conformation dependent library (CDL) restraints added in 2.0 seconds 3750 Ramachandran restraints generated. 1875 Oldfield, 0 Emsley, 1875 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3538 Finding SS restraints... Secondary structure from input PDB file: 94 helices and 22 sheets defined 49.4% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing helix chain 'A' and resid 42 through 58 removed outlier: 3.509A pdb=" N VAL A 51 " --> pdb=" O GLU A 47 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU A 54 " --> pdb=" O GLY A 50 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS A 57 " --> pdb=" O VAL A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 86 removed outlier: 3.543A pdb=" N ILE A 83 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ALA A 84 " --> pdb=" O ALA A 80 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN A 85 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU A 86 " --> pdb=" O ALA A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 101 No H-bonds generated for 'chain 'A' and resid 99 through 101' Processing helix chain 'A' and resid 107 through 117 removed outlier: 3.575A pdb=" N VAL A 111 " --> pdb=" O LYS A 107 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 112 " --> pdb=" O LYS A 108 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N MET A 113 " --> pdb=" O THR A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 244 removed outlier: 3.508A pdb=" N LEU A 243 " --> pdb=" O THR A 239 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP A 244 " --> pdb=" O LEU A 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 239 through 244' Processing helix chain 'A' and resid 275 through 290 removed outlier: 3.638A pdb=" N LYS A 281 " --> pdb=" O GLY A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 307 removed outlier: 3.601A pdb=" N MET A 306 " --> pdb=" O GLU A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 317 removed outlier: 3.578A pdb=" N THR A 313 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N TYR A 314 " --> pdb=" O GLU A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 356 No H-bonds generated for 'chain 'A' and resid 354 through 356' Processing helix chain 'A' and resid 367 through 382 removed outlier: 4.028A pdb=" N LYS A 372 " --> pdb=" O PRO A 368 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLN A 373 " --> pdb=" O GLN A 369 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE A 374 " --> pdb=" O GLU A 370 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU A 382 " --> pdb=" O ARG A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 398 removed outlier: 3.958A pdb=" N HIS A 393 " --> pdb=" O GLU A 389 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 407 removed outlier: 3.969A pdb=" N SER A 406 " --> pdb=" O THR A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 415 removed outlier: 3.585A pdb=" N ALA A 413 " --> pdb=" O LEU A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 434 removed outlier: 3.554A pdb=" N GLU A 432 " --> pdb=" O GLU A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 455 removed outlier: 3.527A pdb=" N ALA A 444 " --> pdb=" O ALA A 440 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE A 446 " --> pdb=" O SER A 442 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP A 452 " --> pdb=" O ALA A 448 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N LYS A 453 " --> pdb=" O ASP A 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 58 removed outlier: 4.315A pdb=" N ALA B 48 " --> pdb=" O ASN B 44 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL B 51 " --> pdb=" O GLU B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.849A pdb=" N ALA B 84 " --> pdb=" O ALA B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 101 No H-bonds generated for 'chain 'B' and resid 99 through 101' Processing helix chain 'B' and resid 107 through 117 removed outlier: 3.977A pdb=" N ASN B 115 " --> pdb=" O VAL B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 247 removed outlier: 3.774A pdb=" N ASP B 244 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA B 246 " --> pdb=" O ASP B 242 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ASN B 247 " --> pdb=" O LEU B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 289 removed outlier: 3.944A pdb=" N LYS B 281 " --> pdb=" O GLY B 277 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL B 282 " --> pdb=" O GLU B 278 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR B 286 " --> pdb=" O VAL B 282 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE B 287 " --> pdb=" O VAL B 283 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP B 288 " --> pdb=" O ASN B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 307 Processing helix chain 'B' and resid 308 through 318 removed outlier: 3.739A pdb=" N THR B 313 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR B 314 " --> pdb=" O GLU B 310 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA B 318 " --> pdb=" O TYR B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 381 removed outlier: 3.760A pdb=" N ILE B 375 " --> pdb=" O MET B 371 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LYS B 376 " --> pdb=" O LYS B 372 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE B 377 " --> pdb=" O GLN B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 395 removed outlier: 3.568A pdb=" N LEU B 391 " --> pdb=" O SER B 387 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N HIS B 393 " --> pdb=" O GLU B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 401 removed outlier: 3.535A pdb=" N LYS B 400 " --> pdb=" O GLU B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 409 removed outlier: 3.510A pdb=" N VAL B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN B 408 " --> pdb=" O ARG B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 420 removed outlier: 3.819A pdb=" N ASN B 420 " --> pdb=" O LEU B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 437 removed outlier: 3.865A pdb=" N VAL B 430 " --> pdb=" O GLU B 426 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLU B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 452 removed outlier: 3.604A pdb=" N ASP B 449 " --> pdb=" O LYS B 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 19 removed outlier: 4.242A pdb=" N SER C 17 " --> pdb=" O ARG C 14 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N HIS C 18 " --> pdb=" O ILE C 15 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N SER C 19 " --> pdb=" O ALA C 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 14 through 19' Processing helix chain 'C' and resid 43 through 58 removed outlier: 3.523A pdb=" N ALA C 48 " --> pdb=" O ASN C 44 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N CYS C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LYS C 57 " --> pdb=" O VAL C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 83 removed outlier: 3.754A pdb=" N ALA C 80 " --> pdb=" O LYS C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 101 No H-bonds generated for 'chain 'C' and resid 99 through 101' Processing helix chain 'C' and resid 108 through 117 removed outlier: 3.898A pdb=" N LEU C 112 " --> pdb=" O LYS C 108 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLU C 114 " --> pdb=" O GLU C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 248 removed outlier: 3.656A pdb=" N VAL C 245 " --> pdb=" O HIS C 241 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ALA C 246 " --> pdb=" O ASP C 242 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN C 247 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA C 248 " --> pdb=" O ASP C 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 241 through 248' Processing helix chain 'C' and resid 274 through 278 Processing helix chain 'C' and resid 279 through 290 removed outlier: 3.984A pdb=" N LYS C 285 " --> pdb=" O LYS C 281 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP C 288 " --> pdb=" O ASN C 284 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN C 289 " --> pdb=" O LYS C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 307 Processing helix chain 'C' and resid 308 through 318 removed outlier: 3.518A pdb=" N PHE C 312 " --> pdb=" O ASP C 308 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N THR C 313 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N TYR C 314 " --> pdb=" O GLU C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 356 removed outlier: 3.693A pdb=" N ASP C 356 " --> pdb=" O LEU C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 383 removed outlier: 3.618A pdb=" N LYS C 372 " --> pdb=" O PRO C 368 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N GLN C 373 " --> pdb=" O GLN C 369 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE C 375 " --> pdb=" O MET C 371 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN C 380 " --> pdb=" O LYS C 376 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU C 382 " --> pdb=" O ARG C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 401 removed outlier: 3.860A pdb=" N LEU C 391 " --> pdb=" O SER C 387 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU C 396 " --> pdb=" O ASN C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 409 removed outlier: 3.900A pdb=" N SER C 406 " --> pdb=" O THR C 402 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU C 409 " --> pdb=" O TYR C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 420 removed outlier: 3.794A pdb=" N ILE C 419 " --> pdb=" O LEU C 415 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN C 420 " --> pdb=" O LEU C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 437 removed outlier: 3.996A pdb=" N VAL C 430 " --> pdb=" O GLU C 426 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU C 435 " --> pdb=" O GLU C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 450 removed outlier: 3.604A pdb=" N ALA C 444 " --> pdb=" O ALA C 440 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LYS C 445 " --> pdb=" O LYS C 441 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE C 446 " --> pdb=" O SER C 442 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU C 447 " --> pdb=" O SER C 443 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA C 448 " --> pdb=" O ALA C 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 65 removed outlier: 3.723A pdb=" N ARG D 54 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY D 57 " --> pdb=" O ARG D 53 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL D 58 " --> pdb=" O ARG D 54 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL D 59 " --> pdb=" O ALA D 55 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG D 64 " --> pdb=" O LEU D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 93 removed outlier: 3.694A pdb=" N ALA D 91 " --> pdb=" O ALA D 87 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLN D 92 " --> pdb=" O MET D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 109 removed outlier: 3.553A 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 124 removed outlier: 3.862A pdb=" N LEU D 119 " --> pdb=" O LYS D 115 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR D 120 " --> pdb=" O THR D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 249 Processing helix chain 'D' and resid 271 through 287 removed outlier: 3.606A pdb=" N ILE D 276 " --> pdb=" O VAL D 272 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASN D 277 " --> pdb=" O ARG D 273 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA D 278 " --> pdb=" O GLU D 274 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLU D 282 " --> pdb=" O ALA D 278 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TRP D 283 " --> pdb=" O LYS D 279 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLU D 285 " --> pdb=" O ALA D 281 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY D 287 " --> pdb=" O TRP D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 304 removed outlier: 3.577A pdb=" N MET D 303 " --> pdb=" O GLU D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 316 removed outlier: 3.612A pdb=" N SER D 310 " --> pdb=" O ILE D 306 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N PHE D 311 " --> pdb=" O GLU D 307 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN D 313 " --> pdb=" O PHE D 309 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG D 314 " --> pdb=" O SER D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 352 removed outlier: 3.702A pdb=" N ASP D 352 " --> pdb=" O ILE D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 378 removed outlier: 3.646A pdb=" N LYS D 368 " --> pdb=" O GLU D 364 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN D 369 " --> pdb=" O LYS D 365 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE D 370 " --> pdb=" O ASP D 366 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU D 376 " --> pdb=" O ARG D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 397 removed outlier: 3.525A pdb=" N THR D 388 " --> pdb=" O GLU D 384 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL D 389 " --> pdb=" O ASP D 385 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ARG D 392 " --> pdb=" O THR D 388 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE D 393 " --> pdb=" O VAL D 389 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU D 396 " --> pdb=" O ARG D 392 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 409 removed outlier: 3.840A pdb=" N ALA D 408 " --> pdb=" O GLN D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 416 Processing helix chain 'D' and resid 422 through 432 removed outlier: 3.702A pdb=" N ILE D 426 " --> pdb=" O GLN D 422 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N SER D 431 " --> pdb=" O LYS D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 453 removed outlier: 3.700A pdb=" N THR D 440 " --> pdb=" O GLU D 436 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLN D 441 " --> pdb=" O SER D 437 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA D 449 " --> pdb=" O GLU D 445 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASN D 453 " --> pdb=" O ALA D 449 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 66 removed outlier: 3.989A pdb=" N ALA E 56 " --> pdb=" O ALA E 52 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLY E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL E 58 " --> pdb=" O ARG E 54 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL E 59 " --> pdb=" O ALA E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 93 removed outlier: 3.662A pdb=" N ALA E 87 " --> pdb=" O LYS E 83 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET E 90 " --> pdb=" O ILE E 86 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA E 91 " --> pdb=" O ALA E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 108 No H-bonds generated for 'chain 'E' and resid 106 through 108' Processing helix chain 'E' and resid 119 through 125 Processing helix chain 'E' and resid 244 through 253 removed outlier: 3.781A pdb=" N ASP E 248 " --> pdb=" O LEU E 244 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ILE E 250 " --> pdb=" O GLU E 246 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASN E 251 " --> pdb=" O ILE E 247 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER E 252 " --> pdb=" O ASP E 248 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ARG E 253 " --> pdb=" O VAL E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 264 Processing helix chain 'E' and resid 270 through 284 removed outlier: 4.188A pdb=" N GLU E 274 " --> pdb=" O SER E 270 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA E 281 " --> pdb=" O ASN E 277 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU E 282 " --> pdb=" O ALA E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 304 Processing helix chain 'E' and resid 305 through 313 removed outlier: 3.532A pdb=" N SER E 310 " --> pdb=" O ILE E 306 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N PHE E 311 " --> pdb=" O GLU E 307 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN E 313 " --> pdb=" O PHE E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 347 through 352 removed outlier: 3.739A pdb=" N ASP E 352 " --> pdb=" O ILE E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 378 removed outlier: 3.632A pdb=" N LYS E 368 " --> pdb=" O GLU E 364 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN E 369 " --> pdb=" O LYS E 365 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N CYS E 375 " --> pdb=" O LEU E 371 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N GLU E 376 " --> pdb=" O ARG E 372 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU E 377 " --> pdb=" O ILE E 373 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU E 378 " --> pdb=" O ARG E 374 " (cutoff:3.500A) Processing helix chain 'E' and resid 385 through 395 removed outlier: 3.593A pdb=" N VAL E 389 " --> pdb=" O ASP E 385 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG E 392 " --> pdb=" O THR E 388 " (cutoff:3.500A) Processing helix chain 'E' and resid 398 through 416 removed outlier: 3.850A pdb=" N ALA E 402 " --> pdb=" O SER E 398 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE E 406 " --> pdb=" O ALA E 402 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N THR E 407 " --> pdb=" O ILE E 403 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ALA E 408 " --> pdb=" O GLN E 404 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU E 411 " --> pdb=" O THR E 407 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N VAL E 412 " --> pdb=" O ALA E 408 " (cutoff:3.500A) Processing helix chain 'E' and resid 422 through 427 removed outlier: 3.856A pdb=" N ILE E 426 " --> pdb=" O GLN E 422 " (cutoff:3.500A) Processing helix chain 'E' and resid 428 through 432 Processing helix chain 'E' and resid 438 through 452 removed outlier: 4.131A pdb=" N TYR E 442 " --> pdb=" O ARG E 438 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N MET E 443 " --> pdb=" O SER E 439 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS E 444 " --> pdb=" O THR E 440 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA E 449 " --> pdb=" O GLU E 445 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE E 452 " --> pdb=" O ASP E 448 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 24 removed outlier: 3.757A pdb=" N GLY F 23 " --> pdb=" O GLU F 20 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ALA F 24 " --> pdb=" O ARG F 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 20 through 24' Processing helix chain 'F' and resid 49 through 65 removed outlier: 3.744A pdb=" N ARG F 54 " --> pdb=" O LEU F 50 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA F 55 " --> pdb=" O ALA F 51 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY F 57 " --> pdb=" O ARG F 53 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL F 58 " --> pdb=" O ARG F 54 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG F 64 " --> pdb=" O LEU F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.935A pdb=" N ALA F 87 " --> pdb=" O LYS F 83 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ALA F 91 " --> pdb=" O ALA F 87 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN F 92 " --> pdb=" O MET F 88 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU F 94 " --> pdb=" O MET F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 109 removed outlier: 3.645A pdb=" N ILE F 108 " --> pdb=" O GLY F 105 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE F 109 " --> pdb=" O SER F 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 105 through 109' Processing helix chain 'F' and resid 119 through 124 Processing helix chain 'F' and resid 244 through 250 removed outlier: 3.633A pdb=" N VAL F 249 " --> pdb=" O GLU F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 264 Processing helix chain 'F' and resid 269 through 280 removed outlier: 3.540A pdb=" N ALA F 278 " --> pdb=" O GLU F 274 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 304 Processing helix chain 'F' and resid 305 through 316 removed outlier: 3.663A pdb=" N SER F 310 " --> pdb=" O ILE F 306 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N PHE F 311 " --> pdb=" O GLU F 307 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASN F 313 " --> pdb=" O PHE F 309 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ARG F 314 " --> pdb=" O SER F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 347 through 352 removed outlier: 3.878A pdb=" N ASP F 352 " --> pdb=" O ILE F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 365 through 377 removed outlier: 3.774A pdb=" N GLN F 369 " --> pdb=" O LYS F 365 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU F 371 " --> pdb=" O THR F 367 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG F 372 " --> pdb=" O LYS F 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 397 removed outlier: 3.647A pdb=" N THR F 388 " --> pdb=" O GLU F 384 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL F 389 " --> pdb=" O ASP F 385 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG F 392 " --> pdb=" O THR F 388 " (cutoff:3.500A) Processing helix chain 'F' and resid 404 through 416 removed outlier: 4.250A pdb=" N ALA F 408 " --> pdb=" O GLN F 404 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N VAL F 412 " --> pdb=" O ALA F 408 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N CYS F 413 " --> pdb=" O ALA F 409 " (cutoff:3.500A) Processing helix chain 'F' and resid 423 through 433 removed outlier: 3.963A pdb=" N VAL F 429 " --> pdb=" O ASP F 425 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER F 431 " --> pdb=" O LYS F 427 " (cutoff:3.500A) Processing helix chain 'F' and resid 440 through 452 removed outlier: 3.560A pdb=" N GLU F 445 " --> pdb=" O GLN F 441 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 36 Processing sheet with id=AA2, first strand: chain 'A' and resid 329 through 331 removed outlier: 6.637A pdb=" N VAL A 66 " --> pdb=" O PHE A 329 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N SER A 331 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU A 68 " --> pdb=" O SER A 331 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ALA A 65 " --> pdb=" O MET A 359 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N ILE A 361 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU A 67 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ILE A 360 " --> pdb=" O LEU D 434 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 93 through 97 removed outlier: 6.437A pdb=" N CYS A 94 " --> pdb=" O PHE A 300 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N ASP A 302 " --> pdb=" O CYS A 94 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N MET A 96 " --> pdb=" O ASP A 302 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 335 through 337 Processing sheet with id=AA5, first strand: chain 'A' and resid 437 through 438 removed outlier: 4.277A pdb=" N ILE F 356 " --> pdb=" O TYR A 438 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N THR F 328 " --> pdb=" O ILE F 75 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N LEU F 296 " --> pdb=" O ILE F 325 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N ALA F 327 " --> pdb=" O LEU F 296 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ILE F 298 " --> pdb=" O ALA F 327 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N THR F 101 " --> pdb=" O PHE F 297 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 35 through 36 Processing sheet with id=AA7, first strand: chain 'B' and resid 93 through 97 removed outlier: 6.601A pdb=" N CYS B 94 " --> pdb=" O PHE B 300 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N ASP B 302 " --> pdb=" O CYS B 94 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N MET B 96 " --> pdb=" O ASP B 302 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LEU B 299 " --> pdb=" O ILE B 328 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N ALA B 330 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N VAL B 301 " --> pdb=" O ALA B 330 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL B 66 " --> pdb=" O PHE B 329 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N SER B 331 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LEU B 68 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ALA B 65 " --> pdb=" O MET B 359 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N ILE B 361 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N LEU B 67 " --> pdb=" O ILE B 361 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ILE B 360 " --> pdb=" O LEU E 434 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 335 through 337 Processing sheet with id=AA9, first strand: chain 'C' and resid 35 through 36 Processing sheet with id=AB1, first strand: chain 'C' and resid 65 through 69 Processing sheet with id=AB2, first strand: chain 'C' and resid 94 through 97 Processing sheet with id=AB3, first strand: chain 'C' and resid 120 through 121 Processing sheet with id=AB4, first strand: chain 'C' and resid 335 through 337 Processing sheet with id=AB5, first strand: chain 'D' and resid 42 through 43 Processing sheet with id=AB6, first strand: chain 'D' and resid 325 through 328 removed outlier: 6.683A pdb=" N VAL D 73 " --> pdb=" O MET D 326 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N THR D 328 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE D 75 " --> pdb=" O THR D 328 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ALA D 72 " --> pdb=" O LEU D 355 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N VAL D 357 " --> pdb=" O ALA D 72 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LEU D 74 " --> pdb=" O VAL D 357 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'D' and resid 102 through 104 removed outlier: 6.737A pdb=" N ILE D 103 " --> pdb=" O ASP D 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'D' and resid 332 through 334 Processing sheet with id=AB9, first strand: chain 'E' and resid 100 through 104 removed outlier: 5.933A pdb=" N THR E 101 " --> pdb=" O PHE E 297 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ASP E 299 " --> pdb=" O THR E 101 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ILE E 103 " --> pdb=" O ASP E 299 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL E 73 " --> pdb=" O MET E 326 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N THR E 328 " --> pdb=" O VAL E 73 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE E 75 " --> pdb=" O THR E 328 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 127 through 130 Processing sheet with id=AC2, first strand: chain 'E' and resid 332 through 334 Processing sheet with id=AC3, first strand: chain 'F' and resid 42 through 43 Processing sheet with id=AC4, first strand: chain 'F' and resid 332 through 334 435 hydrogen bonds defined for protein. 1248 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: 3.77 Time building geometry restraints manager: 4.22 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: 4978 1.34 - 1.46: 2664 1.46 - 1.58: 7195 1.58 - 1.70: 18 1.70 - 1.81: 120 Bond restraints: 14975 Sorted by residual: bond pdb=" N LYS B 7 " pdb=" CA LYS B 7 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.23e-02 6.61e+03 5.88e+00 bond pdb=" CA THR C 10 " pdb=" CB THR C 10 " ideal model delta sigma weight residual 1.532 1.564 -0.033 1.36e-02 5.41e+03 5.79e+00 bond pdb=" N LYS A 7 " pdb=" CA LYS A 7 " ideal model delta sigma weight residual 1.458 1.488 -0.029 1.23e-02 6.61e+03 5.72e+00 bond pdb=" N LYS C 7 " pdb=" CA LYS C 7 " ideal model delta sigma weight residual 1.457 1.488 -0.030 1.29e-02 6.01e+03 5.56e+00 bond pdb=" N GLU C 342 " pdb=" CA GLU C 342 " ideal model delta sigma weight residual 1.459 1.481 -0.022 1.15e-02 7.56e+03 3.59e+00 ... (remaining 14970 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 19429 2.01 - 4.02: 670 4.02 - 6.02: 96 6.02 - 8.03: 26 8.03 - 10.04: 11 Bond angle restraints: 20232 Sorted by residual: angle pdb=" N VAL F 249 " pdb=" CA VAL F 249 " pdb=" C VAL F 249 " ideal model delta sigma weight residual 113.53 106.69 6.84 9.80e-01 1.04e+00 4.87e+01 angle pdb=" C VAL A 6 " pdb=" N LYS A 7 " pdb=" CA LYS A 7 " ideal model delta sigma weight residual 120.82 130.86 -10.04 1.50e+00 4.44e-01 4.48e+01 angle pdb=" C VAL B 6 " pdb=" N LYS B 7 " pdb=" CA LYS B 7 " ideal model delta sigma weight residual 120.82 130.84 -10.02 1.50e+00 4.44e-01 4.46e+01 angle pdb=" C ILE E 13 " pdb=" N ARG E 14 " pdb=" CA ARG E 14 " ideal model delta sigma weight residual 121.19 129.37 -8.18 1.59e+00 3.96e-01 2.65e+01 angle pdb=" C GLU D 378 " pdb=" N ASP D 379 " pdb=" CA ASP D 379 " ideal model delta sigma weight residual 121.54 131.27 -9.73 1.91e+00 2.74e-01 2.60e+01 ... (remaining 20227 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.36: 8927 33.36 - 66.72: 237 66.72 - 100.08: 37 100.08 - 133.44: 3 133.44 - 166.81: 2 Dihedral angle restraints: 9206 sinusoidal: 3737 harmonic: 5469 Sorted by residual: dihedral pdb=" O2A ADP C 501 " pdb=" O3A ADP C 501 " pdb=" PA ADP C 501 " pdb=" PB ADP C 501 " ideal model delta sinusoidal sigma weight residual -60.00 106.81 -166.81 1 2.00e+01 2.50e-03 4.74e+01 dihedral pdb=" O1B ADP C 501 " pdb=" O3A ADP C 501 " pdb=" PB ADP C 501 " pdb=" PA ADP C 501 " ideal model delta sinusoidal sigma weight residual -60.00 81.57 -141.57 1 2.00e+01 2.50e-03 4.28e+01 dihedral pdb=" O1B ADP B 501 " pdb=" O3A ADP B 501 " pdb=" PB ADP B 501 " pdb=" PA ADP B 501 " ideal model delta sinusoidal sigma weight residual -60.00 -179.11 119.10 1 2.00e+01 2.50e-03 3.57e+01 ... (remaining 9203 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1993 0.063 - 0.125: 336 0.125 - 0.188: 52 0.188 - 0.251: 9 0.251 - 0.313: 5 Chirality restraints: 2395 Sorted by residual: chirality pdb=" CB VAL E 10 " pdb=" CA VAL E 10 " pdb=" CG1 VAL E 10 " pdb=" CG2 VAL E 10 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" CB VAL F 10 " pdb=" CA VAL F 10 " pdb=" CG1 VAL F 10 " pdb=" CG2 VAL F 10 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" CA VAL F 16 " pdb=" N VAL F 16 " pdb=" C VAL F 16 " pdb=" CB VAL F 16 " both_signs ideal model delta sigma weight residual False 2.44 2.74 -0.30 2.00e-01 2.50e+01 2.20e+00 ... (remaining 2392 not shown) Planarity restraints: 2578 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 327 " 0.014 2.00e-02 2.50e+03 2.77e-02 7.67e+00 pdb=" C VAL A 327 " -0.048 2.00e-02 2.50e+03 pdb=" O VAL A 327 " 0.018 2.00e-02 2.50e+03 pdb=" N ILE A 328 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL E 10 " 0.045 5.00e-02 4.00e+02 6.80e-02 7.39e+00 pdb=" N PRO E 11 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO E 11 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO E 11 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL F 10 " 0.045 5.00e-02 4.00e+02 6.80e-02 7.39e+00 pdb=" N PRO F 11 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO F 11 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO F 11 " 0.038 5.00e-02 4.00e+02 ... (remaining 2575 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 113 2.58 - 3.16: 10751 3.16 - 3.74: 21197 3.74 - 4.32: 29446 4.32 - 4.90: 48326 Nonbonded interactions: 109833 Sorted by model distance: nonbonded pdb=" CB ARG F 14 " pdb=" CG1 VAL F 242 " model vdw 1.999 3.860 nonbonded pdb=" O VAL A 6 " pdb=" OD2 ASP A 242 " model vdw 2.037 3.040 nonbonded pdb=" OG SER E 243 " pdb=" OE1 GLU E 246 " model vdw 2.300 3.040 nonbonded pdb=" O SER E 363 " pdb=" OG1 THR E 367 " model vdw 2.304 3.040 nonbonded pdb=" OG SER E 114 " pdb=" OE1 GLU E 117 " model vdw 2.314 3.040 ... (remaining 109828 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 2 through 120 or resid 239 through 248 or (resid 274 throu \ gh 276 and (name N or name CA or name C or name O or name CB )) or resid 277 thr \ ough 452 or resid 501)) selection = (chain 'B' and (resid 2 through 120 or resid 239 through 248 or (resid 274 throu \ gh 276 and (name N or name CA or name C or name O or name CB )) or resid 277 thr \ ough 452 or resid 501)) selection = (chain 'C' and (resid 2 through 120 or resid 239 through 248 or resid 274 throug \ h 452 or resid 501)) } ncs_group { reference = (chain 'D' and (resid 23 through 282 or (resid 283 and (name N or name CA or nam \ e C or name O or name CB )) or resid 284 through 453 or resid 501)) selection = (chain 'E' and (resid 23 through 127 or resid 243 through 249 or (resid 270 and \ (name N or name CA or name C or name O or name CB )) or resid 271 through 282 or \ (resid 283 and (name N or name CA or name C or name O or name CB )) or resid 28 \ 4 through 451 or (resid 452 through 453 and (name N or name CA or name C or name \ O or name CB )) or resid 501)) selection = (chain 'F' and (resid 23 through 127 or resid 243 through 249 or resid 270 throu \ gh 451 or (resid 452 through 453 and (name N or name CA or name C or name O or n \ ame CB )) 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=0.01 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 21.200 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: 0.010 Extract box with map and model: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 34.410 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0230 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 : 0.004 0.060 14984 Z= 0.207 Angle : 0.910 10.039 20232 Z= 0.529 Chirality : 0.052 0.313 2395 Planarity : 0.006 0.068 2578 Dihedral : 16.348 166.805 5668 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 0.19 % Allowed : 8.69 % Favored : 91.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -5.84 (0.13), residues: 1875 helix: -4.93 (0.05), residues: 871 sheet: -2.18 (0.33), residues: 199 loop : -2.85 (0.16), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 283 HIS 0.005 0.001 HIS D 245 PHE 0.016 0.001 PHE F 257 TYR 0.009 0.001 TYR B 438 ARG 0.008 0.000 ARG C 404 Details of bonding type rmsd hydrogen bonds : bond 0.34368 ( 435) hydrogen bonds : angle 9.74140 ( 1248) covalent geometry : bond 0.00410 (14975) covalent geometry : angle 0.90958 (20232) Misc. bond : bond 0.00213 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3750 Ramachandran restraints generated. 1875 Oldfield, 0 Emsley, 1875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3750 Ramachandran restraints generated. 1875 Oldfield, 0 Emsley, 1875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 163 time to evaluate : 1.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 11 LYS cc_start: 0.3534 (mttt) cc_final: 0.3241 (tptp) REVERT: B 61 MET cc_start: 0.0763 (tpp) cc_final: 0.0240 (tpt) REVERT: B 365 LEU cc_start: 0.0754 (mt) cc_final: -0.0956 (tt) REVERT: C 113 MET cc_start: 0.0870 (tpt) cc_final: 0.0538 (ttm) REVERT: D 424 ASP cc_start: 0.1234 (m-30) cc_final: 0.0589 (m-30) REVERT: F 41 GLN cc_start: 0.3192 (tp40) cc_final: 0.2046 (mt0) REVERT: F 320 MET cc_start: -0.0532 (ptt) cc_final: -0.1427 (mtt) outliers start: 3 outliers final: 1 residues processed: 166 average time/residue: 0.2931 time to fit residues: 71.8000 Evaluate side-chains 111 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 110 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 323 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 158 optimal weight: 0.4980 chunk 142 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 96 optimal weight: 0.6980 chunk 76 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 57 optimal weight: 0.3980 chunk 89 optimal weight: 6.9990 chunk 109 optimal weight: 3.9990 chunk 170 optimal weight: 9.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN A 305 HIS A 348 HIS A 392 ASN A 420 ASN A 429 HIS B 18 HIS B 85 GLN B 316 HIS C 18 HIS C 42 GLN C 247 ASN ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 393 HIS D 27 HIS D 78 GLN ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 329 ASN D 344 HIS D 369 GLN E 78 GLN E 251 ASN E 344 HIS ** F 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 447 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.229631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.200955 restraints weight = 20919.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.205660 restraints weight = 13384.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.208983 restraints weight = 9626.280| |-----------------------------------------------------------------------------| r_work (final): 0.4324 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4327 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4327 r_free = 0.4327 target_work(ls_wunit_k1) = 0.209 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4326 r_free = 0.4326 target_work(ls_wunit_k1) = 0.209 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4326 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1222 moved from start: 0.3753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 14984 Z= 0.232 Angle : 0.916 10.986 20232 Z= 0.453 Chirality : 0.051 0.330 2395 Planarity : 0.007 0.080 2578 Dihedral : 10.418 168.002 2113 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 1.78 % Allowed : 14.66 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -4.49 (0.15), residues: 1875 helix: -3.66 (0.11), residues: 896 sheet: -1.81 (0.35), residues: 194 loop : -2.20 (0.19), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 283 HIS 0.014 0.003 HIS B 429 PHE 0.023 0.003 PHE A 312 TYR 0.023 0.003 TYR B 438 ARG 0.020 0.001 ARG F 14 Details of bonding type rmsd hydrogen bonds : bond 0.05008 ( 435) hydrogen bonds : angle 5.69108 ( 1248) covalent geometry : bond 0.00506 (14975) covalent geometry : angle 0.91583 (20232) Misc. bond : bond 0.00134 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3750 Ramachandran restraints generated. 1875 Oldfield, 0 Emsley, 1875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3750 Ramachandran restraints generated. 1875 Oldfield, 0 Emsley, 1875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 132 time to evaluate : 1.612 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 371 MET cc_start: 0.1228 (tmm) cc_final: 0.0955 (tmm) REVERT: A 450 GLN cc_start: 0.1884 (tp40) cc_final: 0.1565 (tt0) REVERT: B 61 MET cc_start: 0.1184 (tpp) cc_final: 0.0581 (tpt) REVERT: B 280 ASN cc_start: 0.1235 (t0) cc_final: 0.1020 (t0) REVERT: B 303 GLU cc_start: 0.4631 (mt-10) cc_final: 0.4394 (mt-10) REVERT: C 68 LEU cc_start: 0.0510 (OUTLIER) cc_final: -0.0176 (mp) REVERT: D 380 VAL cc_start: 0.2804 (m) cc_final: 0.2591 (m) REVERT: D 424 ASP cc_start: 0.0783 (m-30) cc_final: 0.0498 (m-30) REVERT: E 320 MET cc_start: -0.0819 (tpt) cc_final: -0.1438 (tpt) REVERT: E 401 TYR cc_start: 0.3788 (t80) cc_final: 0.2814 (t80) REVERT: F 41 GLN cc_start: 0.4722 (tp40) cc_final: 0.3335 (tp40) REVERT: F 113 MET cc_start: -0.0048 (ptp) cc_final: -0.0309 (ptt) REVERT: F 320 MET cc_start: 0.0398 (ptt) cc_final: -0.0535 (mtt) outliers start: 28 outliers final: 11 residues processed: 158 average time/residue: 0.2451 time to fit residues: 59.4971 Evaluate side-chains 119 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 107 time to evaluate : 1.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 245 HIS Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 440 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 143 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 4 optimal weight: 2.9990 chunk 161 optimal weight: 0.0030 chunk 168 optimal weight: 0.0070 chunk 85 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 32 optimal weight: 8.9990 chunk 81 optimal weight: 0.7980 chunk 129 optimal weight: 0.9980 chunk 104 optimal weight: 0.3980 overall best weight: 0.4008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 380 GLN ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 HIS ** E 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 369 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.229749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.201119 restraints weight = 20356.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.205969 restraints weight = 12893.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.209279 restraints weight = 9195.721| |-----------------------------------------------------------------------------| r_work (final): 0.4334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1100 moved from start: 0.3928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14984 Z= 0.113 Angle : 0.646 9.204 20232 Z= 0.309 Chirality : 0.044 0.280 2395 Planarity : 0.004 0.052 2578 Dihedral : 9.529 152.748 2113 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.84 % Allowed : 15.61 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.55 (0.17), residues: 1875 helix: -2.78 (0.14), residues: 921 sheet: -1.39 (0.36), residues: 192 loop : -1.80 (0.20), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP D 283 HIS 0.005 0.001 HIS B 429 PHE 0.013 0.001 PHE C 300 TYR 0.016 0.001 TYR F 340 ARG 0.008 0.000 ARG D 330 Details of bonding type rmsd hydrogen bonds : bond 0.03597 ( 435) hydrogen bonds : angle 4.60000 ( 1248) covalent geometry : bond 0.00231 (14975) covalent geometry : angle 0.64602 (20232) Misc. bond : bond 0.00065 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3750 Ramachandran restraints generated. 1875 Oldfield, 0 Emsley, 1875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3750 Ramachandran restraints generated. 1875 Oldfield, 0 Emsley, 1875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 107 time to evaluate : 2.420 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 364 MET cc_start: 0.1902 (pmm) cc_final: 0.0679 (pmm) REVERT: A 371 MET cc_start: 0.0831 (tmm) cc_final: 0.0533 (tmm) REVERT: A 450 GLN cc_start: 0.2337 (tp40) cc_final: 0.1936 (tt0) REVERT: B 61 MET cc_start: 0.1046 (tpp) cc_final: 0.0063 (tpt) REVERT: D 424 ASP cc_start: 0.0771 (m-30) cc_final: 0.0420 (m-30) REVERT: F 41 GLN cc_start: 0.4612 (tp40) cc_final: 0.3565 (tp40) REVERT: F 113 MET cc_start: -0.0388 (ptp) cc_final: -0.0774 (ptt) REVERT: F 320 MET cc_start: 0.0502 (ptt) cc_final: -0.0491 (mtt) outliers start: 29 outliers final: 11 residues processed: 132 average time/residue: 0.2923 time to fit residues: 60.1991 Evaluate side-chains 108 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 403 ILE Chi-restraints excluded: chain F residue 440 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 46 optimal weight: 1.9990 chunk 138 optimal weight: 5.9990 chunk 62 optimal weight: 9.9990 chunk 105 optimal weight: 0.4980 chunk 1 optimal weight: 9.9990 chunk 132 optimal weight: 0.1980 chunk 149 optimal weight: 3.9990 chunk 145 optimal weight: 0.4980 chunk 94 optimal weight: 10.0000 chunk 30 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 HIS B 241 HIS D 78 GLN ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 GLN ** E 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 404 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.233474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.206388 restraints weight = 20554.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.210911 restraints weight = 13221.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.214221 restraints weight = 9573.955| |-----------------------------------------------------------------------------| r_work (final): 0.4381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1379 moved from start: 0.4938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 14984 Z= 0.134 Angle : 0.695 12.220 20232 Z= 0.329 Chirality : 0.044 0.238 2395 Planarity : 0.004 0.050 2578 Dihedral : 9.056 122.867 2113 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 2.28 % Allowed : 16.62 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.96 (0.17), residues: 1875 helix: -2.13 (0.15), residues: 912 sheet: -1.49 (0.35), residues: 197 loop : -1.64 (0.21), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 283 HIS 0.007 0.001 HIS F 302 PHE 0.021 0.002 PHE C 300 TYR 0.012 0.001 TYR C 366 ARG 0.007 0.001 ARG E 21 Details of bonding type rmsd hydrogen bonds : bond 0.03395 ( 435) hydrogen bonds : angle 4.41428 ( 1248) covalent geometry : bond 0.00294 (14975) covalent geometry : angle 0.69454 (20232) Misc. bond : bond 0.00072 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3750 Ramachandran restraints generated. 1875 Oldfield, 0 Emsley, 1875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3750 Ramachandran restraints generated. 1875 Oldfield, 0 Emsley, 1875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 115 time to evaluate : 1.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 450 GLN cc_start: 0.2389 (tp40) cc_final: 0.2088 (tt0) REVERT: B 61 MET cc_start: 0.1039 (tpp) cc_final: 0.0613 (tpt) REVERT: B 391 LEU cc_start: 0.0035 (OUTLIER) cc_final: -0.0219 (mt) REVERT: C 96 MET cc_start: 0.3724 (mmt) cc_final: 0.3072 (mpp) REVERT: C 364 MET cc_start: 0.2668 (mtt) cc_final: -0.0063 (ttp) REVERT: F 41 GLN cc_start: 0.4825 (tp40) cc_final: 0.3145 (tm-30) REVERT: F 65 GLU cc_start: -0.3227 (OUTLIER) cc_final: -0.3991 (mm-30) REVERT: F 113 MET cc_start: -0.0662 (ptp) cc_final: -0.1280 (ptt) REVERT: F 320 MET cc_start: 0.0989 (ptt) cc_final: -0.0568 (mtt) REVERT: F 404 GLN cc_start: -0.1288 (OUTLIER) cc_final: -0.4812 (tm-30) outliers start: 36 outliers final: 15 residues processed: 145 average time/residue: 0.2614 time to fit residues: 57.8514 Evaluate side-chains 124 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 1.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 346 ILE Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 396 GLU Chi-restraints excluded: chain E residue 403 ILE Chi-restraints excluded: chain F residue 65 GLU Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 369 GLN Chi-restraints excluded: chain F residue 404 GLN Chi-restraints excluded: chain F residue 440 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 154 optimal weight: 0.9990 chunk 171 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 119 optimal weight: 0.0070 chunk 90 optimal weight: 2.9990 chunk 136 optimal weight: 0.6980 chunk 110 optimal weight: 0.0970 chunk 144 optimal weight: 0.1980 chunk 56 optimal weight: 2.9990 chunk 179 optimal weight: 0.7980 overall best weight: 0.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 GLN ** E 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 369 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.233608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.206306 restraints weight = 20526.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.210956 restraints weight = 13290.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.214294 restraints weight = 9627.502| |-----------------------------------------------------------------------------| r_work (final): 0.4378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1301 moved from start: 0.5113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 14984 Z= 0.098 Angle : 0.612 9.748 20232 Z= 0.284 Chirality : 0.042 0.163 2395 Planarity : 0.003 0.047 2578 Dihedral : 8.720 117.165 2113 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.33 % Allowed : 17.77 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.43 (0.18), residues: 1875 helix: -1.68 (0.16), residues: 927 sheet: -1.30 (0.37), residues: 185 loop : -1.37 (0.21), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP E 283 HIS 0.009 0.001 HIS E 245 PHE 0.020 0.001 PHE C 300 TYR 0.011 0.001 TYR B 405 ARG 0.005 0.000 ARG E 372 Details of bonding type rmsd hydrogen bonds : bond 0.02759 ( 435) hydrogen bonds : angle 4.08495 ( 1248) covalent geometry : bond 0.00203 (14975) covalent geometry : angle 0.61239 (20232) Misc. bond : bond 0.00068 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3750 Ramachandran restraints generated. 1875 Oldfield, 0 Emsley, 1875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3750 Ramachandran restraints generated. 1875 Oldfield, 0 Emsley, 1875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 1.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 MET cc_start: 0.1012 (mmp) cc_final: 0.0261 (mmp) REVERT: A 364 MET cc_start: 0.1663 (pmm) cc_final: 0.0661 (pmm) REVERT: A 371 MET cc_start: 0.1595 (tmm) cc_final: 0.0745 (tmm) REVERT: B 61 MET cc_start: 0.0731 (tpp) cc_final: 0.0396 (tpt) REVERT: C 364 MET cc_start: 0.2736 (mtt) cc_final: -0.0048 (ttp) REVERT: D 62 MET cc_start: 0.4033 (tpp) cc_final: 0.3606 (mmp) REVERT: E 88 MET cc_start: 0.5052 (tpp) cc_final: 0.4717 (tpt) REVERT: F 41 GLN cc_start: 0.4707 (tp40) cc_final: 0.4268 (mm-40) REVERT: F 65 GLU cc_start: -0.3456 (OUTLIER) cc_final: -0.5076 (mt-10) REVERT: F 113 MET cc_start: -0.0521 (ptp) cc_final: -0.1071 (ptt) REVERT: F 320 MET cc_start: 0.0924 (ptt) cc_final: -0.0620 (mtt) REVERT: F 401 TYR cc_start: -0.1567 (t80) cc_final: -0.1906 (t80) REVERT: F 404 GLN cc_start: -0.1261 (OUTLIER) cc_final: -0.4743 (tm-30) REVERT: F 432 LEU cc_start: -0.2803 (OUTLIER) cc_final: -0.3309 (mp) outliers start: 21 outliers final: 10 residues processed: 125 average time/residue: 0.3099 time to fit residues: 59.4987 Evaluate side-chains 119 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 106 time to evaluate : 2.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain F residue 65 GLU Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 369 GLN Chi-restraints excluded: chain F residue 404 GLN Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain F residue 440 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 30 optimal weight: 0.9980 chunk 181 optimal weight: 0.9980 chunk 106 optimal weight: 0.5980 chunk 80 optimal weight: 0.9980 chunk 13 optimal weight: 20.0000 chunk 72 optimal weight: 7.9990 chunk 59 optimal weight: 0.5980 chunk 139 optimal weight: 0.7980 chunk 32 optimal weight: 10.0000 chunk 115 optimal weight: 0.4980 chunk 40 optimal weight: 0.2980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 GLN ** E 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.235648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.208580 restraints weight = 20597.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.213231 restraints weight = 13426.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.216466 restraints weight = 9704.370| |-----------------------------------------------------------------------------| r_work (final): 0.4396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1399 moved from start: 0.5499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14984 Z= 0.105 Angle : 0.618 11.073 20232 Z= 0.288 Chirality : 0.042 0.158 2395 Planarity : 0.003 0.044 2578 Dihedral : 8.534 113.141 2113 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 1.52 % Allowed : 18.34 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.02 (0.18), residues: 1875 helix: -1.26 (0.16), residues: 910 sheet: -1.15 (0.37), residues: 181 loop : -1.28 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 283 HIS 0.004 0.001 HIS E 25 PHE 0.018 0.001 PHE C 300 TYR 0.010 0.001 TYR B 405 ARG 0.006 0.000 ARG E 53 Details of bonding type rmsd hydrogen bonds : bond 0.02730 ( 435) hydrogen bonds : angle 4.02064 ( 1248) covalent geometry : bond 0.00222 (14975) covalent geometry : angle 0.61835 (20232) Misc. bond : bond 0.00071 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3750 Ramachandran restraints generated. 1875 Oldfield, 0 Emsley, 1875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3750 Ramachandran restraints generated. 1875 Oldfield, 0 Emsley, 1875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 112 time to evaluate : 1.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 MET cc_start: 0.1092 (mmp) cc_final: 0.0329 (mmp) REVERT: A 371 MET cc_start: 0.2030 (tmm) cc_final: 0.1075 (tmm) REVERT: B 61 MET cc_start: 0.0870 (tpp) cc_final: 0.0636 (tpt) REVERT: C 364 MET cc_start: 0.2650 (mtt) cc_final: -0.0281 (ttp) REVERT: D 49 GLN cc_start: 0.5429 (mm-40) cc_final: 0.4814 (mt0) REVERT: D 62 MET cc_start: 0.4097 (tpp) cc_final: 0.3724 (mmp) REVERT: D 330 ARG cc_start: 0.4807 (ttt90) cc_final: 0.4416 (ttt90) REVERT: D 346 ILE cc_start: 0.1319 (OUTLIER) cc_final: 0.0944 (mt) REVERT: E 88 MET cc_start: 0.4859 (tpp) cc_final: 0.4529 (tpt) REVERT: E 416 ARG cc_start: 0.1665 (ppt170) cc_final: -0.0202 (mmt-90) REVERT: F 41 GLN cc_start: 0.4822 (tp40) cc_final: 0.3776 (tm-30) REVERT: F 65 GLU cc_start: -0.3507 (OUTLIER) cc_final: -0.4200 (mm-30) REVERT: F 90 MET cc_start: 0.1369 (tmm) cc_final: 0.0925 (tmm) REVERT: F 113 MET cc_start: -0.1135 (ptp) cc_final: -0.1860 (ptt) REVERT: F 320 MET cc_start: 0.0470 (ptt) cc_final: -0.0887 (mtt) REVERT: F 401 TYR cc_start: -0.1411 (t80) cc_final: -0.1723 (t80) REVERT: F 404 GLN cc_start: -0.0890 (OUTLIER) cc_final: -0.4695 (tm-30) outliers start: 24 outliers final: 16 residues processed: 134 average time/residue: 0.2705 time to fit residues: 56.2065 Evaluate side-chains 128 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 346 ILE Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 245 HIS Chi-restraints excluded: chain E residue 396 GLU Chi-restraints excluded: chain F residue 65 GLU Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 369 GLN Chi-restraints excluded: chain F residue 404 GLN Chi-restraints excluded: chain F residue 440 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 42 optimal weight: 5.9990 chunk 167 optimal weight: 4.9990 chunk 130 optimal weight: 7.9990 chunk 98 optimal weight: 4.9990 chunk 19 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 166 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 148 optimal weight: 4.9990 chunk 137 optimal weight: 0.9990 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 42 GLN C 236 GLN C 241 HIS ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 344 HIS ** 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 = 0.4594 r_free = 0.4594 target = 0.239872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.213777 restraints weight = 20866.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.218232 restraints weight = 13519.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.221473 restraints weight = 9807.791| |-----------------------------------------------------------------------------| r_work (final): 0.4427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1640 moved from start: 0.6372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 14984 Z= 0.133 Angle : 0.693 10.627 20232 Z= 0.327 Chirality : 0.044 0.175 2395 Planarity : 0.004 0.045 2578 Dihedral : 8.707 116.115 2113 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 1.78 % Allowed : 19.48 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.96 (0.18), residues: 1875 helix: -1.13 (0.16), residues: 898 sheet: -1.42 (0.37), residues: 179 loop : -1.29 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 283 HIS 0.007 0.001 HIS A 305 PHE 0.015 0.002 PHE F 433 TYR 0.015 0.002 TYR C 366 ARG 0.009 0.001 ARG D 54 Details of bonding type rmsd hydrogen bonds : bond 0.03241 ( 435) hydrogen bonds : angle 4.38529 ( 1248) covalent geometry : bond 0.00285 (14975) covalent geometry : angle 0.69307 (20232) Misc. bond : bond 0.00092 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3750 Ramachandran restraints generated. 1875 Oldfield, 0 Emsley, 1875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3750 Ramachandran restraints generated. 1875 Oldfield, 0 Emsley, 1875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 117 time to evaluate : 1.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 MET cc_start: 0.1315 (mmp) cc_final: 0.0649 (mmp) REVERT: A 371 MET cc_start: 0.2424 (tmm) cc_final: 0.1153 (tmm) REVERT: B 61 MET cc_start: 0.1344 (tpp) cc_final: 0.0583 (tpt) REVERT: B 364 MET cc_start: -0.1540 (ptp) cc_final: -0.2011 (ptp) REVERT: C 61 MET cc_start: 0.0182 (ttt) cc_final: -0.0163 (ttt) REVERT: C 116 PHE cc_start: -0.2755 (OUTLIER) cc_final: -0.3481 (m-80) REVERT: C 364 MET cc_start: 0.2972 (mtt) cc_final: 0.0212 (ttp) REVERT: D 62 MET cc_start: 0.4340 (tpp) cc_final: 0.4040 (mmp) REVERT: D 88 MET cc_start: -0.0820 (mtp) cc_final: -0.1732 (mtp) REVERT: D 330 ARG cc_start: 0.5505 (ttt90) cc_final: 0.4856 (ttt90) REVERT: D 346 ILE cc_start: 0.1141 (OUTLIER) cc_final: 0.0794 (mt) REVERT: E 88 MET cc_start: 0.4897 (tpp) cc_final: 0.4555 (tpt) REVERT: E 291 ILE cc_start: -0.2517 (tp) cc_final: -0.2831 (mp) REVERT: F 41 GLN cc_start: 0.4797 (tp40) cc_final: 0.3321 (tm-30) REVERT: F 65 GLU cc_start: -0.3640 (OUTLIER) cc_final: -0.4873 (mm-30) REVERT: F 113 MET cc_start: -0.0736 (ptp) cc_final: -0.1574 (ptt) REVERT: F 320 MET cc_start: 0.0459 (ptt) cc_final: -0.0758 (mtt) REVERT: F 401 TYR cc_start: -0.1046 (t80) cc_final: -0.1317 (t80) REVERT: F 404 GLN cc_start: -0.0422 (OUTLIER) cc_final: -0.4197 (tm-30) REVERT: F 432 LEU cc_start: -0.2517 (OUTLIER) cc_final: -0.2861 (mp) outliers start: 28 outliers final: 20 residues processed: 142 average time/residue: 0.2514 time to fit residues: 54.6383 Evaluate side-chains 136 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 111 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 346 ILE Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 124 ARG Chi-restraints excluded: chain E residue 348 ILE Chi-restraints excluded: chain E residue 396 GLU Chi-restraints excluded: chain F residue 65 GLU Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 369 GLN Chi-restraints excluded: chain F residue 404 GLN Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain F residue 440 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 26 optimal weight: 0.1980 chunk 46 optimal weight: 4.9990 chunk 131 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 137 optimal weight: 0.0980 chunk 187 optimal weight: 5.9990 chunk 148 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 41 optimal weight: 7.9990 chunk 1 optimal weight: 8.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN A 348 HIS B 280 ASN B 380 GLN ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 329 ASN ** E 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 HIS E 49 GLN E 78 GLN E 251 ASN ** E 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 313 ASN ** E 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 329 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4678 r_free = 0.4678 target = 0.249790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.225348 restraints weight = 21922.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.229932 restraints weight = 14039.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.233198 restraints weight = 10027.281| |-----------------------------------------------------------------------------| r_work (final): 0.4523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2123 moved from start: 0.8141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 14984 Z= 0.228 Angle : 0.934 17.271 20232 Z= 0.456 Chirality : 0.051 0.280 2395 Planarity : 0.006 0.055 2578 Dihedral : 9.851 127.093 2113 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 2.47 % Allowed : 19.67 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.79 (0.18), residues: 1875 helix: -1.77 (0.15), residues: 900 sheet: -1.66 (0.39), residues: 152 loop : -1.83 (0.20), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 283 HIS 0.015 0.002 HIS C 305 PHE 0.031 0.004 PHE A 312 TYR 0.025 0.003 TYR C 366 ARG 0.014 0.001 ARG D 53 Details of bonding type rmsd hydrogen bonds : bond 0.04976 ( 435) hydrogen bonds : angle 5.39834 ( 1248) covalent geometry : bond 0.00481 (14975) covalent geometry : angle 0.93384 (20232) Misc. bond : bond 0.00208 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3750 Ramachandran restraints generated. 1875 Oldfield, 0 Emsley, 1875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3750 Ramachandran restraints generated. 1875 Oldfield, 0 Emsley, 1875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 122 time to evaluate : 1.790 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 364 MET cc_start: 0.2360 (pmm) cc_final: 0.0674 (ttm) REVERT: B 113 MET cc_start: 0.1750 (OUTLIER) cc_final: 0.0024 (tpt) REVERT: B 364 MET cc_start: -0.0681 (ptp) cc_final: -0.1336 (ptp) REVERT: C 306 MET cc_start: 0.2712 (pmm) cc_final: 0.1160 (ttp) REVERT: C 364 MET cc_start: 0.3148 (mtt) cc_final: 0.0673 (ttt) REVERT: D 88 MET cc_start: -0.0597 (mtp) cc_final: -0.1431 (mtp) REVERT: D 346 ILE cc_start: 0.1943 (OUTLIER) cc_final: 0.1664 (mt) REVERT: D 416 ARG cc_start: 0.0479 (OUTLIER) cc_final: -0.0334 (mtt90) REVERT: E 62 MET cc_start: -0.0360 (ttm) cc_final: -0.0668 (ttm) REVERT: E 88 MET cc_start: 0.5210 (tpp) cc_final: 0.4847 (tpt) REVERT: E 416 ARG cc_start: 0.1442 (ppt170) cc_final: 0.0552 (mtt90) REVERT: F 65 GLU cc_start: -0.3439 (OUTLIER) cc_final: -0.5286 (mt-10) REVERT: F 320 MET cc_start: 0.0980 (ptt) cc_final: -0.1003 (mtt) REVERT: F 325 ILE cc_start: 0.2853 (OUTLIER) cc_final: 0.2385 (mm) REVERT: F 401 TYR cc_start: -0.0616 (t80) cc_final: -0.1109 (t80) REVERT: F 404 GLN cc_start: 0.0639 (OUTLIER) cc_final: -0.3041 (tm-30) outliers start: 39 outliers final: 15 residues processed: 155 average time/residue: 0.3265 time to fit residues: 76.5852 Evaluate side-chains 135 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 346 ILE Chi-restraints excluded: chain D residue 416 ARG Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 22 ILE Chi-restraints excluded: chain E residue 396 GLU Chi-restraints excluded: chain F residue 65 GLU Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 325 ILE Chi-restraints excluded: chain F residue 404 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 124 optimal weight: 10.0000 chunk 9 optimal weight: 0.1980 chunk 2 optimal weight: 0.0470 chunk 79 optimal weight: 0.4980 chunk 187 optimal weight: 2.9990 chunk 131 optimal weight: 8.9990 chunk 181 optimal weight: 0.4980 chunk 135 optimal weight: 9.9990 chunk 76 optimal weight: 5.9990 chunk 55 optimal weight: 0.0870 chunk 90 optimal weight: 0.0370 overall best weight: 0.1734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 92 GLN ** E 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 GLN ** E 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 313 ASN ** E 344 HIS ** 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 = 0.4664 r_free = 0.4664 target = 0.247917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.222162 restraints weight = 21040.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.226802 restraints weight = 13697.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.230086 restraints weight = 9865.486| |-----------------------------------------------------------------------------| r_work (final): 0.4503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1769 moved from start: 0.7874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14984 Z= 0.113 Angle : 0.675 11.630 20232 Z= 0.319 Chirality : 0.044 0.167 2395 Planarity : 0.004 0.046 2578 Dihedral : 8.920 126.283 2113 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.02 % Allowed : 20.69 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.12 (0.18), residues: 1875 helix: -1.13 (0.16), residues: 918 sheet: -1.55 (0.39), residues: 154 loop : -1.55 (0.21), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 283 HIS 0.006 0.001 HIS E 245 PHE 0.027 0.002 PHE C 300 TYR 0.012 0.001 TYR A 366 ARG 0.015 0.001 ARG E 330 Details of bonding type rmsd hydrogen bonds : bond 0.03100 ( 435) hydrogen bonds : angle 4.42657 ( 1248) covalent geometry : bond 0.00240 (14975) covalent geometry : angle 0.67529 (20232) Misc. bond : bond 0.00141 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3750 Ramachandran restraints generated. 1875 Oldfield, 0 Emsley, 1875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3750 Ramachandran restraints generated. 1875 Oldfield, 0 Emsley, 1875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 1.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 MET cc_start: 0.1964 (mmp) cc_final: 0.1458 (mmp) REVERT: A 364 MET cc_start: 0.1330 (pmm) cc_final: 0.0068 (ttm) REVERT: B 364 MET cc_start: -0.1270 (ptp) cc_final: -0.1734 (ptp) REVERT: C 61 MET cc_start: 0.0817 (ttm) cc_final: 0.0306 (ttp) REVERT: C 306 MET cc_start: 0.3182 (pmm) cc_final: 0.0568 (ttt) REVERT: C 364 MET cc_start: 0.3080 (mtt) cc_final: 0.0444 (ttp) REVERT: D 88 MET cc_start: -0.1074 (mtp) cc_final: -0.1628 (mtp) REVERT: E 88 MET cc_start: 0.4977 (tpp) cc_final: 0.4595 (tpt) REVERT: E 90 MET cc_start: 0.1472 (mtt) cc_final: 0.0750 (ptp) REVERT: E 416 ARG cc_start: 0.1815 (ppt170) cc_final: 0.0645 (mmt-90) REVERT: F 65 GLU cc_start: -0.3621 (OUTLIER) cc_final: -0.5428 (mt-10) REVERT: F 90 MET cc_start: 0.1301 (tmm) cc_final: 0.0126 (tpt) REVERT: F 113 MET cc_start: -0.0795 (ptp) cc_final: -0.3036 (mtp) REVERT: F 320 MET cc_start: 0.0845 (ptt) cc_final: -0.1050 (mtt) REVERT: F 325 ILE cc_start: 0.2356 (OUTLIER) cc_final: 0.1635 (mm) REVERT: F 401 TYR cc_start: -0.1283 (t80) cc_final: -0.1627 (t80) outliers start: 16 outliers final: 8 residues processed: 133 average time/residue: 0.2549 time to fit residues: 51.2800 Evaluate side-chains 122 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain E residue 22 ILE Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 396 GLU Chi-restraints excluded: chain F residue 65 GLU Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 325 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 159 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 41 optimal weight: 0.4980 chunk 129 optimal weight: 0.0670 chunk 98 optimal weight: 2.9990 chunk 32 optimal weight: 8.9990 chunk 150 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 120 optimal weight: 0.2980 chunk 19 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 overall best weight: 1.1722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 GLN ** E 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4673 r_free = 0.4673 target = 0.249198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.223712 restraints weight = 21407.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.228424 restraints weight = 13674.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.231754 restraints weight = 9733.719| |-----------------------------------------------------------------------------| r_work (final): 0.4520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2027 moved from start: 0.8419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 14984 Z= 0.152 Angle : 0.766 11.768 20232 Z= 0.365 Chirality : 0.046 0.187 2395 Planarity : 0.004 0.049 2578 Dihedral : 9.038 124.972 2113 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 1.02 % Allowed : 21.38 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.26 (0.18), residues: 1875 helix: -1.32 (0.16), residues: 914 sheet: -1.60 (0.41), residues: 140 loop : -1.54 (0.21), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 283 HIS 0.007 0.001 HIS E 245 PHE 0.019 0.002 PHE B 93 TYR 0.019 0.002 TYR B 314 ARG 0.008 0.001 ARG D 416 Details of bonding type rmsd hydrogen bonds : bond 0.03842 ( 435) hydrogen bonds : angle 4.75452 ( 1248) covalent geometry : bond 0.00330 (14975) covalent geometry : angle 0.76623 (20232) Misc. bond : bond 0.00140 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3750 Ramachandran restraints generated. 1875 Oldfield, 0 Emsley, 1875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3750 Ramachandran restraints generated. 1875 Oldfield, 0 Emsley, 1875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 1.401 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 364 MET cc_start: 0.2073 (pmm) cc_final: 0.0669 (ttm) REVERT: B 364 MET cc_start: -0.1050 (ptp) cc_final: -0.1256 (ptp) REVERT: C 306 MET cc_start: 0.2751 (pmm) cc_final: 0.0546 (ttt) REVERT: C 364 MET cc_start: 0.3101 (mtt) cc_final: 0.0572 (ttt) REVERT: D 88 MET cc_start: -0.0772 (mtp) cc_final: -0.1440 (mtp) REVERT: E 88 MET cc_start: 0.5193 (tpp) cc_final: 0.4824 (tpt) REVERT: E 244 LEU cc_start: 0.4462 (tt) cc_final: 0.3788 (tp) REVERT: E 416 ARG cc_start: 0.2051 (ppt170) cc_final: 0.0605 (mmt-90) REVERT: E 420 GLU cc_start: 0.6567 (pm20) cc_final: 0.6207 (mp0) REVERT: F 65 GLU cc_start: -0.3807 (OUTLIER) cc_final: -0.5045 (mm-30) REVERT: F 320 MET cc_start: 0.0671 (ptt) cc_final: 0.0336 (ptp) REVERT: F 325 ILE cc_start: 0.2571 (OUTLIER) cc_final: 0.2056 (mm) REVERT: F 401 TYR cc_start: -0.0822 (t80) cc_final: -0.1122 (t80) outliers start: 16 outliers final: 11 residues processed: 121 average time/residue: 0.2918 time to fit residues: 55.4719 Evaluate side-chains 117 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 1.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain E residue 22 ILE Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 396 GLU Chi-restraints excluded: chain F residue 65 GLU Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 325 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 145 optimal weight: 2.9990 chunk 109 optimal weight: 0.6980 chunk 74 optimal weight: 4.9990 chunk 150 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 30 optimal weight: 0.2980 chunk 164 optimal weight: 0.0870 chunk 144 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 chunk 63 optimal weight: 8.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 344 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4683 r_free = 0.4683 target = 0.249728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.223891 restraints weight = 21103.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.228681 restraints weight = 13440.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.232021 restraints weight = 9546.960| |-----------------------------------------------------------------------------| r_work (final): 0.4526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1913 moved from start: 0.8460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14984 Z= 0.118 Angle : 0.702 10.726 20232 Z= 0.329 Chirality : 0.045 0.178 2395 Planarity : 0.004 0.047 2578 Dihedral : 8.796 126.357 2113 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 1.27 % Allowed : 21.19 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.04 (0.19), residues: 1875 helix: -1.13 (0.17), residues: 911 sheet: -1.48 (0.41), residues: 139 loop : -1.45 (0.21), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 283 HIS 0.007 0.001 HIS E 245 PHE 0.020 0.002 PHE C 300 TYR 0.012 0.001 TYR B 314 ARG 0.009 0.001 ARG D 53 Details of bonding type rmsd hydrogen bonds : bond 0.03266 ( 435) hydrogen bonds : angle 4.48630 ( 1248) covalent geometry : bond 0.00252 (14975) covalent geometry : angle 0.70222 (20232) Misc. bond : bond 0.00132 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5046.85 seconds wall clock time: 92 minutes 18.59 seconds (5538.59 seconds total)