Starting phenix.real_space_refine on Sun Jun 22 22:51:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g7m_29816/06_2025/8g7m_29816.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g7m_29816/06_2025/8g7m_29816.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g7m_29816/06_2025/8g7m_29816.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g7m_29816/06_2025/8g7m_29816.map" model { file = "/net/cci-nas-00/data/ceres_data/8g7m_29816/06_2025/8g7m_29816.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g7m_29816/06_2025/8g7m_29816.cif" } resolution = 3.2 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= 0.002 sd= 0.120 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: 7 Type Number sf(0) Gaussians K 7 8.98 5 P 21 5.49 5 Mg 7 5.21 5 S 94 5.16 5 C 16434 2.51 5 N 4491 2.21 5 O 5280 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 69 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 26334 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3932 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 15, 'TRANS': 511} Chain: "B" Number of atoms: 3932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3932 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 15, 'TRANS': 511} Chain: "C" Number of atoms: 3932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3932 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 15, 'TRANS': 511} Chain: "D" Number of atoms: 3932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3932 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 15, 'TRANS': 511} Chain: "E" Number of atoms: 3932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3932 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 15, 'TRANS': 511} Chain: "F" Number of atoms: 3932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3932 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 15, 'TRANS': 511} Chain: "G" Number of atoms: 2511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2511 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 10, 'TRANS': 332} Chain breaks: 1 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 16.67, per 1000 atoms: 0.63 Number of scatterers: 26334 At special positions: 0 Unit cell: (157.59, 160.371, 95.481, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 7 19.00 S 94 16.00 P 21 15.00 Mg 7 11.99 O 5280 8.00 N 4491 7.00 C 16434 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.69 Conformation dependent library (CDL) restraints added in 3.7 seconds 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6396 Finding SS restraints... Secondary structure from input PDB file: 149 helices and 36 sheets defined 59.3% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.29 Creating SS restraints... Processing helix chain 'A' and resid 7 through 27 removed outlier: 3.584A pdb=" N ARG A 11 " --> pdb=" O GLY A 7 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL A 27 " --> pdb=" O ASP A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 56 Processing helix chain 'A' and resid 64 through 83 removed outlier: 3.969A pdb=" N GLY A 68 " --> pdb=" O TYR A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 104 Processing helix chain 'A' and resid 110 through 133 Processing helix chain 'A' and resid 138 through 150 removed outlier: 3.555A pdb=" N ILE A 142 " --> pdb=" O THR A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 168 removed outlier: 3.555A pdb=" N GLY A 157 " --> pdb=" O ASP A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 203 removed outlier: 3.647A pdb=" N PHE A 202 " --> pdb=" O SER A 199 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE A 203 " --> pdb=" O PRO A 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 199 through 203' Processing helix chain 'A' and resid 227 through 230 Processing helix chain 'A' and resid 231 through 242 Processing helix chain 'A' and resid 253 through 267 Processing helix chain 'A' and resid 280 through 295 Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.576A pdb=" N LEU A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 353 removed outlier: 3.692A pdb=" N ASP A 353 " --> pdb=" O ILE A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 373 Processing helix chain 'A' and resid 384 through 408 Processing helix chain 'A' and resid 415 through 420 removed outlier: 3.724A pdb=" N LEU A 419 " --> pdb=" O GLY A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 428 removed outlier: 3.809A pdb=" N SER A 427 " --> pdb=" O ALA A 424 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU A 428 " --> pdb=" O LEU A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 446 Processing helix chain 'A' and resid 447 through 457 Processing helix chain 'A' and resid 460 through 470 Processing helix chain 'A' and resid 487 through 491 Processing helix chain 'A' and resid 496 through 514 removed outlier: 3.796A pdb=" N LEU A 512 " --> pdb=" O GLY A 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 27 removed outlier: 3.672A pdb=" N ARG B 11 " --> pdb=" O GLY B 7 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL B 27 " --> pdb=" O ASP B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 57 removed outlier: 3.709A pdb=" N SER B 57 " --> pdb=" O THR B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 83 removed outlier: 3.961A pdb=" N GLY B 68 " --> pdb=" O TYR B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 104 Processing helix chain 'B' and resid 110 through 133 Processing helix chain 'B' and resid 138 through 150 removed outlier: 3.521A pdb=" N ILE B 142 " --> pdb=" O THR B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 168 Processing helix chain 'B' and resid 199 through 203 removed outlier: 3.769A pdb=" N PHE B 202 " --> pdb=" O SER B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 242 Processing helix chain 'B' and resid 253 through 267 Processing helix chain 'B' and resid 280 through 295 Processing helix chain 'B' and resid 312 through 316 removed outlier: 3.557A pdb=" N LEU B 316 " --> pdb=" O PRO B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 355 removed outlier: 3.504A pdb=" N ILE B 341 " --> pdb=" O ASP B 337 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASP B 353 " --> pdb=" O ILE B 349 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N THR B 355 " --> pdb=" O GLN B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 373 Processing helix chain 'B' and resid 384 through 408 Processing helix chain 'B' and resid 415 through 420 removed outlier: 3.789A pdb=" N LEU B 419 " --> pdb=" O GLY B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 428 removed outlier: 3.753A pdb=" N SER B 427 " --> pdb=" O ALA B 424 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU B 428 " --> pdb=" O LEU B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 446 Processing helix chain 'B' and resid 447 through 457 Processing helix chain 'B' and resid 460 through 470 Processing helix chain 'B' and resid 487 through 491 Processing helix chain 'B' and resid 496 through 514 removed outlier: 3.844A pdb=" N LEU B 512 " --> pdb=" O GLY B 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 27 removed outlier: 3.736A pdb=" N ARG C 11 " --> pdb=" O GLY C 7 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL C 27 " --> pdb=" O ASP C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 57 removed outlier: 3.587A pdb=" N SER C 57 " --> pdb=" O THR C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 83 removed outlier: 3.973A pdb=" N GLY C 68 " --> pdb=" O TYR C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 104 Processing helix chain 'C' and resid 110 through 133 Processing helix chain 'C' and resid 138 through 150 removed outlier: 3.507A pdb=" N ILE C 142 " --> pdb=" O THR C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 168 removed outlier: 3.505A pdb=" N GLY C 157 " --> pdb=" O ASP C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 203 Processing helix chain 'C' and resid 231 through 242 Processing helix chain 'C' and resid 253 through 267 Processing helix chain 'C' and resid 280 through 295 Processing helix chain 'C' and resid 312 through 316 Processing helix chain 'C' and resid 337 through 355 removed outlier: 3.684A pdb=" N ILE C 341 " --> pdb=" O ASP C 337 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP C 353 " --> pdb=" O ILE C 349 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N THR C 355 " --> pdb=" O GLN C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 373 Processing helix chain 'C' and resid 384 through 408 Processing helix chain 'C' and resid 415 through 420 removed outlier: 3.774A pdb=" N LEU C 419 " --> pdb=" O GLY C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 428 removed outlier: 3.722A pdb=" N SER C 427 " --> pdb=" O ALA C 424 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU C 428 " --> pdb=" O LEU C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 446 Processing helix chain 'C' and resid 447 through 457 Processing helix chain 'C' and resid 460 through 470 Processing helix chain 'C' and resid 487 through 491 Processing helix chain 'C' and resid 496 through 514 removed outlier: 3.861A pdb=" N LEU C 512 " --> pdb=" O GLY C 508 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 27 removed outlier: 3.701A pdb=" N ARG D 11 " --> pdb=" O GLY D 7 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL D 27 " --> pdb=" O ASP D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 56 Processing helix chain 'D' and resid 64 through 83 removed outlier: 4.029A pdb=" N GLY D 68 " --> pdb=" O TYR D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 104 Processing helix chain 'D' and resid 110 through 133 Processing helix chain 'D' and resid 138 through 150 removed outlier: 3.536A pdb=" N ILE D 142 " --> pdb=" O THR D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 168 removed outlier: 3.501A pdb=" N GLY D 157 " --> pdb=" O ASP D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 203 removed outlier: 3.663A pdb=" N PHE D 202 " --> pdb=" O SER D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 241 Processing helix chain 'D' and resid 253 through 267 Processing helix chain 'D' and resid 279 through 295 Processing helix chain 'D' and resid 312 through 316 Processing helix chain 'D' and resid 337 through 353 removed outlier: 3.692A pdb=" N ILE D 341 " --> pdb=" O ASP D 337 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP D 353 " --> pdb=" O ILE D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 357 through 373 Processing helix chain 'D' and resid 384 through 408 removed outlier: 3.558A pdb=" N VAL D 388 " --> pdb=" O SER D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 420 removed outlier: 3.649A pdb=" N LEU D 419 " --> pdb=" O GLY D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 428 removed outlier: 3.856A pdb=" N SER D 427 " --> pdb=" O ALA D 424 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU D 428 " --> pdb=" O LEU D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 446 Processing helix chain 'D' and resid 447 through 457 Processing helix chain 'D' and resid 460 through 470 Processing helix chain 'D' and resid 487 through 491 Processing helix chain 'D' and resid 496 through 514 removed outlier: 3.911A pdb=" N LEU D 512 " --> pdb=" O GLY D 508 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 27 removed outlier: 3.635A pdb=" N ARG E 11 " --> pdb=" O GLY E 7 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL E 27 " --> pdb=" O ASP E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 56 Processing helix chain 'E' and resid 64 through 84 removed outlier: 3.977A pdb=" N GLY E 68 " --> pdb=" O TYR E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 104 removed outlier: 3.520A pdb=" N ALA E 90 " --> pdb=" O GLY E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 133 Processing helix chain 'E' and resid 138 through 150 removed outlier: 3.530A pdb=" N ILE E 142 " --> pdb=" O THR E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 168 removed outlier: 3.523A pdb=" N GLY E 157 " --> pdb=" O ASP E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 203 removed outlier: 3.629A pdb=" N PHE E 202 " --> pdb=" O SER E 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 230 Processing helix chain 'E' and resid 231 through 241 Processing helix chain 'E' and resid 253 through 267 Processing helix chain 'E' and resid 280 through 295 Processing helix chain 'E' and resid 312 through 316 Processing helix chain 'E' and resid 337 through 353 removed outlier: 3.580A pdb=" N ASP E 353 " --> pdb=" O ILE E 349 " (cutoff:3.500A) Processing helix chain 'E' and resid 357 through 373 Processing helix chain 'E' and resid 384 through 408 Processing helix chain 'E' and resid 415 through 420 removed outlier: 3.835A pdb=" N LEU E 419 " --> pdb=" O GLY E 415 " (cutoff:3.500A) Processing helix chain 'E' and resid 421 through 428 removed outlier: 3.751A pdb=" N SER E 427 " --> pdb=" O ALA E 424 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU E 428 " --> pdb=" O LEU E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 432 through 446 Processing helix chain 'E' and resid 447 through 457 Processing helix chain 'E' and resid 460 through 470 Processing helix chain 'E' and resid 487 through 491 Processing helix chain 'E' and resid 496 through 514 removed outlier: 3.855A pdb=" N LEU E 512 " --> pdb=" O GLY E 508 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 27 removed outlier: 3.549A pdb=" N ARG F 11 " --> pdb=" O GLY F 7 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL F 27 " --> pdb=" O ASP F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 57 removed outlier: 3.708A pdb=" N SER F 57 " --> pdb=" O THR F 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 83 removed outlier: 3.954A pdb=" N GLY F 68 " --> pdb=" O TYR F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 104 Processing helix chain 'F' and resid 110 through 133 Processing helix chain 'F' and resid 138 through 150 removed outlier: 3.516A pdb=" N ILE F 142 " --> pdb=" O THR F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 153 through 168 removed outlier: 3.528A pdb=" N GLY F 157 " --> pdb=" O ASP F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 199 through 203 removed outlier: 3.693A pdb=" N PHE F 202 " --> pdb=" O SER F 199 " (cutoff:3.500A) Processing helix chain 'F' and resid 231 through 242 Processing helix chain 'F' and resid 253 through 267 Processing helix chain 'F' and resid 280 through 295 Processing helix chain 'F' and resid 312 through 316 Processing helix chain 'F' and resid 337 through 353 removed outlier: 3.569A pdb=" N ASP F 353 " --> pdb=" O ILE F 349 " (cutoff:3.500A) Processing helix chain 'F' and resid 357 through 373 Processing helix chain 'F' and resid 384 through 408 Processing helix chain 'F' and resid 415 through 420 removed outlier: 3.713A pdb=" N LEU F 419 " --> pdb=" O GLY F 415 " (cutoff:3.500A) Processing helix chain 'F' and resid 421 through 428 removed outlier: 3.821A pdb=" N SER F 427 " --> pdb=" O ALA F 424 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU F 428 " --> pdb=" O LEU F 425 " (cutoff:3.500A) Processing helix chain 'F' and resid 432 through 446 Processing helix chain 'F' and resid 447 through 457 Processing helix chain 'F' and resid 460 through 470 Processing helix chain 'F' and resid 487 through 491 Processing helix chain 'F' and resid 496 through 514 removed outlier: 3.933A pdb=" N LEU F 512 " --> pdb=" O GLY F 508 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 27 removed outlier: 3.543A pdb=" N ARG G 11 " --> pdb=" O GLY G 7 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL G 27 " --> pdb=" O ASP G 23 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 57 removed outlier: 3.708A pdb=" N SER G 57 " --> pdb=" O THR G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 83 removed outlier: 3.910A pdb=" N GLY G 68 " --> pdb=" O TYR G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 104 Processing helix chain 'G' and resid 110 through 133 Processing helix chain 'G' and resid 138 through 150 removed outlier: 3.530A pdb=" N ILE G 142 " --> pdb=" O THR G 138 " (cutoff:3.500A) Processing helix chain 'G' and resid 153 through 168 removed outlier: 3.520A pdb=" N GLY G 157 " --> pdb=" O ASP G 153 " (cutoff:3.500A) Processing helix chain 'G' and resid 384 through 408 Processing helix chain 'G' and resid 415 through 420 removed outlier: 3.590A pdb=" N LEU G 419 " --> pdb=" O GLY G 415 " (cutoff:3.500A) Processing helix chain 'G' and resid 421 through 428 removed outlier: 3.858A pdb=" N SER G 427 " --> pdb=" O ALA G 424 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU G 428 " --> pdb=" O LEU G 425 " (cutoff:3.500A) Processing helix chain 'G' and resid 432 through 446 Processing helix chain 'G' and resid 447 through 457 removed outlier: 3.542A pdb=" N ALA G 457 " --> pdb=" O ILE G 453 " (cutoff:3.500A) Processing helix chain 'G' and resid 460 through 470 Processing helix chain 'G' and resid 487 through 491 Processing helix chain 'G' and resid 496 through 514 removed outlier: 3.817A pdb=" N LEU G 512 " --> pdb=" O GLY G 508 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 6 removed outlier: 4.751A pdb=" N ALA A 516 " --> pdb=" O THR B 35 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ILE B 37 " --> pdb=" O ALA A 516 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N VAL A 518 " --> pdb=" O ILE B 37 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 46 through 48 removed outlier: 7.013A pdb=" N THR A 35 " --> pdb=" O VAL G 518 " (cutoff:3.500A) removed outlier: 8.570A pdb=" N VAL G 520 " --> pdb=" O THR A 35 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ILE A 37 " --> pdb=" O VAL G 520 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N GLU G 522 " --> pdb=" O ILE A 37 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 173 through 177 removed outlier: 6.329A pdb=" N THR A 174 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N VAL A 380 " --> pdb=" O THR A 174 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N LYS A 176 " --> pdb=" O VAL A 380 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU A 184 " --> pdb=" O LYS A 379 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 191 through 192 removed outlier: 6.053A pdb=" N LYS A 318 " --> pdb=" O TYR A 217 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N TYR A 217 " --> pdb=" O LYS A 318 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLY A 320 " --> pdb=" O ASP A 215 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N VAL A 246 " --> pdb=" O ASP A 215 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N TYR A 217 " --> pdb=" O VAL A 246 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N ILE A 248 " --> pdb=" O TYR A 217 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N LEU A 219 " --> pdb=" O ILE A 248 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 410 through 412 Processing sheet with id=AA6, first strand: chain 'A' and resid 475 through 478 Processing sheet with id=AA7, first strand: chain 'B' and resid 2 through 6 removed outlier: 4.831A pdb=" N ALA B 516 " --> pdb=" O THR C 35 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N ILE C 37 " --> pdb=" O ALA B 516 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL B 518 " --> pdb=" O ILE C 37 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 173 through 177 removed outlier: 6.499A pdb=" N THR B 174 " --> pdb=" O LEU B 378 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N VAL B 380 " --> pdb=" O THR B 174 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N LYS B 176 " --> pdb=" O VAL B 380 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU B 184 " --> pdb=" O LYS B 379 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 191 through 192 removed outlier: 3.511A pdb=" N LEU B 331 " --> pdb=" O MET B 191 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE B 323 " --> pdb=" O MET B 330 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LYS B 318 " --> pdb=" O TYR B 217 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N TYR B 217 " --> pdb=" O LYS B 318 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N GLY B 320 " --> pdb=" O ASP B 215 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N VAL B 246 " --> pdb=" O ASP B 215 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N TYR B 217 " --> pdb=" O VAL B 246 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N ILE B 248 " --> pdb=" O TYR B 217 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N LEU B 219 " --> pdb=" O ILE B 248 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU B 245 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N VAL B 274 " --> pdb=" O LEU B 245 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ILE B 247 " --> pdb=" O VAL B 274 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 410 through 412 Processing sheet with id=AB2, first strand: chain 'B' and resid 475 through 478 removed outlier: 3.519A pdb=" N ASP B 483 " --> pdb=" O ASP B 478 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 2 through 6 removed outlier: 4.869A pdb=" N ALA C 516 " --> pdb=" O THR D 35 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N ILE D 37 " --> pdb=" O ALA C 516 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N VAL C 518 " --> pdb=" O ILE D 37 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 172 through 177 removed outlier: 6.123A pdb=" N VAL C 172 " --> pdb=" O ALA C 376 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N LEU C 378 " --> pdb=" O VAL C 172 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N THR C 174 " --> pdb=" O LEU C 378 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N VAL C 380 " --> pdb=" O THR C 174 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N LYS C 176 " --> pdb=" O VAL C 380 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 191 through 192 removed outlier: 6.252A pdb=" N LYS C 318 " --> pdb=" O TYR C 217 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N TYR C 217 " --> pdb=" O LYS C 318 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLY C 320 " --> pdb=" O ASP C 215 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N VAL C 246 " --> pdb=" O ASP C 215 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N TYR C 217 " --> pdb=" O VAL C 246 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N ILE C 248 " --> pdb=" O TYR C 217 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU C 219 " --> pdb=" O ILE C 248 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA C 249 " --> pdb=" O VAL C 274 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 191 through 192 removed outlier: 6.252A pdb=" N LYS C 318 " --> pdb=" O TYR C 217 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N TYR C 217 " --> pdb=" O LYS C 318 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLY C 320 " --> pdb=" O ASP C 215 " (cutoff:3.500A) removed outlier: 8.727A pdb=" N PHE C 299 " --> pdb=" O VAL C 218 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N LEU C 220 " --> pdb=" O PHE C 299 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 410 through 412 Processing sheet with id=AB8, first strand: chain 'C' and resid 475 through 478 Processing sheet with id=AB9, first strand: chain 'D' and resid 2 through 6 removed outlier: 4.753A pdb=" N ALA D 516 " --> pdb=" O THR E 35 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N ILE E 37 " --> pdb=" O ALA D 516 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL D 518 " --> pdb=" O ILE E 37 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 173 through 177 Processing sheet with id=AC2, first strand: chain 'D' and resid 191 through 192 removed outlier: 3.513A pdb=" N MET D 191 " --> pdb=" O LEU D 331 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU D 331 " --> pdb=" O MET D 191 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LYS D 318 " --> pdb=" O TYR D 217 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N TYR D 217 " --> pdb=" O LYS D 318 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N GLY D 320 " --> pdb=" O ASP D 215 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N VAL D 246 " --> pdb=" O ASP D 215 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N TYR D 217 " --> pdb=" O VAL D 246 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N ILE D 248 " --> pdb=" O TYR D 217 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LEU D 219 " --> pdb=" O ILE D 248 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA D 249 " --> pdb=" O VAL D 274 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 410 through 412 Processing sheet with id=AC4, first strand: chain 'D' and resid 475 through 478 removed outlier: 3.523A pdb=" N ASP D 483 " --> pdb=" O ASP D 478 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 2 through 6 removed outlier: 4.737A pdb=" N ALA E 516 " --> pdb=" O THR F 35 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N ILE F 37 " --> pdb=" O ALA E 516 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL E 518 " --> pdb=" O ILE F 37 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 172 through 177 removed outlier: 6.139A pdb=" N VAL E 172 " --> pdb=" O ALA E 376 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N LEU E 378 " --> pdb=" O VAL E 172 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N THR E 174 " --> pdb=" O LEU E 378 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N VAL E 380 " --> pdb=" O THR E 174 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N LYS E 176 " --> pdb=" O VAL E 380 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 191 through 192 removed outlier: 3.845A pdb=" N LEU E 331 " --> pdb=" O MET E 191 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LYS E 318 " --> pdb=" O TYR E 217 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N TYR E 217 " --> pdb=" O LYS E 318 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N GLY E 320 " --> pdb=" O ASP E 215 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N VAL E 246 " --> pdb=" O ASP E 215 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N TYR E 217 " --> pdb=" O VAL E 246 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N ILE E 248 " --> pdb=" O TYR E 217 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU E 219 " --> pdb=" O ILE E 248 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA E 249 " --> pdb=" O VAL E 274 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 191 through 192 removed outlier: 3.845A pdb=" N LEU E 331 " --> pdb=" O MET E 191 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LYS E 318 " --> pdb=" O TYR E 217 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N TYR E 217 " --> pdb=" O LYS E 318 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N GLY E 320 " --> pdb=" O ASP E 215 " (cutoff:3.500A) removed outlier: 8.627A pdb=" N PHE E 299 " --> pdb=" O VAL E 218 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N LEU E 220 " --> pdb=" O PHE E 299 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 410 through 412 Processing sheet with id=AD1, first strand: chain 'E' and resid 475 through 478 Processing sheet with id=AD2, first strand: chain 'F' and resid 2 through 6 removed outlier: 4.797A pdb=" N ALA F 516 " --> pdb=" O THR G 35 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N ILE G 37 " --> pdb=" O ALA F 516 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL F 518 " --> pdb=" O ILE G 37 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 173 through 177 removed outlier: 6.512A pdb=" N THR F 174 " --> pdb=" O LEU F 378 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N VAL F 380 " --> pdb=" O THR F 174 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N LYS F 176 " --> pdb=" O VAL F 380 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 191 through 192 removed outlier: 6.141A pdb=" N LYS F 318 " --> pdb=" O TYR F 217 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N TYR F 217 " --> pdb=" O LYS F 318 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N GLY F 320 " --> pdb=" O ASP F 215 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER F 221 " --> pdb=" O ILE F 248 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 410 through 412 Processing sheet with id=AD6, first strand: chain 'F' and resid 475 through 478 removed outlier: 3.504A pdb=" N ASP F 483 " --> pdb=" O ASP F 478 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 173 through 177 removed outlier: 6.495A pdb=" N THR G 174 " --> pdb=" O LEU G 378 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N VAL G 380 " --> pdb=" O THR G 174 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N LYS G 176 " --> pdb=" O VAL G 380 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 410 through 412 Processing sheet with id=AD9, first strand: chain 'G' and resid 475 through 478 1640 hydrogen bonds defined for protein. 4689 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.34 Time building geometry restraints manager: 7.85 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: 8528 1.34 - 1.45: 2040 1.45 - 1.57: 15770 1.57 - 1.69: 35 1.69 - 1.81: 168 Bond restraints: 26541 Sorted by residual: bond pdb=" CA ASP D 289 " pdb=" C ASP D 289 " ideal model delta sigma weight residual 1.524 1.439 0.085 1.29e-02 6.01e+03 4.33e+01 bond pdb=" ND1 HIS C 314 " pdb=" CE1 HIS C 314 " ideal model delta sigma weight residual 1.321 1.374 -0.053 1.00e-02 1.00e+04 2.80e+01 bond pdb=" ND1 HIS D 241 " pdb=" CE1 HIS D 241 " ideal model delta sigma weight residual 1.321 1.374 -0.053 1.00e-02 1.00e+04 2.76e+01 bond pdb=" CD GLN C 351 " pdb=" OE1 GLN C 351 " ideal model delta sigma weight residual 1.231 1.325 -0.094 1.90e-02 2.77e+03 2.43e+01 bond pdb=" CG ASN B 239 " pdb=" OD1 ASN B 239 " ideal model delta sigma weight residual 1.231 1.324 -0.093 1.90e-02 2.77e+03 2.40e+01 ... (remaining 26536 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 35474 1.81 - 3.62: 305 3.62 - 5.43: 64 5.43 - 7.24: 7 7.24 - 9.05: 7 Bond angle restraints: 35857 Sorted by residual: angle pdb=" CB HIS C 314 " pdb=" CG HIS C 314 " pdb=" CD2 HIS C 314 " ideal model delta sigma weight residual 131.20 122.59 8.61 1.30e+00 5.92e-01 4.39e+01 angle pdb=" CB HIS D 241 " pdb=" CG HIS D 241 " pdb=" CD2 HIS D 241 " ideal model delta sigma weight residual 131.20 122.71 8.49 1.30e+00 5.92e-01 4.27e+01 angle pdb=" CA ASP D 289 " pdb=" C ASP D 289 " pdb=" N MET D 290 " ideal model delta sigma weight residual 117.39 110.26 7.13 1.24e+00 6.50e-01 3.30e+01 angle pdb=" CB HIS D 241 " pdb=" CG HIS D 241 " pdb=" ND1 HIS D 241 " ideal model delta sigma weight residual 122.70 131.25 -8.55 1.50e+00 4.44e-01 3.25e+01 angle pdb=" CB HIS C 314 " pdb=" CG HIS C 314 " pdb=" ND1 HIS C 314 " ideal model delta sigma weight residual 122.70 131.25 -8.55 1.50e+00 4.44e-01 3.25e+01 ... (remaining 35852 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 15335 17.93 - 35.85: 927 35.85 - 53.78: 272 53.78 - 71.70: 95 71.70 - 89.63: 25 Dihedral angle restraints: 16654 sinusoidal: 6723 harmonic: 9931 Sorted by residual: dihedral pdb=" CA GLN D 312 " pdb=" C GLN D 312 " pdb=" N PRO D 313 " pdb=" CA PRO D 313 " ideal model delta harmonic sigma weight residual -180.00 -156.39 -23.61 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA VAL G 25 " pdb=" C VAL G 25 " pdb=" N ALA G 26 " pdb=" CA ALA G 26 " ideal model delta harmonic sigma weight residual -180.00 -163.06 -16.94 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA PHE F 6 " pdb=" C PHE F 6 " pdb=" N GLY F 7 " pdb=" CA GLY F 7 " ideal model delta harmonic sigma weight residual 180.00 163.10 16.90 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 16651 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 3033 0.035 - 0.071: 953 0.071 - 0.106: 265 0.106 - 0.141: 125 0.141 - 0.177: 5 Chirality restraints: 4381 Sorted by residual: chirality pdb=" CA GLU C 347 " pdb=" N GLU C 347 " pdb=" C GLU C 347 " pdb=" CB GLU C 347 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.81e-01 chirality pdb=" CA PRO D 313 " pdb=" N PRO D 313 " pdb=" C PRO D 313 " pdb=" CB PRO D 313 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.09e-01 chirality pdb=" CA GLN D 346 " pdb=" N GLN D 346 " pdb=" C GLN D 346 " pdb=" CB GLN D 346 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.41e-01 ... (remaining 4378 not shown) Planarity restraints: 4578 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS D 288 " 0.029 2.00e-02 2.50e+03 5.77e-02 3.33e+01 pdb=" C LYS D 288 " -0.100 2.00e-02 2.50e+03 pdb=" O LYS D 288 " 0.039 2.00e-02 2.50e+03 pdb=" N ASP D 289 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER C 199 " -0.060 5.00e-02 4.00e+02 9.12e-02 1.33e+01 pdb=" N PRO C 200 " 0.158 5.00e-02 4.00e+02 pdb=" CA PRO C 200 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO C 200 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 276 " -0.031 5.00e-02 4.00e+02 4.67e-02 3.49e+00 pdb=" N PRO B 277 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 277 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 277 " -0.026 5.00e-02 4.00e+02 ... (remaining 4575 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.67: 345 2.67 - 3.29: 28226 3.29 - 3.91: 51493 3.91 - 4.52: 64982 4.52 - 5.14: 106747 Nonbonded interactions: 251793 Sorted by model distance: nonbonded pdb=" OD1 ASP D 85 " pdb="MG MG D 602 " model vdw 2.057 2.170 nonbonded pdb=" O2G ATP E 601 " pdb="MG MG E 602 " model vdw 2.079 2.170 nonbonded pdb=" O1A ATP E 601 " pdb="MG MG E 602 " model vdw 2.100 2.170 nonbonded pdb=" O2G ATP A 601 " pdb="MG MG A 602 " model vdw 2.118 2.170 nonbonded pdb=" OD1 ASP F 85 " pdb="MG MG F 602 " model vdw 2.139 2.170 ... (remaining 251788 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.170 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: 0.020 Extract box with map and model: 1.110 Check model and map are aligned: 0.190 Set scattering table: 0.260 Process input model: 61.700 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 26541 Z= 0.167 Angle : 0.487 9.054 35857 Z= 0.281 Chirality : 0.041 0.177 4381 Planarity : 0.004 0.091 4578 Dihedral : 14.085 89.629 10258 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % 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: 2.22 (0.14), residues: 3489 helix: 2.52 (0.12), residues: 1859 sheet: 1.35 (0.24), residues: 455 loop : -0.20 (0.16), residues: 1175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 42 HIS 0.006 0.001 HIS D 314 PHE 0.021 0.001 PHE D 213 TYR 0.012 0.001 TYR C 197 ARG 0.006 0.000 ARG D 344 Details of bonding type rmsd hydrogen bonds : bond 0.15495 ( 1623) hydrogen bonds : angle 5.15375 ( 4689) covalent geometry : bond 0.00301 (26541) covalent geometry : angle 0.48710 (35857) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 3.057 Fit side-chains REVERT: A 209 GLN cc_start: 0.7544 (mm110) cc_final: 0.7045 (tm-30) REVERT: A 505 ASP cc_start: 0.8124 (m-30) cc_final: 0.7726 (m-30) REVERT: B 164 MET cc_start: 0.8341 (ttm) cc_final: 0.8024 (mtt) REVERT: B 343 LYS cc_start: 0.8952 (ttpt) cc_final: 0.8623 (tptt) REVERT: B 505 ASP cc_start: 0.8207 (m-30) cc_final: 0.7884 (m-30) REVERT: C 192 LYS cc_start: 0.7116 (tttt) cc_final: 0.6822 (tttt) REVERT: C 270 GLN cc_start: 0.7248 (mp10) cc_final: 0.6805 (mp10) REVERT: E 123 ASP cc_start: 0.6730 (m-30) cc_final: 0.6496 (m-30) REVERT: E 487 MET cc_start: 0.8772 (mmm) cc_final: 0.8075 (mmt) REVERT: G 74 ASP cc_start: 0.7699 (t70) cc_final: 0.7265 (t0) outliers start: 0 outliers final: 0 residues processed: 217 average time/residue: 0.3453 time to fit residues: 125.4465 Evaluate side-chains 185 residues out of total 2827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 3.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 292 optimal weight: 30.0000 chunk 262 optimal weight: 0.0470 chunk 145 optimal weight: 6.9990 chunk 89 optimal weight: 5.9990 chunk 176 optimal weight: 0.0030 chunk 140 optimal weight: 10.0000 chunk 271 optimal weight: 0.9980 chunk 104 optimal weight: 6.9990 chunk 164 optimal weight: 0.2980 chunk 201 optimal weight: 1.9990 chunk 314 optimal weight: 0.7980 overall best weight: 0.4288 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 GLN C 78 ASN C 470 GLN D 209 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.168284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.102377 restraints weight = 34409.234| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.11 r_work: 0.3123 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.0890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 26541 Z= 0.099 Angle : 0.452 8.819 35857 Z= 0.246 Chirality : 0.041 0.162 4381 Planarity : 0.003 0.056 4578 Dihedral : 9.858 77.978 3886 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 0.46 % Allowed : 3.25 % Favored : 96.29 % 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: 2.30 (0.14), residues: 3489 helix: 2.51 (0.12), residues: 1933 sheet: 1.42 (0.24), residues: 453 loop : -0.25 (0.17), residues: 1103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP G 42 HIS 0.004 0.001 HIS D 241 PHE 0.011 0.001 PHE D 213 TYR 0.013 0.002 TYR C 359 ARG 0.004 0.000 ARG B 344 Details of bonding type rmsd hydrogen bonds : bond 0.04144 ( 1623) hydrogen bonds : angle 4.09956 ( 4689) covalent geometry : bond 0.00192 (26541) covalent geometry : angle 0.45229 (35857) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 204 time to evaluate : 3.109 Fit side-chains revert: symmetry clash REVERT: A 209 GLN cc_start: 0.7721 (mm110) cc_final: 0.7206 (tm-30) REVERT: A 375 VAL cc_start: 0.8724 (t) cc_final: 0.8511 (m) REVERT: A 505 ASP cc_start: 0.8459 (m-30) cc_final: 0.8228 (m-30) REVERT: B 120 LEU cc_start: 0.8500 (tp) cc_final: 0.8281 (mp) REVERT: B 343 LYS cc_start: 0.8898 (ttpt) cc_final: 0.8551 (tptt) REVERT: B 366 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8269 (pm20) REVERT: B 505 ASP cc_start: 0.8613 (m-30) cc_final: 0.8311 (m-30) REVERT: C 270 GLN cc_start: 0.7481 (mp10) cc_final: 0.6969 (mp10) REVERT: C 330 MET cc_start: 0.8160 (mtt) cc_final: 0.7892 (mtt) REVERT: D 3 ASP cc_start: 0.8463 (t0) cc_final: 0.8223 (t0) REVERT: E 123 ASP cc_start: 0.7547 (m-30) cc_final: 0.7283 (m-30) REVERT: F 328 ASP cc_start: 0.7569 (m-30) cc_final: 0.7233 (t0) REVERT: G 74 ASP cc_start: 0.8388 (t70) cc_final: 0.7972 (t0) outliers start: 13 outliers final: 10 residues processed: 211 average time/residue: 0.3486 time to fit residues: 122.5431 Evaluate side-chains 193 residues out of total 2827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 182 time to evaluate : 2.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain B residue 279 PHE Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 366 GLU Chi-restraints excluded: chain B residue 407 GLU Chi-restraints excluded: chain C residue 176 LYS Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 384 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 144 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 259 optimal weight: 2.9990 chunk 292 optimal weight: 20.0000 chunk 255 optimal weight: 8.9990 chunk 55 optimal weight: 0.7980 chunk 341 optimal weight: 0.9980 chunk 72 optimal weight: 20.0000 chunk 181 optimal weight: 7.9990 chunk 51 optimal weight: 0.7980 chunk 126 optimal weight: 10.0000 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 209 GLN D 346 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.162918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.095871 restraints weight = 34665.546| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.10 r_work: 0.3042 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 26541 Z= 0.165 Angle : 0.496 10.410 35857 Z= 0.265 Chirality : 0.043 0.154 4381 Planarity : 0.003 0.044 4578 Dihedral : 9.751 89.572 3886 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 0.92 % Allowed : 4.56 % Favored : 94.52 % 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: 2.18 (0.14), residues: 3489 helix: 2.46 (0.12), residues: 1900 sheet: 1.37 (0.25), residues: 403 loop : -0.21 (0.16), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 42 HIS 0.002 0.000 HIS D 314 PHE 0.012 0.001 PHE D 213 TYR 0.013 0.002 TYR B 197 ARG 0.004 0.000 ARG B 344 Details of bonding type rmsd hydrogen bonds : bond 0.05570 ( 1623) hydrogen bonds : angle 4.12216 ( 4689) covalent geometry : bond 0.00401 (26541) covalent geometry : angle 0.49642 (35857) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 188 time to evaluate : 2.760 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 191 MET cc_start: 0.5743 (mmp) cc_final: 0.5505 (mmm) REVERT: A 209 GLN cc_start: 0.7763 (mm110) cc_final: 0.7216 (tm-30) REVERT: B 217 TYR cc_start: 0.5256 (m-80) cc_final: 0.4402 (m-80) REVERT: B 343 LYS cc_start: 0.8934 (ttpt) cc_final: 0.8622 (tptt) REVERT: B 351 GLN cc_start: 0.8036 (mp10) cc_final: 0.7641 (pm20) REVERT: B 366 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8314 (pm20) REVERT: B 505 ASP cc_start: 0.8676 (m-30) cc_final: 0.8352 (m-30) REVERT: C 59 ASP cc_start: 0.8192 (m-30) cc_final: 0.7869 (m-30) REVERT: C 270 GLN cc_start: 0.7579 (mp10) cc_final: 0.7016 (mp10) REVERT: D 3 ASP cc_start: 0.8521 (t0) cc_final: 0.8277 (t0) REVERT: E 123 ASP cc_start: 0.7653 (m-30) cc_final: 0.7402 (m-30) REVERT: G 74 ASP cc_start: 0.8483 (t70) cc_final: 0.8111 (t0) REVERT: G 77 ASN cc_start: 0.9016 (t0) cc_final: 0.8651 (m-40) outliers start: 26 outliers final: 14 residues processed: 203 average time/residue: 0.3362 time to fit residues: 114.9222 Evaluate side-chains 191 residues out of total 2827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 176 time to evaluate : 2.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 366 GLU Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain C residue 176 LYS Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 392 LYS Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 384 SER Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 172 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 157 optimal weight: 0.9980 chunk 76 optimal weight: 8.9990 chunk 104 optimal weight: 5.9990 chunk 87 optimal weight: 30.0000 chunk 73 optimal weight: 3.9990 chunk 276 optimal weight: 8.9990 chunk 4 optimal weight: 2.9990 chunk 237 optimal weight: 30.0000 chunk 22 optimal weight: 3.9990 chunk 89 optimal weight: 10.0000 chunk 154 optimal weight: 1.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 239 ASN D 209 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.160974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.094070 restraints weight = 35097.332| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 2.10 r_work: 0.2997 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 26541 Z= 0.187 Angle : 0.516 8.835 35857 Z= 0.276 Chirality : 0.044 0.166 4381 Planarity : 0.003 0.045 4578 Dihedral : 9.524 84.020 3886 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 0.99 % Allowed : 5.98 % Favored : 93.03 % 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: 1.94 (0.14), residues: 3489 helix: 2.28 (0.12), residues: 1895 sheet: 1.21 (0.26), residues: 403 loop : -0.31 (0.16), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 42 HIS 0.004 0.001 HIS D 314 PHE 0.012 0.001 PHE D 6 TYR 0.015 0.002 TYR B 197 ARG 0.002 0.000 ARG C 116 Details of bonding type rmsd hydrogen bonds : bond 0.05892 ( 1623) hydrogen bonds : angle 4.13637 ( 4689) covalent geometry : bond 0.00458 (26541) covalent geometry : angle 0.51608 (35857) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 181 time to evaluate : 2.875 Fit side-chains revert: symmetry clash REVERT: A 191 MET cc_start: 0.5836 (mmp) cc_final: 0.5553 (mmm) REVERT: A 209 GLN cc_start: 0.7808 (mm110) cc_final: 0.7292 (tm-30) REVERT: B 343 LYS cc_start: 0.8878 (ttpt) cc_final: 0.8600 (tptt) REVERT: B 351 GLN cc_start: 0.7866 (mp10) cc_final: 0.7513 (tt0) REVERT: B 366 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8355 (pm20) REVERT: C 59 ASP cc_start: 0.8248 (m-30) cc_final: 0.7923 (m-30) REVERT: C 270 GLN cc_start: 0.7654 (mp10) cc_final: 0.7055 (mp10) REVERT: C 330 MET cc_start: 0.8093 (mtp) cc_final: 0.7463 (mmm) REVERT: D 3 ASP cc_start: 0.8492 (t0) cc_final: 0.8217 (t0) REVERT: E 123 ASP cc_start: 0.7634 (m-30) cc_final: 0.7376 (m-30) REVERT: G 74 ASP cc_start: 0.8430 (t70) cc_final: 0.8034 (t0) REVERT: G 505 ASP cc_start: 0.8624 (m-30) cc_final: 0.8295 (m-30) outliers start: 28 outliers final: 17 residues processed: 196 average time/residue: 0.3341 time to fit residues: 109.8084 Evaluate side-chains 192 residues out of total 2827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 174 time to evaluate : 2.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 279 PHE Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 366 GLU Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 469 MET Chi-restraints excluded: chain D residue 183 ASP Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 384 SER Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 330 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 57 optimal weight: 0.0470 chunk 78 optimal weight: 7.9990 chunk 19 optimal weight: 20.0000 chunk 192 optimal weight: 9.9990 chunk 220 optimal weight: 1.9990 chunk 202 optimal weight: 0.8980 chunk 217 optimal weight: 0.8980 chunk 321 optimal weight: 0.8980 chunk 252 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 249 optimal weight: 8.9990 overall best weight: 0.9480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 209 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.164533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.098945 restraints weight = 34717.828| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 2.10 r_work: 0.3066 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 26541 Z= 0.102 Angle : 0.448 10.861 35857 Z= 0.239 Chirality : 0.042 0.290 4381 Planarity : 0.003 0.047 4578 Dihedral : 8.904 80.051 3886 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 0.64 % Allowed : 7.04 % Favored : 92.32 % 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: 2.17 (0.14), residues: 3489 helix: 2.52 (0.12), residues: 1909 sheet: 1.28 (0.25), residues: 423 loop : -0.38 (0.16), residues: 1157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP G 42 HIS 0.004 0.001 HIS D 314 PHE 0.010 0.001 PHE D 213 TYR 0.013 0.001 TYR B 197 ARG 0.003 0.000 ARG B 344 Details of bonding type rmsd hydrogen bonds : bond 0.04207 ( 1623) hydrogen bonds : angle 3.88213 ( 4689) covalent geometry : bond 0.00215 (26541) covalent geometry : angle 0.44801 (35857) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 190 time to evaluate : 3.242 Fit side-chains REVERT: A 209 GLN cc_start: 0.7895 (mm110) cc_final: 0.7388 (tm-30) REVERT: B 141 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7612 (mt-10) REVERT: B 343 LYS cc_start: 0.8932 (ttpt) cc_final: 0.8530 (tppt) REVERT: B 351 GLN cc_start: 0.7768 (mp10) cc_final: 0.7535 (tt0) REVERT: B 366 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8308 (pm20) REVERT: C 59 ASP cc_start: 0.8248 (m-30) cc_final: 0.7912 (m-30) REVERT: C 176 LYS cc_start: 0.7282 (OUTLIER) cc_final: 0.7082 (ptmt) REVERT: C 270 GLN cc_start: 0.7473 (mp10) cc_final: 0.6862 (mp10) REVERT: C 328 ASP cc_start: 0.8064 (t0) cc_final: 0.7742 (t0) REVERT: E 123 ASP cc_start: 0.7569 (m-30) cc_final: 0.7308 (m-30) REVERT: F 14 MET cc_start: 0.9389 (mtm) cc_final: 0.9161 (mtm) REVERT: G 74 ASP cc_start: 0.8383 (t70) cc_final: 0.7950 (t0) outliers start: 18 outliers final: 13 residues processed: 197 average time/residue: 0.3410 time to fit residues: 113.4051 Evaluate side-chains 192 residues out of total 2827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 177 time to evaluate : 3.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain B residue 279 PHE Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 366 GLU Chi-restraints excluded: chain B residue 407 GLU Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain C residue 176 LYS Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 384 SER Chi-restraints excluded: chain E residue 469 MET Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 330 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 223 optimal weight: 3.9990 chunk 75 optimal weight: 8.9990 chunk 214 optimal weight: 0.2980 chunk 235 optimal weight: 8.9990 chunk 30 optimal weight: 5.9990 chunk 192 optimal weight: 7.9990 chunk 130 optimal weight: 5.9990 chunk 172 optimal weight: 0.9980 chunk 131 optimal weight: 7.9990 chunk 86 optimal weight: 5.9990 chunk 227 optimal weight: 6.9990 overall best weight: 3.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 209 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.159085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.092526 restraints weight = 34944.137| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 2.06 r_work: 0.2967 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 26541 Z= 0.222 Angle : 0.547 10.666 35857 Z= 0.290 Chirality : 0.045 0.151 4381 Planarity : 0.004 0.050 4578 Dihedral : 9.596 85.376 3886 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.74 % Allowed : 8.28 % Favored : 90.98 % 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: 1.79 (0.14), residues: 3489 helix: 2.19 (0.12), residues: 1895 sheet: 1.05 (0.26), residues: 403 loop : -0.42 (0.16), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 42 HIS 0.004 0.001 HIS D 314 PHE 0.013 0.001 PHE D 6 TYR 0.016 0.002 TYR B 197 ARG 0.002 0.000 ARG G 169 Details of bonding type rmsd hydrogen bonds : bond 0.06459 ( 1623) hydrogen bonds : angle 4.13980 ( 4689) covalent geometry : bond 0.00550 (26541) covalent geometry : angle 0.54710 (35857) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 182 time to evaluate : 2.881 Fit side-chains REVERT: B 343 LYS cc_start: 0.8875 (ttpt) cc_final: 0.8605 (tptt) REVERT: B 366 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8309 (pm20) REVERT: C 59 ASP cc_start: 0.8341 (m-30) cc_final: 0.8029 (m-30) REVERT: C 270 GLN cc_start: 0.7623 (mp10) cc_final: 0.6949 (mp10) REVERT: C 330 MET cc_start: 0.7996 (mmm) cc_final: 0.7759 (mmt) REVERT: C 390 GLU cc_start: 0.8101 (tm-30) cc_final: 0.7246 (tm-30) REVERT: D 3 ASP cc_start: 0.8526 (t0) cc_final: 0.8237 (t0) REVERT: E 123 ASP cc_start: 0.7670 (m-30) cc_final: 0.7414 (m-30) REVERT: F 390 GLU cc_start: 0.8068 (tp30) cc_final: 0.7787 (tp30) REVERT: G 74 ASP cc_start: 0.8435 (t70) cc_final: 0.8051 (t0) REVERT: G 505 ASP cc_start: 0.8626 (m-30) cc_final: 0.8284 (m-30) outliers start: 21 outliers final: 15 residues processed: 191 average time/residue: 0.3515 time to fit residues: 111.9227 Evaluate side-chains 190 residues out of total 2827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 174 time to evaluate : 3.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 279 PHE Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 366 GLU Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain C residue 176 LYS Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 469 MET Chi-restraints excluded: chain D residue 183 ASP Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 384 SER Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 330 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 321 optimal weight: 0.7980 chunk 124 optimal weight: 0.0020 chunk 33 optimal weight: 0.0370 chunk 6 optimal weight: 3.9990 chunk 294 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 265 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 302 optimal weight: 0.3980 chunk 204 optimal weight: 0.9990 chunk 329 optimal weight: 0.9990 overall best weight: 0.4468 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 209 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.164714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.099650 restraints weight = 34816.094| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.09 r_work: 0.3073 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 26541 Z= 0.102 Angle : 0.455 11.335 35857 Z= 0.240 Chirality : 0.041 0.166 4381 Planarity : 0.003 0.053 4578 Dihedral : 8.774 79.895 3886 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 0.57 % Allowed : 8.56 % Favored : 90.87 % 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: 2.16 (0.14), residues: 3489 helix: 2.55 (0.12), residues: 1925 sheet: 1.20 (0.25), residues: 423 loop : -0.46 (0.17), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP G 42 HIS 0.002 0.000 HIS D 314 PHE 0.010 0.001 PHE C 193 TYR 0.012 0.001 TYR B 197 ARG 0.003 0.000 ARG A 367 Details of bonding type rmsd hydrogen bonds : bond 0.03890 ( 1623) hydrogen bonds : angle 3.82583 ( 4689) covalent geometry : bond 0.00195 (26541) covalent geometry : angle 0.45510 (35857) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 187 time to evaluate : 2.826 Fit side-chains REVERT: A 505 ASP cc_start: 0.8488 (m-30) cc_final: 0.8114 (m-30) REVERT: B 141 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7600 (mt-10) REVERT: B 343 LYS cc_start: 0.8800 (ttpt) cc_final: 0.8484 (tptt) REVERT: B 366 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8312 (pm20) REVERT: C 59 ASP cc_start: 0.8284 (m-30) cc_final: 0.7948 (m-30) REVERT: C 270 GLN cc_start: 0.7602 (mp10) cc_final: 0.6857 (mp10) REVERT: C 330 MET cc_start: 0.7881 (mmm) cc_final: 0.7474 (mmm) REVERT: E 123 ASP cc_start: 0.7551 (m-30) cc_final: 0.7290 (m-30) REVERT: F 14 MET cc_start: 0.9385 (mtm) cc_final: 0.9168 (mtm) REVERT: F 390 GLU cc_start: 0.7823 (tp30) cc_final: 0.7517 (tp30) REVERT: F 487 MET cc_start: 0.8943 (mmm) cc_final: 0.8719 (mmt) REVERT: G 74 ASP cc_start: 0.8368 (t70) cc_final: 0.7959 (t0) outliers start: 16 outliers final: 11 residues processed: 195 average time/residue: 0.4336 time to fit residues: 138.8449 Evaluate side-chains 191 residues out of total 2827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 179 time to evaluate : 3.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain B residue 279 PHE Chi-restraints excluded: chain B residue 366 GLU Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 330 MET Chi-restraints excluded: chain G residue 387 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 71 optimal weight: 20.0000 chunk 304 optimal weight: 1.9990 chunk 159 optimal weight: 0.7980 chunk 329 optimal weight: 0.1980 chunk 209 optimal weight: 0.9990 chunk 185 optimal weight: 20.0000 chunk 156 optimal weight: 6.9990 chunk 179 optimal weight: 20.0000 chunk 142 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 chunk 104 optimal weight: 6.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 351 GLN D 209 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.164183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.098947 restraints weight = 34779.559| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.09 r_work: 0.3071 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 26541 Z= 0.102 Angle : 0.452 11.868 35857 Z= 0.236 Chirality : 0.041 0.146 4381 Planarity : 0.003 0.057 4578 Dihedral : 8.724 80.226 3886 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.50 % Allowed : 8.63 % Favored : 90.87 % 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: 2.28 (0.14), residues: 3489 helix: 2.65 (0.12), residues: 1897 sheet: 1.23 (0.25), residues: 423 loop : -0.34 (0.16), residues: 1169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP G 42 HIS 0.002 0.000 HIS D 314 PHE 0.008 0.001 PHE D 6 TYR 0.013 0.001 TYR B 197 ARG 0.007 0.000 ARG B 344 Details of bonding type rmsd hydrogen bonds : bond 0.04176 ( 1623) hydrogen bonds : angle 3.78465 ( 4689) covalent geometry : bond 0.00220 (26541) covalent geometry : angle 0.45172 (35857) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 189 time to evaluate : 3.340 Fit side-chains REVERT: B 343 LYS cc_start: 0.8824 (ttpt) cc_final: 0.8546 (tptt) REVERT: B 366 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8286 (pm20) REVERT: C 59 ASP cc_start: 0.8282 (m-30) cc_final: 0.7948 (m-30) REVERT: C 164 MET cc_start: 0.8585 (mtt) cc_final: 0.8347 (mtm) REVERT: C 330 MET cc_start: 0.7938 (mmm) cc_final: 0.7609 (mmt) REVERT: E 123 ASP cc_start: 0.7567 (m-30) cc_final: 0.7309 (m-30) REVERT: G 74 ASP cc_start: 0.8395 (t70) cc_final: 0.8004 (t0) outliers start: 14 outliers final: 10 residues processed: 196 average time/residue: 0.3437 time to fit residues: 112.0853 Evaluate side-chains 192 residues out of total 2827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 181 time to evaluate : 3.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain B residue 279 PHE Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 366 GLU Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 330 MET Chi-restraints excluded: chain F residue 331 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 0 optimal weight: 6.9990 chunk 302 optimal weight: 4.9990 chunk 257 optimal weight: 0.9980 chunk 187 optimal weight: 10.0000 chunk 95 optimal weight: 0.8980 chunk 77 optimal weight: 5.9990 chunk 133 optimal weight: 5.9990 chunk 315 optimal weight: 6.9990 chunk 109 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 98 optimal weight: 0.7980 overall best weight: 1.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 209 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.162820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.097096 restraints weight = 34968.023| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.09 r_work: 0.3041 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26541 Z= 0.130 Angle : 0.482 11.311 35857 Z= 0.251 Chirality : 0.042 0.146 4381 Planarity : 0.003 0.060 4578 Dihedral : 8.853 81.803 3886 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.50 % Allowed : 8.77 % Favored : 90.73 % 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: 2.22 (0.14), residues: 3489 helix: 2.59 (0.12), residues: 1897 sheet: 1.21 (0.26), residues: 402 loop : -0.29 (0.16), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP G 42 HIS 0.003 0.000 HIS D 314 PHE 0.010 0.001 PHE D 6 TYR 0.013 0.001 TYR B 197 ARG 0.012 0.000 ARG E 283 Details of bonding type rmsd hydrogen bonds : bond 0.04695 ( 1623) hydrogen bonds : angle 3.82934 ( 4689) covalent geometry : bond 0.00307 (26541) covalent geometry : angle 0.48173 (35857) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 185 time to evaluate : 3.553 Fit side-chains REVERT: B 366 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8309 (pm20) REVERT: C 59 ASP cc_start: 0.8275 (m-30) cc_final: 0.7928 (m-30) REVERT: C 330 MET cc_start: 0.7944 (mmm) cc_final: 0.7522 (mmt) REVERT: E 123 ASP cc_start: 0.7584 (m-30) cc_final: 0.7323 (m-30) REVERT: F 390 GLU cc_start: 0.7858 (tp30) cc_final: 0.7553 (tp30) REVERT: G 74 ASP cc_start: 0.8409 (t70) cc_final: 0.8016 (t0) outliers start: 14 outliers final: 12 residues processed: 192 average time/residue: 0.4002 time to fit residues: 128.2582 Evaluate side-chains 194 residues out of total 2827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 181 time to evaluate : 3.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 279 PHE Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 366 GLU Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 330 MET Chi-restraints excluded: chain F residue 331 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 209 optimal weight: 0.2980 chunk 306 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 162 optimal weight: 0.8980 chunk 244 optimal weight: 8.9990 chunk 312 optimal weight: 5.9990 chunk 230 optimal weight: 8.9990 chunk 23 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 19 optimal weight: 20.0000 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 209 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.162042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.096287 restraints weight = 34733.366| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 2.08 r_work: 0.3034 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26541 Z= 0.138 Angle : 0.489 11.172 35857 Z= 0.255 Chirality : 0.042 0.145 4381 Planarity : 0.003 0.062 4578 Dihedral : 8.968 83.191 3886 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 0.53 % Allowed : 8.74 % Favored : 90.73 % 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: 2.17 (0.14), residues: 3489 helix: 2.56 (0.12), residues: 1895 sheet: 1.17 (0.26), residues: 402 loop : -0.32 (0.16), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP G 42 HIS 0.003 0.001 HIS D 314 PHE 0.011 0.001 PHE D 6 TYR 0.014 0.001 TYR B 197 ARG 0.009 0.000 ARG E 283 Details of bonding type rmsd hydrogen bonds : bond 0.04936 ( 1623) hydrogen bonds : angle 3.85878 ( 4689) covalent geometry : bond 0.00326 (26541) covalent geometry : angle 0.48892 (35857) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 182 time to evaluate : 3.575 Fit side-chains REVERT: B 366 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8277 (pm20) REVERT: C 59 ASP cc_start: 0.8279 (m-30) cc_final: 0.7942 (m-30) REVERT: C 330 MET cc_start: 0.7985 (mmm) cc_final: 0.7487 (mmm) REVERT: D 3 ASP cc_start: 0.8484 (t0) cc_final: 0.8181 (t0) REVERT: E 123 ASP cc_start: 0.7597 (m-30) cc_final: 0.7343 (m-30) REVERT: F 390 GLU cc_start: 0.7895 (tp30) cc_final: 0.7598 (tp30) REVERT: G 74 ASP cc_start: 0.8419 (t70) cc_final: 0.8025 (t0) outliers start: 15 outliers final: 13 residues processed: 189 average time/residue: 0.3456 time to fit residues: 109.9014 Evaluate side-chains 192 residues out of total 2827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 178 time to evaluate : 2.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 279 PHE Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 366 GLU Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 330 MET Chi-restraints excluded: chain F residue 331 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 197 optimal weight: 6.9990 chunk 94 optimal weight: 0.9990 chunk 159 optimal weight: 1.9990 chunk 206 optimal weight: 0.9990 chunk 226 optimal weight: 4.9990 chunk 282 optimal weight: 9.9990 chunk 151 optimal weight: 5.9990 chunk 305 optimal weight: 0.1980 chunk 208 optimal weight: 6.9990 chunk 44 optimal weight: 0.2980 chunk 64 optimal weight: 1.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 209 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.164171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.099023 restraints weight = 34790.009| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.10 r_work: 0.3077 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 26541 Z= 0.102 Angle : 0.470 10.949 35857 Z= 0.245 Chirality : 0.041 0.157 4381 Planarity : 0.003 0.062 4578 Dihedral : 8.663 82.058 3886 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 0.50 % Allowed : 8.88 % Favored : 90.63 % 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: 2.28 (0.14), residues: 3489 helix: 2.65 (0.12), residues: 1909 sheet: 1.28 (0.25), residues: 418 loop : -0.38 (0.16), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP G 42 HIS 0.002 0.000 HIS D 314 PHE 0.008 0.001 PHE D 213 TYR 0.012 0.001 TYR B 197 ARG 0.010 0.000 ARG E 283 Details of bonding type rmsd hydrogen bonds : bond 0.04114 ( 1623) hydrogen bonds : angle 3.77780 ( 4689) covalent geometry : bond 0.00218 (26541) covalent geometry : angle 0.46955 (35857) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15662.89 seconds wall clock time: 270 minutes 36.51 seconds (16236.51 seconds total)