Starting phenix.real_space_refine on Mon Aug 25 08:05:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g7m_29816/08_2025/8g7m_29816.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g7m_29816/08_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_29816/08_2025/8g7m_29816.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g7m_29816/08_2025/8g7m_29816.map" model { file = "/net/cci-nas-00/data/ceres_data/8g7m_29816/08_2025/8g7m_29816.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g7m_29816/08_2025/8g7m_29816.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 6.56, per 1000 atoms: 0.25 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: 1.77 Conformation dependent library (CDL) restraints added in 982.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.19 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: 6.16 Time building geometry restraints manager: 2.43 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: 4.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 25.800 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.070 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.550 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 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 ARG 0.006 0.000 ARG D 344 TYR 0.012 0.001 TYR C 197 PHE 0.021 0.001 PHE D 213 TRP 0.008 0.001 TRP G 42 HIS 0.006 0.001 HIS D 314 Details of bonding type rmsd covalent geometry : bond 0.00301 (26541) covalent geometry : angle 0.48710 (35857) hydrogen bonds : bond 0.15495 ( 1623) hydrogen bonds : angle 5.15375 ( 4689) *********************** 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 : 0.723 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: 0.1382 time to fit residues: 50.5627 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 : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 7.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 = 0.4016 r_free = 0.4016 target = 0.163979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.097056 restraints weight = 34669.185| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.10 r_work: 0.3043 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.0877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 26541 Z= 0.151 Angle : 0.489 7.718 35857 Z= 0.266 Chirality : 0.043 0.161 4381 Planarity : 0.004 0.056 4578 Dihedral : 10.187 80.291 3886 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.57 % Allowed : 3.18 % Favored : 96.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.11 (0.14), residues: 3489 helix: 2.40 (0.12), residues: 1899 sheet: 1.31 (0.24), residues: 432 loop : -0.25 (0.16), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 344 TYR 0.014 0.002 TYR C 197 PHE 0.015 0.001 PHE D 213 TRP 0.005 0.001 TRP G 42 HIS 0.003 0.001 HIS D 314 Details of bonding type rmsd covalent geometry : bond 0.00346 (26541) covalent geometry : angle 0.48882 (35857) hydrogen bonds : bond 0.05458 ( 1623) hydrogen bonds : angle 4.26930 ( 4689) *********************** 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 212 residues out of total 2827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 196 time to evaluate : 0.825 Fit side-chains revert: symmetry clash REVERT: A 209 GLN cc_start: 0.7684 (mm110) cc_final: 0.7162 (tm-30) REVERT: B 343 LYS cc_start: 0.8904 (ttpt) cc_final: 0.8562 (tptt) REVERT: B 351 GLN cc_start: 0.8098 (mp10) cc_final: 0.7886 (mp10) REVERT: B 366 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8276 (pm20) REVERT: B 505 ASP cc_start: 0.8654 (m-30) cc_final: 0.8304 (m-30) REVERT: C 59 ASP cc_start: 0.8181 (m-30) cc_final: 0.7952 (m-30) REVERT: C 270 GLN cc_start: 0.7527 (mp10) cc_final: 0.7006 (mp10) REVERT: C 330 MET cc_start: 0.8236 (mtt) cc_final: 0.7954 (mtt) REVERT: E 123 ASP cc_start: 0.7623 (m-30) cc_final: 0.7353 (m-30) REVERT: F 328 ASP cc_start: 0.7498 (m-30) cc_final: 0.7128 (t0) REVERT: G 74 ASP cc_start: 0.8436 (t70) cc_final: 0.8030 (t0) outliers start: 16 outliers final: 12 residues processed: 205 average time/residue: 0.1398 time to fit residues: 48.4470 Evaluate side-chains 193 residues out of total 2827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 180 time to evaluate : 0.957 ------------------------------------------------------------------------------- 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 523 ILE 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 Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain F residue 172 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 34 optimal weight: 4.9990 chunk 257 optimal weight: 4.9990 chunk 284 optimal weight: 8.9990 chunk 225 optimal weight: 10.0000 chunk 88 optimal weight: 6.9990 chunk 318 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 242 optimal weight: 5.9990 chunk 323 optimal weight: 3.9990 chunk 137 optimal weight: 8.9990 chunk 61 optimal weight: 0.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3980 r_free = 0.3980 target = 0.160714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.093693 restraints weight = 35073.800| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 2.09 r_work: 0.2992 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1395 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= 0.189 Angle : 0.528 10.242 35857 Z= 0.282 Chirality : 0.044 0.152 4381 Planarity : 0.004 0.046 4578 Dihedral : 9.924 83.226 3886 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 0.88 % Allowed : 5.09 % Favored : 94.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.89 (0.14), residues: 3489 helix: 2.23 (0.12), residues: 1898 sheet: 1.24 (0.26), residues: 403 loop : -0.35 (0.16), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 344 TYR 0.016 0.002 TYR B 197 PHE 0.012 0.001 PHE D 6 TRP 0.006 0.001 TRP G 42 HIS 0.003 0.001 HIS B 241 Details of bonding type rmsd covalent geometry : bond 0.00463 (26541) covalent geometry : angle 0.52809 (35857) hydrogen bonds : bond 0.06181 ( 1623) hydrogen bonds : angle 4.19433 ( 4689) *********************** 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 218 residues out of total 2827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 193 time to evaluate : 0.827 Fit side-chains revert: symmetry clash REVERT: A 209 GLN cc_start: 0.7795 (mm110) cc_final: 0.7236 (tm-30) REVERT: B 343 LYS cc_start: 0.8944 (ttpt) cc_final: 0.8635 (tptt) REVERT: B 366 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8368 (pm20) REVERT: C 59 ASP cc_start: 0.8245 (m-30) cc_final: 0.7925 (m-30) REVERT: C 270 GLN cc_start: 0.7638 (mp10) cc_final: 0.7059 (mp10) REVERT: C 330 MET cc_start: 0.8309 (mtt) cc_final: 0.7482 (mtp) REVERT: E 123 ASP cc_start: 0.7649 (m-30) cc_final: 0.7390 (m-30) REVERT: F 188 ILE cc_start: 0.6743 (OUTLIER) cc_final: 0.6539 (pt) REVERT: G 74 ASP cc_start: 0.8441 (t70) cc_final: 0.8044 (t0) REVERT: G 186 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.7076 (pp20) REVERT: G 505 ASP cc_start: 0.8627 (m-30) cc_final: 0.8284 (m-30) outliers start: 25 outliers final: 13 residues processed: 207 average time/residue: 0.1492 time to fit residues: 51.2989 Evaluate side-chains 194 residues out of total 2827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 178 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 G residue 186 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 10 optimal weight: 0.0970 chunk 204 optimal weight: 0.9990 chunk 343 optimal weight: 4.9990 chunk 264 optimal weight: 3.9990 chunk 134 optimal weight: 30.0000 chunk 189 optimal weight: 6.9990 chunk 27 optimal weight: 9.9990 chunk 52 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 65 optimal weight: 0.4980 chunk 294 optimal weight: 6.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 239 ASN C 351 GLN D 209 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.162068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.095639 restraints weight = 34838.654| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 2.08 r_work: 0.3022 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 26541 Z= 0.142 Angle : 0.480 8.826 35857 Z= 0.257 Chirality : 0.042 0.156 4381 Planarity : 0.003 0.048 4578 Dihedral : 9.413 86.816 3886 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 0.99 % Allowed : 6.47 % Favored : 92.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.96 (0.14), residues: 3489 helix: 2.33 (0.12), residues: 1895 sheet: 1.21 (0.26), residues: 403 loop : -0.37 (0.16), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 344 TYR 0.015 0.001 TYR B 197 PHE 0.013 0.001 PHE C 193 TRP 0.003 0.001 TRP G 42 HIS 0.005 0.001 HIS D 314 Details of bonding type rmsd covalent geometry : bond 0.00335 (26541) covalent geometry : angle 0.47979 (35857) hydrogen bonds : bond 0.05189 ( 1623) hydrogen bonds : angle 4.05076 ( 4689) *********************** 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 213 residues out of total 2827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 185 time to evaluate : 1.008 Fit side-chains REVERT: A 209 GLN cc_start: 0.7821 (mm110) cc_final: 0.7315 (tm-30) REVERT: B 343 LYS cc_start: 0.8892 (ttpt) cc_final: 0.8571 (tptt) REVERT: B 366 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8341 (pm20) REVERT: B 505 ASP cc_start: 0.8615 (m-30) cc_final: 0.8390 (m-30) REVERT: C 59 ASP cc_start: 0.8253 (m-30) cc_final: 0.7926 (m-30) REVERT: C 270 GLN cc_start: 0.7648 (mp10) cc_final: 0.6990 (mp10) REVERT: C 330 MET cc_start: 0.8242 (mtt) cc_final: 0.7812 (ptp) REVERT: E 123 ASP cc_start: 0.7611 (m-30) cc_final: 0.7354 (m-30) REVERT: F 14 MET cc_start: 0.9431 (mtm) cc_final: 0.9190 (mtm) REVERT: F 188 ILE cc_start: 0.6753 (OUTLIER) cc_final: 0.6553 (pt) REVERT: G 74 ASP cc_start: 0.8420 (t70) cc_final: 0.8026 (t0) REVERT: G 186 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.7009 (pp20) REVERT: G 505 ASP cc_start: 0.8609 (m-30) cc_final: 0.8296 (m-30) outliers start: 28 outliers final: 17 residues processed: 199 average time/residue: 0.1393 time to fit residues: 47.0093 Evaluate side-chains 198 residues out of total 2827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 178 time to evaluate : 1.040 ------------------------------------------------------------------------------- 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 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 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 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 188 ILE Chi-restraints excluded: chain F residue 330 MET Chi-restraints excluded: chain F residue 331 LEU Chi-restraints excluded: chain G residue 186 GLU Chi-restraints excluded: chain G residue 521 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 246 optimal weight: 0.9980 chunk 258 optimal weight: 3.9990 chunk 6 optimal weight: 0.3980 chunk 17 optimal weight: 10.0000 chunk 21 optimal weight: 20.0000 chunk 32 optimal weight: 6.9990 chunk 78 optimal weight: 9.9990 chunk 243 optimal weight: 20.0000 chunk 198 optimal weight: 0.8980 chunk 159 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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 = 0.3997 r_free = 0.3997 target = 0.162338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.096221 restraints weight = 34859.882| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.10 r_work: 0.3031 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26541 Z= 0.131 Angle : 0.473 11.223 35857 Z= 0.252 Chirality : 0.042 0.178 4381 Planarity : 0.003 0.048 4578 Dihedral : 9.180 80.814 3886 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.99 % Allowed : 7.36 % Favored : 91.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.02 (0.14), residues: 3489 helix: 2.40 (0.12), residues: 1897 sheet: 1.20 (0.26), residues: 403 loop : -0.38 (0.16), residues: 1189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 344 TYR 0.014 0.001 TYR B 197 PHE 0.010 0.001 PHE D 6 TRP 0.003 0.000 TRP G 42 HIS 0.004 0.001 HIS D 314 Details of bonding type rmsd covalent geometry : bond 0.00303 (26541) covalent geometry : angle 0.47255 (35857) hydrogen bonds : bond 0.04920 ( 1623) hydrogen bonds : angle 3.98726 ( 4689) *********************** 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 218 residues out of total 2827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 190 time to evaluate : 0.766 Fit side-chains REVERT: A 153 ASP cc_start: 0.8875 (OUTLIER) cc_final: 0.8595 (m-30) REVERT: B 343 LYS cc_start: 0.8876 (ttpt) cc_final: 0.8606 (tptt) REVERT: B 366 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8336 (pm20) REVERT: B 505 ASP cc_start: 0.8640 (m-30) cc_final: 0.8377 (m-30) REVERT: C 59 ASP cc_start: 0.8294 (m-30) cc_final: 0.7982 (m-30) REVERT: C 270 GLN cc_start: 0.7543 (mp10) cc_final: 0.6848 (mp10) REVERT: C 330 MET cc_start: 0.8475 (mtt) cc_final: 0.8114 (mtp) REVERT: E 123 ASP cc_start: 0.7603 (m-30) cc_final: 0.7348 (m-30) REVERT: F 188 ILE cc_start: 0.6758 (OUTLIER) cc_final: 0.6535 (pt) REVERT: G 74 ASP cc_start: 0.8402 (t70) cc_final: 0.8022 (t0) REVERT: G 186 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.7008 (pp20) REVERT: G 505 ASP cc_start: 0.8603 (m-30) cc_final: 0.8281 (m-30) outliers start: 28 outliers final: 19 residues processed: 203 average time/residue: 0.1453 time to fit residues: 50.0373 Evaluate side-chains 204 residues out of total 2827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 181 time to evaluate : 0.667 ------------------------------------------------------------------------------- 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 164 MET 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 523 ILE Chi-restraints excluded: chain C residue 176 LYS Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 262 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 Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 469 MET Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 330 MET Chi-restraints excluded: chain F residue 331 LEU Chi-restraints excluded: chain G residue 186 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 119 optimal weight: 1.9990 chunk 24 optimal weight: 8.9990 chunk 294 optimal weight: 0.5980 chunk 80 optimal weight: 9.9990 chunk 33 optimal weight: 7.9990 chunk 124 optimal weight: 0.0170 chunk 267 optimal weight: 0.7980 chunk 167 optimal weight: 3.9990 chunk 291 optimal weight: 6.9990 chunk 27 optimal weight: 7.9990 chunk 161 optimal weight: 0.7980 overall best weight: 0.8420 ------------------------------------------------------------------------------- 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 = 0.164566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.099416 restraints weight = 34798.995| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.09 r_work: 0.3098 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 26541 Z= 0.098 Angle : 0.445 10.600 35857 Z= 0.236 Chirality : 0.041 0.207 4381 Planarity : 0.003 0.051 4578 Dihedral : 8.780 81.962 3886 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 0.85 % Allowed : 8.03 % Favored : 91.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.19 (0.14), residues: 3489 helix: 2.55 (0.12), residues: 1909 sheet: 1.27 (0.26), residues: 403 loop : -0.36 (0.16), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 344 TYR 0.012 0.001 TYR B 197 PHE 0.011 0.001 PHE C 193 TRP 0.003 0.000 TRP G 42 HIS 0.003 0.000 HIS D 314 Details of bonding type rmsd covalent geometry : bond 0.00206 (26541) covalent geometry : angle 0.44501 (35857) hydrogen bonds : bond 0.04023 ( 1623) hydrogen bonds : angle 3.84666 ( 4689) *********************** 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 214 residues out of total 2827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 190 time to evaluate : 1.040 Fit side-chains revert: symmetry clash REVERT: A 153 ASP cc_start: 0.8924 (OUTLIER) cc_final: 0.8650 (m-30) REVERT: B 343 LYS cc_start: 0.8858 (ttpt) cc_final: 0.8558 (tptt) REVERT: B 366 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8286 (pm20) REVERT: B 505 ASP cc_start: 0.8632 (m-30) cc_final: 0.8360 (m-30) REVERT: C 59 ASP cc_start: 0.8286 (m-30) cc_final: 0.7950 (m-30) REVERT: C 176 LYS cc_start: 0.7318 (OUTLIER) cc_final: 0.7083 (ptmt) REVERT: C 270 GLN cc_start: 0.7597 (mp10) cc_final: 0.6852 (mp10) REVERT: D 3 ASP cc_start: 0.8430 (t0) cc_final: 0.8173 (t0) REVERT: E 123 ASP cc_start: 0.7586 (m-30) cc_final: 0.7329 (m-30) REVERT: F 188 ILE cc_start: 0.6806 (OUTLIER) cc_final: 0.6593 (pt) REVERT: G 74 ASP cc_start: 0.8415 (t70) cc_final: 0.7997 (t0) REVERT: G 186 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.7079 (pp20) outliers start: 24 outliers final: 14 residues processed: 202 average time/residue: 0.1602 time to fit residues: 54.6111 Evaluate side-chains 200 residues out of total 2827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 181 time to evaluate : 1.137 ------------------------------------------------------------------------------- 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 366 GLU Chi-restraints excluded: chain B residue 407 GLU Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 176 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 E residue 469 MET Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 330 MET Chi-restraints excluded: chain F residue 331 LEU Chi-restraints excluded: chain G residue 186 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 120 optimal weight: 6.9990 chunk 71 optimal weight: 8.9990 chunk 270 optimal weight: 2.9990 chunk 201 optimal weight: 0.5980 chunk 86 optimal weight: 5.9990 chunk 19 optimal weight: 20.0000 chunk 263 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 306 optimal weight: 1.9990 chunk 213 optimal weight: 0.0770 overall best weight: 1.5344 ------------------------------------------------------------------------------- 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 = 0.4002 r_free = 0.4002 target = 0.162847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.097622 restraints weight = 34682.936| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.08 r_work: 0.3071 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 26541 Z= 0.122 Angle : 0.472 12.925 35857 Z= 0.246 Chirality : 0.042 0.148 4381 Planarity : 0.003 0.055 4578 Dihedral : 8.880 83.072 3886 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 0.96 % Allowed : 8.24 % Favored : 90.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.18 (0.14), residues: 3489 helix: 2.55 (0.12), residues: 1897 sheet: 1.25 (0.26), residues: 403 loop : -0.33 (0.16), residues: 1189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 344 TYR 0.013 0.001 TYR B 197 PHE 0.010 0.001 PHE D 6 TRP 0.003 0.000 TRP G 42 HIS 0.003 0.000 HIS D 314 Details of bonding type rmsd covalent geometry : bond 0.00280 (26541) covalent geometry : angle 0.47233 (35857) hydrogen bonds : bond 0.04600 ( 1623) hydrogen bonds : angle 3.88867 ( 4689) *********************** 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 216 residues out of total 2827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 189 time to evaluate : 1.073 Fit side-chains revert: symmetry clash REVERT: A 153 ASP cc_start: 0.8919 (OUTLIER) cc_final: 0.8658 (m-30) REVERT: B 343 LYS cc_start: 0.8837 (ttpt) cc_final: 0.8553 (tptt) REVERT: B 366 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8291 (pm20) REVERT: B 505 ASP cc_start: 0.8681 (m-30) cc_final: 0.8363 (m-30) REVERT: C 59 ASP cc_start: 0.8268 (m-30) cc_final: 0.7950 (m-30) REVERT: C 176 LYS cc_start: 0.7364 (OUTLIER) cc_final: 0.7113 (ptmt) REVERT: C 270 GLN cc_start: 0.7615 (mp10) cc_final: 0.6852 (mp10) REVERT: E 123 ASP cc_start: 0.7613 (m-30) cc_final: 0.7357 (m-30) REVERT: F 188 ILE cc_start: 0.6918 (OUTLIER) cc_final: 0.6695 (pt) REVERT: F 390 GLU cc_start: 0.7861 (tp30) cc_final: 0.7546 (tp30) REVERT: G 74 ASP cc_start: 0.8431 (t70) cc_final: 0.8052 (t0) REVERT: G 186 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.7080 (pp20) REVERT: G 505 ASP cc_start: 0.8590 (m-30) cc_final: 0.8266 (m-30) outliers start: 27 outliers final: 19 residues processed: 205 average time/residue: 0.1507 time to fit residues: 51.3627 Evaluate side-chains 207 residues out of total 2827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 183 time to evaluate : 0.791 ------------------------------------------------------------------------------- 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 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 122 VAL Chi-restraints excluded: chain C residue 176 LYS Chi-restraints excluded: chain C residue 371 LEU Chi-restraints excluded: chain C residue 469 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 D residue 384 SER Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 469 MET Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 330 MET Chi-restraints excluded: chain F residue 331 LEU Chi-restraints excluded: chain F residue 422 ILE Chi-restraints excluded: chain G residue 186 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 132 optimal weight: 1.9990 chunk 120 optimal weight: 6.9990 chunk 17 optimal weight: 9.9990 chunk 135 optimal weight: 3.9990 chunk 293 optimal weight: 6.9990 chunk 233 optimal weight: 8.9990 chunk 193 optimal weight: 9.9990 chunk 97 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 266 optimal weight: 3.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 209 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.161839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.096001 restraints weight = 34949.354| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.10 r_work: 0.3046 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26541 Z= 0.138 Angle : 0.490 15.430 35857 Z= 0.256 Chirality : 0.042 0.203 4381 Planarity : 0.003 0.057 4578 Dihedral : 9.023 84.977 3886 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 1.06 % Allowed : 8.35 % Favored : 90.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.09 (0.14), residues: 3489 helix: 2.47 (0.12), residues: 1897 sheet: 1.20 (0.26), residues: 403 loop : -0.34 (0.16), residues: 1189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 344 TYR 0.014 0.001 TYR B 197 PHE 0.011 0.001 PHE D 6 TRP 0.003 0.001 TRP E 42 HIS 0.003 0.001 HIS D 314 Details of bonding type rmsd covalent geometry : bond 0.00326 (26541) covalent geometry : angle 0.48958 (35857) hydrogen bonds : bond 0.05007 ( 1623) hydrogen bonds : angle 3.95286 ( 4689) *********************** 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 221 residues out of total 2827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 191 time to evaluate : 0.808 Fit side-chains revert: symmetry clash REVERT: A 153 ASP cc_start: 0.8931 (OUTLIER) cc_final: 0.8665 (m-30) REVERT: B 343 LYS cc_start: 0.8834 (ttpt) cc_final: 0.8505 (tptt) REVERT: B 366 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8368 (pm20) REVERT: B 505 ASP cc_start: 0.8695 (m-30) cc_final: 0.8381 (m-30) REVERT: C 59 ASP cc_start: 0.8307 (m-30) cc_final: 0.7991 (m-30) REVERT: C 176 LYS cc_start: 0.7384 (OUTLIER) cc_final: 0.7129 (ptmt) REVERT: D 215 ASP cc_start: 0.8176 (t0) cc_final: 0.7383 (t0) REVERT: E 123 ASP cc_start: 0.7639 (m-30) cc_final: 0.7388 (m-30) REVERT: F 188 ILE cc_start: 0.6876 (OUTLIER) cc_final: 0.6648 (pt) REVERT: F 390 GLU cc_start: 0.7914 (tp30) cc_final: 0.7617 (tp30) REVERT: G 74 ASP cc_start: 0.8438 (t70) cc_final: 0.8074 (t0) REVERT: G 186 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.7076 (pp20) REVERT: G 505 ASP cc_start: 0.8618 (m-30) cc_final: 0.8270 (m-30) outliers start: 30 outliers final: 19 residues processed: 211 average time/residue: 0.1482 time to fit residues: 51.8385 Evaluate side-chains 207 residues out of total 2827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 183 time to evaluate : 0.987 ------------------------------------------------------------------------------- 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 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 122 VAL Chi-restraints excluded: chain C residue 176 LYS Chi-restraints excluded: chain C residue 371 LEU 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 D residue 384 SER Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 469 MET Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 330 MET Chi-restraints excluded: chain F residue 331 LEU Chi-restraints excluded: chain F residue 422 ILE Chi-restraints excluded: chain G residue 186 GLU Chi-restraints excluded: chain G residue 521 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 176 optimal weight: 0.4980 chunk 95 optimal weight: 0.7980 chunk 227 optimal weight: 20.0000 chunk 143 optimal weight: 1.9990 chunk 158 optimal weight: 2.9990 chunk 260 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 chunk 335 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 289 optimal weight: 10.0000 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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 = 0.3995 r_free = 0.3995 target = 0.162281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.096717 restraints weight = 34841.561| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.10 r_work: 0.3040 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1933 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 : 0.499 17.695 35857 Z= 0.258 Chirality : 0.042 0.204 4381 Planarity : 0.003 0.061 4578 Dihedral : 8.956 84.127 3886 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 0.88 % Allowed : 8.77 % Favored : 90.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.11 (0.14), residues: 3489 helix: 2.49 (0.12), residues: 1894 sheet: 1.20 (0.26), residues: 403 loop : -0.35 (0.16), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 283 TYR 0.017 0.001 TYR B 197 PHE 0.010 0.001 PHE D 6 TRP 0.002 0.000 TRP E 42 HIS 0.003 0.001 HIS D 314 Details of bonding type rmsd covalent geometry : bond 0.00303 (26541) covalent geometry : angle 0.49913 (35857) hydrogen bonds : bond 0.04774 ( 1623) hydrogen bonds : angle 3.92646 ( 4689) *********************** 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 214 residues out of total 2827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 189 time to evaluate : 0.917 Fit side-chains REVERT: A 153 ASP cc_start: 0.8936 (OUTLIER) cc_final: 0.8652 (m-30) REVERT: B 343 LYS cc_start: 0.8820 (ttpt) cc_final: 0.8559 (tptt) REVERT: B 505 ASP cc_start: 0.8692 (m-30) cc_final: 0.8368 (m-30) REVERT: C 59 ASP cc_start: 0.8303 (m-30) cc_final: 0.7990 (m-30) REVERT: C 176 LYS cc_start: 0.7351 (OUTLIER) cc_final: 0.7109 (ptmt) REVERT: C 330 MET cc_start: 0.8368 (mtt) cc_final: 0.8091 (ptp) REVERT: D 215 ASP cc_start: 0.8150 (t0) cc_final: 0.7398 (t0) REVERT: E 123 ASP cc_start: 0.7604 (m-30) cc_final: 0.7348 (m-30) REVERT: F 188 ILE cc_start: 0.6857 (OUTLIER) cc_final: 0.6634 (pt) REVERT: F 390 GLU cc_start: 0.7876 (tp30) cc_final: 0.7565 (tp30) REVERT: G 74 ASP cc_start: 0.8398 (t70) cc_final: 0.8018 (t0) REVERT: G 186 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.7037 (pp20) REVERT: G 505 ASP cc_start: 0.8601 (m-30) cc_final: 0.8287 (m-30) outliers start: 25 outliers final: 19 residues processed: 205 average time/residue: 0.1570 time to fit residues: 53.7851 Evaluate side-chains 210 residues out of total 2827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 187 time to evaluate : 0.975 ------------------------------------------------------------------------------- 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 164 MET Chi-restraints excluded: chain B residue 279 PHE Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 176 LYS Chi-restraints excluded: chain C residue 371 LEU 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 D residue 384 SER Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 469 MET Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 330 MET Chi-restraints excluded: chain F residue 331 LEU Chi-restraints excluded: chain F residue 422 ILE Chi-restraints excluded: chain G residue 186 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 196 optimal weight: 0.0870 chunk 137 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 120 optimal weight: 5.9990 chunk 129 optimal weight: 7.9990 chunk 56 optimal weight: 0.6980 chunk 18 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 253 optimal weight: 0.0170 chunk 244 optimal weight: 5.9990 chunk 54 optimal weight: 0.2980 overall best weight: 1.4198 ------------------------------------------------------------------------------- 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 = 0.162799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.097575 restraints weight = 34790.828| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.07 r_work: 0.3053 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26541 Z= 0.120 Angle : 0.491 17.038 35857 Z= 0.255 Chirality : 0.042 0.168 4381 Planarity : 0.003 0.062 4578 Dihedral : 8.855 82.330 3886 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 0.88 % Allowed : 8.98 % Favored : 90.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.16 (0.14), residues: 3489 helix: 2.53 (0.12), residues: 1894 sheet: 1.30 (0.26), residues: 398 loop : -0.34 (0.16), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 283 TYR 0.016 0.001 TYR B 197 PHE 0.009 0.001 PHE D 6 TRP 0.002 0.000 TRP G 42 HIS 0.003 0.001 HIS D 314 Details of bonding type rmsd covalent geometry : bond 0.00273 (26541) covalent geometry : angle 0.49105 (35857) hydrogen bonds : bond 0.04557 ( 1623) hydrogen bonds : angle 3.88840 ( 4689) ********************** 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 216 residues out of total 2827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 191 time to evaluate : 1.032 Fit side-chains REVERT: A 153 ASP cc_start: 0.8933 (OUTLIER) cc_final: 0.8655 (m-30) REVERT: A 189 GLU cc_start: 0.6582 (pm20) cc_final: 0.5963 (mm-30) REVERT: B 217 TYR cc_start: 0.4807 (m-80) cc_final: 0.4589 (m-10) REVERT: B 343 LYS cc_start: 0.8790 (ttpt) cc_final: 0.8545 (tptt) REVERT: B 505 ASP cc_start: 0.8687 (m-30) cc_final: 0.8363 (m-30) REVERT: C 59 ASP cc_start: 0.8305 (m-30) cc_final: 0.7992 (m-30) REVERT: C 176 LYS cc_start: 0.7338 (OUTLIER) cc_final: 0.7112 (ptmt) REVERT: C 330 MET cc_start: 0.8317 (mtt) cc_final: 0.8054 (ptp) REVERT: D 215 ASP cc_start: 0.8130 (t0) cc_final: 0.7382 (t0) REVERT: E 123 ASP cc_start: 0.7591 (m-30) cc_final: 0.7334 (m-30) REVERT: F 188 ILE cc_start: 0.6844 (OUTLIER) cc_final: 0.6626 (pt) REVERT: F 390 GLU cc_start: 0.7836 (tp30) cc_final: 0.7516 (tp30) REVERT: F 487 MET cc_start: 0.8943 (mmm) cc_final: 0.8705 (mmt) REVERT: G 74 ASP cc_start: 0.8389 (t70) cc_final: 0.7992 (t0) REVERT: G 186 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.7043 (pp20) REVERT: G 505 ASP cc_start: 0.8596 (m-30) cc_final: 0.8261 (m-30) outliers start: 25 outliers final: 21 residues processed: 205 average time/residue: 0.1581 time to fit residues: 53.9927 Evaluate side-chains 210 residues out of total 2827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 185 time to evaluate : 1.068 ------------------------------------------------------------------------------- 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 164 MET Chi-restraints excluded: chain B residue 279 PHE Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 328 ASP Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 176 LYS Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 371 LEU 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 D residue 384 SER Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 469 MET Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 330 MET Chi-restraints excluded: chain F residue 331 LEU Chi-restraints excluded: chain F residue 422 ILE Chi-restraints excluded: chain G residue 186 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 217 optimal weight: 0.6980 chunk 329 optimal weight: 4.9990 chunk 215 optimal weight: 1.9990 chunk 182 optimal weight: 0.0040 chunk 29 optimal weight: 0.0770 chunk 124 optimal weight: 1.9990 chunk 297 optimal weight: 10.0000 chunk 342 optimal weight: 5.9990 chunk 232 optimal weight: 1.9990 chunk 249 optimal weight: 5.9990 chunk 174 optimal weight: 5.9990 overall best weight: 0.9554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.164416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.099893 restraints weight = 34588.407| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.06 r_work: 0.3088 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2025 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= 0.101 Angle : 0.469 17.277 35857 Z= 0.243 Chirality : 0.041 0.166 4381 Planarity : 0.003 0.062 4578 Dihedral : 8.570 81.565 3886 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 0.71 % Allowed : 9.34 % Favored : 89.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.25 (0.14), residues: 3489 helix: 2.63 (0.12), residues: 1904 sheet: 1.33 (0.26), residues: 418 loop : -0.40 (0.16), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 283 TYR 0.015 0.001 TYR B 197 PHE 0.009 0.001 PHE C 193 TRP 0.003 0.000 TRP G 42 HIS 0.003 0.000 HIS D 314 Details of bonding type rmsd covalent geometry : bond 0.00214 (26541) covalent geometry : angle 0.46937 (35857) hydrogen bonds : bond 0.03983 ( 1623) hydrogen bonds : angle 3.80520 ( 4689) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7042.58 seconds wall clock time: 121 minutes 6.54 seconds (7266.54 seconds total)