Starting phenix.real_space_refine on Tue Jun 17 19:25:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tf3_41218/06_2025/8tf3_41218_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tf3_41218/06_2025/8tf3_41218.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tf3_41218/06_2025/8tf3_41218.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tf3_41218/06_2025/8tf3_41218.map" model { file = "/net/cci-nas-00/data/ceres_data/8tf3_41218/06_2025/8tf3_41218_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tf3_41218/06_2025/8tf3_41218_neut.cif" } resolution = 2.94 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.046 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 4 5.49 5 S 136 5.16 5 Cl 12 4.86 5 C 13008 2.51 5 N 3268 2.21 5 O 3460 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 140 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 19888 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4822 Classifications: {'peptide': 602} Link IDs: {'PTRANS': 24, 'TRANS': 577} Chain breaks: 2 Chain: "A" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 150 Unusual residues: {'CPL': 2, 'ECN': 1, 'ERG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CPL:plan-4': 1, 'CPL:plan-3': 1, 'CPL:plan-2': 1, 'CPL:plan-1': 1} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 150 Unusual residues: {'CPL': 2, 'ECN': 1, 'ERG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CPL:plan-4': 1, 'CPL:plan-3': 1, 'CPL:plan-2': 1, 'CPL:plan-1': 1} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 150 Unusual residues: {'CPL': 2, 'ECN': 1, 'ERG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CPL:plan-4': 1, 'CPL:plan-3': 1, 'CPL:plan-2': 1, 'CPL:plan-1': 1} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 150 Unusual residues: {'CPL': 2, 'ECN': 1, 'ERG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CPL:plan-4': 1, 'CPL:plan-3': 1, 'CPL:plan-2': 1, 'CPL:plan-1': 1} Unresolved non-hydrogen planarities: 14 Restraints were copied for chains: B, C, D Time building chain proxies: 12.08, per 1000 atoms: 0.61 Number of scatterers: 19888 At special positions: 0 Unit cell: (136.95, 136.95, 122.01, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 12 17.00 S 136 16.00 P 4 15.00 O 3460 8.00 N 3268 7.00 C 13008 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: 5.13 Conformation dependent library (CDL) restraints added in 2.5 seconds 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4544 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 8 sheets defined 71.8% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.27 Creating SS restraints... Processing helix chain 'A' and resid 28 through 47 Processing helix chain 'A' and resid 47 through 56 Processing helix chain 'A' and resid 57 through 67 Processing helix chain 'A' and resid 81 through 89 Processing helix chain 'A' and resid 91 through 102 Processing helix chain 'A' and resid 103 through 108 Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 129 through 138 Processing helix chain 'A' and resid 149 through 153 Processing helix chain 'A' and resid 165 through 174 Processing helix chain 'A' and resid 175 through 185 Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 208 through 221 removed outlier: 3.979A pdb=" N GLN A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 235 Processing helix chain 'A' and resid 242 through 250 Processing helix chain 'A' and resid 252 through 261 Processing helix chain 'A' and resid 280 through 285 removed outlier: 3.537A pdb=" N SER A 285 " --> pdb=" O THR A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 298 Processing helix chain 'A' and resid 303 through 309 Processing helix chain 'A' and resid 310 through 324 removed outlier: 4.114A pdb=" N GLU A 315 " --> pdb=" O THR A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 349 Processing helix chain 'A' and resid 379 through 411 removed outlier: 3.514A pdb=" N GLY A 388 " --> pdb=" O ILE A 384 " (cutoff:3.500A) Proline residue: A 405 - end of helix removed outlier: 3.612A pdb=" N PHE A 408 " --> pdb=" O ILE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 418 Processing helix chain 'A' and resid 422 through 445 Processing helix chain 'A' and resid 450 through 464 Processing helix chain 'A' and resid 465 through 472 removed outlier: 3.592A pdb=" N ARG A 470 " --> pdb=" O TYR A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 488 Processing helix chain 'A' and resid 488 through 513 removed outlier: 3.683A pdb=" N VAL A 499 " --> pdb=" O TRP A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 524 removed outlier: 4.403A pdb=" N PHE A 523 " --> pdb=" O LEU A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 538 Processing helix chain 'A' and resid 552 through 566 removed outlier: 3.691A pdb=" N CYS A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 608 removed outlier: 3.614A pdb=" N ASN A 572 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE A 575 " --> pdb=" O LEU A 571 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TRP A 583 " --> pdb=" O GLY A 579 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG A 584 " --> pdb=" O ASP A 580 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N GLN A 587 " --> pdb=" O TRP A 583 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N GLU A 588 " --> pdb=" O ARG A 584 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP A 590 " --> pdb=" O ALA A 586 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL A 598 " --> pdb=" O ARG A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 613 Processing helix chain 'A' and resid 621 through 624 Processing helix chain 'B' and resid 29 through 47 Processing helix chain 'B' and resid 47 through 56 Processing helix chain 'B' and resid 57 through 67 Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 91 through 102 Processing helix chain 'B' and resid 103 through 108 Processing helix chain 'B' and resid 119 through 127 Processing helix chain 'B' and resid 129 through 138 Processing helix chain 'B' and resid 149 through 153 Processing helix chain 'B' and resid 165 through 174 Processing helix chain 'B' and resid 175 through 185 Processing helix chain 'B' and resid 198 through 205 Processing helix chain 'B' and resid 208 through 221 removed outlier: 3.980A pdb=" N GLN B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 235 Processing helix chain 'B' and resid 242 through 250 Processing helix chain 'B' and resid 252 through 261 Processing helix chain 'B' and resid 280 through 285 removed outlier: 3.537A pdb=" N SER B 285 " --> pdb=" O THR B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 298 Processing helix chain 'B' and resid 303 through 309 Processing helix chain 'B' and resid 310 through 324 removed outlier: 4.115A pdb=" N GLU B 315 " --> pdb=" O THR B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 349 Processing helix chain 'B' and resid 379 through 411 removed outlier: 3.514A pdb=" N GLY B 388 " --> pdb=" O ILE B 384 " (cutoff:3.500A) Proline residue: B 405 - end of helix removed outlier: 3.612A pdb=" N PHE B 408 " --> pdb=" O ILE B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 418 Processing helix chain 'B' and resid 422 through 445 Processing helix chain 'B' and resid 450 through 464 Processing helix chain 'B' and resid 465 through 472 removed outlier: 3.592A pdb=" N ARG B 470 " --> pdb=" O TYR B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 488 Processing helix chain 'B' and resid 488 through 513 removed outlier: 3.682A pdb=" N VAL B 499 " --> pdb=" O TRP B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 524 removed outlier: 4.403A pdb=" N PHE B 523 " --> pdb=" O LEU B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 538 Processing helix chain 'B' and resid 552 through 566 removed outlier: 3.690A pdb=" N CYS B 556 " --> pdb=" O PRO B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 608 removed outlier: 3.615A pdb=" N ASN B 572 " --> pdb=" O LEU B 568 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE B 575 " --> pdb=" O LEU B 571 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TRP B 583 " --> pdb=" O GLY B 579 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG B 584 " --> pdb=" O ASP B 580 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N GLN B 587 " --> pdb=" O TRP B 583 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N GLU B 588 " --> pdb=" O ARG B 584 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP B 590 " --> pdb=" O ALA B 586 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL B 598 " --> pdb=" O ARG B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 613 Processing helix chain 'B' and resid 621 through 624 Processing helix chain 'C' and resid 29 through 47 Processing helix chain 'C' and resid 47 through 56 Processing helix chain 'C' and resid 57 through 67 Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 91 through 102 Processing helix chain 'C' and resid 103 through 108 Processing helix chain 'C' and resid 119 through 127 Processing helix chain 'C' and resid 129 through 138 Processing helix chain 'C' and resid 149 through 153 Processing helix chain 'C' and resid 165 through 174 Processing helix chain 'C' and resid 175 through 185 Processing helix chain 'C' and resid 198 through 205 Processing helix chain 'C' and resid 208 through 221 removed outlier: 3.979A pdb=" N GLN C 214 " --> pdb=" O THR C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 235 Processing helix chain 'C' and resid 242 through 250 Processing helix chain 'C' and resid 252 through 261 Processing helix chain 'C' and resid 280 through 285 removed outlier: 3.537A pdb=" N SER C 285 " --> pdb=" O THR C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 298 Processing helix chain 'C' and resid 303 through 309 Processing helix chain 'C' and resid 310 through 324 removed outlier: 4.114A pdb=" N GLU C 315 " --> pdb=" O THR C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 349 Processing helix chain 'C' and resid 379 through 411 removed outlier: 3.514A pdb=" N GLY C 388 " --> pdb=" O ILE C 384 " (cutoff:3.500A) Proline residue: C 405 - end of helix removed outlier: 3.612A pdb=" N PHE C 408 " --> pdb=" O ILE C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 418 Processing helix chain 'C' and resid 422 through 445 Processing helix chain 'C' and resid 450 through 464 Processing helix chain 'C' and resid 465 through 472 removed outlier: 3.592A pdb=" N ARG C 470 " --> pdb=" O TYR C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 488 Processing helix chain 'C' and resid 488 through 513 removed outlier: 3.682A pdb=" N VAL C 499 " --> pdb=" O TRP C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 524 removed outlier: 4.403A pdb=" N PHE C 523 " --> pdb=" O LEU C 520 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 538 Processing helix chain 'C' and resid 552 through 566 removed outlier: 3.691A pdb=" N CYS C 556 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 608 removed outlier: 3.614A pdb=" N ASN C 572 " --> pdb=" O LEU C 568 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE C 575 " --> pdb=" O LEU C 571 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TRP C 583 " --> pdb=" O GLY C 579 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG C 584 " --> pdb=" O ASP C 580 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N GLN C 587 " --> pdb=" O TRP C 583 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N GLU C 588 " --> pdb=" O ARG C 584 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP C 590 " --> pdb=" O ALA C 586 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL C 598 " --> pdb=" O ARG C 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 609 through 613 Processing helix chain 'C' and resid 621 through 624 Processing helix chain 'D' and resid 29 through 47 Processing helix chain 'D' and resid 47 through 56 Processing helix chain 'D' and resid 57 through 67 Processing helix chain 'D' and resid 81 through 89 Processing helix chain 'D' and resid 91 through 102 Processing helix chain 'D' and resid 103 through 108 Processing helix chain 'D' and resid 119 through 127 Processing helix chain 'D' and resid 129 through 138 Processing helix chain 'D' and resid 149 through 153 Processing helix chain 'D' and resid 165 through 174 Processing helix chain 'D' and resid 175 through 185 Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 208 through 221 removed outlier: 3.979A pdb=" N GLN D 214 " --> pdb=" O THR D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 235 Processing helix chain 'D' and resid 242 through 250 Processing helix chain 'D' and resid 252 through 261 Processing helix chain 'D' and resid 280 through 285 removed outlier: 3.537A pdb=" N SER D 285 " --> pdb=" O THR D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 298 Processing helix chain 'D' and resid 303 through 309 Processing helix chain 'D' and resid 310 through 324 removed outlier: 4.115A pdb=" N GLU D 315 " --> pdb=" O THR D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 349 Processing helix chain 'D' and resid 379 through 411 removed outlier: 3.514A pdb=" N GLY D 388 " --> pdb=" O ILE D 384 " (cutoff:3.500A) Proline residue: D 405 - end of helix removed outlier: 3.611A pdb=" N PHE D 408 " --> pdb=" O ILE D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 418 Processing helix chain 'D' and resid 422 through 445 Processing helix chain 'D' and resid 450 through 464 Processing helix chain 'D' and resid 465 through 472 removed outlier: 3.592A pdb=" N ARG D 470 " --> pdb=" O TYR D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 488 Processing helix chain 'D' and resid 488 through 513 removed outlier: 3.683A pdb=" N VAL D 499 " --> pdb=" O TRP D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 524 removed outlier: 4.402A pdb=" N PHE D 523 " --> pdb=" O LEU D 520 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 538 Processing helix chain 'D' and resid 552 through 566 removed outlier: 3.690A pdb=" N CYS D 556 " --> pdb=" O PRO D 552 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 608 removed outlier: 3.614A pdb=" N ASN D 572 " --> pdb=" O LEU D 568 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE D 575 " --> pdb=" O LEU D 571 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TRP D 583 " --> pdb=" O GLY D 579 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG D 584 " --> pdb=" O ASP D 580 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N GLN D 587 " --> pdb=" O TRP D 583 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N GLU D 588 " --> pdb=" O ARG D 584 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP D 590 " --> pdb=" O ALA D 586 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL D 598 " --> pdb=" O ARG D 594 " (cutoff:3.500A) Processing helix chain 'D' and resid 609 through 613 Processing helix chain 'D' and resid 621 through 624 Processing sheet with id=AA1, first strand: chain 'A' and resid 264 through 270 removed outlier: 6.535A pdb=" N LYS A 264 " --> pdb=" O ASP A 279 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASP A 279 " --> pdb=" O LYS A 264 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N VAL A 266 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU A 277 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TRP A 268 " --> pdb=" O SER A 275 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 352 through 354 Processing sheet with id=AA3, first strand: chain 'B' and resid 264 through 270 removed outlier: 6.536A pdb=" N LYS B 264 " --> pdb=" O ASP B 279 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASP B 279 " --> pdb=" O LYS B 264 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N VAL B 266 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU B 277 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TRP B 268 " --> pdb=" O SER B 275 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 352 through 354 Processing sheet with id=AA5, first strand: chain 'C' and resid 264 through 270 removed outlier: 6.535A pdb=" N LYS C 264 " --> pdb=" O ASP C 279 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ASP C 279 " --> pdb=" O LYS C 264 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N VAL C 266 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU C 277 " --> pdb=" O VAL C 266 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TRP C 268 " --> pdb=" O SER C 275 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 352 through 354 Processing sheet with id=AA7, first strand: chain 'D' and resid 264 through 270 removed outlier: 6.535A pdb=" N LYS D 264 " --> pdb=" O ASP D 279 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASP D 279 " --> pdb=" O LYS D 264 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N VAL D 266 " --> pdb=" O LEU D 277 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU D 277 " --> pdb=" O VAL D 266 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TRP D 268 " --> pdb=" O SER D 275 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 352 through 354 1189 hydrogen bonds defined for protein. 3315 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: 6.70 Time building geometry restraints manager: 5.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3096 1.30 - 1.43: 5424 1.43 - 1.56: 11580 1.56 - 1.69: 16 1.69 - 1.82: 236 Bond restraints: 20352 Sorted by residual: bond pdb=" C PRO B 312 " pdb=" O PRO B 312 " ideal model delta sigma weight residual 1.237 1.172 0.066 1.20e-02 6.94e+03 3.00e+01 bond pdb=" C PRO C 312 " pdb=" O PRO C 312 " ideal model delta sigma weight residual 1.237 1.173 0.065 1.20e-02 6.94e+03 2.90e+01 bond pdb=" C PRO D 312 " pdb=" O PRO D 312 " ideal model delta sigma weight residual 1.237 1.173 0.065 1.20e-02 6.94e+03 2.90e+01 bond pdb=" C PRO A 312 " pdb=" O PRO A 312 " ideal model delta sigma weight residual 1.237 1.173 0.065 1.20e-02 6.94e+03 2.90e+01 bond pdb=" CA ALA D 545 " pdb=" CB ALA D 545 " ideal model delta sigma weight residual 1.530 1.461 0.069 1.69e-02 3.50e+03 1.69e+01 ... (remaining 20347 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 20326 1.94 - 3.88: 6371 3.88 - 5.82: 794 5.82 - 7.76: 96 7.76 - 9.69: 25 Bond angle restraints: 27612 Sorted by residual: angle pdb=" N PRO A 312 " pdb=" CA PRO A 312 " pdb=" C PRO A 312 " ideal model delta sigma weight residual 113.40 105.19 8.21 1.34e+00 5.57e-01 3.75e+01 angle pdb=" N PRO D 312 " pdb=" CA PRO D 312 " pdb=" C PRO D 312 " ideal model delta sigma weight residual 113.40 105.23 8.17 1.34e+00 5.57e-01 3.72e+01 angle pdb=" N PRO B 312 " pdb=" CA PRO B 312 " pdb=" C PRO B 312 " ideal model delta sigma weight residual 113.40 105.23 8.17 1.34e+00 5.57e-01 3.72e+01 angle pdb=" N PRO C 312 " pdb=" CA PRO C 312 " pdb=" C PRO C 312 " ideal model delta sigma weight residual 113.40 105.23 8.17 1.34e+00 5.57e-01 3.71e+01 angle pdb=" N ILE B 540 " pdb=" CA ILE B 540 " pdb=" C ILE B 540 " ideal model delta sigma weight residual 112.83 107.07 5.76 9.90e-01 1.02e+00 3.39e+01 ... (remaining 27607 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.57: 12032 25.57 - 51.14: 384 51.14 - 76.71: 84 76.71 - 102.28: 32 102.28 - 127.85: 4 Dihedral angle restraints: 12536 sinusoidal: 5508 harmonic: 7028 Sorted by residual: dihedral pdb=" C THR D 539 " pdb=" N THR D 539 " pdb=" CA THR D 539 " pdb=" CB THR D 539 " ideal model delta harmonic sigma weight residual -122.00 -133.51 11.51 0 2.50e+00 1.60e-01 2.12e+01 dihedral pdb=" C THR A 539 " pdb=" N THR A 539 " pdb=" CA THR A 539 " pdb=" CB THR A 539 " ideal model delta harmonic sigma weight residual -122.00 -133.47 11.47 0 2.50e+00 1.60e-01 2.10e+01 dihedral pdb=" C THR B 539 " pdb=" N THR B 539 " pdb=" CA THR B 539 " pdb=" CB THR B 539 " ideal model delta harmonic sigma weight residual -122.00 -133.46 11.46 0 2.50e+00 1.60e-01 2.10e+01 ... (remaining 12533 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1631 0.061 - 0.121: 978 0.121 - 0.182: 393 0.182 - 0.243: 100 0.243 - 0.303: 26 Chirality restraints: 3128 Sorted by residual: chirality pdb=" CA THR D 539 " pdb=" N THR D 539 " pdb=" C THR D 539 " pdb=" CB THR D 539 " both_signs ideal model delta sigma weight residual False 2.53 2.22 0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" CA THR A 539 " pdb=" N THR A 539 " pdb=" C THR A 539 " pdb=" CB THR A 539 " both_signs ideal model delta sigma weight residual False 2.53 2.22 0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" CA THR B 539 " pdb=" N THR B 539 " pdb=" C THR B 539 " pdb=" CB THR B 539 " both_signs ideal model delta sigma weight residual False 2.53 2.22 0.30 2.00e-01 2.50e+01 2.28e+00 ... (remaining 3125 not shown) Planarity restraints: 3424 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C38 CPL C 801 " -0.098 2.00e-02 2.50e+03 2.60e-01 6.76e+02 pdb=" C39 CPL C 801 " 0.344 2.00e-02 2.50e+03 pdb=" C40 CPL C 801 " -0.360 2.00e-02 2.50e+03 pdb=" C41 CPL C 801 " 0.114 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C38 CPL D 801 " 0.098 2.00e-02 2.50e+03 2.60e-01 6.75e+02 pdb=" C39 CPL D 801 " -0.344 2.00e-02 2.50e+03 pdb=" C40 CPL D 801 " 0.359 2.00e-02 2.50e+03 pdb=" C41 CPL D 801 " -0.114 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C38 CPL A 805 " 0.099 2.00e-02 2.50e+03 2.60e-01 6.75e+02 pdb=" C39 CPL A 805 " -0.345 2.00e-02 2.50e+03 pdb=" C40 CPL A 805 " 0.358 2.00e-02 2.50e+03 pdb=" C41 CPL A 805 " -0.113 2.00e-02 2.50e+03 ... (remaining 3421 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.86: 6192 2.86 - 3.37: 20079 3.37 - 3.88: 35004 3.88 - 4.39: 41539 4.39 - 4.90: 69305 Nonbonded interactions: 172119 Sorted by model distance: nonbonded pdb=" O LEU A 368 " pdb=" OG1 THR D 514 " model vdw 2.356 3.040 nonbonded pdb=" OG1 THR C 514 " pdb=" O LEU D 368 " model vdw 2.361 3.040 nonbonded pdb=" OG1 THR B 514 " pdb=" O LEU C 368 " model vdw 2.362 3.040 nonbonded pdb=" OG1 THR A 514 " pdb=" O LEU B 368 " model vdw 2.366 3.040 nonbonded pdb=" O ALA D 563 " pdb=" OG1 THR D 567 " model vdw 2.388 3.040 ... (remaining 172114 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: 0.04 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 28 through 637 or resid 802)) selection = (chain 'B' and (resid 28 through 637 or resid 802)) selection = (chain 'C' and (resid 28 through 637 or resid 802)) selection = (chain 'D' and (resid 28 through 637 or resid 802)) } 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: 1.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.690 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 44.560 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 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 : 0.012 0.069 20352 Z= 0.742 Angle : 1.798 9.695 27612 Z= 1.223 Chirality : 0.088 0.303 3128 Planarity : 0.016 0.260 3424 Dihedral : 14.586 127.848 7992 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.16), residues: 2384 helix: -1.01 (0.11), residues: 1500 sheet: 0.88 (0.51), residues: 80 loop : 0.47 (0.24), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.147 0.021 TRP C 593 HIS 0.011 0.003 HIS A 238 PHE 0.058 0.011 PHE C 256 TYR 0.110 0.020 TYR B 432 ARG 0.009 0.001 ARG D 492 Details of bonding type rmsd hydrogen bonds : bond 0.16942 ( 1189) hydrogen bonds : angle 6.73925 ( 3315) covalent geometry : bond 0.01202 (20352) covalent geometry : angle 1.79784 (27612) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 414 time to evaluate : 2.306 Fit side-chains REVERT: A 33 ARG cc_start: 0.6544 (ttt90) cc_final: 0.6341 (ttp-170) REVERT: A 74 GLN cc_start: 0.7121 (mt0) cc_final: 0.6894 (mt0) REVERT: A 93 GLU cc_start: 0.7416 (mp0) cc_final: 0.7110 (mp0) REVERT: A 214 GLN cc_start: 0.7683 (mm-40) cc_final: 0.7245 (mt0) REVERT: A 301 LYS cc_start: 0.7837 (mmmt) cc_final: 0.7357 (mmmt) REVERT: A 306 GLN cc_start: 0.7612 (mt0) cc_final: 0.6833 (mp10) REVERT: A 380 HIS cc_start: 0.7138 (t-170) cc_final: 0.6854 (t-90) REVERT: A 381 GLN cc_start: 0.6758 (mp10) cc_final: 0.5816 (mm-40) REVERT: A 448 ASN cc_start: 0.7710 (t0) cc_final: 0.7438 (t0) REVERT: A 483 GLN cc_start: 0.7712 (tt0) cc_final: 0.7417 (tm-30) REVERT: A 491 MET cc_start: 0.7517 (mmm) cc_final: 0.6797 (mmp) REVERT: B 33 ARG cc_start: 0.6515 (ttt90) cc_final: 0.6296 (ttp-170) REVERT: B 93 GLU cc_start: 0.7468 (mp0) cc_final: 0.7042 (mp0) REVERT: B 214 GLN cc_start: 0.7672 (mm-40) cc_final: 0.7249 (mt0) REVERT: B 301 LYS cc_start: 0.7818 (mmmt) cc_final: 0.7335 (mmmt) REVERT: B 306 GLN cc_start: 0.7602 (mt0) cc_final: 0.6830 (mp10) REVERT: B 380 HIS cc_start: 0.7096 (t-170) cc_final: 0.6836 (t-90) REVERT: B 448 ASN cc_start: 0.7723 (t0) cc_final: 0.7454 (t0) REVERT: B 491 MET cc_start: 0.7523 (mmm) cc_final: 0.6811 (mmp) REVERT: C 33 ARG cc_start: 0.6511 (ttt90) cc_final: 0.6294 (ttp-170) REVERT: C 93 GLU cc_start: 0.7467 (mp0) cc_final: 0.7036 (mp0) REVERT: C 214 GLN cc_start: 0.7676 (mm-40) cc_final: 0.7243 (mt0) REVERT: C 301 LYS cc_start: 0.7836 (mmmt) cc_final: 0.7357 (mmmt) REVERT: C 306 GLN cc_start: 0.7608 (mt0) cc_final: 0.6835 (mp10) REVERT: C 380 HIS cc_start: 0.7115 (t-170) cc_final: 0.6855 (t-90) REVERT: C 448 ASN cc_start: 0.7721 (t0) cc_final: 0.7451 (t0) REVERT: C 491 MET cc_start: 0.7515 (mmm) cc_final: 0.6804 (mmp) REVERT: D 33 ARG cc_start: 0.6505 (ttt90) cc_final: 0.6285 (ttp-170) REVERT: D 74 GLN cc_start: 0.7214 (mt0) cc_final: 0.7004 (mt0) REVERT: D 93 GLU cc_start: 0.7441 (mp0) cc_final: 0.7100 (mp0) REVERT: D 214 GLN cc_start: 0.7675 (mm-40) cc_final: 0.7250 (mt0) REVERT: D 301 LYS cc_start: 0.7837 (mmmt) cc_final: 0.7359 (mmmt) REVERT: D 306 GLN cc_start: 0.7597 (mt0) cc_final: 0.6832 (mp10) REVERT: D 380 HIS cc_start: 0.7121 (t-170) cc_final: 0.6860 (t-90) REVERT: D 448 ASN cc_start: 0.7714 (t0) cc_final: 0.7442 (t0) REVERT: D 491 MET cc_start: 0.7516 (mmm) cc_final: 0.6804 (mmp) outliers start: 0 outliers final: 0 residues processed: 414 average time/residue: 1.4284 time to fit residues: 662.2777 Evaluate side-chains 300 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 300 time to evaluate : 2.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 0.7980 chunk 181 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 188 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 114 optimal weight: 0.6980 chunk 140 optimal weight: 0.9990 chunk 217 optimal weight: 3.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 261 GLN A 473 GLN A 483 GLN A 596 GLN B 261 GLN B 473 GLN B 483 GLN B 596 GLN C 261 GLN C 473 GLN C 483 GLN C 596 GLN D 261 GLN D 473 GLN D 483 GLN D 596 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.151313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.113635 restraints weight = 21737.184| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.62 r_work: 0.3074 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20352 Z= 0.136 Angle : 0.575 5.784 27612 Z= 0.299 Chirality : 0.040 0.146 3128 Planarity : 0.004 0.031 3424 Dihedral : 10.646 93.100 3428 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 1.25 % Allowed : 7.36 % Favored : 91.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.17), residues: 2384 helix: 1.24 (0.13), residues: 1512 sheet: 0.65 (0.52), residues: 88 loop : 0.83 (0.24), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 593 HIS 0.003 0.001 HIS B 185 PHE 0.016 0.002 PHE D 456 TYR 0.016 0.001 TYR C 555 ARG 0.004 0.001 ARG B 355 Details of bonding type rmsd hydrogen bonds : bond 0.04793 ( 1189) hydrogen bonds : angle 4.26336 ( 3315) covalent geometry : bond 0.00301 (20352) covalent geometry : angle 0.57536 (27612) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 356 time to evaluate : 2.035 Fit side-chains REVERT: A 35 ARG cc_start: 0.7993 (ttt-90) cc_final: 0.7768 (ttt90) REVERT: A 93 GLU cc_start: 0.7633 (mp0) cc_final: 0.7320 (mp0) REVERT: A 173 VAL cc_start: 0.8511 (t) cc_final: 0.8187 (m) REVERT: A 184 GLU cc_start: 0.7581 (mt-10) cc_final: 0.7275 (tp30) REVERT: A 214 GLN cc_start: 0.8005 (mm-40) cc_final: 0.7630 (mt0) REVERT: A 302 ARG cc_start: 0.7802 (mtm110) cc_final: 0.7419 (ttp80) REVERT: A 306 GLN cc_start: 0.7932 (mt0) cc_final: 0.7395 (mp10) REVERT: A 381 GLN cc_start: 0.6958 (mp10) cc_final: 0.5971 (mm-40) REVERT: A 448 ASN cc_start: 0.7952 (t0) cc_final: 0.7749 (t0) REVERT: A 491 MET cc_start: 0.7940 (mmm) cc_final: 0.7450 (mmp) REVERT: B 35 ARG cc_start: 0.8007 (ttt-90) cc_final: 0.7753 (ttt90) REVERT: B 93 GLU cc_start: 0.7657 (mp0) cc_final: 0.7316 (mp0) REVERT: B 173 VAL cc_start: 0.8511 (t) cc_final: 0.8217 (m) REVERT: B 184 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7286 (tp30) REVERT: B 214 GLN cc_start: 0.8003 (mm-40) cc_final: 0.7624 (mt0) REVERT: B 302 ARG cc_start: 0.7775 (mtm110) cc_final: 0.7410 (ttp80) REVERT: B 306 GLN cc_start: 0.7955 (mt0) cc_final: 0.7412 (mp10) REVERT: B 381 GLN cc_start: 0.6932 (mp10) cc_final: 0.5952 (mm-40) REVERT: B 448 ASN cc_start: 0.7945 (t0) cc_final: 0.7735 (t0) REVERT: B 491 MET cc_start: 0.7958 (mmm) cc_final: 0.7472 (mmp) REVERT: C 35 ARG cc_start: 0.8021 (ttt-90) cc_final: 0.7762 (ttt90) REVERT: C 93 GLU cc_start: 0.7660 (mp0) cc_final: 0.7325 (mp0) REVERT: C 173 VAL cc_start: 0.8520 (t) cc_final: 0.8221 (m) REVERT: C 184 GLU cc_start: 0.7589 (mt-10) cc_final: 0.7278 (tp30) REVERT: C 214 GLN cc_start: 0.7994 (mm-40) cc_final: 0.7627 (mt0) REVERT: C 302 ARG cc_start: 0.7782 (mtm110) cc_final: 0.7410 (ttp80) REVERT: C 306 GLN cc_start: 0.7973 (mt0) cc_final: 0.7421 (mp10) REVERT: C 381 GLN cc_start: 0.6913 (mp10) cc_final: 0.5941 (mm-40) REVERT: C 448 ASN cc_start: 0.7945 (t0) cc_final: 0.7737 (t0) REVERT: C 491 MET cc_start: 0.7941 (mmm) cc_final: 0.7454 (mmp) REVERT: D 35 ARG cc_start: 0.8029 (ttt-90) cc_final: 0.7772 (ttt90) REVERT: D 93 GLU cc_start: 0.7679 (mp0) cc_final: 0.7343 (mp0) REVERT: D 173 VAL cc_start: 0.8506 (t) cc_final: 0.8212 (m) REVERT: D 184 GLU cc_start: 0.7566 (mt-10) cc_final: 0.7282 (tp30) REVERT: D 214 GLN cc_start: 0.8002 (mm-40) cc_final: 0.7603 (mt0) REVERT: D 302 ARG cc_start: 0.7781 (mtm110) cc_final: 0.7411 (ttp80) REVERT: D 306 GLN cc_start: 0.7954 (mt0) cc_final: 0.7421 (mp10) REVERT: D 381 GLN cc_start: 0.6930 (mp10) cc_final: 0.5974 (mm-40) REVERT: D 421 LEU cc_start: 0.8569 (mp) cc_final: 0.8369 (mm) REVERT: D 491 MET cc_start: 0.7944 (mmm) cc_final: 0.7455 (mmp) outliers start: 26 outliers final: 11 residues processed: 365 average time/residue: 1.3008 time to fit residues: 538.8262 Evaluate side-chains 311 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 300 time to evaluate : 2.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 603 MET Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 603 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 102 optimal weight: 2.9990 chunk 198 optimal weight: 4.9990 chunk 69 optimal weight: 10.0000 chunk 113 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 221 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 chunk 177 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS A 197 ASN A 261 GLN B 185 HIS B 261 GLN C 185 HIS C 261 GLN D 185 HIS D 261 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.153143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.118556 restraints weight = 21584.316| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 1.45 r_work: 0.3060 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20352 Z= 0.153 Angle : 0.547 5.855 27612 Z= 0.281 Chirality : 0.039 0.156 3128 Planarity : 0.004 0.034 3424 Dihedral : 9.920 82.384 3428 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.88 % Allowed : 9.66 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.17), residues: 2384 helix: 1.49 (0.13), residues: 1540 sheet: -0.04 (0.53), residues: 80 loop : 0.94 (0.25), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 593 HIS 0.006 0.001 HIS C 201 PHE 0.016 0.002 PHE A 534 TYR 0.014 0.002 TYR A 89 ARG 0.006 0.001 ARG C 139 Details of bonding type rmsd hydrogen bonds : bond 0.04744 ( 1189) hydrogen bonds : angle 4.04841 ( 3315) covalent geometry : bond 0.00367 (20352) covalent geometry : angle 0.54654 (27612) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 321 time to evaluate : 2.308 Fit side-chains REVERT: A 93 GLU cc_start: 0.7636 (mp0) cc_final: 0.7300 (mp0) REVERT: A 139 ARG cc_start: 0.7890 (mtt-85) cc_final: 0.7680 (mtp180) REVERT: A 173 VAL cc_start: 0.8538 (t) cc_final: 0.8294 (m) REVERT: A 184 GLU cc_start: 0.7605 (mt-10) cc_final: 0.7343 (tp30) REVERT: A 190 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7577 (mtm180) REVERT: A 214 GLN cc_start: 0.8024 (mm-40) cc_final: 0.7687 (mt0) REVERT: A 302 ARG cc_start: 0.7835 (mtm110) cc_final: 0.7459 (ttp80) REVERT: A 306 GLN cc_start: 0.7879 (mt0) cc_final: 0.7358 (mp10) REVERT: A 381 GLN cc_start: 0.6994 (mp10) cc_final: 0.6043 (mm-40) REVERT: A 448 ASN cc_start: 0.8041 (t0) cc_final: 0.7825 (t0) REVERT: A 491 MET cc_start: 0.7879 (mmm) cc_final: 0.7376 (mmp) REVERT: B 93 GLU cc_start: 0.7651 (mp0) cc_final: 0.7282 (mp0) REVERT: B 173 VAL cc_start: 0.8529 (t) cc_final: 0.8293 (m) REVERT: B 184 GLU cc_start: 0.7674 (mt-10) cc_final: 0.7369 (tp30) REVERT: B 190 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.7603 (mtm180) REVERT: B 214 GLN cc_start: 0.8023 (mm-40) cc_final: 0.7690 (mt0) REVERT: B 302 ARG cc_start: 0.7824 (mtm110) cc_final: 0.7453 (ttp80) REVERT: B 306 GLN cc_start: 0.7883 (mt0) cc_final: 0.7357 (mp10) REVERT: B 381 GLN cc_start: 0.6966 (mp10) cc_final: 0.6010 (mm-40) REVERT: B 421 LEU cc_start: 0.8751 (mm) cc_final: 0.8439 (mp) REVERT: B 491 MET cc_start: 0.7898 (mmm) cc_final: 0.7393 (mmp) REVERT: C 80 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8358 (pm20) REVERT: C 93 GLU cc_start: 0.7642 (mp0) cc_final: 0.7268 (mp0) REVERT: C 139 ARG cc_start: 0.7870 (mtt-85) cc_final: 0.7670 (mtp180) REVERT: C 173 VAL cc_start: 0.8533 (t) cc_final: 0.8300 (m) REVERT: C 184 GLU cc_start: 0.7674 (mt-10) cc_final: 0.7375 (tp30) REVERT: C 190 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7587 (mtm180) REVERT: C 214 GLN cc_start: 0.8027 (mm-40) cc_final: 0.7686 (mt0) REVERT: C 302 ARG cc_start: 0.7826 (mtm110) cc_final: 0.7452 (ttp80) REVERT: C 306 GLN cc_start: 0.7897 (mt0) cc_final: 0.7376 (mp10) REVERT: C 381 GLN cc_start: 0.6963 (mp10) cc_final: 0.6013 (mm-40) REVERT: C 421 LEU cc_start: 0.8725 (mm) cc_final: 0.8408 (mp) REVERT: C 448 ASN cc_start: 0.8031 (t0) cc_final: 0.7827 (t0) REVERT: C 491 MET cc_start: 0.7879 (mmm) cc_final: 0.7376 (mmp) REVERT: D 93 GLU cc_start: 0.7654 (mp0) cc_final: 0.7282 (mp0) REVERT: D 173 VAL cc_start: 0.8533 (t) cc_final: 0.8301 (m) REVERT: D 184 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7362 (tp30) REVERT: D 190 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7593 (mtm180) REVERT: D 214 GLN cc_start: 0.8022 (mm-40) cc_final: 0.7676 (mt0) REVERT: D 302 ARG cc_start: 0.7834 (mtm110) cc_final: 0.7462 (ttp80) REVERT: D 306 GLN cc_start: 0.7904 (mt0) cc_final: 0.7379 (mp10) REVERT: D 381 GLN cc_start: 0.6968 (mp10) cc_final: 0.6014 (mm-40) REVERT: D 491 MET cc_start: 0.7886 (mmm) cc_final: 0.7381 (mmp) outliers start: 39 outliers final: 19 residues processed: 344 average time/residue: 1.3369 time to fit residues: 516.9693 Evaluate side-chains 328 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 304 time to evaluate : 2.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 603 MET Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 190 ARG Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 603 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 122 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 140 optimal weight: 3.9990 chunk 209 optimal weight: 0.9990 chunk 204 optimal weight: 5.9990 chunk 182 optimal weight: 5.9990 chunk 119 optimal weight: 6.9990 chunk 85 optimal weight: 8.9990 chunk 20 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 169 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN A 418 GLN B 261 GLN C 261 GLN D 261 GLN D 418 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.148129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.112609 restraints weight = 21773.542| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 1.45 r_work: 0.3011 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 20352 Z= 0.234 Angle : 0.612 6.528 27612 Z= 0.310 Chirality : 0.042 0.171 3128 Planarity : 0.005 0.035 3424 Dihedral : 9.706 85.767 3428 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.79 % Allowed : 9.28 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.17), residues: 2384 helix: 1.24 (0.13), residues: 1536 sheet: -0.66 (0.55), residues: 80 loop : 0.83 (0.24), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 593 HIS 0.006 0.001 HIS A 201 PHE 0.017 0.002 PHE D 534 TYR 0.017 0.002 TYR C 89 ARG 0.007 0.001 ARG C 35 Details of bonding type rmsd hydrogen bonds : bond 0.05242 ( 1189) hydrogen bonds : angle 4.12245 ( 3315) covalent geometry : bond 0.00582 (20352) covalent geometry : angle 0.61196 (27612) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 338 time to evaluate : 2.113 Fit side-chains REVERT: A 57 ASP cc_start: 0.8005 (p0) cc_final: 0.7766 (p0) REVERT: A 74 GLN cc_start: 0.7460 (mt0) cc_final: 0.7254 (mt0) REVERT: A 93 GLU cc_start: 0.7636 (mp0) cc_final: 0.7306 (mp0) REVERT: A 173 VAL cc_start: 0.8586 (t) cc_final: 0.8283 (m) REVERT: A 184 GLU cc_start: 0.7620 (mt-10) cc_final: 0.7315 (tp30) REVERT: A 190 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7645 (mtm180) REVERT: A 214 GLN cc_start: 0.7979 (mm-40) cc_final: 0.7665 (mt0) REVERT: A 215 MET cc_start: 0.8795 (mmm) cc_final: 0.8491 (mmt) REVERT: A 306 GLN cc_start: 0.7864 (mt0) cc_final: 0.7328 (mp10) REVERT: A 381 GLN cc_start: 0.6954 (mp10) cc_final: 0.5986 (mm-40) REVERT: A 421 LEU cc_start: 0.8837 (mm) cc_final: 0.8540 (mp) REVERT: A 447 MET cc_start: 0.8021 (ttp) cc_final: 0.7782 (mtp) REVERT: A 448 ASN cc_start: 0.8039 (t0) cc_final: 0.7814 (t0) REVERT: A 491 MET cc_start: 0.7836 (mmm) cc_final: 0.7321 (mmp) REVERT: B 57 ASP cc_start: 0.7991 (p0) cc_final: 0.7751 (p0) REVERT: B 74 GLN cc_start: 0.7517 (mt0) cc_final: 0.7316 (mt0) REVERT: B 80 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8329 (pm20) REVERT: B 93 GLU cc_start: 0.7618 (mp0) cc_final: 0.7238 (mp0) REVERT: B 173 VAL cc_start: 0.8561 (t) cc_final: 0.8254 (m) REVERT: B 184 GLU cc_start: 0.7711 (mt-10) cc_final: 0.7366 (tp30) REVERT: B 190 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7663 (mtm180) REVERT: B 214 GLN cc_start: 0.7977 (mm-40) cc_final: 0.7665 (mt0) REVERT: B 215 MET cc_start: 0.8797 (mmm) cc_final: 0.8461 (mmt) REVERT: B 306 GLN cc_start: 0.7861 (mt0) cc_final: 0.7324 (mp10) REVERT: B 381 GLN cc_start: 0.6937 (mp10) cc_final: 0.5950 (mm-40) REVERT: B 421 LEU cc_start: 0.8807 (mm) cc_final: 0.8504 (mp) REVERT: B 491 MET cc_start: 0.7854 (mmm) cc_final: 0.7333 (mmp) REVERT: C 57 ASP cc_start: 0.7978 (p0) cc_final: 0.7737 (p0) REVERT: C 80 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8312 (pm20) REVERT: C 93 GLU cc_start: 0.7630 (mp0) cc_final: 0.7250 (mp0) REVERT: C 173 VAL cc_start: 0.8574 (t) cc_final: 0.8275 (m) REVERT: C 184 GLU cc_start: 0.7721 (mt-10) cc_final: 0.7362 (tp30) REVERT: C 190 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7665 (mtm180) REVERT: C 214 GLN cc_start: 0.7976 (mm-40) cc_final: 0.7660 (mt0) REVERT: C 215 MET cc_start: 0.8793 (mmm) cc_final: 0.8458 (mmt) REVERT: C 306 GLN cc_start: 0.7879 (mt0) cc_final: 0.7340 (mp10) REVERT: C 381 GLN cc_start: 0.6929 (mp10) cc_final: 0.5945 (mm-40) REVERT: C 421 LEU cc_start: 0.8810 (mm) cc_final: 0.8513 (mp) REVERT: C 448 ASN cc_start: 0.8047 (t0) cc_final: 0.7829 (t0) REVERT: C 491 MET cc_start: 0.7857 (mmm) cc_final: 0.7334 (mmp) REVERT: D 57 ASP cc_start: 0.7978 (p0) cc_final: 0.7732 (p0) REVERT: D 80 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8332 (pm20) REVERT: D 93 GLU cc_start: 0.7612 (mp0) cc_final: 0.7314 (mp0) REVERT: D 173 VAL cc_start: 0.8565 (t) cc_final: 0.8265 (m) REVERT: D 184 GLU cc_start: 0.7706 (mt-10) cc_final: 0.7368 (tp30) REVERT: D 190 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7664 (mtm180) REVERT: D 214 GLN cc_start: 0.7963 (mm-40) cc_final: 0.7644 (mt0) REVERT: D 215 MET cc_start: 0.8787 (mmm) cc_final: 0.8450 (mmt) REVERT: D 306 GLN cc_start: 0.7887 (mt0) cc_final: 0.7348 (mp10) REVERT: D 381 GLN cc_start: 0.6951 (mp10) cc_final: 0.5968 (mm-40) REVERT: D 491 MET cc_start: 0.7847 (mmm) cc_final: 0.7329 (mmp) outliers start: 58 outliers final: 32 residues processed: 376 average time/residue: 1.2533 time to fit residues: 533.5313 Evaluate side-chains 361 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 322 time to evaluate : 2.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 548 SER Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 548 SER Chi-restraints excluded: chain C residue 603 MET Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 190 ARG Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 318 SER Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 548 SER Chi-restraints excluded: chain D residue 603 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 166 optimal weight: 2.9990 chunk 127 optimal weight: 0.5980 chunk 216 optimal weight: 0.9990 chunk 235 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 70 optimal weight: 0.7980 chunk 220 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 126 optimal weight: 4.9990 chunk 139 optimal weight: 5.9990 chunk 74 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN B 418 GLN C 418 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.148645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.110569 restraints weight = 21933.810| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 1.63 r_work: 0.3035 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20352 Z= 0.116 Angle : 0.503 5.724 27612 Z= 0.258 Chirality : 0.038 0.140 3128 Planarity : 0.004 0.037 3424 Dihedral : 8.866 81.732 3428 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.84 % Allowed : 9.04 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.17), residues: 2384 helix: 1.57 (0.13), residues: 1536 sheet: -0.88 (0.53), residues: 80 loop : 0.92 (0.25), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 593 HIS 0.003 0.001 HIS A 201 PHE 0.012 0.001 PHE C 534 TYR 0.011 0.001 TYR C 555 ARG 0.007 0.000 ARG B 139 Details of bonding type rmsd hydrogen bonds : bond 0.04170 ( 1189) hydrogen bonds : angle 3.91890 ( 3315) covalent geometry : bond 0.00259 (20352) covalent geometry : angle 0.50301 (27612) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 356 time to evaluate : 2.066 Fit side-chains REVERT: A 35 ARG cc_start: 0.8234 (ttt90) cc_final: 0.7980 (tpt-90) REVERT: A 57 ASP cc_start: 0.8030 (p0) cc_final: 0.7815 (p0) REVERT: A 74 GLN cc_start: 0.7430 (mt0) cc_final: 0.7215 (mt0) REVERT: A 93 GLU cc_start: 0.7593 (mp0) cc_final: 0.7264 (mp0) REVERT: A 184 GLU cc_start: 0.7649 (mt-10) cc_final: 0.7329 (tp30) REVERT: A 190 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7741 (mtm180) REVERT: A 214 GLN cc_start: 0.7948 (mm-40) cc_final: 0.7574 (mt0) REVERT: A 302 ARG cc_start: 0.7857 (mtm110) cc_final: 0.7594 (mtp-110) REVERT: A 306 GLN cc_start: 0.7831 (mt0) cc_final: 0.7296 (mp10) REVERT: A 381 GLN cc_start: 0.6833 (mp10) cc_final: 0.5881 (mm-40) REVERT: A 421 LEU cc_start: 0.8734 (mm) cc_final: 0.8399 (mp) REVERT: A 448 ASN cc_start: 0.8057 (t0) cc_final: 0.7825 (t0) REVERT: A 487 PHE cc_start: 0.8922 (m-10) cc_final: 0.8722 (m-10) REVERT: A 491 MET cc_start: 0.7879 (mmm) cc_final: 0.7341 (mmp) REVERT: B 35 ARG cc_start: 0.8186 (ttt90) cc_final: 0.7921 (tpt-90) REVERT: B 57 ASP cc_start: 0.7972 (p0) cc_final: 0.7729 (p0) REVERT: B 74 GLN cc_start: 0.7464 (mt0) cc_final: 0.7260 (mt0) REVERT: B 93 GLU cc_start: 0.7615 (mp0) cc_final: 0.7248 (mp0) REVERT: B 184 GLU cc_start: 0.7612 (mt-10) cc_final: 0.7280 (tp30) REVERT: B 190 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.7742 (mtm180) REVERT: B 214 GLN cc_start: 0.7948 (mm-40) cc_final: 0.7583 (mt0) REVERT: B 302 ARG cc_start: 0.7890 (mtm110) cc_final: 0.7610 (mtp-110) REVERT: B 306 GLN cc_start: 0.7819 (mt0) cc_final: 0.7276 (mp10) REVERT: B 381 GLN cc_start: 0.6836 (mp10) cc_final: 0.5884 (mm-40) REVERT: B 421 LEU cc_start: 0.8719 (mm) cc_final: 0.8350 (mp) REVERT: B 491 MET cc_start: 0.7891 (mmm) cc_final: 0.7351 (mmp) REVERT: C 35 ARG cc_start: 0.8150 (ttt90) cc_final: 0.7865 (tpt-90) REVERT: C 57 ASP cc_start: 0.7992 (p0) cc_final: 0.7751 (p0) REVERT: C 93 GLU cc_start: 0.7610 (mp0) cc_final: 0.7244 (mp0) REVERT: C 184 GLU cc_start: 0.7620 (mt-10) cc_final: 0.7280 (tp30) REVERT: C 190 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.7737 (mtm180) REVERT: C 214 GLN cc_start: 0.7973 (mm-40) cc_final: 0.7608 (mt0) REVERT: C 302 ARG cc_start: 0.7883 (mtm110) cc_final: 0.7605 (mtp-110) REVERT: C 306 GLN cc_start: 0.7820 (mt0) cc_final: 0.7285 (mp10) REVERT: C 381 GLN cc_start: 0.6834 (mp10) cc_final: 0.5878 (mm-40) REVERT: C 421 LEU cc_start: 0.8715 (mm) cc_final: 0.8379 (mp) REVERT: C 448 ASN cc_start: 0.8005 (t0) cc_final: 0.7802 (t0) REVERT: C 491 MET cc_start: 0.7889 (mmm) cc_final: 0.7355 (mmp) REVERT: D 35 ARG cc_start: 0.8164 (ttt90) cc_final: 0.7876 (tpt-90) REVERT: D 57 ASP cc_start: 0.7954 (p0) cc_final: 0.7708 (p0) REVERT: D 93 GLU cc_start: 0.7607 (mp0) cc_final: 0.7243 (mp0) REVERT: D 184 GLU cc_start: 0.7603 (mt-10) cc_final: 0.7277 (tp30) REVERT: D 190 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7746 (mtm180) REVERT: D 214 GLN cc_start: 0.7965 (mm-40) cc_final: 0.7592 (mt0) REVERT: D 302 ARG cc_start: 0.7853 (mtm110) cc_final: 0.7593 (mtp-110) REVERT: D 306 GLN cc_start: 0.7829 (mt0) cc_final: 0.7289 (mp10) REVERT: D 381 GLN cc_start: 0.6861 (mp10) cc_final: 0.5916 (mm-40) REVERT: D 421 LEU cc_start: 0.8763 (mm) cc_final: 0.8442 (mp) REVERT: D 487 PHE cc_start: 0.8929 (m-10) cc_final: 0.8727 (m-10) REVERT: D 491 MET cc_start: 0.7898 (mmm) cc_final: 0.7361 (mmp) outliers start: 59 outliers final: 29 residues processed: 395 average time/residue: 1.2783 time to fit residues: 572.1445 Evaluate side-chains 350 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 317 time to evaluate : 2.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 548 SER Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 548 SER Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 190 ARG Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 318 SER Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 548 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 84 optimal weight: 5.9990 chunk 176 optimal weight: 0.6980 chunk 12 optimal weight: 0.0040 chunk 16 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 179 optimal weight: 0.3980 chunk 172 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 171 optimal weight: 0.0870 overall best weight: 0.4372 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN B 261 GLN C 261 GLN D 261 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.151095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.113354 restraints weight = 21898.758| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.63 r_work: 0.3079 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 20352 Z= 0.105 Angle : 0.504 6.112 27612 Z= 0.255 Chirality : 0.037 0.137 3128 Planarity : 0.004 0.040 3424 Dihedral : 8.483 77.594 3428 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.73 % Allowed : 11.35 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.17), residues: 2384 helix: 1.83 (0.13), residues: 1532 sheet: -1.14 (0.51), residues: 80 loop : 0.95 (0.25), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 593 HIS 0.003 0.001 HIS B 201 PHE 0.011 0.001 PHE A 534 TYR 0.010 0.001 TYR D 555 ARG 0.009 0.000 ARG B 409 Details of bonding type rmsd hydrogen bonds : bond 0.03915 ( 1189) hydrogen bonds : angle 3.87833 ( 3315) covalent geometry : bond 0.00221 (20352) covalent geometry : angle 0.50417 (27612) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 325 time to evaluate : 2.213 Fit side-chains REVERT: A 35 ARG cc_start: 0.8122 (ttt90) cc_final: 0.7882 (tpt-90) REVERT: A 93 GLU cc_start: 0.7545 (mp0) cc_final: 0.7213 (mp0) REVERT: A 108 GLU cc_start: 0.7691 (mm-30) cc_final: 0.7416 (mm-30) REVERT: A 184 GLU cc_start: 0.7506 (mt-10) cc_final: 0.7266 (tp30) REVERT: A 190 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7543 (mtm180) REVERT: A 214 GLN cc_start: 0.7965 (mm-40) cc_final: 0.7595 (mt0) REVERT: A 306 GLN cc_start: 0.7791 (mt0) cc_final: 0.7300 (mp10) REVERT: A 318 SER cc_start: 0.8664 (t) cc_final: 0.8302 (m) REVERT: A 381 GLN cc_start: 0.6791 (mp10) cc_final: 0.5823 (mm-40) REVERT: A 421 LEU cc_start: 0.8672 (mm) cc_final: 0.8326 (mp) REVERT: A 448 ASN cc_start: 0.8002 (t0) cc_final: 0.7780 (t0) REVERT: A 487 PHE cc_start: 0.8847 (m-10) cc_final: 0.8638 (m-10) REVERT: A 491 MET cc_start: 0.7907 (mmm) cc_final: 0.7359 (mmp) REVERT: B 35 ARG cc_start: 0.8105 (ttt90) cc_final: 0.7863 (tpt-90) REVERT: B 80 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7583 (pt0) REVERT: B 93 GLU cc_start: 0.7594 (mp0) cc_final: 0.7266 (mp0) REVERT: B 108 GLU cc_start: 0.7639 (mm-30) cc_final: 0.7360 (mm-30) REVERT: B 184 GLU cc_start: 0.7593 (mt-10) cc_final: 0.7276 (tp30) REVERT: B 190 ARG cc_start: 0.8121 (OUTLIER) cc_final: 0.7555 (mtm180) REVERT: B 214 GLN cc_start: 0.7966 (mm-40) cc_final: 0.7609 (mt0) REVERT: B 302 ARG cc_start: 0.7807 (mtm110) cc_final: 0.7554 (mtp-110) REVERT: B 306 GLN cc_start: 0.7732 (mt0) cc_final: 0.7227 (mp10) REVERT: B 381 GLN cc_start: 0.6791 (mp10) cc_final: 0.5833 (mm-40) REVERT: B 421 LEU cc_start: 0.8656 (mm) cc_final: 0.8310 (mp) REVERT: B 491 MET cc_start: 0.7908 (mmm) cc_final: 0.7356 (mmp) REVERT: C 35 ARG cc_start: 0.8022 (ttt90) cc_final: 0.7768 (tpt-90) REVERT: C 80 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7536 (pt0) REVERT: C 93 GLU cc_start: 0.7578 (mp0) cc_final: 0.7245 (mp0) REVERT: C 108 GLU cc_start: 0.7664 (mm-30) cc_final: 0.7391 (mm-30) REVERT: C 184 GLU cc_start: 0.7536 (mt-10) cc_final: 0.7282 (tp30) REVERT: C 190 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7541 (mtm180) REVERT: C 214 GLN cc_start: 0.8006 (mm-40) cc_final: 0.7635 (mt0) REVERT: C 302 ARG cc_start: 0.7835 (mtm110) cc_final: 0.7579 (mtp-110) REVERT: C 306 GLN cc_start: 0.7773 (mt0) cc_final: 0.7286 (mp10) REVERT: C 381 GLN cc_start: 0.6777 (mp10) cc_final: 0.5826 (mm-40) REVERT: C 421 LEU cc_start: 0.8680 (mm) cc_final: 0.8340 (mp) REVERT: C 448 ASN cc_start: 0.7983 (t0) cc_final: 0.7779 (t0) REVERT: C 491 MET cc_start: 0.7905 (mmm) cc_final: 0.7358 (mmp) REVERT: D 35 ARG cc_start: 0.8029 (ttt90) cc_final: 0.7766 (tpt-90) REVERT: D 80 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7558 (pt0) REVERT: D 93 GLU cc_start: 0.7572 (mp0) cc_final: 0.7242 (mp0) REVERT: D 108 GLU cc_start: 0.7669 (mm-30) cc_final: 0.7393 (mm-30) REVERT: D 184 GLU cc_start: 0.7571 (mt-10) cc_final: 0.7300 (tp30) REVERT: D 190 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.7493 (mtm180) REVERT: D 214 GLN cc_start: 0.7991 (mm-40) cc_final: 0.7617 (mt0) REVERT: D 306 GLN cc_start: 0.7781 (mt0) cc_final: 0.7288 (mp10) REVERT: D 381 GLN cc_start: 0.6792 (mp10) cc_final: 0.5834 (mm-40) REVERT: D 421 LEU cc_start: 0.8683 (mm) cc_final: 0.8357 (mp) REVERT: D 487 PHE cc_start: 0.8852 (m-10) cc_final: 0.8640 (m-10) REVERT: D 491 MET cc_start: 0.7900 (mmm) cc_final: 0.7352 (mmp) outliers start: 36 outliers final: 19 residues processed: 353 average time/residue: 1.3101 time to fit residues: 520.8309 Evaluate side-chains 327 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 301 time to evaluate : 2.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 190 ARG Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 335 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 38 optimal weight: 4.9990 chunk 154 optimal weight: 3.9990 chunk 234 optimal weight: 1.9990 chunk 236 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 169 optimal weight: 0.5980 chunk 58 optimal weight: 0.7980 chunk 220 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN B 261 GLN C 261 GLN D 261 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.149791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.112135 restraints weight = 21823.865| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 1.63 r_work: 0.3054 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 20352 Z= 0.115 Angle : 0.506 5.690 27612 Z= 0.256 Chirality : 0.038 0.175 3128 Planarity : 0.004 0.057 3424 Dihedral : 8.416 76.110 3428 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.83 % Allowed : 11.63 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.17), residues: 2384 helix: 1.87 (0.13), residues: 1540 sheet: -1.40 (0.51), residues: 80 loop : 1.09 (0.25), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 593 HIS 0.003 0.001 HIS C 201 PHE 0.017 0.001 PHE B 611 TYR 0.010 0.001 TYR B 555 ARG 0.013 0.001 ARG B 409 Details of bonding type rmsd hydrogen bonds : bond 0.04016 ( 1189) hydrogen bonds : angle 3.83777 ( 3315) covalent geometry : bond 0.00263 (20352) covalent geometry : angle 0.50574 (27612) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 304 time to evaluate : 2.168 Fit side-chains REVERT: A 35 ARG cc_start: 0.8162 (ttt90) cc_final: 0.7948 (tpt-90) REVERT: A 93 GLU cc_start: 0.7529 (mp0) cc_final: 0.7214 (mp0) REVERT: A 108 GLU cc_start: 0.7614 (mm-30) cc_final: 0.7280 (mm-30) REVERT: A 184 GLU cc_start: 0.7495 (mt-10) cc_final: 0.7281 (tp30) REVERT: A 190 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7700 (mtm180) REVERT: A 214 GLN cc_start: 0.8022 (mm-40) cc_final: 0.7666 (mt0) REVERT: A 302 ARG cc_start: 0.7807 (mtm110) cc_final: 0.7135 (ttt-90) REVERT: A 306 GLN cc_start: 0.7800 (mt0) cc_final: 0.7307 (mp10) REVERT: A 318 SER cc_start: 0.8674 (OUTLIER) cc_final: 0.8318 (m) REVERT: A 381 GLN cc_start: 0.6822 (mp10) cc_final: 0.5875 (mm-40) REVERT: A 421 LEU cc_start: 0.8667 (mm) cc_final: 0.8334 (mp) REVERT: A 448 ASN cc_start: 0.8053 (t0) cc_final: 0.7831 (t0) REVERT: A 487 PHE cc_start: 0.8887 (m-10) cc_final: 0.8642 (m-10) REVERT: A 491 MET cc_start: 0.7931 (mmm) cc_final: 0.7396 (mmp) REVERT: B 35 ARG cc_start: 0.8155 (ttt90) cc_final: 0.7928 (tpt-90) REVERT: B 80 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7574 (pt0) REVERT: B 93 GLU cc_start: 0.7584 (mp0) cc_final: 0.7190 (mp0) REVERT: B 108 GLU cc_start: 0.7614 (mm-30) cc_final: 0.7385 (mm-30) REVERT: B 184 GLU cc_start: 0.7518 (mt-10) cc_final: 0.7212 (tp30) REVERT: B 190 ARG cc_start: 0.8150 (OUTLIER) cc_final: 0.7627 (mtm180) REVERT: B 214 GLN cc_start: 0.8012 (mm-40) cc_final: 0.7669 (mt0) REVERT: B 306 GLN cc_start: 0.7782 (mt0) cc_final: 0.7296 (mp10) REVERT: B 318 SER cc_start: 0.8688 (t) cc_final: 0.8297 (m) REVERT: B 381 GLN cc_start: 0.6839 (mp10) cc_final: 0.5902 (mm-40) REVERT: B 421 LEU cc_start: 0.8669 (mm) cc_final: 0.8346 (mp) REVERT: B 491 MET cc_start: 0.7930 (mmm) cc_final: 0.7396 (mmp) REVERT: C 35 ARG cc_start: 0.8098 (ttt90) cc_final: 0.7853 (tpt-90) REVERT: C 80 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7554 (pt0) REVERT: C 93 GLU cc_start: 0.7565 (mp0) cc_final: 0.7170 (mp0) REVERT: C 108 GLU cc_start: 0.7588 (mm-30) cc_final: 0.7272 (mm-30) REVERT: C 184 GLU cc_start: 0.7496 (mt-10) cc_final: 0.7209 (tp30) REVERT: C 190 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.7551 (mtm180) REVERT: C 214 GLN cc_start: 0.8028 (mm-40) cc_final: 0.7671 (mt0) REVERT: C 306 GLN cc_start: 0.7795 (mt0) cc_final: 0.7316 (mp10) REVERT: C 318 SER cc_start: 0.8679 (t) cc_final: 0.8287 (m) REVERT: C 381 GLN cc_start: 0.6839 (mp10) cc_final: 0.5901 (mm-40) REVERT: C 421 LEU cc_start: 0.8666 (mm) cc_final: 0.8350 (mp) REVERT: C 448 ASN cc_start: 0.8036 (t0) cc_final: 0.7829 (t0) REVERT: C 491 MET cc_start: 0.7930 (mmm) cc_final: 0.7396 (mmp) REVERT: D 35 ARG cc_start: 0.8078 (ttt90) cc_final: 0.7837 (tpt-90) REVERT: D 80 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7569 (pt0) REVERT: D 93 GLU cc_start: 0.7576 (mp0) cc_final: 0.7185 (mp0) REVERT: D 108 GLU cc_start: 0.7579 (mm-30) cc_final: 0.7261 (mm-30) REVERT: D 184 GLU cc_start: 0.7504 (mt-10) cc_final: 0.7208 (tp30) REVERT: D 190 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7628 (mtm180) REVERT: D 214 GLN cc_start: 0.8028 (mm-40) cc_final: 0.7670 (mt0) REVERT: D 302 ARG cc_start: 0.7843 (mtm110) cc_final: 0.7157 (ttt-90) REVERT: D 306 GLN cc_start: 0.7790 (mt0) cc_final: 0.7298 (mp10) REVERT: D 318 SER cc_start: 0.8690 (t) cc_final: 0.8303 (m) REVERT: D 381 GLN cc_start: 0.6816 (mp10) cc_final: 0.5877 (mm-40) REVERT: D 421 LEU cc_start: 0.8703 (mm) cc_final: 0.8371 (mp) REVERT: D 487 PHE cc_start: 0.8865 (m-10) cc_final: 0.8625 (m-10) REVERT: D 491 MET cc_start: 0.7930 (mmm) cc_final: 0.7392 (mmp) outliers start: 38 outliers final: 21 residues processed: 333 average time/residue: 1.3815 time to fit residues: 518.5975 Evaluate side-chains 327 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 298 time to evaluate : 2.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 190 ARG Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 390 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 50 optimal weight: 0.8980 chunk 168 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 205 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 chunk 166 optimal weight: 0.5980 chunk 105 optimal weight: 0.9980 chunk 229 optimal weight: 4.9990 chunk 53 optimal weight: 0.5980 chunk 94 optimal weight: 4.9990 chunk 208 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN A 261 GLN B 261 GLN C 261 GLN D 261 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.149933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.112184 restraints weight = 21998.695| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 1.63 r_work: 0.3066 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20352 Z= 0.115 Angle : 0.516 6.495 27612 Z= 0.258 Chirality : 0.038 0.188 3128 Planarity : 0.004 0.058 3424 Dihedral : 8.343 75.003 3428 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.92 % Allowed : 11.92 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.17), residues: 2384 helix: 1.85 (0.13), residues: 1540 sheet: -1.42 (0.51), residues: 80 loop : 1.14 (0.25), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 593 HIS 0.003 0.001 HIS B 201 PHE 0.016 0.001 PHE A 611 TYR 0.010 0.001 TYR B 555 ARG 0.014 0.000 ARG B 409 Details of bonding type rmsd hydrogen bonds : bond 0.04025 ( 1189) hydrogen bonds : angle 3.83470 ( 3315) covalent geometry : bond 0.00260 (20352) covalent geometry : angle 0.51575 (27612) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 301 time to evaluate : 2.009 Fit side-chains REVERT: A 35 ARG cc_start: 0.8099 (ttt90) cc_final: 0.7895 (tpt-90) REVERT: A 93 GLU cc_start: 0.7526 (mp0) cc_final: 0.7234 (mp0) REVERT: A 108 GLU cc_start: 0.7584 (mm-30) cc_final: 0.7253 (mm-30) REVERT: A 139 ARG cc_start: 0.8040 (mtp180) cc_final: 0.7765 (mtp85) REVERT: A 184 GLU cc_start: 0.7489 (mt-10) cc_final: 0.7250 (tp30) REVERT: A 190 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7665 (mtm180) REVERT: A 214 GLN cc_start: 0.7978 (mm-40) cc_final: 0.7610 (mt0) REVERT: A 215 MET cc_start: 0.8766 (mmm) cc_final: 0.8501 (mmt) REVERT: A 302 ARG cc_start: 0.7819 (mtm110) cc_final: 0.7127 (ttt-90) REVERT: A 306 GLN cc_start: 0.7780 (mt0) cc_final: 0.7272 (mp10) REVERT: A 318 SER cc_start: 0.8627 (OUTLIER) cc_final: 0.8282 (m) REVERT: A 381 GLN cc_start: 0.6798 (mp10) cc_final: 0.5853 (mm-40) REVERT: A 421 LEU cc_start: 0.8648 (mm) cc_final: 0.8319 (mp) REVERT: A 448 ASN cc_start: 0.8047 (t0) cc_final: 0.7823 (t0) REVERT: A 487 PHE cc_start: 0.8845 (m-10) cc_final: 0.8609 (m-10) REVERT: A 491 MET cc_start: 0.7908 (mmm) cc_final: 0.7359 (mmp) REVERT: B 35 ARG cc_start: 0.8096 (ttt90) cc_final: 0.7880 (tpt-90) REVERT: B 80 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7622 (pt0) REVERT: B 93 GLU cc_start: 0.7576 (mp0) cc_final: 0.7192 (mp0) REVERT: B 108 GLU cc_start: 0.7589 (mm-30) cc_final: 0.7246 (mm-30) REVERT: B 184 GLU cc_start: 0.7533 (mt-10) cc_final: 0.7263 (tp30) REVERT: B 190 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7664 (mtm180) REVERT: B 214 GLN cc_start: 0.7983 (mm-40) cc_final: 0.7618 (mt0) REVERT: B 302 ARG cc_start: 0.7827 (mtm110) cc_final: 0.7085 (ttt-90) REVERT: B 306 GLN cc_start: 0.7762 (mt0) cc_final: 0.7251 (mp10) REVERT: B 318 SER cc_start: 0.8669 (OUTLIER) cc_final: 0.8283 (m) REVERT: B 381 GLN cc_start: 0.6799 (mp10) cc_final: 0.5858 (mm-40) REVERT: B 421 LEU cc_start: 0.8652 (mm) cc_final: 0.8329 (mp) REVERT: B 491 MET cc_start: 0.7905 (mmm) cc_final: 0.7357 (mmp) REVERT: C 35 ARG cc_start: 0.8041 (ttt90) cc_final: 0.7802 (tpt-90) REVERT: C 80 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7563 (pt0) REVERT: C 93 GLU cc_start: 0.7577 (mp0) cc_final: 0.7186 (mp0) REVERT: C 107 LYS cc_start: 0.7627 (mtmm) cc_final: 0.7312 (mtpp) REVERT: C 108 GLU cc_start: 0.7572 (mm-30) cc_final: 0.7248 (mm-30) REVERT: C 139 ARG cc_start: 0.8038 (mtp180) cc_final: 0.7739 (mtp85) REVERT: C 184 GLU cc_start: 0.7518 (mt-10) cc_final: 0.7264 (tp30) REVERT: C 190 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7651 (mtm180) REVERT: C 214 GLN cc_start: 0.8000 (mm-40) cc_final: 0.7624 (mt0) REVERT: C 302 ARG cc_start: 0.7854 (mtm110) cc_final: 0.7088 (ttt-90) REVERT: C 306 GLN cc_start: 0.7776 (mt0) cc_final: 0.7274 (mp10) REVERT: C 318 SER cc_start: 0.8661 (OUTLIER) cc_final: 0.8275 (m) REVERT: C 381 GLN cc_start: 0.6809 (mp10) cc_final: 0.5867 (mm-40) REVERT: C 421 LEU cc_start: 0.8628 (mm) cc_final: 0.8315 (mp) REVERT: C 448 ASN cc_start: 0.8026 (t0) cc_final: 0.7813 (t0) REVERT: C 491 MET cc_start: 0.7913 (mmm) cc_final: 0.7364 (mmp) REVERT: D 35 ARG cc_start: 0.8031 (ttt90) cc_final: 0.7784 (tpt-90) REVERT: D 80 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7618 (pt0) REVERT: D 93 GLU cc_start: 0.7570 (mp0) cc_final: 0.7185 (mp0) REVERT: D 108 GLU cc_start: 0.7600 (mm-30) cc_final: 0.7278 (mm-30) REVERT: D 184 GLU cc_start: 0.7533 (mt-10) cc_final: 0.7271 (tp30) REVERT: D 190 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7590 (mtm180) REVERT: D 214 GLN cc_start: 0.7964 (mm-40) cc_final: 0.7591 (mt0) REVERT: D 302 ARG cc_start: 0.7861 (mtm110) cc_final: 0.7152 (ttt-90) REVERT: D 306 GLN cc_start: 0.7774 (mt0) cc_final: 0.7270 (mp10) REVERT: D 318 SER cc_start: 0.8670 (t) cc_final: 0.8285 (m) REVERT: D 381 GLN cc_start: 0.6800 (mp10) cc_final: 0.5864 (mm-40) REVERT: D 421 LEU cc_start: 0.8699 (mm) cc_final: 0.8377 (mp) REVERT: D 487 PHE cc_start: 0.8846 (m-10) cc_final: 0.8617 (m-10) REVERT: D 491 MET cc_start: 0.7910 (mmm) cc_final: 0.7358 (mmp) outliers start: 40 outliers final: 22 residues processed: 331 average time/residue: 1.3635 time to fit residues: 508.1137 Evaluate side-chains 329 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 297 time to evaluate : 2.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 190 ARG Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 335 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 57 optimal weight: 0.7980 chunk 147 optimal weight: 1.9990 chunk 75 optimal weight: 6.9990 chunk 101 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 71 optimal weight: 8.9990 chunk 127 optimal weight: 0.5980 chunk 121 optimal weight: 0.6980 chunk 111 optimal weight: 2.9990 chunk 119 optimal weight: 6.9990 chunk 106 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN A 261 GLN B 40 GLN B 261 GLN C 261 GLN D 74 GLN D 261 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.150005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.112881 restraints weight = 21822.491| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 1.55 r_work: 0.3071 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20352 Z= 0.114 Angle : 0.509 6.431 27612 Z= 0.259 Chirality : 0.038 0.162 3128 Planarity : 0.004 0.055 3424 Dihedral : 8.257 73.844 3428 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.73 % Allowed : 11.63 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.17), residues: 2384 helix: 1.87 (0.13), residues: 1536 sheet: -1.47 (0.51), residues: 80 loop : 1.25 (0.25), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 593 HIS 0.003 0.001 HIS D 201 PHE 0.016 0.001 PHE A 611 TYR 0.010 0.001 TYR A 555 ARG 0.014 0.000 ARG B 409 Details of bonding type rmsd hydrogen bonds : bond 0.04011 ( 1189) hydrogen bonds : angle 3.84422 ( 3315) covalent geometry : bond 0.00262 (20352) covalent geometry : angle 0.50905 (27612) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 304 time to evaluate : 2.069 Fit side-chains REVERT: A 35 ARG cc_start: 0.8149 (ttt90) cc_final: 0.7930 (tpt-90) REVERT: A 93 GLU cc_start: 0.7581 (mp0) cc_final: 0.7294 (mp0) REVERT: A 108 GLU cc_start: 0.7538 (mm-30) cc_final: 0.7251 (mm-30) REVERT: A 139 ARG cc_start: 0.8109 (mtp180) cc_final: 0.7844 (mtp85) REVERT: A 214 GLN cc_start: 0.7979 (mm-40) cc_final: 0.7639 (mt0) REVERT: A 215 MET cc_start: 0.8784 (mmm) cc_final: 0.8535 (mmt) REVERT: A 302 ARG cc_start: 0.7834 (mtm110) cc_final: 0.7163 (ttt-90) REVERT: A 306 GLN cc_start: 0.7790 (mt0) cc_final: 0.7322 (mp10) REVERT: A 318 SER cc_start: 0.8667 (OUTLIER) cc_final: 0.8340 (m) REVERT: A 381 GLN cc_start: 0.6838 (mp10) cc_final: 0.5905 (mm-40) REVERT: A 421 LEU cc_start: 0.8713 (mm) cc_final: 0.8409 (mp) REVERT: A 487 PHE cc_start: 0.8850 (m-10) cc_final: 0.8612 (m-10) REVERT: A 491 MET cc_start: 0.7971 (mmm) cc_final: 0.7457 (mmp) REVERT: B 40 GLN cc_start: 0.7829 (OUTLIER) cc_final: 0.7593 (mt0) REVERT: B 80 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7686 (pt0) REVERT: B 93 GLU cc_start: 0.7611 (mp0) cc_final: 0.7252 (mp0) REVERT: B 107 LYS cc_start: 0.7622 (mtmm) cc_final: 0.7270 (mtpp) REVERT: B 108 GLU cc_start: 0.7524 (mm-30) cc_final: 0.7238 (mm-30) REVERT: B 139 ARG cc_start: 0.8158 (mtp180) cc_final: 0.7876 (mtp85) REVERT: B 184 GLU cc_start: 0.7514 (mt-10) cc_final: 0.7301 (tp30) REVERT: B 214 GLN cc_start: 0.8004 (mm-40) cc_final: 0.7668 (mt0) REVERT: B 302 ARG cc_start: 0.7876 (mtm110) cc_final: 0.7189 (ttt-90) REVERT: B 306 GLN cc_start: 0.7777 (mt0) cc_final: 0.7311 (mp10) REVERT: B 318 SER cc_start: 0.8712 (OUTLIER) cc_final: 0.8344 (m) REVERT: B 381 GLN cc_start: 0.6858 (mp10) cc_final: 0.5912 (mm-40) REVERT: B 421 LEU cc_start: 0.8675 (mm) cc_final: 0.8386 (mp) REVERT: B 491 MET cc_start: 0.7984 (mmm) cc_final: 0.7472 (mmp) REVERT: C 35 ARG cc_start: 0.8104 (ttt90) cc_final: 0.7887 (tpt-90) REVERT: C 57 ASP cc_start: 0.7900 (p0) cc_final: 0.7661 (p0) REVERT: C 80 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7675 (pt0) REVERT: C 93 GLU cc_start: 0.7604 (mp0) cc_final: 0.7253 (mp0) REVERT: C 107 LYS cc_start: 0.7631 (mtmm) cc_final: 0.7284 (mtpp) REVERT: C 108 GLU cc_start: 0.7511 (mm-30) cc_final: 0.7234 (mm-30) REVERT: C 139 ARG cc_start: 0.8121 (mtp180) cc_final: 0.7829 (mtp85) REVERT: C 214 GLN cc_start: 0.7993 (mm-40) cc_final: 0.7666 (mt0) REVERT: C 302 ARG cc_start: 0.7909 (mtm110) cc_final: 0.7199 (ttt-90) REVERT: C 306 GLN cc_start: 0.7792 (mt0) cc_final: 0.7337 (mp10) REVERT: C 318 SER cc_start: 0.8699 (OUTLIER) cc_final: 0.8334 (m) REVERT: C 381 GLN cc_start: 0.6859 (mp10) cc_final: 0.5912 (mm-40) REVERT: C 421 LEU cc_start: 0.8702 (mm) cc_final: 0.8413 (mp) REVERT: C 448 ASN cc_start: 0.8010 (t0) cc_final: 0.7806 (t0) REVERT: C 491 MET cc_start: 0.7977 (mmm) cc_final: 0.7465 (mmp) REVERT: D 35 ARG cc_start: 0.8105 (ttt90) cc_final: 0.7889 (tpt-90) REVERT: D 80 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7682 (pt0) REVERT: D 93 GLU cc_start: 0.7597 (mp0) cc_final: 0.7252 (mp0) REVERT: D 107 LYS cc_start: 0.7628 (mtmm) cc_final: 0.7272 (mtpp) REVERT: D 108 GLU cc_start: 0.7530 (mm-30) cc_final: 0.7253 (mm-30) REVERT: D 139 ARG cc_start: 0.8147 (mtp180) cc_final: 0.7859 (mtp85) REVERT: D 190 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7597 (mtm180) REVERT: D 214 GLN cc_start: 0.7988 (mm-40) cc_final: 0.7650 (mt0) REVERT: D 302 ARG cc_start: 0.7895 (mtm110) cc_final: 0.7199 (ttt-90) REVERT: D 306 GLN cc_start: 0.7785 (mt0) cc_final: 0.7327 (mp10) REVERT: D 318 SER cc_start: 0.8707 (OUTLIER) cc_final: 0.8343 (m) REVERT: D 381 GLN cc_start: 0.6836 (mp10) cc_final: 0.5915 (mm-40) REVERT: D 421 LEU cc_start: 0.8731 (mm) cc_final: 0.8438 (mp) REVERT: D 487 PHE cc_start: 0.8838 (m-10) cc_final: 0.8606 (m-10) REVERT: D 491 MET cc_start: 0.7968 (mmm) cc_final: 0.7451 (mmp) outliers start: 36 outliers final: 23 residues processed: 328 average time/residue: 1.3252 time to fit residues: 489.4595 Evaluate side-chains 325 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 293 time to evaluate : 2.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 129 ASN Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain B residue 40 GLN Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 190 ARG Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 318 SER Chi-restraints excluded: chain D residue 335 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 239 optimal weight: 6.9990 chunk 9 optimal weight: 7.9990 chunk 114 optimal weight: 0.9980 chunk 120 optimal weight: 10.0000 chunk 68 optimal weight: 0.0970 chunk 4 optimal weight: 0.9980 chunk 94 optimal weight: 5.9990 chunk 234 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 overall best weight: 1.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN B 40 GLN B 74 GLN B 261 GLN C 74 GLN C 261 GLN D 74 GLN D 261 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.146838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.109477 restraints weight = 21845.504| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 1.54 r_work: 0.3032 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 20352 Z= 0.163 Angle : 0.572 7.939 27612 Z= 0.289 Chirality : 0.041 0.241 3128 Planarity : 0.004 0.062 3424 Dihedral : 8.522 75.902 3428 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.12 % Allowed : 12.50 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.17), residues: 2384 helix: 1.71 (0.13), residues: 1532 sheet: -1.38 (0.53), residues: 80 loop : 1.16 (0.25), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 593 HIS 0.004 0.001 HIS A 201 PHE 0.015 0.002 PHE A 611 TYR 0.012 0.001 TYR D 89 ARG 0.014 0.001 ARG B 409 Details of bonding type rmsd hydrogen bonds : bond 0.04464 ( 1189) hydrogen bonds : angle 3.97201 ( 3315) covalent geometry : bond 0.00400 (20352) covalent geometry : angle 0.57230 (27612) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 300 time to evaluate : 2.342 Fit side-chains REVERT: A 93 GLU cc_start: 0.7534 (mp0) cc_final: 0.7247 (mp0) REVERT: A 108 GLU cc_start: 0.7539 (mm-30) cc_final: 0.7244 (mm-30) REVERT: A 214 GLN cc_start: 0.7973 (mm-40) cc_final: 0.7651 (mt0) REVERT: A 215 MET cc_start: 0.8784 (mmm) cc_final: 0.8534 (mmt) REVERT: A 306 GLN cc_start: 0.7842 (mt0) cc_final: 0.7382 (mp10) REVERT: A 318 SER cc_start: 0.8685 (OUTLIER) cc_final: 0.8314 (m) REVERT: A 381 GLN cc_start: 0.6908 (mp10) cc_final: 0.5945 (mm-40) REVERT: A 421 LEU cc_start: 0.8711 (mm) cc_final: 0.8413 (mp) REVERT: A 491 MET cc_start: 0.7999 (mmm) cc_final: 0.7498 (mmp) REVERT: B 57 ASP cc_start: 0.7860 (p0) cc_final: 0.7622 (p0) REVERT: B 80 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7811 (pt0) REVERT: B 93 GLU cc_start: 0.7607 (mp0) cc_final: 0.7236 (mp0) REVERT: B 108 GLU cc_start: 0.7527 (mm-30) cc_final: 0.7234 (mm-30) REVERT: B 139 ARG cc_start: 0.8042 (mtp180) cc_final: 0.7776 (mtp85) REVERT: B 184 GLU cc_start: 0.7556 (mt-10) cc_final: 0.7336 (tp30) REVERT: B 214 GLN cc_start: 0.7984 (mm-40) cc_final: 0.7664 (mt0) REVERT: B 302 ARG cc_start: 0.7881 (mtm110) cc_final: 0.7195 (ttt-90) REVERT: B 306 GLN cc_start: 0.7837 (mt0) cc_final: 0.7364 (mp10) REVERT: B 381 GLN cc_start: 0.6895 (mp10) cc_final: 0.5943 (mm-40) REVERT: B 421 LEU cc_start: 0.8704 (mm) cc_final: 0.8414 (mp) REVERT: B 491 MET cc_start: 0.8008 (mmm) cc_final: 0.7505 (mmp) REVERT: C 35 ARG cc_start: 0.8125 (ttt90) cc_final: 0.7892 (tpt-90) REVERT: C 57 ASP cc_start: 0.7960 (p0) cc_final: 0.7718 (p0) REVERT: C 93 GLU cc_start: 0.7591 (mp0) cc_final: 0.7239 (mp0) REVERT: C 107 LYS cc_start: 0.7636 (mtmm) cc_final: 0.7321 (mtpp) REVERT: C 108 GLU cc_start: 0.7530 (mm-30) cc_final: 0.7235 (mm-30) REVERT: C 139 ARG cc_start: 0.8069 (mtp180) cc_final: 0.7766 (mtp85) REVERT: C 214 GLN cc_start: 0.7993 (mm-40) cc_final: 0.7666 (mt0) REVERT: C 302 ARG cc_start: 0.7923 (mtm110) cc_final: 0.7206 (ttt-90) REVERT: C 306 GLN cc_start: 0.7848 (mt0) cc_final: 0.7382 (mp10) REVERT: C 381 GLN cc_start: 0.6887 (mp10) cc_final: 0.5936 (mm-40) REVERT: C 421 LEU cc_start: 0.8695 (mm) cc_final: 0.8430 (mp) REVERT: C 491 MET cc_start: 0.8000 (mmm) cc_final: 0.7499 (mmp) REVERT: D 35 ARG cc_start: 0.8126 (ttt90) cc_final: 0.7891 (tpt-90) REVERT: D 57 ASP cc_start: 0.7915 (p0) cc_final: 0.7675 (p0) REVERT: D 80 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7763 (pt0) REVERT: D 93 GLU cc_start: 0.7597 (mp0) cc_final: 0.7305 (mp0) REVERT: D 107 LYS cc_start: 0.7650 (mtmm) cc_final: 0.7323 (mtpp) REVERT: D 108 GLU cc_start: 0.7546 (mm-30) cc_final: 0.7247 (mm-30) REVERT: D 139 ARG cc_start: 0.8064 (mtp180) cc_final: 0.7770 (mtp85) REVERT: D 190 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.7697 (mtm180) REVERT: D 214 GLN cc_start: 0.7985 (mm-40) cc_final: 0.7644 (mt0) REVERT: D 306 GLN cc_start: 0.7860 (mt0) cc_final: 0.7394 (mp10) REVERT: D 381 GLN cc_start: 0.6902 (mp10) cc_final: 0.5952 (mm-40) REVERT: D 421 LEU cc_start: 0.8757 (mm) cc_final: 0.8460 (mp) REVERT: D 487 PHE cc_start: 0.8896 (m-10) cc_final: 0.8649 (m-10) REVERT: D 491 MET cc_start: 0.7994 (mmm) cc_final: 0.7493 (mmp) outliers start: 44 outliers final: 28 residues processed: 336 average time/residue: 1.3292 time to fit residues: 508.9217 Evaluate side-chains 327 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 295 time to evaluate : 2.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 190 ARG Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 318 SER Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 514 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 57 optimal weight: 0.2980 chunk 152 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 50 optimal weight: 0.3980 chunk 16 optimal weight: 0.7980 chunk 157 optimal weight: 3.9990 chunk 177 optimal weight: 0.9980 chunk 147 optimal weight: 0.5980 chunk 146 optimal weight: 0.7980 chunk 12 optimal weight: 5.9990 chunk 108 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN A 74 GLN A 261 GLN B 40 GLN B 261 GLN C 40 GLN C 74 GLN C 261 GLN D 40 GLN D 261 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.150720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.113861 restraints weight = 21867.767| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.53 r_work: 0.3082 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 20352 Z= 0.112 Angle : 0.521 7.950 27612 Z= 0.266 Chirality : 0.038 0.214 3128 Planarity : 0.004 0.062 3424 Dihedral : 8.290 73.447 3428 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.54 % Allowed : 12.74 % Favored : 85.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.17), residues: 2384 helix: 1.83 (0.13), residues: 1532 sheet: -1.58 (0.50), residues: 80 loop : 1.25 (0.25), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 593 HIS 0.002 0.001 HIS A 201 PHE 0.017 0.001 PHE A 611 TYR 0.010 0.001 TYR A 555 ARG 0.015 0.001 ARG B 409 Details of bonding type rmsd hydrogen bonds : bond 0.03951 ( 1189) hydrogen bonds : angle 3.93858 ( 3315) covalent geometry : bond 0.00257 (20352) covalent geometry : angle 0.52078 (27612) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14841.67 seconds wall clock time: 253 minutes 19.82 seconds (15199.82 seconds total)