Starting phenix.real_space_refine on Sun Aug 24 13:42:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tf3_41218/08_2025/8tf3_41218_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tf3_41218/08_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_41218/08_2025/8tf3_41218.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tf3_41218/08_2025/8tf3_41218.map" model { file = "/net/cci-nas-00/data/ceres_data/8tf3_41218/08_2025/8tf3_41218_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tf3_41218/08_2025/8tf3_41218_neut.cif" } resolution = 2.94 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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-1': 1, 'CPL:plan-2': 1, 'CPL:plan-3': 1, 'CPL:plan-4': 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-1': 1, 'CPL:plan-2': 1, 'CPL:plan-3': 1, 'CPL:plan-4': 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-1': 1, 'CPL:plan-2': 1, 'CPL:plan-3': 1, 'CPL:plan-4': 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-1': 1, 'CPL:plan-2': 1, 'CPL:plan-3': 1, 'CPL:plan-4': 1} Unresolved non-hydrogen planarities: 14 Restraints were copied for chains: B, C, D Time building chain proxies: 4.64, per 1000 atoms: 0.23 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: 1.95 Conformation dependent library (CDL) restraints added in 789.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.80 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: 3.56 Time building geometry restraints manager: 2.54 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: 0.02 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: 1.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.030 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.990 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.009 0.001 ARG D 492 TYR 0.110 0.020 TYR B 432 PHE 0.058 0.011 PHE C 256 TRP 0.147 0.021 TRP C 593 HIS 0.011 0.003 HIS A 238 Details of bonding type rmsd covalent geometry : bond 0.01202 (20352) covalent geometry : angle 1.79784 (27612) hydrogen bonds : bond 0.16942 ( 1189) hydrogen bonds : angle 6.73925 ( 3315) *********************** 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 : 0.720 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: 0.6609 time to fit residues: 305.1844 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 : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.8980 chunk 227 optimal weight: 0.7980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 chunk 235 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3640 r_free = 0.3640 target = 0.151726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.115842 restraints weight = 21813.075| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 1.52 r_work: 0.3097 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2018 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= 0.137 Angle : 0.579 5.823 27612 Z= 0.302 Chirality : 0.040 0.150 3128 Planarity : 0.004 0.030 3424 Dihedral : 10.729 95.817 3428 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 1.44 % Allowed : 7.16 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.39 (0.17), residues: 2384 helix: 1.16 (0.13), residues: 1508 sheet: 0.63 (0.51), residues: 88 loop : 0.76 (0.24), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 355 TYR 0.017 0.002 TYR C 555 PHE 0.016 0.002 PHE B 456 TRP 0.021 0.002 TRP B 593 HIS 0.003 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00305 (20352) covalent geometry : angle 0.57905 (27612) hydrogen bonds : bond 0.04906 ( 1189) hydrogen bonds : angle 4.28383 ( 3315) *********************** 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 387 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 357 time to evaluate : 0.531 Fit side-chains REVERT: A 35 ARG cc_start: 0.8038 (ttt-90) cc_final: 0.7801 (ttt90) REVERT: A 93 GLU cc_start: 0.7636 (mp0) cc_final: 0.7320 (mp0) REVERT: A 173 VAL cc_start: 0.8577 (t) cc_final: 0.8250 (m) REVERT: A 184 GLU cc_start: 0.7564 (mt-10) cc_final: 0.7343 (tp30) REVERT: A 214 GLN cc_start: 0.8046 (mm-40) cc_final: 0.7730 (mt0) REVERT: A 302 ARG cc_start: 0.7805 (mtm110) cc_final: 0.7443 (ttp80) REVERT: A 306 GLN cc_start: 0.7951 (mt0) cc_final: 0.7461 (mp10) REVERT: A 381 GLN cc_start: 0.6987 (mp10) cc_final: 0.6019 (mm-40) REVERT: A 448 ASN cc_start: 0.7970 (t0) cc_final: 0.7769 (t0) REVERT: A 491 MET cc_start: 0.7955 (mmm) cc_final: 0.7504 (mmp) REVERT: B 35 ARG cc_start: 0.8036 (ttt-90) cc_final: 0.7783 (ttt90) REVERT: B 93 GLU cc_start: 0.7673 (mp0) cc_final: 0.7327 (mp0) REVERT: B 173 VAL cc_start: 0.8573 (t) cc_final: 0.8274 (m) REVERT: B 184 GLU cc_start: 0.7638 (mt-10) cc_final: 0.7363 (tp30) REVERT: B 214 GLN cc_start: 0.8047 (mm-40) cc_final: 0.7715 (mt0) REVERT: B 302 ARG cc_start: 0.7793 (mtm110) cc_final: 0.7449 (ttp80) REVERT: B 306 GLN cc_start: 0.7978 (mt0) cc_final: 0.7488 (mp10) REVERT: B 381 GLN cc_start: 0.7015 (mp10) cc_final: 0.6044 (mm-40) REVERT: B 382 ASP cc_start: 0.8266 (m-30) cc_final: 0.8057 (m-30) REVERT: B 421 LEU cc_start: 0.8614 (mp) cc_final: 0.8412 (mm) REVERT: B 448 ASN cc_start: 0.7968 (t0) cc_final: 0.7766 (t0) REVERT: B 491 MET cc_start: 0.7961 (mmm) cc_final: 0.7517 (mmp) REVERT: C 35 ARG cc_start: 0.8043 (ttt-90) cc_final: 0.7791 (ttt90) REVERT: C 93 GLU cc_start: 0.7674 (mp0) cc_final: 0.7335 (mp0) REVERT: C 173 VAL cc_start: 0.8581 (t) cc_final: 0.8282 (m) REVERT: C 184 GLU cc_start: 0.7646 (mt-10) cc_final: 0.7364 (tp30) REVERT: C 214 GLN cc_start: 0.8033 (mm-40) cc_final: 0.7712 (mt0) REVERT: C 302 ARG cc_start: 0.7792 (mtm110) cc_final: 0.7445 (ttp80) REVERT: C 306 GLN cc_start: 0.7984 (mt0) cc_final: 0.7490 (mp10) REVERT: C 381 GLN cc_start: 0.6994 (mp10) cc_final: 0.6031 (mm-40) REVERT: C 448 ASN cc_start: 0.7966 (t0) cc_final: 0.7760 (t0) REVERT: C 491 MET cc_start: 0.7955 (mmm) cc_final: 0.7512 (mmp) REVERT: D 35 ARG cc_start: 0.8064 (ttt-90) cc_final: 0.7811 (ttt90) REVERT: D 93 GLU cc_start: 0.7661 (mp0) cc_final: 0.7312 (mp0) REVERT: D 173 VAL cc_start: 0.8566 (t) cc_final: 0.8271 (m) REVERT: D 184 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7364 (tp30) REVERT: D 214 GLN cc_start: 0.8043 (mm-40) cc_final: 0.7700 (mt0) REVERT: D 302 ARG cc_start: 0.7790 (mtm110) cc_final: 0.7446 (ttp80) REVERT: D 306 GLN cc_start: 0.7976 (mt0) cc_final: 0.7492 (mp10) REVERT: D 381 GLN cc_start: 0.6990 (mp10) cc_final: 0.6059 (mm-40) REVERT: D 421 LEU cc_start: 0.8618 (mp) cc_final: 0.8416 (mm) REVERT: D 491 MET cc_start: 0.7949 (mmm) cc_final: 0.7500 (mmp) outliers start: 30 outliers final: 20 residues processed: 369 average time/residue: 0.5975 time to fit residues: 248.4988 Evaluate side-chains 322 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 302 time to evaluate : 0.760 ------------------------------------------------------------------------------- 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 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 B residue 143 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 603 MET 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 335 LEU 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 143 VAL Chi-restraints excluded: chain D residue 335 LEU 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 218 optimal weight: 5.9990 chunk 113 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 206 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 145 optimal weight: 0.0070 chunk 87 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 chunk 131 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 overall best weight: 0.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.158956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.123459 restraints weight = 21688.370| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.46 r_work: 0.3103 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20352 Z= 0.119 Angle : 0.513 5.714 27612 Z= 0.264 Chirality : 0.038 0.145 3128 Planarity : 0.004 0.034 3424 Dihedral : 9.407 80.216 3428 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 1.92 % Allowed : 9.42 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.03 (0.17), residues: 2384 helix: 1.77 (0.13), residues: 1508 sheet: 0.08 (0.52), residues: 88 loop : 0.88 (0.24), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 139 TYR 0.012 0.001 TYR A 555 PHE 0.017 0.002 PHE C 211 TRP 0.017 0.001 TRP B 593 HIS 0.004 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00267 (20352) covalent geometry : angle 0.51258 (27612) hydrogen bonds : bond 0.04289 ( 1189) hydrogen bonds : angle 3.98082 ( 3315) *********************** 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 379 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 339 time to evaluate : 0.669 Fit side-chains REVERT: A 80 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8414 (pm20) REVERT: A 93 GLU cc_start: 0.7636 (mp0) cc_final: 0.7263 (mp0) REVERT: A 173 VAL cc_start: 0.8477 (t) cc_final: 0.8272 (m) REVERT: A 184 GLU cc_start: 0.7572 (mt-10) cc_final: 0.7316 (tp30) REVERT: A 190 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7505 (mtm180) REVERT: A 214 GLN cc_start: 0.8006 (mm-40) cc_final: 0.7672 (mt0) REVERT: A 302 ARG cc_start: 0.7800 (mtm110) cc_final: 0.7438 (ttp80) REVERT: A 306 GLN cc_start: 0.7886 (mt0) cc_final: 0.7342 (mp10) REVERT: A 381 GLN cc_start: 0.6968 (mp10) cc_final: 0.6008 (mm-40) REVERT: A 421 LEU cc_start: 0.8665 (mm) cc_final: 0.8387 (mp) REVERT: A 448 ASN cc_start: 0.7953 (t0) cc_final: 0.7750 (t0) REVERT: A 491 MET cc_start: 0.7856 (mmm) cc_final: 0.7332 (mmp) REVERT: B 93 GLU cc_start: 0.7625 (mp0) cc_final: 0.7237 (mp0) REVERT: B 184 GLU cc_start: 0.7621 (mt-10) cc_final: 0.7327 (tp30) REVERT: B 190 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.7506 (mtm180) REVERT: B 214 GLN cc_start: 0.8012 (mm-40) cc_final: 0.7675 (mt0) REVERT: B 302 ARG cc_start: 0.7784 (mtm110) cc_final: 0.7446 (ttp80) REVERT: B 306 GLN cc_start: 0.7887 (mt0) cc_final: 0.7350 (mp10) REVERT: B 381 GLN cc_start: 0.6939 (mp10) cc_final: 0.5938 (mm-40) REVERT: B 491 MET cc_start: 0.7864 (mmm) cc_final: 0.7342 (mmp) REVERT: C 93 GLU cc_start: 0.7636 (mp0) cc_final: 0.7247 (mp0) REVERT: C 184 GLU cc_start: 0.7626 (mt-10) cc_final: 0.7340 (tp30) REVERT: C 190 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7518 (mtm180) REVERT: C 214 GLN cc_start: 0.8036 (mm-40) cc_final: 0.7691 (mt0) REVERT: C 302 ARG cc_start: 0.7787 (mtm110) cc_final: 0.7445 (ttp80) REVERT: C 306 GLN cc_start: 0.7901 (mt0) cc_final: 0.7363 (mp10) REVERT: C 381 GLN cc_start: 0.6946 (mp10) cc_final: 0.5985 (mm-40) REVERT: C 421 LEU cc_start: 0.8646 (mm) cc_final: 0.8362 (mp) REVERT: C 448 ASN cc_start: 0.7956 (t0) cc_final: 0.7752 (t0) REVERT: C 491 MET cc_start: 0.7842 (mmm) cc_final: 0.7319 (mmp) REVERT: D 93 GLU cc_start: 0.7639 (mp0) cc_final: 0.7270 (mp0) REVERT: D 184 GLU cc_start: 0.7624 (mt-10) cc_final: 0.7352 (tp30) REVERT: D 190 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.7506 (mtm180) REVERT: D 214 GLN cc_start: 0.8022 (mm-40) cc_final: 0.7679 (mt0) REVERT: D 302 ARG cc_start: 0.7791 (mtm110) cc_final: 0.7450 (ttp80) REVERT: D 306 GLN cc_start: 0.7907 (mt0) cc_final: 0.7370 (mp10) REVERT: D 381 GLN cc_start: 0.6949 (mp10) cc_final: 0.5986 (mm-40) REVERT: D 491 MET cc_start: 0.7841 (mmm) cc_final: 0.7310 (mmp) outliers start: 40 outliers final: 8 residues processed: 364 average time/residue: 0.6169 time to fit residues: 252.6980 Evaluate side-chains 313 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 300 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 548 SER Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 548 SER Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 190 ARG Chi-restraints excluded: chain D residue 548 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 185 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 196 optimal weight: 9.9990 chunk 96 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 234 optimal weight: 2.9990 chunk 204 optimal weight: 6.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.151977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.116195 restraints weight = 21930.698| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 1.45 r_work: 0.3053 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20352 Z= 0.144 Angle : 0.529 5.812 27612 Z= 0.269 Chirality : 0.039 0.154 3128 Planarity : 0.004 0.035 3424 Dihedral : 8.777 80.044 3428 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.78 % Allowed : 11.01 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.95 (0.17), residues: 2384 helix: 1.66 (0.13), residues: 1540 sheet: -0.47 (0.53), residues: 80 loop : 0.97 (0.24), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 35 TYR 0.012 0.001 TYR A 89 PHE 0.015 0.002 PHE C 534 TRP 0.013 0.001 TRP A 593 HIS 0.005 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00341 (20352) covalent geometry : angle 0.52897 (27612) hydrogen bonds : bond 0.04472 ( 1189) hydrogen bonds : angle 3.94510 ( 3315) *********************** 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 361 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 324 time to evaluate : 0.749 Fit side-chains REVERT: A 35 ARG cc_start: 0.8207 (ttt90) cc_final: 0.7891 (tpt-90) REVERT: A 80 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8349 (pm20) REVERT: A 93 GLU cc_start: 0.7623 (mp0) cc_final: 0.7307 (mp0) REVERT: A 173 VAL cc_start: 0.8539 (t) cc_final: 0.8270 (m) REVERT: A 184 GLU cc_start: 0.7612 (mt-10) cc_final: 0.7389 (tp30) REVERT: A 190 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7681 (mtm180) REVERT: A 214 GLN cc_start: 0.8001 (mm-40) cc_final: 0.7697 (mt0) REVERT: A 306 GLN cc_start: 0.7911 (mt0) cc_final: 0.7440 (mp10) REVERT: A 381 GLN cc_start: 0.6948 (mp10) cc_final: 0.5990 (mm-40) REVERT: A 421 LEU cc_start: 0.8755 (mm) cc_final: 0.8426 (mp) REVERT: A 448 ASN cc_start: 0.8024 (t0) cc_final: 0.7810 (t0) REVERT: A 487 PHE cc_start: 0.8921 (m-10) cc_final: 0.8714 (m-10) REVERT: A 491 MET cc_start: 0.7898 (mmm) cc_final: 0.7380 (mmp) REVERT: B 93 GLU cc_start: 0.7633 (mp0) cc_final: 0.7314 (mp0) REVERT: B 184 GLU cc_start: 0.7636 (mt-10) cc_final: 0.7353 (tp30) REVERT: B 190 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.7688 (mtm180) REVERT: B 214 GLN cc_start: 0.8009 (mm-40) cc_final: 0.7706 (mt0) REVERT: B 302 ARG cc_start: 0.7759 (mtm110) cc_final: 0.7527 (mtp-110) REVERT: B 306 GLN cc_start: 0.7863 (mt0) cc_final: 0.7402 (mp10) REVERT: B 381 GLN cc_start: 0.6917 (mp10) cc_final: 0.5961 (mm-40) REVERT: B 487 PHE cc_start: 0.8916 (m-10) cc_final: 0.8714 (m-10) REVERT: B 491 MET cc_start: 0.7892 (mmm) cc_final: 0.7379 (mmp) REVERT: C 93 GLU cc_start: 0.7645 (mp0) cc_final: 0.7252 (mp0) REVERT: C 184 GLU cc_start: 0.7650 (mt-10) cc_final: 0.7356 (tp30) REVERT: C 190 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7684 (mtm180) REVERT: C 214 GLN cc_start: 0.8010 (mm-40) cc_final: 0.7700 (mt0) REVERT: C 302 ARG cc_start: 0.7790 (mtm110) cc_final: 0.7548 (mtp-110) REVERT: C 306 GLN cc_start: 0.7865 (mt0) cc_final: 0.7410 (mp10) REVERT: C 381 GLN cc_start: 0.6950 (mp10) cc_final: 0.5980 (mm-40) REVERT: C 421 LEU cc_start: 0.8732 (mm) cc_final: 0.8410 (mp) REVERT: C 448 ASN cc_start: 0.8025 (t0) cc_final: 0.7817 (t0) REVERT: C 487 PHE cc_start: 0.8914 (m-10) cc_final: 0.8713 (m-10) REVERT: C 491 MET cc_start: 0.7893 (mmm) cc_final: 0.7382 (mmp) REVERT: D 93 GLU cc_start: 0.7636 (mp0) cc_final: 0.7314 (mp0) REVERT: D 184 GLU cc_start: 0.7630 (mt-10) cc_final: 0.7349 (tp30) REVERT: D 190 ARG cc_start: 0.8231 (OUTLIER) cc_final: 0.7685 (mtm180) REVERT: D 214 GLN cc_start: 0.8012 (mm-40) cc_final: 0.7693 (mt0) REVERT: D 215 MET cc_start: 0.8826 (mmm) cc_final: 0.8530 (mmt) REVERT: D 302 ARG cc_start: 0.7777 (mtm110) cc_final: 0.7544 (mtp-110) REVERT: D 306 GLN cc_start: 0.7865 (mt0) cc_final: 0.7408 (mp10) REVERT: D 381 GLN cc_start: 0.6954 (mp10) cc_final: 0.5990 (mm-40) REVERT: D 487 PHE cc_start: 0.8921 (m-10) cc_final: 0.8716 (m-10) REVERT: D 491 MET cc_start: 0.7872 (mmm) cc_final: 0.7361 (mmp) outliers start: 37 outliers final: 17 residues processed: 352 average time/residue: 0.6256 time to fit residues: 248.3117 Evaluate side-chains 325 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 303 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 318 SER 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 318 SER Chi-restraints excluded: chain B residue 335 LEU 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 318 SER Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 514 THR 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 318 SER Chi-restraints excluded: chain D residue 335 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 155 optimal weight: 1.9990 chunk 160 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 234 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 206 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 173 optimal weight: 0.8980 chunk 190 optimal weight: 0.1980 chunk 124 optimal weight: 7.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- 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 = 0.3582 r_free = 0.3582 target = 0.147229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.108982 restraints weight = 22024.736| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 1.63 r_work: 0.3013 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20352 Z= 0.146 Angle : 0.525 5.811 27612 Z= 0.268 Chirality : 0.039 0.150 3128 Planarity : 0.004 0.047 3424 Dihedral : 8.718 80.027 3428 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.21 % Allowed : 10.43 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.95 (0.17), residues: 2384 helix: 1.68 (0.13), residues: 1540 sheet: -0.81 (0.53), residues: 80 loop : 0.94 (0.24), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 409 TYR 0.012 0.001 TYR A 89 PHE 0.014 0.001 PHE C 534 TRP 0.013 0.001 TRP D 593 HIS 0.004 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00348 (20352) covalent geometry : angle 0.52514 (27612) hydrogen bonds : bond 0.04445 ( 1189) hydrogen bonds : angle 3.93071 ( 3315) *********************** 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 364 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 318 time to evaluate : 0.877 Fit side-chains REVERT: A 35 ARG cc_start: 0.8163 (ttt90) cc_final: 0.7872 (tpt-90) REVERT: A 80 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.8286 (pm20) REVERT: A 93 GLU cc_start: 0.7602 (mp0) cc_final: 0.7227 (mp0) REVERT: A 173 VAL cc_start: 0.8459 (t) cc_final: 0.8194 (m) REVERT: A 184 GLU cc_start: 0.7618 (mt-10) cc_final: 0.7341 (tp30) REVERT: A 190 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.7733 (mtm180) REVERT: A 214 GLN cc_start: 0.7958 (mm-40) cc_final: 0.7613 (mt0) REVERT: A 215 MET cc_start: 0.8749 (mmm) cc_final: 0.8461 (mmt) REVERT: A 302 ARG cc_start: 0.7591 (mtp-110) cc_final: 0.7140 (ttp80) REVERT: A 306 GLN cc_start: 0.7892 (mt0) cc_final: 0.7373 (mp10) REVERT: A 381 GLN cc_start: 0.6856 (mp10) cc_final: 0.5862 (mm-40) REVERT: A 421 LEU cc_start: 0.8739 (mm) cc_final: 0.8397 (mp) REVERT: A 448 ASN cc_start: 0.8046 (t0) cc_final: 0.7823 (t0) REVERT: A 491 MET cc_start: 0.7919 (mmm) cc_final: 0.7366 (mmp) REVERT: B 35 ARG cc_start: 0.8198 (ttt90) cc_final: 0.7933 (tpt-90) REVERT: B 57 ASP cc_start: 0.7945 (p0) cc_final: 0.7669 (p0) REVERT: B 80 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7629 (pt0) REVERT: B 93 GLU cc_start: 0.7624 (mp0) cc_final: 0.7242 (mp0) REVERT: B 184 GLU cc_start: 0.7634 (mt-10) cc_final: 0.7256 (tp30) REVERT: B 190 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.7784 (mtm180) REVERT: B 214 GLN cc_start: 0.7995 (mm-40) cc_final: 0.7640 (mt0) REVERT: B 215 MET cc_start: 0.8777 (mmm) cc_final: 0.8475 (mmt) REVERT: B 306 GLN cc_start: 0.7860 (mt0) cc_final: 0.7350 (mp10) REVERT: B 381 GLN cc_start: 0.6827 (mp10) cc_final: 0.5872 (mm-40) REVERT: B 491 MET cc_start: 0.7920 (mmm) cc_final: 0.7369 (mmp) REVERT: C 35 ARG cc_start: 0.8185 (ttt90) cc_final: 0.7924 (tpt-90) REVERT: C 57 ASP cc_start: 0.7939 (p0) cc_final: 0.7658 (p0) REVERT: C 93 GLU cc_start: 0.7618 (mp0) cc_final: 0.7238 (mp0) REVERT: C 184 GLU cc_start: 0.7644 (mt-10) cc_final: 0.7274 (tp30) REVERT: C 190 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.7734 (mtm180) REVERT: C 214 GLN cc_start: 0.7994 (mm-40) cc_final: 0.7643 (mt0) REVERT: C 306 GLN cc_start: 0.7878 (mt0) cc_final: 0.7373 (mp10) REVERT: C 381 GLN cc_start: 0.6861 (mp10) cc_final: 0.5896 (mm-40) REVERT: C 421 LEU cc_start: 0.8733 (mm) cc_final: 0.8381 (mp) REVERT: C 448 ASN cc_start: 0.8066 (t0) cc_final: 0.7849 (t0) REVERT: C 491 MET cc_start: 0.7922 (mmm) cc_final: 0.7370 (mmp) REVERT: D 35 ARG cc_start: 0.8204 (ttt90) cc_final: 0.7944 (tpt-90) REVERT: D 80 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7642 (pt0) REVERT: D 93 GLU cc_start: 0.7599 (mp0) cc_final: 0.7216 (mp0) REVERT: D 184 GLU cc_start: 0.7634 (mt-10) cc_final: 0.7267 (tp30) REVERT: D 190 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.7755 (mtm180) REVERT: D 214 GLN cc_start: 0.7975 (mm-40) cc_final: 0.7625 (mt0) REVERT: D 215 MET cc_start: 0.8780 (mmm) cc_final: 0.8444 (mmt) REVERT: D 306 GLN cc_start: 0.7869 (mt0) cc_final: 0.7362 (mp10) REVERT: D 381 GLN cc_start: 0.6869 (mp10) cc_final: 0.5917 (mm-40) REVERT: D 491 MET cc_start: 0.7917 (mmm) cc_final: 0.7363 (mmp) outliers start: 46 outliers final: 25 residues processed: 352 average time/residue: 0.6395 time to fit residues: 254.6038 Evaluate side-chains 344 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 312 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU 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 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 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 64 optimal weight: 10.0000 chunk 195 optimal weight: 10.0000 chunk 170 optimal weight: 0.6980 chunk 214 optimal weight: 7.9990 chunk 139 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 chunk 140 optimal weight: 0.8980 chunk 156 optimal weight: 0.9990 chunk 177 optimal weight: 0.9980 chunk 60 optimal weight: 10.0000 chunk 199 optimal weight: 7.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 B 418 GLN C 261 GLN C 418 GLN D 261 GLN D 418 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.148908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.111444 restraints weight = 21893.064| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.58 r_work: 0.3062 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2914 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= 0.120 Angle : 0.513 5.702 27612 Z= 0.259 Chirality : 0.038 0.149 3128 Planarity : 0.004 0.052 3424 Dihedral : 8.475 78.282 3428 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 2.26 % Allowed : 10.53 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.07 (0.17), residues: 2384 helix: 1.80 (0.13), residues: 1536 sheet: -1.08 (0.52), residues: 80 loop : 0.98 (0.24), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 409 TYR 0.010 0.001 TYR C 555 PHE 0.013 0.001 PHE C 534 TRP 0.014 0.001 TRP D 593 HIS 0.003 0.001 HIS D 201 Details of bonding type rmsd covalent geometry : bond 0.00274 (20352) covalent geometry : angle 0.51342 (27612) hydrogen bonds : bond 0.04137 ( 1189) hydrogen bonds : angle 3.88162 ( 3315) *********************** 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 378 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 331 time to evaluate : 0.863 Fit side-chains REVERT: A 35 ARG cc_start: 0.8210 (ttt90) cc_final: 0.7957 (tpt-90) REVERT: A 93 GLU cc_start: 0.7593 (mp0) cc_final: 0.7259 (mp0) REVERT: A 108 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7511 (mm-30) REVERT: A 173 VAL cc_start: 0.8455 (t) cc_final: 0.8226 (m) REVERT: A 184 GLU cc_start: 0.7552 (mt-10) cc_final: 0.7340 (tp30) REVERT: A 190 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.7694 (mtm180) REVERT: A 214 GLN cc_start: 0.8022 (mm-40) cc_final: 0.7696 (mt0) REVERT: A 306 GLN cc_start: 0.7875 (mt0) cc_final: 0.7405 (mp10) REVERT: A 381 GLN cc_start: 0.6917 (mp10) cc_final: 0.5970 (mm-40) REVERT: A 421 LEU cc_start: 0.8738 (mm) cc_final: 0.8393 (mp) REVERT: A 448 ASN cc_start: 0.8047 (t0) cc_final: 0.7825 (t0) REVERT: A 487 PHE cc_start: 0.8917 (m-10) cc_final: 0.8715 (m-10) REVERT: A 491 MET cc_start: 0.7968 (mmm) cc_final: 0.7475 (mmp) REVERT: B 35 ARG cc_start: 0.8214 (ttt90) cc_final: 0.7971 (tpt-90) REVERT: B 80 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7718 (pt0) REVERT: B 93 GLU cc_start: 0.7622 (mp0) cc_final: 0.7269 (mp0) REVERT: B 184 GLU cc_start: 0.7608 (mt-10) cc_final: 0.7359 (tp30) REVERT: B 190 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.7828 (mtm180) REVERT: B 214 GLN cc_start: 0.8043 (mm-40) cc_final: 0.7715 (mt0) REVERT: B 302 ARG cc_start: 0.7807 (mtm110) cc_final: 0.7234 (ttp80) REVERT: B 306 GLN cc_start: 0.7871 (mt0) cc_final: 0.7407 (mp10) REVERT: B 381 GLN cc_start: 0.6882 (mp10) cc_final: 0.5951 (mm-40) REVERT: B 421 LEU cc_start: 0.8725 (mm) cc_final: 0.8419 (mp) REVERT: B 491 MET cc_start: 0.7975 (mmm) cc_final: 0.7483 (mmp) REVERT: C 35 ARG cc_start: 0.8217 (ttt90) cc_final: 0.7976 (tpt-90) REVERT: C 93 GLU cc_start: 0.7634 (mp0) cc_final: 0.7279 (mp0) REVERT: C 108 GLU cc_start: 0.7722 (mm-30) cc_final: 0.7485 (mm-30) REVERT: C 184 GLU cc_start: 0.7608 (mt-10) cc_final: 0.7366 (tp30) REVERT: C 190 ARG cc_start: 0.8279 (OUTLIER) cc_final: 0.7752 (mtm180) REVERT: C 214 GLN cc_start: 0.8061 (mm-40) cc_final: 0.7733 (mt0) REVERT: C 215 MET cc_start: 0.8831 (mmm) cc_final: 0.8521 (mmt) REVERT: C 302 ARG cc_start: 0.7825 (mtm110) cc_final: 0.7250 (ttp80) REVERT: C 306 GLN cc_start: 0.7874 (mt0) cc_final: 0.7410 (mp10) REVERT: C 381 GLN cc_start: 0.6955 (mp10) cc_final: 0.5977 (mm-40) REVERT: C 421 LEU cc_start: 0.8741 (mm) cc_final: 0.8390 (mp) REVERT: C 448 ASN cc_start: 0.8051 (t0) cc_final: 0.7832 (t0) REVERT: C 491 MET cc_start: 0.7971 (mmm) cc_final: 0.7479 (mmp) REVERT: D 35 ARG cc_start: 0.8222 (ttt90) cc_final: 0.7984 (tpt-90) REVERT: D 80 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7703 (pt0) REVERT: D 93 GLU cc_start: 0.7620 (mp0) cc_final: 0.7269 (mp0) REVERT: D 108 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7495 (mm-30) REVERT: D 184 GLU cc_start: 0.7616 (mt-10) cc_final: 0.7367 (tp30) REVERT: D 190 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.7822 (mtm180) REVERT: D 214 GLN cc_start: 0.8049 (mm-40) cc_final: 0.7727 (mt0) REVERT: D 215 MET cc_start: 0.8834 (mmm) cc_final: 0.8547 (mmt) REVERT: D 302 ARG cc_start: 0.7813 (mtm110) cc_final: 0.7240 (ttp80) REVERT: D 306 GLN cc_start: 0.7892 (mt0) cc_final: 0.7424 (mp10) REVERT: D 381 GLN cc_start: 0.6918 (mp10) cc_final: 0.5998 (mm-40) REVERT: D 421 LEU cc_start: 0.8730 (mm) cc_final: 0.8424 (mp) REVERT: D 487 PHE cc_start: 0.8920 (m-10) cc_final: 0.8717 (m-10) REVERT: D 491 MET cc_start: 0.7975 (mmm) cc_final: 0.7481 (mmp) outliers start: 47 outliers final: 23 residues processed: 370 average time/residue: 0.6317 time to fit residues: 264.5865 Evaluate side-chains 341 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 312 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ASP 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 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 311 THR 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 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 C residue 548 SER 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 514 THR Chi-restraints excluded: chain D residue 548 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 224 optimal weight: 0.7980 chunk 12 optimal weight: 0.0980 chunk 229 optimal weight: 0.7980 chunk 177 optimal weight: 2.9990 chunk 228 optimal weight: 1.9990 chunk 167 optimal weight: 0.6980 chunk 208 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 15 optimal weight: 7.9990 chunk 77 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3603 r_free = 0.3603 target = 0.149362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.112062 restraints weight = 22053.561| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 1.57 r_work: 0.3056 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20352 Z= 0.120 Angle : 0.517 5.746 27612 Z= 0.262 Chirality : 0.038 0.176 3128 Planarity : 0.004 0.047 3424 Dihedral : 8.391 76.738 3428 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.21 % Allowed : 10.87 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.16 (0.17), residues: 2384 helix: 1.87 (0.13), residues: 1536 sheet: -1.19 (0.52), residues: 80 loop : 1.04 (0.24), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 409 TYR 0.016 0.001 TYR D 467 PHE 0.014 0.001 PHE A 611 TRP 0.013 0.001 TRP A 593 HIS 0.003 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00274 (20352) covalent geometry : angle 0.51667 (27612) hydrogen bonds : bond 0.04127 ( 1189) hydrogen bonds : angle 3.86876 ( 3315) *********************** 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 361 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 315 time to evaluate : 0.778 Fit side-chains REVERT: A 35 ARG cc_start: 0.8154 (ttt90) cc_final: 0.7909 (tpt-90) REVERT: A 80 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7619 (pt0) REVERT: A 93 GLU cc_start: 0.7563 (mp0) cc_final: 0.7226 (mp0) REVERT: A 108 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7439 (mm-30) REVERT: A 139 ARG cc_start: 0.8136 (mtp180) cc_final: 0.7846 (mtp85) REVERT: A 173 VAL cc_start: 0.8414 (t) cc_final: 0.8175 (m) REVERT: A 190 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.7591 (mtm180) REVERT: A 214 GLN cc_start: 0.8004 (mm-40) cc_final: 0.7663 (mt0) REVERT: A 302 ARG cc_start: 0.7494 (mtp-110) cc_final: 0.7024 (ttp80) REVERT: A 306 GLN cc_start: 0.7827 (mt0) cc_final: 0.7357 (mp10) REVERT: A 318 SER cc_start: 0.8680 (t) cc_final: 0.8298 (m) REVERT: A 381 GLN cc_start: 0.6870 (mp10) cc_final: 0.5934 (mm-40) REVERT: A 421 LEU cc_start: 0.8654 (mm) cc_final: 0.8327 (mp) REVERT: A 448 ASN cc_start: 0.8031 (t0) cc_final: 0.7804 (t0) REVERT: A 487 PHE cc_start: 0.8890 (m-10) cc_final: 0.8665 (m-10) REVERT: A 491 MET cc_start: 0.7938 (mmm) cc_final: 0.7434 (mmp) REVERT: B 35 ARG cc_start: 0.8160 (ttt90) cc_final: 0.7925 (tpt-90) REVERT: B 80 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7672 (pt0) REVERT: B 93 GLU cc_start: 0.7601 (mp0) cc_final: 0.7255 (mp0) REVERT: B 108 GLU cc_start: 0.7622 (mm-30) cc_final: 0.7397 (mm-30) REVERT: B 184 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7313 (tp30) REVERT: B 190 ARG cc_start: 0.8252 (OUTLIER) cc_final: 0.7766 (mtm180) REVERT: B 214 GLN cc_start: 0.8003 (mm-40) cc_final: 0.7661 (mt0) REVERT: B 306 GLN cc_start: 0.7811 (mt0) cc_final: 0.7332 (mp10) REVERT: B 318 SER cc_start: 0.8683 (OUTLIER) cc_final: 0.8275 (m) REVERT: B 381 GLN cc_start: 0.6834 (mp10) cc_final: 0.5902 (mm-40) REVERT: B 421 LEU cc_start: 0.8718 (mm) cc_final: 0.8402 (mp) REVERT: B 491 MET cc_start: 0.7941 (mmm) cc_final: 0.7436 (mmp) REVERT: C 35 ARG cc_start: 0.8168 (ttt90) cc_final: 0.7934 (tpt-90) REVERT: C 80 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7620 (pt0) REVERT: C 93 GLU cc_start: 0.7623 (mp0) cc_final: 0.7271 (mp0) REVERT: C 108 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7433 (mm-30) REVERT: C 184 GLU cc_start: 0.7541 (mt-10) cc_final: 0.7314 (tp30) REVERT: C 190 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.7771 (mtm180) REVERT: C 214 GLN cc_start: 0.7993 (mm-40) cc_final: 0.7653 (mt0) REVERT: C 215 MET cc_start: 0.8828 (mmm) cc_final: 0.8579 (mmt) REVERT: C 306 GLN cc_start: 0.7825 (mt0) cc_final: 0.7349 (mp10) REVERT: C 318 SER cc_start: 0.8683 (OUTLIER) cc_final: 0.8274 (m) REVERT: C 381 GLN cc_start: 0.6867 (mp10) cc_final: 0.5940 (mm-40) REVERT: C 421 LEU cc_start: 0.8667 (mm) cc_final: 0.8333 (mp) REVERT: C 448 ASN cc_start: 0.8044 (t0) cc_final: 0.7818 (t0) REVERT: C 487 PHE cc_start: 0.8889 (m-10) cc_final: 0.8688 (m-10) REVERT: C 491 MET cc_start: 0.7932 (mmm) cc_final: 0.7427 (mmp) REVERT: D 35 ARG cc_start: 0.8178 (ttt90) cc_final: 0.7948 (tpt-90) REVERT: D 80 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7677 (pt0) REVERT: D 93 GLU cc_start: 0.7611 (mp0) cc_final: 0.7268 (mp0) REVERT: D 108 GLU cc_start: 0.7681 (mm-30) cc_final: 0.7461 (mm-30) REVERT: D 184 GLU cc_start: 0.7546 (mt-10) cc_final: 0.7321 (tp30) REVERT: D 190 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.7766 (mtm180) REVERT: D 214 GLN cc_start: 0.8004 (mm-40) cc_final: 0.7672 (mt0) REVERT: D 215 MET cc_start: 0.8806 (mmm) cc_final: 0.8521 (mmt) REVERT: D 306 GLN cc_start: 0.7818 (mt0) cc_final: 0.7339 (mp10) REVERT: D 318 SER cc_start: 0.8684 (OUTLIER) cc_final: 0.8278 (m) REVERT: D 381 GLN cc_start: 0.6861 (mp10) cc_final: 0.5942 (mm-40) REVERT: D 421 LEU cc_start: 0.8723 (mm) cc_final: 0.8403 (mp) REVERT: D 487 PHE cc_start: 0.8891 (m-10) cc_final: 0.8667 (m-10) REVERT: D 491 MET cc_start: 0.7943 (mmm) cc_final: 0.7439 (mmp) outliers start: 46 outliers final: 23 residues processed: 353 average time/residue: 0.6623 time to fit residues: 263.4689 Evaluate side-chains 331 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 297 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 90 ASP 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 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 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 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 548 SER 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 Chi-restraints excluded: chain D residue 548 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 107 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 147 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 4 optimal weight: 0.0980 chunk 26 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 223 optimal weight: 2.9990 chunk 184 optimal weight: 7.9990 chunk 92 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 40 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.159319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.124678 restraints weight = 21705.137| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.44 r_work: 0.3110 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.3116 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= 0.115 Angle : 0.519 6.726 27612 Z= 0.261 Chirality : 0.038 0.202 3128 Planarity : 0.004 0.052 3424 Dihedral : 8.296 75.228 3428 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.40 % Allowed : 11.68 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.26 (0.17), residues: 2384 helix: 1.90 (0.13), residues: 1532 sheet: -1.41 (0.51), residues: 80 loop : 1.23 (0.25), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 409 TYR 0.013 0.001 TYR C 467 PHE 0.015 0.001 PHE A 611 TRP 0.013 0.001 TRP B 593 HIS 0.003 0.001 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00262 (20352) covalent geometry : angle 0.51871 (27612) hydrogen bonds : bond 0.04057 ( 1189) hydrogen bonds : angle 3.84847 ( 3315) *********************** 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 357 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 307 time to evaluate : 0.813 Fit side-chains REVERT: A 40 GLN cc_start: 0.8049 (OUTLIER) cc_final: 0.7795 (mt0) REVERT: A 80 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7617 (pt0) REVERT: A 93 GLU cc_start: 0.7597 (mp0) cc_final: 0.7291 (mp0) REVERT: A 108 GLU cc_start: 0.7623 (mm-30) cc_final: 0.7369 (mm-30) REVERT: A 139 ARG cc_start: 0.8230 (mtp180) cc_final: 0.7955 (mtp85) REVERT: A 190 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.7748 (mtm180) REVERT: A 214 GLN cc_start: 0.8086 (mm-40) cc_final: 0.7791 (mt0) REVERT: A 215 MET cc_start: 0.8894 (mmm) cc_final: 0.8618 (mmt) REVERT: A 302 ARG cc_start: 0.7500 (mtp-110) cc_final: 0.7078 (ttp80) REVERT: A 306 GLN cc_start: 0.7850 (mt0) cc_final: 0.7483 (mp10) REVERT: A 318 SER cc_start: 0.8706 (OUTLIER) cc_final: 0.8367 (m) REVERT: A 381 GLN cc_start: 0.6965 (mp10) cc_final: 0.6069 (mm-40) REVERT: A 421 LEU cc_start: 0.8726 (mm) cc_final: 0.8445 (mp) REVERT: A 448 ASN cc_start: 0.8037 (t0) cc_final: 0.7826 (t0) REVERT: A 487 PHE cc_start: 0.8844 (m-10) cc_final: 0.8636 (m-10) REVERT: A 491 MET cc_start: 0.7951 (mmm) cc_final: 0.7517 (mmp) REVERT: B 40 GLN cc_start: 0.8043 (OUTLIER) cc_final: 0.7794 (mt0) REVERT: B 80 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7687 (pt0) REVERT: B 93 GLU cc_start: 0.7609 (mp0) cc_final: 0.7316 (mp0) REVERT: B 107 LYS cc_start: 0.7916 (mtmm) cc_final: 0.7551 (mtpp) REVERT: B 108 GLU cc_start: 0.7604 (mm-30) cc_final: 0.7398 (mm-30) REVERT: B 139 ARG cc_start: 0.8197 (mtp180) cc_final: 0.7912 (mtp85) REVERT: B 190 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.7881 (mtm180) REVERT: B 214 GLN cc_start: 0.8103 (mm-40) cc_final: 0.7828 (mt0) REVERT: B 215 MET cc_start: 0.8898 (mmm) cc_final: 0.8605 (mmt) REVERT: B 302 ARG cc_start: 0.7847 (mtm110) cc_final: 0.7263 (ttp80) REVERT: B 306 GLN cc_start: 0.7839 (mt0) cc_final: 0.7465 (mp10) REVERT: B 318 SER cc_start: 0.8719 (OUTLIER) cc_final: 0.8352 (m) REVERT: B 381 GLN cc_start: 0.6961 (mp10) cc_final: 0.6087 (mm-40) REVERT: B 421 LEU cc_start: 0.8787 (mm) cc_final: 0.8485 (mp) REVERT: B 491 MET cc_start: 0.7972 (mmm) cc_final: 0.7538 (mmp) REVERT: C 80 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7692 (pt0) REVERT: C 93 GLU cc_start: 0.7602 (mp0) cc_final: 0.7309 (mp0) REVERT: C 107 LYS cc_start: 0.7869 (mtmm) cc_final: 0.7509 (mtpp) REVERT: C 108 GLU cc_start: 0.7590 (mm-30) cc_final: 0.7388 (mm-30) REVERT: C 139 ARG cc_start: 0.8217 (mtp180) cc_final: 0.7933 (mtp85) REVERT: C 190 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.7811 (mtm180) REVERT: C 214 GLN cc_start: 0.8113 (mm-40) cc_final: 0.7823 (mt0) REVERT: C 302 ARG cc_start: 0.7860 (mtm110) cc_final: 0.7280 (ttp80) REVERT: C 306 GLN cc_start: 0.7840 (mt0) cc_final: 0.7482 (mp10) REVERT: C 318 SER cc_start: 0.8717 (OUTLIER) cc_final: 0.8348 (m) REVERT: C 381 GLN cc_start: 0.6995 (mp10) cc_final: 0.6088 (mm-40) REVERT: C 421 LEU cc_start: 0.8727 (mm) cc_final: 0.8448 (mp) REVERT: C 448 ASN cc_start: 0.8047 (t0) cc_final: 0.7836 (t0) REVERT: C 491 MET cc_start: 0.7959 (mmm) cc_final: 0.7525 (mmp) REVERT: D 40 GLN cc_start: 0.8054 (OUTLIER) cc_final: 0.7804 (mt0) REVERT: D 80 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7698 (pt0) REVERT: D 93 GLU cc_start: 0.7612 (mp0) cc_final: 0.7315 (mp0) REVERT: D 107 LYS cc_start: 0.7931 (mtmm) cc_final: 0.7561 (mtpp) REVERT: D 108 GLU cc_start: 0.7615 (mm-30) cc_final: 0.7408 (mm-30) REVERT: D 139 ARG cc_start: 0.8225 (mtp180) cc_final: 0.7947 (mtp85) REVERT: D 190 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.7819 (mtm180) REVERT: D 214 GLN cc_start: 0.8119 (mm-40) cc_final: 0.7818 (mt0) REVERT: D 215 MET cc_start: 0.8891 (mmm) cc_final: 0.8609 (mmt) REVERT: D 302 ARG cc_start: 0.7874 (mtm110) cc_final: 0.7288 (ttp80) REVERT: D 306 GLN cc_start: 0.7845 (mt0) cc_final: 0.7474 (mp10) REVERT: D 318 SER cc_start: 0.8721 (OUTLIER) cc_final: 0.8354 (m) REVERT: D 381 GLN cc_start: 0.6965 (mp10) cc_final: 0.6095 (mm-40) REVERT: D 421 LEU cc_start: 0.8803 (mm) cc_final: 0.8502 (mp) REVERT: D 487 PHE cc_start: 0.8847 (m-10) cc_final: 0.8639 (m-10) REVERT: D 491 MET cc_start: 0.7958 (mmm) cc_final: 0.7523 (mmp) outliers start: 50 outliers final: 26 residues processed: 338 average time/residue: 0.6895 time to fit residues: 261.5582 Evaluate side-chains 334 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 293 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLN Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 90 ASP 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 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 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 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 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 311 THR Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 548 SER Chi-restraints excluded: chain D residue 40 GLN 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 33 optimal weight: 5.9990 chunk 187 optimal weight: 6.9990 chunk 141 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 216 optimal weight: 0.7980 chunk 177 optimal weight: 0.0570 chunk 171 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 224 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 overall best weight: 0.6902 ------------------------------------------------------------------------------- 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 74 GLN B 261 GLN C 74 GLN C 261 GLN D 40 GLN D 74 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.150830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.113564 restraints weight = 21752.648| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 1.57 r_work: 0.3078 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20352 Z= 0.112 Angle : 0.513 6.679 27612 Z= 0.260 Chirality : 0.037 0.171 3128 Planarity : 0.004 0.059 3424 Dihedral : 8.196 73.851 3428 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.88 % Allowed : 12.36 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.33 (0.17), residues: 2384 helix: 1.94 (0.13), residues: 1536 sheet: -1.46 (0.51), residues: 80 loop : 1.32 (0.25), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 409 TYR 0.013 0.001 TYR B 467 PHE 0.015 0.001 PHE A 611 TRP 0.013 0.001 TRP D 593 HIS 0.003 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00254 (20352) covalent geometry : angle 0.51279 (27612) hydrogen bonds : bond 0.03973 ( 1189) hydrogen bonds : angle 3.81154 ( 3315) *********************** 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 343 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 304 time to evaluate : 0.808 Fit side-chains REVERT: A 93 GLU cc_start: 0.7557 (mp0) cc_final: 0.7196 (mp0) REVERT: A 107 LYS cc_start: 0.7741 (mtmm) cc_final: 0.7326 (mtpp) REVERT: A 108 GLU cc_start: 0.7578 (mm-30) cc_final: 0.7253 (mm-30) REVERT: A 139 ARG cc_start: 0.8148 (mtp180) cc_final: 0.7846 (mtp85) REVERT: A 190 ARG cc_start: 0.8249 (OUTLIER) cc_final: 0.7648 (mtm180) REVERT: A 214 GLN cc_start: 0.8030 (mm-40) cc_final: 0.7686 (mt0) REVERT: A 215 MET cc_start: 0.8831 (mmm) cc_final: 0.8571 (mmt) REVERT: A 306 GLN cc_start: 0.7821 (mt0) cc_final: 0.7360 (mp10) REVERT: A 318 SER cc_start: 0.8654 (OUTLIER) cc_final: 0.8320 (m) REVERT: A 381 GLN cc_start: 0.6856 (mp10) cc_final: 0.5923 (mm-40) REVERT: A 409 ARG cc_start: 0.7098 (mtp-110) cc_final: 0.6833 (ttm-80) REVERT: A 421 LEU cc_start: 0.8663 (mm) cc_final: 0.8364 (mp) REVERT: A 448 ASN cc_start: 0.8050 (t0) cc_final: 0.7845 (t0) REVERT: A 487 PHE cc_start: 0.8856 (m-10) cc_final: 0.8623 (m-10) REVERT: A 491 MET cc_start: 0.7926 (mmm) cc_final: 0.7427 (mmp) REVERT: B 40 GLN cc_start: 0.7752 (OUTLIER) cc_final: 0.7508 (mt0) REVERT: B 80 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7642 (pt0) REVERT: B 93 GLU cc_start: 0.7565 (mp0) cc_final: 0.7196 (mp0) REVERT: B 107 LYS cc_start: 0.7718 (mtmm) cc_final: 0.7315 (mtpp) REVERT: B 108 GLU cc_start: 0.7557 (mm-30) cc_final: 0.7255 (mm-30) REVERT: B 139 ARG cc_start: 0.8131 (mtp180) cc_final: 0.7829 (mtp85) REVERT: B 190 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7772 (mtm180) REVERT: B 214 GLN cc_start: 0.8024 (mm-40) cc_final: 0.7681 (mt0) REVERT: B 215 MET cc_start: 0.8835 (mmm) cc_final: 0.8564 (mmt) REVERT: B 302 ARG cc_start: 0.7851 (mtm110) cc_final: 0.7276 (ttp80) REVERT: B 306 GLN cc_start: 0.7803 (mt0) cc_final: 0.7337 (mp10) REVERT: B 318 SER cc_start: 0.8689 (OUTLIER) cc_final: 0.8317 (m) REVERT: B 381 GLN cc_start: 0.6855 (mp10) cc_final: 0.5924 (mm-40) REVERT: B 421 LEU cc_start: 0.8695 (mm) cc_final: 0.8373 (mp) REVERT: B 491 MET cc_start: 0.7934 (mmm) cc_final: 0.7435 (mmp) REVERT: C 80 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7625 (pt0) REVERT: C 93 GLU cc_start: 0.7567 (mp0) cc_final: 0.7200 (mp0) REVERT: C 107 LYS cc_start: 0.7733 (mtmm) cc_final: 0.7318 (mtpp) REVERT: C 108 GLU cc_start: 0.7545 (mm-30) cc_final: 0.7246 (mm-30) REVERT: C 139 ARG cc_start: 0.8154 (mtp180) cc_final: 0.7857 (mtp85) REVERT: C 190 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.7679 (mtm180) REVERT: C 214 GLN cc_start: 0.8058 (mm-40) cc_final: 0.7699 (mt0) REVERT: C 302 ARG cc_start: 0.7862 (mtm110) cc_final: 0.7288 (ttp80) REVERT: C 306 GLN cc_start: 0.7838 (mt0) cc_final: 0.7400 (mp10) REVERT: C 318 SER cc_start: 0.8693 (OUTLIER) cc_final: 0.8317 (m) REVERT: C 381 GLN cc_start: 0.6924 (mp10) cc_final: 0.5956 (mm-40) REVERT: C 421 LEU cc_start: 0.8655 (mm) cc_final: 0.8359 (mp) REVERT: C 448 ASN cc_start: 0.8061 (t0) cc_final: 0.7858 (t0) REVERT: C 491 MET cc_start: 0.7928 (mmm) cc_final: 0.7429 (mmp) REVERT: D 40 GLN cc_start: 0.7754 (OUTLIER) cc_final: 0.7502 (mt0) REVERT: D 80 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7674 (pt0) REVERT: D 93 GLU cc_start: 0.7568 (mp0) cc_final: 0.7196 (mp0) REVERT: D 107 LYS cc_start: 0.7740 (mtmm) cc_final: 0.7329 (mtpp) REVERT: D 108 GLU cc_start: 0.7549 (mm-30) cc_final: 0.7248 (mm-30) REVERT: D 139 ARG cc_start: 0.8161 (mtp180) cc_final: 0.7860 (mtp85) REVERT: D 190 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.7766 (mtm180) REVERT: D 214 GLN cc_start: 0.8057 (mm-40) cc_final: 0.7706 (mt0) REVERT: D 215 MET cc_start: 0.8820 (mmm) cc_final: 0.8543 (mmt) REVERT: D 302 ARG cc_start: 0.7864 (mtm110) cc_final: 0.7291 (ttp80) REVERT: D 306 GLN cc_start: 0.7813 (mt0) cc_final: 0.7350 (mp10) REVERT: D 318 SER cc_start: 0.8710 (OUTLIER) cc_final: 0.8340 (m) REVERT: D 381 GLN cc_start: 0.6889 (mp10) cc_final: 0.5951 (mm-40) REVERT: D 421 LEU cc_start: 0.8684 (mm) cc_final: 0.8378 (mp) REVERT: D 487 PHE cc_start: 0.8855 (m-10) cc_final: 0.8617 (m-10) REVERT: D 491 MET cc_start: 0.7934 (mmm) cc_final: 0.7431 (mmp) outliers start: 39 outliers final: 19 residues processed: 331 average time/residue: 0.6736 time to fit residues: 250.3621 Evaluate side-chains 330 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 298 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ASP 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 40 GLN Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 90 ASP 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 80 GLU Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 96 THR 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 548 SER Chi-restraints excluded: chain D residue 40 GLN Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 90 ASP 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 548 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 182 optimal weight: 0.1980 chunk 45 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 127 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 157 optimal weight: 6.9990 chunk 192 optimal weight: 0.0010 chunk 203 optimal weight: 0.9980 chunk 154 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- 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 74 GLN B 261 GLN C 74 GLN C 261 GLN D 40 GLN D 74 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.151251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.114174 restraints weight = 21817.167| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 1.55 r_work: 0.3089 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 20352 Z= 0.108 Angle : 0.518 8.290 27612 Z= 0.260 Chirality : 0.037 0.151 3128 Planarity : 0.004 0.062 3424 Dihedral : 8.094 72.448 3428 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 1.78 % Allowed : 13.03 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.36 (0.17), residues: 2384 helix: 1.95 (0.13), residues: 1536 sheet: -1.50 (0.51), residues: 80 loop : 1.34 (0.25), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 409 TYR 0.014 0.001 TYR C 467 PHE 0.015 0.001 PHE D 611 TRP 0.014 0.001 TRP C 593 HIS 0.003 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00241 (20352) covalent geometry : angle 0.51826 (27612) hydrogen bonds : bond 0.03910 ( 1189) hydrogen bonds : angle 3.80711 ( 3315) ********************** 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 347 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 310 time to evaluate : 0.700 Fit side-chains REVERT: A 93 GLU cc_start: 0.7580 (mp0) cc_final: 0.7249 (mp0) REVERT: A 107 LYS cc_start: 0.7652 (mtmm) cc_final: 0.7231 (mtpp) REVERT: A 108 GLU cc_start: 0.7505 (mm-30) cc_final: 0.7217 (mm-30) REVERT: A 139 ARG cc_start: 0.8118 (mtp180) cc_final: 0.7810 (mtp85) REVERT: A 214 GLN cc_start: 0.8001 (mm-40) cc_final: 0.7673 (mt0) REVERT: A 215 MET cc_start: 0.8827 (mmm) cc_final: 0.8576 (mmt) REVERT: A 221 SER cc_start: 0.8957 (t) cc_final: 0.8530 (p) REVERT: A 302 ARG cc_start: 0.7471 (mtp-110) cc_final: 0.7033 (ttp-110) REVERT: A 306 GLN cc_start: 0.7831 (mt0) cc_final: 0.7396 (mp10) REVERT: A 318 SER cc_start: 0.8673 (OUTLIER) cc_final: 0.8355 (m) REVERT: A 381 GLN cc_start: 0.6862 (mp10) cc_final: 0.5922 (mm-40) REVERT: A 409 ARG cc_start: 0.7040 (mtp-110) cc_final: 0.6823 (ttm-80) REVERT: A 421 LEU cc_start: 0.8672 (mm) cc_final: 0.8393 (mp) REVERT: A 491 MET cc_start: 0.7919 (mmm) cc_final: 0.7409 (mmp) REVERT: B 40 GLN cc_start: 0.7831 (OUTLIER) cc_final: 0.7594 (mt0) REVERT: B 80 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7648 (pt0) REVERT: B 93 GLU cc_start: 0.7592 (mp0) cc_final: 0.7249 (mp0) REVERT: B 107 LYS cc_start: 0.7617 (mtmm) cc_final: 0.7213 (mtpp) REVERT: B 108 GLU cc_start: 0.7511 (mm-30) cc_final: 0.7224 (mm-30) REVERT: B 139 ARG cc_start: 0.8129 (mtp180) cc_final: 0.7837 (mtp85) REVERT: B 190 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.7709 (mtm180) REVERT: B 214 GLN cc_start: 0.8001 (mm-40) cc_final: 0.7679 (mt0) REVERT: B 215 MET cc_start: 0.8822 (mmm) cc_final: 0.8549 (mmt) REVERT: B 302 ARG cc_start: 0.7830 (mtm110) cc_final: 0.7261 (ttp80) REVERT: B 306 GLN cc_start: 0.7769 (mt0) cc_final: 0.7323 (mp10) REVERT: B 318 SER cc_start: 0.8705 (OUTLIER) cc_final: 0.8356 (m) REVERT: B 381 GLN cc_start: 0.6827 (mp10) cc_final: 0.5901 (mm-40) REVERT: B 409 ARG cc_start: 0.7090 (mtp-110) cc_final: 0.6840 (ttm-80) REVERT: B 421 LEU cc_start: 0.8702 (mm) cc_final: 0.8400 (mp) REVERT: B 491 MET cc_start: 0.7919 (mmm) cc_final: 0.7412 (mmp) REVERT: C 80 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7739 (pt0) REVERT: C 93 GLU cc_start: 0.7601 (mp0) cc_final: 0.7253 (mp0) REVERT: C 107 LYS cc_start: 0.7635 (mtmm) cc_final: 0.7217 (mtpp) REVERT: C 108 GLU cc_start: 0.7491 (mm-30) cc_final: 0.7218 (mm-30) REVERT: C 139 ARG cc_start: 0.8118 (mtp180) cc_final: 0.7825 (mtp85) REVERT: C 214 GLN cc_start: 0.8022 (mm-40) cc_final: 0.7696 (mt0) REVERT: C 221 SER cc_start: 0.8956 (t) cc_final: 0.8526 (p) REVERT: C 302 ARG cc_start: 0.7869 (mtm110) cc_final: 0.7296 (ttp80) REVERT: C 306 GLN cc_start: 0.7820 (mt0) cc_final: 0.7396 (mp10) REVERT: C 318 SER cc_start: 0.8692 (OUTLIER) cc_final: 0.8344 (m) REVERT: C 381 GLN cc_start: 0.6875 (mp10) cc_final: 0.5919 (mm-40) REVERT: C 409 ARG cc_start: 0.7076 (mtp-110) cc_final: 0.6812 (ttm-80) REVERT: C 421 LEU cc_start: 0.8656 (mm) cc_final: 0.8369 (mp) REVERT: C 448 ASN cc_start: 0.8062 (t0) cc_final: 0.7860 (t0) REVERT: C 491 MET cc_start: 0.7931 (mmm) cc_final: 0.7425 (mmp) REVERT: D 93 GLU cc_start: 0.7599 (mp0) cc_final: 0.7250 (mp0) REVERT: D 107 LYS cc_start: 0.7642 (mtmm) cc_final: 0.7234 (mtpp) REVERT: D 108 GLU cc_start: 0.7504 (mm-30) cc_final: 0.7219 (mm-30) REVERT: D 139 ARG cc_start: 0.8141 (mtp180) cc_final: 0.7850 (mtp85) REVERT: D 190 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.7670 (mtm180) REVERT: D 214 GLN cc_start: 0.8021 (mm-40) cc_final: 0.7690 (mt0) REVERT: D 215 MET cc_start: 0.8814 (mmm) cc_final: 0.8539 (mmt) REVERT: D 221 SER cc_start: 0.8961 (t) cc_final: 0.8531 (p) REVERT: D 302 ARG cc_start: 0.7873 (mtm110) cc_final: 0.7301 (ttp80) REVERT: D 306 GLN cc_start: 0.7783 (mt0) cc_final: 0.7330 (mp10) REVERT: D 318 SER cc_start: 0.8696 (OUTLIER) cc_final: 0.8345 (m) REVERT: D 381 GLN cc_start: 0.6872 (mp10) cc_final: 0.5937 (mm-40) REVERT: D 409 ARG cc_start: 0.7054 (mtp-110) cc_final: 0.6800 (ttm-80) REVERT: D 421 LEU cc_start: 0.8705 (mm) cc_final: 0.8403 (mp) REVERT: D 491 MET cc_start: 0.7914 (mmm) cc_final: 0.7401 (mmp) outliers start: 37 outliers final: 19 residues processed: 336 average time/residue: 0.6251 time to fit residues: 236.3165 Evaluate side-chains 326 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 298 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ASP 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 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 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 C residue 80 GLU Chi-restraints excluded: chain C residue 90 ASP 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 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 548 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 178 optimal weight: 4.9990 chunk 87 optimal weight: 0.8980 chunk 150 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 117 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 204 optimal weight: 6.9990 chunk 134 optimal weight: 0.9990 chunk 60 optimal weight: 10.0000 chunk 222 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 40 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 = 0.3609 r_free = 0.3609 target = 0.150322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.113298 restraints weight = 21801.583| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.53 r_work: 0.3071 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20352 Z= 0.120 Angle : 0.523 6.975 27612 Z= 0.265 Chirality : 0.038 0.209 3128 Planarity : 0.004 0.060 3424 Dihedral : 8.135 72.234 3428 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.54 % Allowed : 13.03 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.32 (0.17), residues: 2384 helix: 1.92 (0.13), residues: 1540 sheet: -1.52 (0.51), residues: 80 loop : 1.34 (0.25), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 409 TYR 0.011 0.001 TYR D 467 PHE 0.014 0.001 PHE A 611 TRP 0.012 0.001 TRP A 593 HIS 0.003 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00277 (20352) covalent geometry : angle 0.52280 (27612) hydrogen bonds : bond 0.04071 ( 1189) hydrogen bonds : angle 3.83143 ( 3315) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7223.94 seconds wall clock time: 123 minutes 59.76 seconds (7439.76 seconds total)