Starting phenix.real_space_refine on Thu Feb 5 20:39:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tf3_41218/02_2026/8tf3_41218_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tf3_41218/02_2026/8tf3_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_41218/02_2026/8tf3_41218.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tf3_41218/02_2026/8tf3_41218.map" model { file = "/net/cci-nas-00/data/ceres_data/8tf3_41218/02_2026/8tf3_41218_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tf3_41218/02_2026/8tf3_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19888 Number of models: 1 Model: "" Number of chains: 8 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: "B" 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: "C" 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: "D" 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 Time building chain proxies: 4.60, 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: 1.51 Conformation dependent library (CDL) restraints added in 987.4 milliseconds 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: 0.65 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: 3.57 Time building geometry restraints manager: 2.07 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: 1.670 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: 0.350 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 18.400 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.030 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:7.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.850 ------------------------------------------------------------------------------- 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 are 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 : 0.791 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: 0.7415 (mp0) cc_final: 0.7110 (mp0) REVERT: A 214 GLN cc_start: 0.7683 (mm-40) cc_final: 0.7244 (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: 0.7819 (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: 0.7097 (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: 0.6510 (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: 0.6451 time to fit residues: 298.4279 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 : 0.672 ------------------------------------------------------------------------------- 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 = 0.151723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.114946 restraints weight = 21813.202| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 1.51 r_work: 0.3061 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 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 5.822 27612 Z= 0.302 Chirality : 0.040 0.150 3128 Planarity : 0.004 0.030 3424 Dihedral : 10.729 95.820 3428 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.51 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 are 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 4.28388 ( 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 : 0.795 Fit side-chains REVERT: A 35 ARG cc_start: 0.7993 (ttt-90) cc_final: 0.7731 (ttt90) REVERT: A 93 GLU cc_start: 0.7615 (mp0) cc_final: 0.7289 (mp0) REVERT: A 173 VAL cc_start: 0.8521 (t) cc_final: 0.8183 (m) REVERT: A 184 GLU cc_start: 0.7571 (mt-10) cc_final: 0.7279 (tp30) REVERT: A 214 GLN cc_start: 0.7987 (mm-40) cc_final: 0.7612 (mt0) REVERT: A 302 ARG cc_start: 0.7835 (mtm110) cc_final: 0.7439 (ttp80) REVERT: A 306 GLN cc_start: 0.7923 (mt0) cc_final: 0.7376 (mp10) REVERT: A 381 GLN cc_start: 0.6902 (mp10) cc_final: 0.5912 (mm-40) REVERT: A 448 ASN cc_start: 0.7983 (t0) cc_final: 0.7771 (t0) REVERT: A 491 MET cc_start: 0.7956 (mmm) cc_final: 0.7467 (mmp) REVERT: B 35 ARG cc_start: 0.7995 (ttt-90) cc_final: 0.7716 (ttt90) REVERT: B 93 GLU cc_start: 0.7653 (mp0) cc_final: 0.7298 (mp0) REVERT: B 173 VAL cc_start: 0.8515 (t) cc_final: 0.8206 (m) REVERT: B 184 GLU cc_start: 0.7632 (mt-10) cc_final: 0.7306 (tp30) REVERT: B 214 GLN cc_start: 0.7990 (mm-40) cc_final: 0.7603 (mt0) REVERT: B 302 ARG cc_start: 0.7820 (mtm110) cc_final: 0.7443 (ttp80) REVERT: B 306 GLN cc_start: 0.7944 (mt0) cc_final: 0.7406 (mp10) REVERT: B 381 GLN cc_start: 0.6935 (mp10) cc_final: 0.5945 (mm-40) REVERT: B 382 ASP cc_start: 0.8202 (m-30) cc_final: 0.7990 (m-30) REVERT: B 448 ASN cc_start: 0.7977 (t0) cc_final: 0.7761 (t0) REVERT: B 491 MET cc_start: 0.7961 (mmm) cc_final: 0.7479 (mmp) REVERT: C 35 ARG cc_start: 0.7997 (ttt-90) cc_final: 0.7722 (ttt90) REVERT: C 93 GLU cc_start: 0.7647 (mp0) cc_final: 0.7296 (mp0) REVERT: C 173 VAL cc_start: 0.8524 (t) cc_final: 0.8215 (m) REVERT: C 184 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7306 (tp30) REVERT: C 214 GLN cc_start: 0.7975 (mm-40) cc_final: 0.7595 (mt0) REVERT: C 302 ARG cc_start: 0.7818 (mtm110) cc_final: 0.7436 (ttp80) REVERT: C 306 GLN cc_start: 0.7948 (mt0) cc_final: 0.7399 (mp10) REVERT: C 381 GLN cc_start: 0.6917 (mp10) cc_final: 0.5934 (mm-40) REVERT: C 382 ASP cc_start: 0.8185 (m-30) cc_final: 0.7983 (m-30) REVERT: C 448 ASN cc_start: 0.7970 (t0) cc_final: 0.7759 (t0) REVERT: C 491 MET cc_start: 0.7955 (mmm) cc_final: 0.7471 (mmp) REVERT: D 35 ARG cc_start: 0.8010 (ttt-90) cc_final: 0.7735 (ttt90) REVERT: D 93 GLU cc_start: 0.7645 (mp0) cc_final: 0.7286 (mp0) REVERT: D 173 VAL cc_start: 0.8518 (t) cc_final: 0.8208 (m) REVERT: D 184 GLU cc_start: 0.7612 (mt-10) cc_final: 0.7300 (tp30) REVERT: D 214 GLN cc_start: 0.7982 (mm-40) cc_final: 0.7585 (mt0) REVERT: D 302 ARG cc_start: 0.7818 (mtm110) cc_final: 0.7442 (ttp80) REVERT: D 306 GLN cc_start: 0.7945 (mt0) cc_final: 0.7406 (mp10) REVERT: D 381 GLN cc_start: 0.6892 (mp10) cc_final: 0.5936 (mm-40) REVERT: D 448 ASN cc_start: 0.7990 (t0) cc_final: 0.7785 (t0) REVERT: D 491 MET cc_start: 0.7953 (mmm) cc_final: 0.7464 (mmp) outliers start: 30 outliers final: 20 residues processed: 369 average time/residue: 0.5766 time to fit residues: 239.9968 Evaluate side-chains 324 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 304 time to evaluate : 0.566 ------------------------------------------------------------------------------- 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: 0.9990 chunk 206 optimal weight: 0.9990 chunk 91 optimal weight: 0.4980 chunk 145 optimal weight: 0.3980 chunk 87 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 chunk 131 optimal weight: 9.9990 chunk 40 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3780 r_free = 0.3780 target = 0.162730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.127927 restraints weight = 21562.118| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.45 r_work: 0.3114 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20352 Z= 0.117 Angle : 0.509 5.696 27612 Z= 0.262 Chirality : 0.038 0.146 3128 Planarity : 0.004 0.035 3424 Dihedral : 9.345 79.965 3428 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.97 % Allowed : 9.28 % Favored : 88.75 % 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 are not related in a simple way. whole: 2.05 (0.17), residues: 2384 helix: 1.78 (0.13), residues: 1508 sheet: 0.09 (0.52), residues: 88 loop : 0.89 (0.24), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 139 TYR 0.012 0.001 TYR A 555 PHE 0.018 0.001 PHE C 211 TRP 0.018 0.001 TRP B 593 HIS 0.004 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00260 (20352) covalent geometry : angle 0.50865 (27612) hydrogen bonds : bond 0.04248 ( 1189) hydrogen bonds : angle 3.98018 ( 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 382 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 341 time to evaluate : 0.658 Fit side-chains REVERT: A 93 GLU cc_start: 0.7643 (mp0) cc_final: 0.7268 (mp0) REVERT: A 184 GLU cc_start: 0.7600 (mt-10) cc_final: 0.7326 (tp30) REVERT: A 190 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7504 (mtm180) REVERT: A 214 GLN cc_start: 0.8002 (mm-40) cc_final: 0.7673 (mt0) REVERT: A 302 ARG cc_start: 0.7791 (mtm110) cc_final: 0.7433 (ttp80) REVERT: A 306 GLN cc_start: 0.7887 (mt0) cc_final: 0.7341 (mp10) REVERT: A 381 GLN cc_start: 0.6964 (mp10) cc_final: 0.6005 (mm-40) REVERT: A 421 LEU cc_start: 0.8669 (mm) cc_final: 0.8389 (mp) REVERT: A 448 ASN cc_start: 0.7958 (t0) cc_final: 0.7751 (t0) REVERT: A 491 MET cc_start: 0.7881 (mmm) cc_final: 0.7349 (mmp) REVERT: B 93 GLU cc_start: 0.7627 (mp0) cc_final: 0.7251 (mp0) REVERT: B 184 GLU cc_start: 0.7619 (mt-10) cc_final: 0.7328 (tp30) REVERT: B 190 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.7519 (mtm180) REVERT: B 214 GLN cc_start: 0.8014 (mm-40) cc_final: 0.7677 (mt0) REVERT: B 302 ARG cc_start: 0.7791 (mtm110) cc_final: 0.7441 (ttp80) REVERT: B 306 GLN cc_start: 0.7890 (mt0) cc_final: 0.7357 (mp10) REVERT: B 381 GLN cc_start: 0.6947 (mp10) cc_final: 0.5946 (mm-40) REVERT: B 421 LEU cc_start: 0.8634 (mm) cc_final: 0.8356 (mp) REVERT: B 491 MET cc_start: 0.7840 (mmm) cc_final: 0.7322 (mmp) REVERT: C 93 GLU cc_start: 0.7636 (mp0) cc_final: 0.7242 (mp0) REVERT: C 184 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7339 (tp30) REVERT: C 190 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.7517 (mtm180) REVERT: C 214 GLN cc_start: 0.8037 (mm-40) cc_final: 0.7696 (mt0) REVERT: C 302 ARG cc_start: 0.7787 (mtm110) cc_final: 0.7439 (ttp80) REVERT: C 306 GLN cc_start: 0.7878 (mt0) cc_final: 0.7342 (mp10) REVERT: C 381 GLN cc_start: 0.6941 (mp10) cc_final: 0.5944 (mm-40) REVERT: C 382 ASP cc_start: 0.8194 (m-30) cc_final: 0.7980 (m-30) REVERT: C 421 LEU cc_start: 0.8639 (mm) cc_final: 0.8357 (mp) REVERT: C 448 ASN cc_start: 0.7954 (t0) cc_final: 0.7750 (t0) REVERT: C 491 MET cc_start: 0.7842 (mmm) cc_final: 0.7319 (mmp) REVERT: D 93 GLU cc_start: 0.7677 (mp0) cc_final: 0.7311 (mp0) REVERT: D 184 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7356 (tp30) REVERT: D 190 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.7512 (mtm180) REVERT: D 214 GLN cc_start: 0.8028 (mm-40) cc_final: 0.7682 (mt0) REVERT: D 302 ARG cc_start: 0.7797 (mtm110) cc_final: 0.7443 (ttp80) REVERT: D 306 GLN cc_start: 0.7911 (mt0) cc_final: 0.7377 (mp10) REVERT: D 381 GLN cc_start: 0.6992 (mp10) cc_final: 0.6023 (mm-40) REVERT: D 421 LEU cc_start: 0.8647 (mm) cc_final: 0.8362 (mp) REVERT: D 448 ASN cc_start: 0.7954 (t0) cc_final: 0.7749 (t0) REVERT: D 491 MET cc_start: 0.7834 (mmm) cc_final: 0.7307 (mmp) outliers start: 41 outliers final: 8 residues processed: 366 average time/residue: 0.5713 time to fit residues: 236.0429 Evaluate side-chains 313 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 301 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 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: 0.4980 chunk 196 optimal weight: 9.9990 chunk 96 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 234 optimal weight: 0.8980 chunk 204 optimal weight: 7.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- 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 = 0.3664 r_free = 0.3664 target = 0.153198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.117716 restraints weight = 21887.630| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.43 r_work: 0.3074 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20352 Z= 0.128 Angle : 0.513 5.758 27612 Z= 0.261 Chirality : 0.038 0.150 3128 Planarity : 0.004 0.039 3424 Dihedral : 8.652 78.725 3428 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.73 % Allowed : 11.20 % Favored : 87.07 % 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 are not related in a simple way. whole: 2.05 (0.17), residues: 2384 helix: 1.73 (0.13), residues: 1540 sheet: -0.45 (0.53), residues: 80 loop : 1.02 (0.25), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 35 TYR 0.011 0.001 TYR B 555 PHE 0.015 0.001 PHE C 534 TRP 0.014 0.001 TRP A 593 HIS 0.004 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00297 (20352) covalent geometry : angle 0.51345 (27612) hydrogen bonds : bond 0.04281 ( 1189) hydrogen bonds : angle 3.91170 ( 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 362 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 326 time to evaluate : 0.632 Fit side-chains REVERT: A 35 ARG cc_start: 0.8216 (ttt90) cc_final: 0.7912 (tpt-90) REVERT: A 93 GLU cc_start: 0.7599 (mp0) cc_final: 0.7277 (mp0) REVERT: A 184 GLU cc_start: 0.7611 (mt-10) cc_final: 0.7392 (tp30) REVERT: A 190 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.7658 (mtm180) REVERT: A 214 GLN cc_start: 0.7981 (mm-40) cc_final: 0.7695 (mt0) REVERT: A 215 MET cc_start: 0.8799 (mmm) cc_final: 0.8473 (mmt) REVERT: A 302 ARG cc_start: 0.7741 (mtm110) cc_final: 0.7430 (ttp80) REVERT: A 306 GLN cc_start: 0.7892 (mt0) cc_final: 0.7428 (mp10) REVERT: A 381 GLN cc_start: 0.6950 (mp10) cc_final: 0.5997 (mm-40) REVERT: A 421 LEU cc_start: 0.8699 (mm) cc_final: 0.8394 (mp) REVERT: A 448 ASN cc_start: 0.7995 (t0) cc_final: 0.7788 (t0) REVERT: A 487 PHE cc_start: 0.8924 (m-10) cc_final: 0.8717 (m-10) REVERT: A 491 MET cc_start: 0.7948 (mmm) cc_final: 0.7477 (mmp) REVERT: B 93 GLU cc_start: 0.7638 (mp0) cc_final: 0.7310 (mp0) REVERT: B 184 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7343 (tp30) REVERT: B 190 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.7666 (mtm180) REVERT: B 214 GLN cc_start: 0.7996 (mm-40) cc_final: 0.7705 (mt0) REVERT: B 302 ARG cc_start: 0.7728 (mtm110) cc_final: 0.7447 (ttp80) REVERT: B 306 GLN cc_start: 0.7865 (mt0) cc_final: 0.7412 (mp10) REVERT: B 381 GLN cc_start: 0.6906 (mp10) cc_final: 0.5989 (mm-40) REVERT: B 421 LEU cc_start: 0.8696 (mm) cc_final: 0.8360 (mp) REVERT: B 491 MET cc_start: 0.7911 (mmm) cc_final: 0.7443 (mmp) REVERT: C 80 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8337 (pm20) REVERT: C 93 GLU cc_start: 0.7618 (mp0) cc_final: 0.7296 (mp0) REVERT: C 184 GLU cc_start: 0.7638 (mt-10) cc_final: 0.7348 (tp30) REVERT: C 190 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7662 (mtm180) REVERT: C 214 GLN cc_start: 0.8037 (mm-40) cc_final: 0.7729 (mt0) REVERT: C 302 ARG cc_start: 0.7765 (mtm110) cc_final: 0.7467 (ttp80) REVERT: C 306 GLN cc_start: 0.7869 (mt0) cc_final: 0.7418 (mp10) REVERT: C 381 GLN cc_start: 0.6937 (mp10) cc_final: 0.5989 (mm-40) REVERT: C 421 LEU cc_start: 0.8694 (mm) cc_final: 0.8366 (mp) REVERT: C 448 ASN cc_start: 0.8001 (t0) cc_final: 0.7795 (t0) REVERT: C 491 MET cc_start: 0.7894 (mmm) cc_final: 0.7433 (mmp) REVERT: D 80 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8294 (pm20) REVERT: D 93 GLU cc_start: 0.7643 (mp0) cc_final: 0.7318 (mp0) REVERT: D 184 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7347 (tp30) REVERT: D 190 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.7660 (mtm180) REVERT: D 214 GLN cc_start: 0.8019 (mm-40) cc_final: 0.7719 (mt0) REVERT: D 302 ARG cc_start: 0.7746 (mtm110) cc_final: 0.7459 (ttp80) REVERT: D 306 GLN cc_start: 0.7859 (mt0) cc_final: 0.7414 (mp10) REVERT: D 381 GLN cc_start: 0.6925 (mp10) cc_final: 0.6016 (mm-40) REVERT: D 421 LEU cc_start: 0.8695 (mm) cc_final: 0.8369 (mp) REVERT: D 448 ASN cc_start: 0.8005 (t0) cc_final: 0.7796 (t0) REVERT: D 487 PHE cc_start: 0.8917 (m-10) cc_final: 0.8710 (m-10) REVERT: D 491 MET cc_start: 0.7904 (mmm) cc_final: 0.7438 (mmp) outliers start: 36 outliers final: 16 residues processed: 352 average time/residue: 0.5889 time to fit residues: 233.8293 Evaluate side-chains 330 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 308 time to evaluate : 0.577 ------------------------------------------------------------------------------- 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 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 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 318 SER Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 190 ARG Chi-restraints excluded: chain D residue 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: 3.9990 chunk 160 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 234 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 206 optimal weight: 6.9990 chunk 89 optimal weight: 0.8980 chunk 70 optimal weight: 6.9990 chunk 173 optimal weight: 0.7980 chunk 190 optimal weight: 0.7980 chunk 124 optimal weight: 9.9990 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 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 = 0.3605 r_free = 0.3605 target = 0.149534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.111635 restraints weight = 21956.735| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.63 r_work: 0.3062 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 20352 Z= 0.118 Angle : 0.497 5.707 27612 Z= 0.254 Chirality : 0.037 0.142 3128 Planarity : 0.004 0.044 3424 Dihedral : 8.446 77.129 3428 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.07 % Allowed : 10.87 % Favored : 87.07 % 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 are not related in a simple way. whole: 2.16 (0.17), residues: 2384 helix: 1.88 (0.13), residues: 1532 sheet: -0.76 (0.52), residues: 80 loop : 0.97 (0.24), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 409 TYR 0.010 0.001 TYR B 555 PHE 0.013 0.001 PHE C 534 TRP 0.014 0.001 TRP D 593 HIS 0.003 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00267 (20352) covalent geometry : angle 0.49693 (27612) hydrogen bonds : bond 0.04097 ( 1189) hydrogen bonds : angle 3.85080 ( 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 383 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 340 time to evaluate : 0.744 Fit side-chains REVERT: A 35 ARG cc_start: 0.8194 (ttt90) cc_final: 0.7933 (tpt-90) REVERT: A 93 GLU cc_start: 0.7611 (mp0) cc_final: 0.7238 (mp0) REVERT: A 184 GLU cc_start: 0.7575 (mt-10) cc_final: 0.7351 (tp30) REVERT: A 190 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7670 (mtm180) REVERT: A 214 GLN cc_start: 0.8005 (mm-40) cc_final: 0.7658 (mt0) REVERT: A 306 GLN cc_start: 0.7872 (mt0) cc_final: 0.7381 (mp10) REVERT: A 381 GLN cc_start: 0.6885 (mp10) cc_final: 0.5951 (mm-40) REVERT: A 421 LEU cc_start: 0.8690 (mm) cc_final: 0.8338 (mp) REVERT: A 448 ASN cc_start: 0.8010 (t0) cc_final: 0.7792 (t0) REVERT: A 491 MET cc_start: 0.7960 (mmm) cc_final: 0.7468 (mmp) REVERT: B 35 ARG cc_start: 0.8211 (ttt90) cc_final: 0.7956 (tpt-90) REVERT: B 80 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7568 (pt0) REVERT: B 93 GLU cc_start: 0.7647 (mp0) cc_final: 0.7268 (mp0) REVERT: B 184 GLU cc_start: 0.7570 (mt-10) cc_final: 0.7319 (tp30) REVERT: B 190 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.7721 (mtm180) REVERT: B 214 GLN cc_start: 0.8023 (mm-40) cc_final: 0.7680 (mt0) REVERT: B 306 GLN cc_start: 0.7862 (mt0) cc_final: 0.7372 (mp10) REVERT: B 381 GLN cc_start: 0.6878 (mp10) cc_final: 0.5925 (mm-40) REVERT: B 421 LEU cc_start: 0.8667 (mm) cc_final: 0.8302 (mp) REVERT: B 487 PHE cc_start: 0.8899 (m-10) cc_final: 0.8699 (m-10) REVERT: B 491 MET cc_start: 0.7953 (mmm) cc_final: 0.7462 (mmp) REVERT: C 35 ARG cc_start: 0.8214 (ttt90) cc_final: 0.7963 (tpt-90) REVERT: C 93 GLU cc_start: 0.7644 (mp0) cc_final: 0.7264 (mp0) REVERT: C 184 GLU cc_start: 0.7584 (mt-10) cc_final: 0.7330 (tp30) REVERT: C 190 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.7629 (mtm180) REVERT: C 214 GLN cc_start: 0.8043 (mm-40) cc_final: 0.7698 (mt0) REVERT: C 306 GLN cc_start: 0.7865 (mt0) cc_final: 0.7379 (mp10) REVERT: C 381 GLN cc_start: 0.6872 (mp10) cc_final: 0.5929 (mm-40) REVERT: C 421 LEU cc_start: 0.8666 (mm) cc_final: 0.8315 (mp) REVERT: C 448 ASN cc_start: 0.8033 (t0) cc_final: 0.7810 (t0) REVERT: C 487 PHE cc_start: 0.8895 (m-10) cc_final: 0.8693 (m-10) REVERT: C 491 MET cc_start: 0.7937 (mmm) cc_final: 0.7450 (mmp) REVERT: D 35 ARG cc_start: 0.8213 (ttt90) cc_final: 0.7959 (tpt-90) REVERT: D 93 GLU cc_start: 0.7638 (mp0) cc_final: 0.7328 (mp0) REVERT: D 184 GLU cc_start: 0.7584 (mt-10) cc_final: 0.7321 (tp30) REVERT: D 190 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7711 (mtm180) REVERT: D 214 GLN cc_start: 0.8034 (mm-40) cc_final: 0.7688 (mt0) REVERT: D 306 GLN cc_start: 0.7866 (mt0) cc_final: 0.7376 (mp10) REVERT: D 381 GLN cc_start: 0.6889 (mp10) cc_final: 0.5950 (mm-40) REVERT: D 421 LEU cc_start: 0.8673 (mm) cc_final: 0.8319 (mp) REVERT: D 448 ASN cc_start: 0.8024 (t0) cc_final: 0.7801 (t0) REVERT: D 491 MET cc_start: 0.7957 (mmm) cc_final: 0.7466 (mmp) outliers start: 43 outliers final: 20 residues processed: 368 average time/residue: 0.5635 time to fit residues: 234.9225 Evaluate side-chains 347 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 322 time to evaluate : 0.681 ------------------------------------------------------------------------------- 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 318 SER Chi-restraints excluded: chain A residue 335 LEU 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 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 D residue 90 ASP Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 190 ARG Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 318 SER Chi-restraints excluded: chain D residue 335 LEU Rotamers are restrained with sigma=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: 3.9990 chunk 214 optimal weight: 7.9990 chunk 139 optimal weight: 6.9990 chunk 18 optimal weight: 7.9990 chunk 140 optimal weight: 0.0050 chunk 156 optimal weight: 2.9990 chunk 177 optimal weight: 2.9990 chunk 60 optimal weight: 10.0000 chunk 199 optimal weight: 4.9990 overall best weight: 3.0002 ------------------------------------------------------------------------------- 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 C 418 GLN D 261 GLN D 418 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.143349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.104855 restraints weight = 22139.007| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.63 r_work: 0.2959 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 20352 Z= 0.247 Angle : 0.621 7.724 27612 Z= 0.312 Chirality : 0.043 0.203 3128 Planarity : 0.005 0.050 3424 Dihedral : 9.188 83.622 3428 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.69 % Allowed : 11.01 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.17), residues: 2384 helix: 1.44 (0.13), residues: 1540 sheet: -1.00 (0.55), residues: 80 loop : 0.89 (0.24), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 409 TYR 0.017 0.002 TYR B 89 PHE 0.016 0.002 PHE D 534 TRP 0.010 0.002 TRP D 593 HIS 0.006 0.001 HIS D 201 Details of bonding type rmsd covalent geometry : bond 0.00617 (20352) covalent geometry : angle 0.62050 (27612) hydrogen bonds : bond 0.05186 ( 1189) hydrogen bonds : angle 4.06249 ( 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 367 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 311 time to evaluate : 0.675 Fit side-chains REVERT: A 93 GLU cc_start: 0.7618 (mp0) cc_final: 0.7231 (mp0) REVERT: A 184 GLU cc_start: 0.7650 (mt-10) cc_final: 0.7344 (tp30) REVERT: A 190 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7588 (mtm180) REVERT: A 214 GLN cc_start: 0.7976 (mm-40) cc_final: 0.7641 (mt0) REVERT: A 306 GLN cc_start: 0.7924 (mt0) cc_final: 0.7370 (mp10) REVERT: A 381 GLN cc_start: 0.6884 (mp10) cc_final: 0.5905 (mm-40) REVERT: A 421 LEU cc_start: 0.8767 (mm) cc_final: 0.8457 (mp) REVERT: A 448 ASN cc_start: 0.8060 (t0) cc_final: 0.7835 (t0) REVERT: A 491 MET cc_start: 0.7991 (mmm) cc_final: 0.7454 (mmp) REVERT: B 35 ARG cc_start: 0.8192 (ttt90) cc_final: 0.7903 (tpt-90) REVERT: B 57 ASP cc_start: 0.7910 (p0) cc_final: 0.7634 (p0) REVERT: B 80 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7796 (pt0) REVERT: B 93 GLU cc_start: 0.7647 (mp0) cc_final: 0.7272 (mp0) REVERT: B 184 GLU cc_start: 0.7653 (mt-10) cc_final: 0.7252 (tp30) REVERT: B 190 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7653 (mtm180) REVERT: B 214 GLN cc_start: 0.7991 (mm-40) cc_final: 0.7654 (mt0) REVERT: B 215 MET cc_start: 0.8737 (mmm) cc_final: 0.8467 (mmt) REVERT: B 306 GLN cc_start: 0.7915 (mt0) cc_final: 0.7363 (mp10) REVERT: B 381 GLN cc_start: 0.6874 (mp10) cc_final: 0.5874 (mm-40) REVERT: B 421 LEU cc_start: 0.8747 (mm) cc_final: 0.8411 (mp) REVERT: B 491 MET cc_start: 0.7995 (mmm) cc_final: 0.7462 (mmp) REVERT: C 35 ARG cc_start: 0.8186 (ttt90) cc_final: 0.7903 (tpt-90) REVERT: C 93 GLU cc_start: 0.7638 (mp0) cc_final: 0.7250 (mp0) REVERT: C 184 GLU cc_start: 0.7675 (mt-10) cc_final: 0.7284 (tp30) REVERT: C 190 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7600 (mtm180) REVERT: C 214 GLN cc_start: 0.8016 (mm-40) cc_final: 0.7666 (mt0) REVERT: C 215 MET cc_start: 0.8747 (mmm) cc_final: 0.8477 (mmt) REVERT: C 306 GLN cc_start: 0.7918 (mt0) cc_final: 0.7373 (mp10) REVERT: C 381 GLN cc_start: 0.6842 (mp10) cc_final: 0.5864 (mm-40) REVERT: C 421 LEU cc_start: 0.8768 (mm) cc_final: 0.8427 (mp) REVERT: C 448 ASN cc_start: 0.8086 (t0) cc_final: 0.7878 (t0) REVERT: C 487 PHE cc_start: 0.8963 (m-10) cc_final: 0.8761 (m-10) REVERT: C 491 MET cc_start: 0.7979 (mmm) cc_final: 0.7444 (mmp) REVERT: D 35 ARG cc_start: 0.8194 (ttt90) cc_final: 0.7915 (tpt-90) REVERT: D 57 ASP cc_start: 0.7893 (p0) cc_final: 0.7578 (p0) REVERT: D 80 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.7808 (pt0) REVERT: D 93 GLU cc_start: 0.7640 (mp0) cc_final: 0.7263 (mp0) REVERT: D 184 GLU cc_start: 0.7660 (mt-10) cc_final: 0.7333 (tp30) REVERT: D 190 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.7638 (mtm180) REVERT: D 214 GLN cc_start: 0.7991 (mm-40) cc_final: 0.7664 (mt0) REVERT: D 215 MET cc_start: 0.8743 (mmm) cc_final: 0.8483 (mmt) REVERT: D 306 GLN cc_start: 0.7925 (mt0) cc_final: 0.7380 (mp10) REVERT: D 381 GLN cc_start: 0.6888 (mp10) cc_final: 0.5889 (mm-40) REVERT: D 421 LEU cc_start: 0.8760 (mm) cc_final: 0.8435 (mp) REVERT: D 448 ASN cc_start: 0.8095 (t0) cc_final: 0.7887 (t0) REVERT: D 491 MET cc_start: 0.7977 (mmm) cc_final: 0.7439 (mmp) outliers start: 56 outliers final: 31 residues processed: 361 average time/residue: 0.5611 time to fit residues: 229.5194 Evaluate side-chains 336 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 299 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 548 SER Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 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 387 VAL Chi-restraints excluded: chain C residue 514 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 224 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 229 optimal weight: 1.9990 chunk 177 optimal weight: 0.9980 chunk 228 optimal weight: 0.9990 chunk 167 optimal weight: 0.8980 chunk 208 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 77 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN B 40 GLN B 261 GLN C 261 GLN D 40 GLN D 261 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.148441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.110565 restraints weight = 22024.751| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 1.63 r_work: 0.3037 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2995 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= 0.122 Angle : 0.519 5.828 27612 Z= 0.264 Chirality : 0.038 0.156 3128 Planarity : 0.004 0.053 3424 Dihedral : 8.634 80.136 3428 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.68 % Allowed : 11.63 % Favored : 86.68 % 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 are not related in a simple way. whole: 1.93 (0.17), residues: 2384 helix: 1.66 (0.13), residues: 1544 sheet: -1.22 (0.52), residues: 80 loop : 1.01 (0.25), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 409 TYR 0.012 0.001 TYR A 467 PHE 0.015 0.001 PHE C 611 TRP 0.016 0.001 TRP D 593 HIS 0.002 0.001 HIS A 122 Details of bonding type rmsd covalent geometry : bond 0.00277 (20352) covalent geometry : angle 0.51915 (27612) hydrogen bonds : bond 0.04183 ( 1189) hydrogen bonds : angle 3.91895 ( 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 339 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 304 time to evaluate : 0.785 Fit side-chains REVERT: A 35 ARG cc_start: 0.8183 (ttt90) cc_final: 0.7948 (tpt-90) REVERT: A 93 GLU cc_start: 0.7543 (mp0) cc_final: 0.7194 (mp0) REVERT: A 108 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7485 (mm-30) REVERT: A 184 GLU cc_start: 0.7540 (mt-10) cc_final: 0.7306 (tp30) REVERT: A 214 GLN cc_start: 0.8007 (mm-40) cc_final: 0.7639 (mt0) REVERT: A 306 GLN cc_start: 0.7858 (mt0) cc_final: 0.7352 (mp10) REVERT: A 381 GLN cc_start: 0.6833 (mp10) cc_final: 0.5884 (mm-40) REVERT: A 421 LEU cc_start: 0.8677 (mm) cc_final: 0.8357 (mp) REVERT: A 448 ASN cc_start: 0.8046 (t0) cc_final: 0.7828 (t0) REVERT: A 491 MET cc_start: 0.7950 (mmm) cc_final: 0.7427 (mmp) REVERT: B 35 ARG cc_start: 0.8145 (ttt90) cc_final: 0.7900 (tpt-90) REVERT: B 57 ASP cc_start: 0.7887 (p0) cc_final: 0.7646 (p0) REVERT: B 93 GLU cc_start: 0.7589 (mp0) cc_final: 0.7229 (mp0) REVERT: B 108 GLU cc_start: 0.7748 (mm-30) cc_final: 0.7482 (mm-30) REVERT: B 184 GLU cc_start: 0.7533 (mt-10) cc_final: 0.7214 (tp30) REVERT: B 214 GLN cc_start: 0.8019 (mm-40) cc_final: 0.7669 (mt0) REVERT: B 215 MET cc_start: 0.8766 (mmm) cc_final: 0.8509 (mmt) REVERT: B 302 ARG cc_start: 0.7897 (mtm110) cc_final: 0.7246 (ttp80) REVERT: B 306 GLN cc_start: 0.7819 (mt0) cc_final: 0.7329 (mp10) REVERT: B 381 GLN cc_start: 0.6817 (mp10) cc_final: 0.5876 (mm-40) REVERT: B 421 LEU cc_start: 0.8661 (mm) cc_final: 0.8320 (mp) REVERT: B 491 MET cc_start: 0.7965 (mmm) cc_final: 0.7440 (mmp) REVERT: C 35 ARG cc_start: 0.8151 (ttt90) cc_final: 0.7904 (tpt-90) REVERT: C 57 ASP cc_start: 0.7865 (p0) cc_final: 0.7601 (p0) REVERT: C 93 GLU cc_start: 0.7596 (mp0) cc_final: 0.7237 (mp0) REVERT: C 184 GLU cc_start: 0.7521 (mt-10) cc_final: 0.7219 (tp30) REVERT: C 214 GLN cc_start: 0.8040 (mm-40) cc_final: 0.7674 (mt0) REVERT: C 215 MET cc_start: 0.8773 (mmm) cc_final: 0.8519 (mmt) REVERT: C 306 GLN cc_start: 0.7850 (mt0) cc_final: 0.7316 (mp10) REVERT: C 381 GLN cc_start: 0.6824 (mp10) cc_final: 0.5880 (mm-40) REVERT: C 421 LEU cc_start: 0.8663 (mm) cc_final: 0.8335 (mp) REVERT: C 448 ASN cc_start: 0.8062 (t0) cc_final: 0.7848 (t0) REVERT: C 487 PHE cc_start: 0.8914 (m-10) cc_final: 0.8695 (m-10) REVERT: C 491 MET cc_start: 0.7945 (mmm) cc_final: 0.7419 (mmp) REVERT: D 35 ARG cc_start: 0.8156 (ttt90) cc_final: 0.7910 (tpt-90) REVERT: D 57 ASP cc_start: 0.7880 (p0) cc_final: 0.7603 (p0) REVERT: D 93 GLU cc_start: 0.7596 (mp0) cc_final: 0.7238 (mp0) REVERT: D 108 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7488 (mm-30) REVERT: D 184 GLU cc_start: 0.7566 (mt-10) cc_final: 0.7246 (tp30) REVERT: D 214 GLN cc_start: 0.8031 (mm-40) cc_final: 0.7663 (mt0) REVERT: D 215 MET cc_start: 0.8754 (mmm) cc_final: 0.8419 (mmt) REVERT: D 306 GLN cc_start: 0.7812 (mt0) cc_final: 0.7278 (mp10) REVERT: D 381 GLN cc_start: 0.6877 (mp10) cc_final: 0.5900 (mm-40) REVERT: D 421 LEU cc_start: 0.8670 (mm) cc_final: 0.8344 (mp) REVERT: D 448 ASN cc_start: 0.8065 (t0) cc_final: 0.7845 (t0) REVERT: D 491 MET cc_start: 0.7956 (mmm) cc_final: 0.7431 (mmp) outliers start: 35 outliers final: 18 residues processed: 330 average time/residue: 0.5901 time to fit residues: 219.6978 Evaluate side-chains 309 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 291 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ASP 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 B residue 90 ASP 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 C residue 90 ASP Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 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 311 THR Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 514 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 107 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 147 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 109 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 223 optimal weight: 0.0270 chunk 184 optimal weight: 0.0270 chunk 92 optimal weight: 0.0870 overall best weight: 0.2674 ------------------------------------------------------------------------------- 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 = 0.3645 r_free = 0.3645 target = 0.153421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.116448 restraints weight = 21817.110| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.58 r_work: 0.3130 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 20352 Z= 0.099 Angle : 0.502 7.706 27612 Z= 0.251 Chirality : 0.037 0.166 3128 Planarity : 0.004 0.046 3424 Dihedral : 8.167 74.074 3428 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 0.77 % Allowed : 12.98 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.29 (0.17), residues: 2384 helix: 1.90 (0.13), residues: 1540 sheet: -1.43 (0.50), residues: 80 loop : 1.30 (0.25), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 409 TYR 0.014 0.001 TYR A 467 PHE 0.015 0.001 PHE C 611 TRP 0.017 0.001 TRP D 593 HIS 0.002 0.001 HIS A 122 Details of bonding type rmsd covalent geometry : bond 0.00207 (20352) covalent geometry : angle 0.50195 (27612) hydrogen bonds : bond 0.03702 ( 1189) hydrogen bonds : angle 3.83133 ( 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 331 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 315 time to evaluate : 0.733 Fit side-chains REVERT: A 35 ARG cc_start: 0.8165 (ttt90) cc_final: 0.7952 (tpt-90) REVERT: A 93 GLU cc_start: 0.7577 (mp0) cc_final: 0.7206 (mp0) REVERT: A 108 GLU cc_start: 0.7596 (mm-30) cc_final: 0.7310 (mm-30) REVERT: A 139 ARG cc_start: 0.8169 (mtp180) cc_final: 0.7932 (mtp85) REVERT: A 214 GLN cc_start: 0.8042 (mm-40) cc_final: 0.7702 (mt0) REVERT: A 221 SER cc_start: 0.9000 (t) cc_final: 0.8574 (p) REVERT: A 302 ARG cc_start: 0.7853 (mtm110) cc_final: 0.7136 (ttt-90) REVERT: A 306 GLN cc_start: 0.7817 (mt0) cc_final: 0.7385 (mp10) REVERT: A 318 SER cc_start: 0.8686 (t) cc_final: 0.8361 (m) REVERT: A 381 GLN cc_start: 0.6872 (mp10) cc_final: 0.5954 (mm-40) REVERT: A 421 LEU cc_start: 0.8659 (mm) cc_final: 0.8364 (mp) REVERT: A 491 MET cc_start: 0.7908 (mmm) cc_final: 0.7412 (mmp) REVERT: B 35 ARG cc_start: 0.8178 (ttt90) cc_final: 0.7974 (tpt-90) REVERT: B 93 GLU cc_start: 0.7586 (mp0) cc_final: 0.7269 (mp0) REVERT: B 107 LYS cc_start: 0.7785 (mtmm) cc_final: 0.7414 (mtpp) REVERT: B 108 GLU cc_start: 0.7579 (mm-30) cc_final: 0.7340 (mm-30) REVERT: B 139 ARG cc_start: 0.8125 (mtp180) cc_final: 0.7843 (mtp85) REVERT: B 214 GLN cc_start: 0.8059 (mm-40) cc_final: 0.7696 (mt0) REVERT: B 221 SER cc_start: 0.8974 (t) cc_final: 0.8537 (p) REVERT: B 302 ARG cc_start: 0.7847 (mtm110) cc_final: 0.7181 (ttt-90) REVERT: B 306 GLN cc_start: 0.7799 (mt0) cc_final: 0.7371 (mp10) REVERT: B 318 SER cc_start: 0.8690 (t) cc_final: 0.8363 (m) REVERT: B 381 GLN cc_start: 0.6860 (mp10) cc_final: 0.5955 (mm-40) REVERT: B 421 LEU cc_start: 0.8680 (mm) cc_final: 0.8371 (mp) REVERT: B 491 MET cc_start: 0.7914 (mmm) cc_final: 0.7417 (mmp) REVERT: C 35 ARG cc_start: 0.8162 (ttt90) cc_final: 0.7961 (tpt-90) REVERT: C 93 GLU cc_start: 0.7561 (mp0) cc_final: 0.7183 (mp0) REVERT: C 107 LYS cc_start: 0.7780 (mtmm) cc_final: 0.7415 (mtpp) REVERT: C 108 GLU cc_start: 0.7559 (mm-30) cc_final: 0.7318 (mm-30) REVERT: C 139 ARG cc_start: 0.8128 (mtp180) cc_final: 0.7853 (mtp85) REVERT: C 214 GLN cc_start: 0.8078 (mm-40) cc_final: 0.7701 (mt0) REVERT: C 221 SER cc_start: 0.8988 (t) cc_final: 0.8558 (p) REVERT: C 302 ARG cc_start: 0.7832 (mtm110) cc_final: 0.7148 (ttt-90) REVERT: C 306 GLN cc_start: 0.7810 (mt0) cc_final: 0.7386 (mp10) REVERT: C 318 SER cc_start: 0.8677 (t) cc_final: 0.8338 (m) REVERT: C 381 GLN cc_start: 0.6852 (mp10) cc_final: 0.5932 (mm-40) REVERT: C 409 ARG cc_start: 0.7072 (mtp-110) cc_final: 0.6846 (ttm-80) REVERT: C 421 LEU cc_start: 0.8667 (mm) cc_final: 0.8374 (mp) REVERT: C 487 PHE cc_start: 0.8835 (m-10) cc_final: 0.8617 (m-10) REVERT: C 491 MET cc_start: 0.7891 (mmm) cc_final: 0.7398 (mmp) REVERT: D 93 GLU cc_start: 0.7580 (mp0) cc_final: 0.7266 (mp0) REVERT: D 107 LYS cc_start: 0.7792 (mtmm) cc_final: 0.7419 (mtpp) REVERT: D 108 GLU cc_start: 0.7572 (mm-30) cc_final: 0.7334 (mm-30) REVERT: D 139 ARG cc_start: 0.8152 (mtp180) cc_final: 0.7877 (mtp85) REVERT: D 184 GLU cc_start: 0.7567 (mt-10) cc_final: 0.7364 (tp30) REVERT: D 214 GLN cc_start: 0.8055 (mm-40) cc_final: 0.7691 (mt0) REVERT: D 215 MET cc_start: 0.8836 (mmm) cc_final: 0.8570 (mmt) REVERT: D 221 SER cc_start: 0.8954 (t) cc_final: 0.8529 (p) REVERT: D 302 ARG cc_start: 0.7816 (mtm110) cc_final: 0.7136 (ttt-90) REVERT: D 306 GLN cc_start: 0.7809 (mt0) cc_final: 0.7385 (mp10) REVERT: D 318 SER cc_start: 0.8694 (t) cc_final: 0.8365 (m) REVERT: D 381 GLN cc_start: 0.6863 (mp10) cc_final: 0.5964 (mm-40) REVERT: D 409 ARG cc_start: 0.7071 (mtp-110) cc_final: 0.6842 (ttm-80) REVERT: D 421 LEU cc_start: 0.8666 (mm) cc_final: 0.8381 (mp) REVERT: D 491 MET cc_start: 0.7918 (mmm) cc_final: 0.7419 (mmp) outliers start: 16 outliers final: 10 residues processed: 329 average time/residue: 0.5912 time to fit residues: 219.7290 Evaluate side-chains 304 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 294 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain D residue 129 ASN Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 335 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 33 optimal weight: 0.7980 chunk 187 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 chunk 102 optimal weight: 0.9980 chunk 216 optimal weight: 2.9990 chunk 177 optimal weight: 0.7980 chunk 171 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 224 optimal weight: 0.5980 chunk 61 optimal weight: 4.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 GLN B 40 GLN B 261 GLN ** C 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 GLN D 40 GLN D 261 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.149840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.111908 restraints weight = 21746.050| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 1.63 r_work: 0.3051 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.3239 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= 0.126 Angle : 0.523 6.607 27612 Z= 0.263 Chirality : 0.038 0.185 3128 Planarity : 0.004 0.056 3424 Dihedral : 8.256 74.361 3428 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.62 % Allowed : 13.41 % Favored : 85.96 % 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 are not related in a simple way. whole: 2.26 (0.17), residues: 2384 helix: 1.88 (0.13), residues: 1540 sheet: -1.49 (0.51), residues: 80 loop : 1.29 (0.25), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 409 TYR 0.011 0.001 TYR B 555 PHE 0.016 0.001 PHE D 611 TRP 0.012 0.001 TRP C 593 HIS 0.003 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00294 (20352) covalent geometry : angle 0.52293 (27612) hydrogen bonds : bond 0.04093 ( 1189) hydrogen bonds : angle 3.84010 ( 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 311 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 298 time to evaluate : 0.786 Fit side-chains REVERT: A 35 ARG cc_start: 0.8104 (ttt90) cc_final: 0.7902 (tpt-90) REVERT: A 93 GLU cc_start: 0.7560 (mp0) cc_final: 0.7204 (mp0) REVERT: A 108 GLU cc_start: 0.7562 (mm-30) cc_final: 0.7223 (mm-30) REVERT: A 139 ARG cc_start: 0.8111 (mtp180) cc_final: 0.7857 (mtp85) REVERT: A 214 GLN cc_start: 0.7984 (mm-40) cc_final: 0.7602 (mt0) REVERT: A 302 ARG cc_start: 0.7914 (mtm110) cc_final: 0.7118 (ttt-90) REVERT: A 306 GLN cc_start: 0.7809 (mt0) cc_final: 0.7312 (mp10) REVERT: A 318 SER cc_start: 0.8680 (t) cc_final: 0.8325 (m) REVERT: A 381 GLN cc_start: 0.6831 (mp10) cc_final: 0.5879 (mm-40) REVERT: A 421 LEU cc_start: 0.8621 (mm) cc_final: 0.8308 (mp) REVERT: A 487 PHE cc_start: 0.8888 (m-10) cc_final: 0.8682 (m-10) REVERT: A 491 MET cc_start: 0.7923 (mmm) cc_final: 0.7401 (mmp) REVERT: B 35 ARG cc_start: 0.8103 (ttt90) cc_final: 0.7895 (tpt-90) REVERT: B 93 GLU cc_start: 0.7568 (mp0) cc_final: 0.7188 (mp0) REVERT: B 107 LYS cc_start: 0.7754 (mtmm) cc_final: 0.7389 (mtpp) REVERT: B 108 GLU cc_start: 0.7576 (mm-30) cc_final: 0.7247 (mm-30) REVERT: B 139 ARG cc_start: 0.8116 (mtp180) cc_final: 0.7816 (mtp85) REVERT: B 214 GLN cc_start: 0.7989 (mm-40) cc_final: 0.7626 (mt0) REVERT: B 302 ARG cc_start: 0.7872 (mtm110) cc_final: 0.7146 (ttt-90) REVERT: B 306 GLN cc_start: 0.7807 (mt0) cc_final: 0.7308 (mp10) REVERT: B 318 SER cc_start: 0.8674 (t) cc_final: 0.8318 (m) REVERT: B 381 GLN cc_start: 0.6833 (mp10) cc_final: 0.5892 (mm-40) REVERT: B 421 LEU cc_start: 0.8636 (mm) cc_final: 0.8304 (mp) REVERT: B 491 MET cc_start: 0.7930 (mmm) cc_final: 0.7406 (mmp) REVERT: C 57 ASP cc_start: 0.7836 (p0) cc_final: 0.7573 (p0) REVERT: C 80 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7741 (pt0) REVERT: C 93 GLU cc_start: 0.7539 (mp0) cc_final: 0.7156 (mp0) REVERT: C 107 LYS cc_start: 0.7743 (mtmm) cc_final: 0.7376 (mtpp) REVERT: C 108 GLU cc_start: 0.7575 (mm-30) cc_final: 0.7239 (mm-30) REVERT: C 139 ARG cc_start: 0.8111 (mtp180) cc_final: 0.7815 (mtp85) REVERT: C 214 GLN cc_start: 0.7994 (mm-40) cc_final: 0.7615 (mt0) REVERT: C 302 ARG cc_start: 0.7916 (mtm110) cc_final: 0.7141 (ttt-90) REVERT: C 306 GLN cc_start: 0.7797 (mt0) cc_final: 0.7308 (mp10) REVERT: C 318 SER cc_start: 0.8663 (t) cc_final: 0.8285 (m) REVERT: C 381 GLN cc_start: 0.6800 (mp10) cc_final: 0.5852 (mm-40) REVERT: C 421 LEU cc_start: 0.8623 (mm) cc_final: 0.8318 (mp) REVERT: C 487 PHE cc_start: 0.8861 (m-10) cc_final: 0.8619 (m-10) REVERT: C 491 MET cc_start: 0.7926 (mmm) cc_final: 0.7402 (mmp) REVERT: D 93 GLU cc_start: 0.7551 (mp0) cc_final: 0.7177 (mp0) REVERT: D 107 LYS cc_start: 0.7736 (mtmm) cc_final: 0.7372 (mtpp) REVERT: D 108 GLU cc_start: 0.7559 (mm-30) cc_final: 0.7203 (mm-30) REVERT: D 139 ARG cc_start: 0.8122 (mtp180) cc_final: 0.7827 (mtp85) REVERT: D 184 GLU cc_start: 0.7550 (mt-10) cc_final: 0.7302 (tp30) REVERT: D 214 GLN cc_start: 0.7988 (mm-40) cc_final: 0.7608 (mt0) REVERT: D 302 ARG cc_start: 0.7903 (mtm110) cc_final: 0.7133 (ttt-90) REVERT: D 306 GLN cc_start: 0.7802 (mt0) cc_final: 0.7304 (mp10) REVERT: D 318 SER cc_start: 0.8677 (t) cc_final: 0.8316 (m) REVERT: D 381 GLN cc_start: 0.6852 (mp10) cc_final: 0.5898 (mm-40) REVERT: D 421 LEU cc_start: 0.8636 (mm) cc_final: 0.8333 (mp) REVERT: D 487 PHE cc_start: 0.8879 (m-10) cc_final: 0.8673 (m-10) REVERT: D 491 MET cc_start: 0.7929 (mmm) cc_final: 0.7404 (mmp) outliers start: 13 outliers final: 10 residues processed: 309 average time/residue: 0.5850 time to fit residues: 203.8203 Evaluate side-chains 303 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 292 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 335 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 182 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 5 optimal weight: 8.9990 chunk 127 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 157 optimal weight: 1.9990 chunk 192 optimal weight: 0.1980 chunk 203 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN A 261 GLN B 40 GLN B 261 GLN C 74 GLN C 261 GLN D 40 GLN D 74 GLN D 261 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.148579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.111107 restraints weight = 21890.778| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 1.55 r_work: 0.3045 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.3206 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= 0.136 Angle : 0.542 7.136 27612 Z= 0.271 Chirality : 0.038 0.169 3128 Planarity : 0.004 0.061 3424 Dihedral : 8.355 74.972 3428 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 0.72 % Allowed : 13.65 % Favored : 85.62 % 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 are not related in a simple way. whole: 2.19 (0.17), residues: 2384 helix: 1.84 (0.13), residues: 1532 sheet: -1.54 (0.51), residues: 80 loop : 1.23 (0.25), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 409 TYR 0.011 0.001 TYR B 555 PHE 0.016 0.001 PHE D 611 TRP 0.012 0.001 TRP C 593 HIS 0.005 0.001 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00325 (20352) covalent geometry : angle 0.54211 (27612) hydrogen bonds : bond 0.04240 ( 1189) hydrogen bonds : angle 3.88753 ( 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 314 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 299 time to evaluate : 0.777 Fit side-chains REVERT: A 35 ARG cc_start: 0.8152 (ttt90) cc_final: 0.7949 (tpt-90) REVERT: A 57 ASP cc_start: 0.7972 (p0) cc_final: 0.7734 (p0) REVERT: A 93 GLU cc_start: 0.7599 (mp0) cc_final: 0.7262 (mp0) REVERT: A 108 GLU cc_start: 0.7522 (mm-30) cc_final: 0.7224 (mm-30) REVERT: A 139 ARG cc_start: 0.8075 (mtp180) cc_final: 0.7819 (mtp85) REVERT: A 214 GLN cc_start: 0.7979 (mm-40) cc_final: 0.7653 (mt0) REVERT: A 302 ARG cc_start: 0.7971 (mtm110) cc_final: 0.7188 (ttt-90) REVERT: A 306 GLN cc_start: 0.7846 (mt0) cc_final: 0.7381 (mp10) REVERT: A 318 SER cc_start: 0.8711 (t) cc_final: 0.8352 (m) REVERT: A 381 GLN cc_start: 0.6845 (mp10) cc_final: 0.5914 (mm-40) REVERT: A 421 LEU cc_start: 0.8689 (mm) cc_final: 0.8412 (mp) REVERT: A 487 PHE cc_start: 0.8905 (m-10) cc_final: 0.8699 (m-10) REVERT: A 491 MET cc_start: 0.7999 (mmm) cc_final: 0.7507 (mmp) REVERT: B 57 ASP cc_start: 0.7953 (p0) cc_final: 0.7717 (p0) REVERT: B 93 GLU cc_start: 0.7607 (mp0) cc_final: 0.7309 (mp0) REVERT: B 107 LYS cc_start: 0.7707 (mtmm) cc_final: 0.7316 (mtpp) REVERT: B 108 GLU cc_start: 0.7541 (mm-30) cc_final: 0.7235 (mm-30) REVERT: B 139 ARG cc_start: 0.8067 (mtp180) cc_final: 0.7766 (mtp85) REVERT: B 214 GLN cc_start: 0.7987 (mm-40) cc_final: 0.7671 (mt0) REVERT: B 215 MET cc_start: 0.8840 (mmm) cc_final: 0.8552 (mmt) REVERT: B 306 GLN cc_start: 0.7842 (mt0) cc_final: 0.7398 (mp10) REVERT: B 318 SER cc_start: 0.8711 (t) cc_final: 0.8352 (m) REVERT: B 381 GLN cc_start: 0.6860 (mp10) cc_final: 0.5937 (mm-40) REVERT: B 421 LEU cc_start: 0.8687 (mm) cc_final: 0.8390 (mp) REVERT: B 448 ASN cc_start: 0.7822 (t0) cc_final: 0.7568 (m-40) REVERT: B 491 MET cc_start: 0.8008 (mmm) cc_final: 0.7516 (mmp) REVERT: C 57 ASP cc_start: 0.7943 (p0) cc_final: 0.7693 (p0) REVERT: C 93 GLU cc_start: 0.7599 (mp0) cc_final: 0.7249 (mp0) REVERT: C 107 LYS cc_start: 0.7709 (mtmm) cc_final: 0.7318 (mtpp) REVERT: C 108 GLU cc_start: 0.7524 (mm-30) cc_final: 0.7220 (mm-30) REVERT: C 139 ARG cc_start: 0.8062 (mtp180) cc_final: 0.7768 (mtp85) REVERT: C 214 GLN cc_start: 0.7991 (mm-40) cc_final: 0.7673 (mt0) REVERT: C 215 MET cc_start: 0.8840 (mmm) cc_final: 0.8558 (mmt) REVERT: C 302 ARG cc_start: 0.7967 (mtm110) cc_final: 0.7201 (ttt-90) REVERT: C 306 GLN cc_start: 0.7848 (mt0) cc_final: 0.7387 (mp10) REVERT: C 381 GLN cc_start: 0.6826 (mp10) cc_final: 0.5904 (mm-40) REVERT: C 421 LEU cc_start: 0.8673 (mm) cc_final: 0.8387 (mp) REVERT: C 487 PHE cc_start: 0.8890 (m-10) cc_final: 0.8658 (m-10) REVERT: C 491 MET cc_start: 0.7999 (mmm) cc_final: 0.7511 (mmp) REVERT: D 57 ASP cc_start: 0.7953 (p0) cc_final: 0.7722 (p0) REVERT: D 93 GLU cc_start: 0.7582 (mp0) cc_final: 0.7289 (mp0) REVERT: D 107 LYS cc_start: 0.7722 (mtmm) cc_final: 0.7328 (mtpp) REVERT: D 108 GLU cc_start: 0.7527 (mm-30) cc_final: 0.7262 (mm-30) REVERT: D 139 ARG cc_start: 0.8075 (mtp180) cc_final: 0.7781 (mtp85) REVERT: D 184 GLU cc_start: 0.7517 (mt-10) cc_final: 0.7297 (tp30) REVERT: D 214 GLN cc_start: 0.7983 (mm-40) cc_final: 0.7657 (mt0) REVERT: D 302 ARG cc_start: 0.7957 (mtm110) cc_final: 0.7209 (ttt-90) REVERT: D 306 GLN cc_start: 0.7855 (mt0) cc_final: 0.7390 (mp10) REVERT: D 318 SER cc_start: 0.8706 (t) cc_final: 0.8342 (m) REVERT: D 381 GLN cc_start: 0.6920 (mp10) cc_final: 0.5952 (mm-40) REVERT: D 421 LEU cc_start: 0.8680 (mm) cc_final: 0.8396 (mp) REVERT: D 487 PHE cc_start: 0.8903 (m-10) cc_final: 0.8691 (m-10) REVERT: D 491 MET cc_start: 0.7990 (mmm) cc_final: 0.7499 (mmp) outliers start: 15 outliers final: 11 residues processed: 314 average time/residue: 0.6113 time to fit residues: 216.4220 Evaluate side-chains 308 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 297 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 335 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 178 optimal weight: 9.9990 chunk 87 optimal weight: 1.9990 chunk 150 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 117 optimal weight: 0.0870 chunk 27 optimal weight: 0.9980 chunk 204 optimal weight: 5.9990 chunk 134 optimal weight: 0.6980 chunk 60 optimal weight: 10.0000 chunk 222 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN B 40 GLN B 261 GLN C 261 GLN D 40 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.150765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.113675 restraints weight = 21810.632| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.55 r_work: 0.3081 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.3325 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= 0.113 Angle : 0.513 6.933 27612 Z= 0.259 Chirality : 0.037 0.151 3128 Planarity : 0.004 0.065 3424 Dihedral : 8.207 73.266 3428 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 0.58 % Allowed : 13.56 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.30 (0.17), residues: 2384 helix: 1.93 (0.13), residues: 1536 sheet: -1.64 (0.50), residues: 80 loop : 1.28 (0.25), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 409 TYR 0.010 0.001 TYR B 555 PHE 0.016 0.001 PHE D 611 TRP 0.014 0.001 TRP C 593 HIS 0.002 0.001 HIS D 201 Details of bonding type rmsd covalent geometry : bond 0.00254 (20352) covalent geometry : angle 0.51267 (27612) hydrogen bonds : bond 0.03959 ( 1189) hydrogen bonds : angle 3.84888 ( 3315) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6444.32 seconds wall clock time: 110 minutes 36.16 seconds (6636.16 seconds total)