Starting phenix.real_space_refine on Wed May 21 21:20:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gka_40181/05_2025/8gka_40181.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gka_40181/05_2025/8gka_40181.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gka_40181/05_2025/8gka_40181.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gka_40181/05_2025/8gka_40181.map" model { file = "/net/cci-nas-00/data/ceres_data/8gka_40181/05_2025/8gka_40181.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gka_40181/05_2025/8gka_40181.cif" } resolution = 2.55 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.128 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 33 5.49 5 S 124 5.16 5 Na 1 4.78 5 C 14361 2.51 5 N 3409 2.21 5 O 3884 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 21812 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 625, 5090 Classifications: {'peptide': 625} Link IDs: {'PTRANS': 15, 'TRANS': 609} Chain breaks: 1 Chain: "B" Number of atoms: 5090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 625, 5090 Classifications: {'peptide': 625} Link IDs: {'PTRANS': 15, 'TRANS': 609} Chain breaks: 1 Chain: "C" Number of atoms: 5090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 625, 5090 Classifications: {'peptide': 625} Link IDs: {'PTRANS': 15, 'TRANS': 609} Chain breaks: 1 Chain: "D" Number of atoms: 5090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 625, 5090 Classifications: {'peptide': 625} Link IDs: {'PTRANS': 15, 'TRANS': 609} Chain breaks: 1 Chain: "A" Number of atoms: 354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 354 Unusual residues: {' NA': 1, 'POV': 8} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'POV:plan-1': 3} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 435 Unusual residues: {'POV': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 85 Planarities with less than four sites: {'POV:plan-1': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 291 Unusual residues: {'POV': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 73 Planarities with less than four sites: {'POV:plan-1': 3} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 372 Unusual residues: {'POV': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'POV:plan-1': 3} Unresolved non-hydrogen planarities: 6 Time building chain proxies: 11.92, per 1000 atoms: 0.55 Number of scatterers: 21812 At special positions: 0 Unit cell: (164.628, 164.628, 129.12, 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) S 124 16.00 P 33 15.00 Na 1 11.00 O 3884 8.00 N 3409 7.00 C 14361 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 612 " - pdb=" SG CYS A 619 " distance=2.03 Simple disulfide: pdb=" SG CYS B 612 " - pdb=" SG CYS B 619 " distance=2.03 Simple disulfide: pdb=" SG CYS C 612 " - pdb=" SG CYS C 619 " distance=2.03 Simple disulfide: pdb=" SG CYS D 612 " - pdb=" SG CYS D 619 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.10 Conformation dependent library (CDL) restraints added in 2.5 seconds 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4776 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 4 sheets defined 64.6% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.79 Creating SS restraints... Processing helix chain 'A' and resid 118 through 130 Processing helix chain 'A' and resid 134 through 148 removed outlier: 3.586A pdb=" N ARG A 147 " --> pdb=" O GLN A 143 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ARG A 148 " --> pdb=" O GLU A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 163 removed outlier: 3.954A pdb=" N PHE A 157 " --> pdb=" O ASP A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 178 Processing helix chain 'A' and resid 182 through 197 Processing helix chain 'A' and resid 199 through 205 removed outlier: 3.699A pdb=" N ASN A 205 " --> pdb=" O GLY A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 225 Processing helix chain 'A' and resid 227 through 238 Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 274 through 284 Processing helix chain 'A' and resid 298 through 307 Processing helix chain 'A' and resid 315 through 329 Processing helix chain 'A' and resid 343 through 352 removed outlier: 3.724A pdb=" N ALA A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 362 Processing helix chain 'A' and resid 402 through 410 Processing helix chain 'A' and resid 415 through 420 Processing helix chain 'A' and resid 422 through 434 removed outlier: 3.525A pdb=" N THR A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 461 Processing helix chain 'A' and resid 483 through 509 removed outlier: 3.539A pdb=" N ARG A 487 " --> pdb=" O GLN A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 520 Processing helix chain 'A' and resid 520 through 542 removed outlier: 3.659A pdb=" N PHE A 527 " --> pdb=" O HIS A 523 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE A 542 " --> pdb=" O PHE A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 561 Processing helix chain 'A' and resid 562 through 567 Processing helix chain 'A' and resid 569 through 586 Processing helix chain 'A' and resid 586 through 608 removed outlier: 3.614A pdb=" N VAL A 593 " --> pdb=" O LYS A 589 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA A 604 " --> pdb=" O GLY A 600 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU A 608 " --> pdb=" O ALA A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 637 Processing helix chain 'A' and resid 650 through 666 Processing helix chain 'A' and resid 668 through 686 removed outlier: 3.898A pdb=" N ILE A 674 " --> pdb=" O LEU A 670 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA A 675 " --> pdb=" O ASN A 671 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS A 686 " --> pdb=" O GLU A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 707 removed outlier: 3.537A pdb=" N THR A 699 " --> pdb=" O GLN A 695 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU A 707 " --> pdb=" O PHE A 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 130 Processing helix chain 'B' and resid 134 through 148 removed outlier: 3.587A pdb=" N ARG B 147 " --> pdb=" O GLN B 143 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ARG B 148 " --> pdb=" O GLU B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 163 removed outlier: 3.955A pdb=" N PHE B 157 " --> pdb=" O ASP B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 178 Processing helix chain 'B' and resid 182 through 197 Processing helix chain 'B' and resid 199 through 205 removed outlier: 3.699A pdb=" N ASN B 205 " --> pdb=" O GLY B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 225 Processing helix chain 'B' and resid 227 through 238 Processing helix chain 'B' and resid 264 through 272 Processing helix chain 'B' and resid 274 through 284 Processing helix chain 'B' and resid 298 through 307 Processing helix chain 'B' and resid 315 through 329 Processing helix chain 'B' and resid 343 through 352 removed outlier: 3.724A pdb=" N ALA B 349 " --> pdb=" O LEU B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 362 Processing helix chain 'B' and resid 402 through 410 Processing helix chain 'B' and resid 415 through 420 Processing helix chain 'B' and resid 422 through 434 removed outlier: 3.525A pdb=" N THR B 427 " --> pdb=" O GLU B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 461 Processing helix chain 'B' and resid 483 through 509 removed outlier: 3.539A pdb=" N ARG B 487 " --> pdb=" O GLN B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 520 Processing helix chain 'B' and resid 520 through 542 removed outlier: 3.659A pdb=" N PHE B 527 " --> pdb=" O HIS B 523 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE B 542 " --> pdb=" O PHE B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 561 Processing helix chain 'B' and resid 562 through 567 Processing helix chain 'B' and resid 569 through 586 Processing helix chain 'B' and resid 586 through 608 removed outlier: 3.614A pdb=" N VAL B 593 " --> pdb=" O LYS B 589 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA B 604 " --> pdb=" O GLY B 600 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU B 608 " --> pdb=" O ALA B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 637 Processing helix chain 'B' and resid 650 through 666 Processing helix chain 'B' and resid 668 through 686 removed outlier: 3.897A pdb=" N ILE B 674 " --> pdb=" O LEU B 670 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA B 675 " --> pdb=" O ASN B 671 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS B 686 " --> pdb=" O GLU B 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 707 removed outlier: 3.537A pdb=" N THR B 699 " --> pdb=" O GLN B 695 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU B 707 " --> pdb=" O PHE B 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 130 Processing helix chain 'C' and resid 134 through 148 removed outlier: 3.587A pdb=" N ARG C 147 " --> pdb=" O GLN C 143 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ARG C 148 " --> pdb=" O GLU C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 163 removed outlier: 3.954A pdb=" N PHE C 157 " --> pdb=" O ASP C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 178 Processing helix chain 'C' and resid 182 through 197 Processing helix chain 'C' and resid 199 through 205 removed outlier: 3.699A pdb=" N ASN C 205 " --> pdb=" O GLY C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 225 Processing helix chain 'C' and resid 227 through 238 Processing helix chain 'C' and resid 264 through 272 Processing helix chain 'C' and resid 274 through 284 Processing helix chain 'C' and resid 298 through 307 Processing helix chain 'C' and resid 315 through 329 Processing helix chain 'C' and resid 343 through 352 removed outlier: 3.724A pdb=" N ALA C 349 " --> pdb=" O LEU C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 362 Processing helix chain 'C' and resid 402 through 410 Processing helix chain 'C' and resid 415 through 420 Processing helix chain 'C' and resid 422 through 434 removed outlier: 3.525A pdb=" N THR C 427 " --> pdb=" O GLU C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 461 Processing helix chain 'C' and resid 483 through 509 removed outlier: 3.539A pdb=" N ARG C 487 " --> pdb=" O GLN C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 520 Processing helix chain 'C' and resid 520 through 542 removed outlier: 3.659A pdb=" N PHE C 527 " --> pdb=" O HIS C 523 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE C 542 " --> pdb=" O PHE C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 561 Processing helix chain 'C' and resid 562 through 567 Processing helix chain 'C' and resid 569 through 586 Processing helix chain 'C' and resid 586 through 608 removed outlier: 3.614A pdb=" N VAL C 593 " --> pdb=" O LYS C 589 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA C 604 " --> pdb=" O GLY C 600 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU C 608 " --> pdb=" O ALA C 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 637 Processing helix chain 'C' and resid 650 through 666 Processing helix chain 'C' and resid 668 through 686 removed outlier: 3.898A pdb=" N ILE C 674 " --> pdb=" O LEU C 670 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA C 675 " --> pdb=" O ASN C 671 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS C 686 " --> pdb=" O GLU C 682 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 707 removed outlier: 3.537A pdb=" N THR C 699 " --> pdb=" O GLN C 695 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU C 707 " --> pdb=" O PHE C 703 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 130 Processing helix chain 'D' and resid 134 through 148 removed outlier: 3.587A pdb=" N ARG D 147 " --> pdb=" O GLN D 143 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ARG D 148 " --> pdb=" O GLU D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 163 removed outlier: 3.954A pdb=" N PHE D 157 " --> pdb=" O ASP D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 178 Processing helix chain 'D' and resid 182 through 197 Processing helix chain 'D' and resid 199 through 205 removed outlier: 3.699A pdb=" N ASN D 205 " --> pdb=" O GLY D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 225 Processing helix chain 'D' and resid 227 through 238 Processing helix chain 'D' and resid 264 through 272 Processing helix chain 'D' and resid 274 through 284 Processing helix chain 'D' and resid 298 through 307 Processing helix chain 'D' and resid 315 through 329 Processing helix chain 'D' and resid 343 through 352 removed outlier: 3.724A pdb=" N ALA D 349 " --> pdb=" O LEU D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 362 Processing helix chain 'D' and resid 402 through 410 Processing helix chain 'D' and resid 415 through 420 Processing helix chain 'D' and resid 422 through 434 removed outlier: 3.525A pdb=" N THR D 427 " --> pdb=" O GLU D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 461 Processing helix chain 'D' and resid 483 through 509 removed outlier: 3.540A pdb=" N ARG D 487 " --> pdb=" O GLN D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 512 through 520 Processing helix chain 'D' and resid 520 through 542 removed outlier: 3.659A pdb=" N PHE D 527 " --> pdb=" O HIS D 523 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE D 542 " --> pdb=" O PHE D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 561 Processing helix chain 'D' and resid 562 through 567 Processing helix chain 'D' and resid 569 through 586 Processing helix chain 'D' and resid 586 through 608 removed outlier: 3.614A pdb=" N VAL D 593 " --> pdb=" O LYS D 589 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA D 604 " --> pdb=" O GLY D 600 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU D 608 " --> pdb=" O ALA D 604 " (cutoff:3.500A) Processing helix chain 'D' and resid 624 through 637 Processing helix chain 'D' and resid 650 through 666 Processing helix chain 'D' and resid 668 through 686 removed outlier: 3.898A pdb=" N ILE D 674 " --> pdb=" O LEU D 670 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA D 675 " --> pdb=" O ASN D 671 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS D 686 " --> pdb=" O GLU D 682 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 707 removed outlier: 3.537A pdb=" N THR D 699 " --> pdb=" O GLN D 695 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU D 707 " --> pdb=" O PHE D 703 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 376 through 382 removed outlier: 3.546A pdb=" N ASP A 379 " --> pdb=" O SER A 387 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N SER A 387 " --> pdb=" O ASP A 379 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N ALA A 381 " --> pdb=" O VAL A 385 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N VAL A 385 " --> pdb=" O ALA A 381 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL A 723 " --> pdb=" O ASP A 727 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ARG A 729 " --> pdb=" O CYS A 721 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N CYS A 721 " --> pdb=" O ARG A 729 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N CYS A 731 " --> pdb=" O GLU A 719 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N GLU A 719 " --> pdb=" O CYS A 731 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 376 through 382 removed outlier: 3.547A pdb=" N ASP B 379 " --> pdb=" O SER B 387 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N SER B 387 " --> pdb=" O ASP B 379 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N ALA B 381 " --> pdb=" O VAL B 385 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N VAL B 385 " --> pdb=" O ALA B 381 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL B 723 " --> pdb=" O ASP B 727 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ARG B 729 " --> pdb=" O CYS B 721 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N CYS B 721 " --> pdb=" O ARG B 729 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N CYS B 731 " --> pdb=" O GLU B 719 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N GLU B 719 " --> pdb=" O CYS B 731 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 376 through 382 removed outlier: 3.547A pdb=" N ASP C 379 " --> pdb=" O SER C 387 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N SER C 387 " --> pdb=" O ASP C 379 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N ALA C 381 " --> pdb=" O VAL C 385 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N VAL C 385 " --> pdb=" O ALA C 381 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL C 723 " --> pdb=" O ASP C 727 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ARG C 729 " --> pdb=" O CYS C 721 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N CYS C 721 " --> pdb=" O ARG C 729 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N CYS C 731 " --> pdb=" O GLU C 719 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N GLU C 719 " --> pdb=" O CYS C 731 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 376 through 382 removed outlier: 3.548A pdb=" N ASP D 379 " --> pdb=" O SER D 387 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N SER D 387 " --> pdb=" O ASP D 379 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ALA D 381 " --> pdb=" O VAL D 385 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N VAL D 385 " --> pdb=" O ALA D 381 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL D 723 " --> pdb=" O ASP D 727 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ARG D 729 " --> pdb=" O CYS D 721 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N CYS D 721 " --> pdb=" O ARG D 729 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N CYS D 731 " --> pdb=" O GLU D 719 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N GLU D 719 " --> pdb=" O CYS D 731 " (cutoff:3.500A) 1124 hydrogen bonds defined for protein. 3324 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.08 Time building geometry restraints manager: 5.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3578 1.32 - 1.45: 5647 1.45 - 1.57: 12727 1.57 - 1.69: 66 1.69 - 1.81: 204 Bond restraints: 22222 Sorted by residual: bond pdb=" CA ASP C 151 " pdb=" CB ASP C 151 " ideal model delta sigma weight residual 1.530 1.544 -0.013 1.69e-02 3.50e+03 6.36e-01 bond pdb=" CA ASP B 151 " pdb=" CB ASP B 151 " ideal model delta sigma weight residual 1.530 1.544 -0.013 1.69e-02 3.50e+03 6.36e-01 bond pdb=" CA ASP A 151 " pdb=" CB ASP A 151 " ideal model delta sigma weight residual 1.530 1.543 -0.013 1.69e-02 3.50e+03 5.77e-01 bond pdb=" CA ASP D 151 " pdb=" CB ASP D 151 " ideal model delta sigma weight residual 1.530 1.543 -0.012 1.69e-02 3.50e+03 5.38e-01 bond pdb=" CB PRO C 510 " pdb=" CG PRO C 510 " ideal model delta sigma weight residual 1.492 1.529 -0.037 5.00e-02 4.00e+02 5.36e-01 ... (remaining 22217 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 29597 1.60 - 3.20: 176 3.20 - 4.79: 33 4.79 - 6.39: 8 6.39 - 7.99: 8 Bond angle restraints: 29822 Sorted by residual: angle pdb=" C HIS B 150 " pdb=" N ASP B 151 " pdb=" CA ASP B 151 " ideal model delta sigma weight residual 121.54 128.21 -6.67 1.91e+00 2.74e-01 1.22e+01 angle pdb=" C HIS C 150 " pdb=" N ASP C 151 " pdb=" CA ASP C 151 " ideal model delta sigma weight residual 121.54 128.20 -6.66 1.91e+00 2.74e-01 1.22e+01 angle pdb=" C HIS A 150 " pdb=" N ASP A 151 " pdb=" CA ASP A 151 " ideal model delta sigma weight residual 121.54 128.18 -6.64 1.91e+00 2.74e-01 1.21e+01 angle pdb=" C HIS D 150 " pdb=" N ASP D 151 " pdb=" CA ASP D 151 " ideal model delta sigma weight residual 121.54 128.17 -6.63 1.91e+00 2.74e-01 1.21e+01 angle pdb=" CA LEU D 608 " pdb=" CB LEU D 608 " pdb=" CG LEU D 608 " ideal model delta sigma weight residual 116.30 124.29 -7.99 3.50e+00 8.16e-02 5.21e+00 ... (remaining 29817 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.39: 12994 24.39 - 48.78: 433 48.78 - 73.18: 131 73.18 - 97.57: 17 97.57 - 121.96: 6 Dihedral angle restraints: 13581 sinusoidal: 6221 harmonic: 7360 Sorted by residual: dihedral pdb=" C27 POV B 803 " pdb=" C28 POV B 803 " pdb=" C29 POV B 803 " pdb="C210 POV B 803 " ideal model delta sinusoidal sigma weight residual 127.48 -110.56 -121.96 1 3.00e+01 1.11e-03 1.63e+01 dihedral pdb=" C27 POV A 809 " pdb=" C28 POV A 809 " pdb=" C29 POV A 809 " pdb="C210 POV A 809 " ideal model delta sinusoidal sigma weight residual 127.48 -116.73 -115.79 1 3.00e+01 1.11e-03 1.53e+01 dihedral pdb=" C3 POV B 808 " pdb=" C31 POV B 808 " pdb=" O31 POV B 808 " pdb=" C32 POV B 808 " ideal model delta sinusoidal sigma weight residual 172.61 -76.70 -110.69 1 3.00e+01 1.11e-03 1.44e+01 ... (remaining 13578 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 2038 0.024 - 0.047: 729 0.047 - 0.071: 342 0.071 - 0.095: 83 0.095 - 0.119: 41 Chirality restraints: 3233 Sorted by residual: chirality pdb=" CA ILE B 734 " pdb=" N ILE B 734 " pdb=" C ILE B 734 " pdb=" CB ILE B 734 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.51e-01 chirality pdb=" CA ILE A 734 " pdb=" N ILE A 734 " pdb=" C ILE A 734 " pdb=" CB ILE A 734 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.39e-01 chirality pdb=" CA ILE D 734 " pdb=" N ILE D 734 " pdb=" C ILE D 734 " pdb=" CB ILE D 734 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.35e-01 ... (remaining 3230 not shown) Planarity restraints: 3600 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 180 " 0.020 5.00e-02 4.00e+02 3.04e-02 1.48e+00 pdb=" N PRO C 181 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO C 181 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 181 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN D 180 " 0.020 5.00e-02 4.00e+02 3.04e-02 1.48e+00 pdb=" N PRO D 181 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO D 181 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO D 181 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 180 " -0.020 5.00e-02 4.00e+02 3.03e-02 1.47e+00 pdb=" N PRO A 181 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 181 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 181 " -0.017 5.00e-02 4.00e+02 ... (remaining 3597 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 5905 2.81 - 3.33: 21514 3.33 - 3.86: 35968 3.86 - 4.38: 44100 4.38 - 4.90: 74799 Nonbonded interactions: 182286 Sorted by model distance: nonbonded pdb=" O GLY B 638 " pdb="NA NA A 801 " model vdw 2.291 2.470 nonbonded pdb=" O GLY C 638 " pdb="NA NA A 801 " model vdw 2.292 2.470 nonbonded pdb=" O GLY A 638 " pdb="NA NA A 801 " model vdw 2.292 2.470 nonbonded pdb=" O GLY D 638 " pdb="NA NA A 801 " model vdw 2.293 2.470 nonbonded pdb=" NZ LYS C 589 " pdb=" O14 POV C 805 " model vdw 2.297 3.120 ... (remaining 182281 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 117 through 756 or (resid 802 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name O11 or name O12 or name O13 or name O14 or name O21 or \ name O22 or name O31 or name O32 or name P or name C210)) or (resid 803 and (nam \ e N or name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or na \ me C2 or name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or \ name C27 or name C28 or name C29 or name C3 or name C31 or name C32 or name C33 \ or name C34 or name C35 or name C36 or name C37 or name C38 or name O11 or name \ O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name O32 or \ name P )) or (resid 804 and (name N or name C1 or name C11 or name C12 or name C \ 13 or name C14 or name C15 or name C2 or name C21 or name C22 or name C23 or nam \ e C24 or name C25 or name C26 or name C27 or name C3 or name C31 or name C32 or \ name C33 or name O11 or name O12 or name O13 or name O14 or name O21 or name O22 \ or name O31 or name O32 or name P )) or resid 805 or (resid 806 and (name N or \ name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or name C2 o \ r name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C \ 27 or name C3 or name C31 or name C32 or name C33 or name C34 or name O11 or nam \ e O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name O32 or \ name P )) or resid 807)) selection = (chain 'B' and (resid 117 through 756 or (resid 802 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name O11 or name O12 or name O13 or name O14 or name O21 or \ name O22 or name O31 or name O32 or name P or name C210)) or (resid 803 and (nam \ e N or name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or na \ me C2 or name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or \ name C27 or name C28 or name C29 or name C3 or name C31 or name C32 or name C33 \ or name C34 or name C35 or name C36 or name C37 or name C38 or name O11 or name \ O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name O32 or \ name P )) or (resid 804 and (name N or name C1 or name C11 or name C12 or name C \ 13 or name C14 or name C15 or name C2 or name C21 or name C22 or name C23 or nam \ e C24 or name C25 or name C26 or name C27 or name C3 or name C31 or name C32 or \ name C33 or name O11 or name O12 or name O13 or name O14 or name O21 or name O22 \ or name O31 or name O32 or name P )) or (resid 805 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name C37 or name C38 or name O11 or name O12 or name O13 or \ name O14 or name O21 or name O22 or name O31 or name O32 or name P or name C210) \ ) or (resid 806 and (name N or name C1 or name C11 or name C12 or name C13 or na \ me C14 or name C15 or name C2 or name C21 or name C22 or name C23 or name C24 or \ name C25 or name C26 or name C27 or name C3 or name C31 or name C32 or name C33 \ or name C34 or name O11 or name O12 or name O13 or name O14 or name O21 or name \ O22 or name O31 or name O32 or name P )) or (resid 807 and (name N or name C1 o \ r name C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C2 \ 1 or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or nam \ e C28 or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or \ name C36 or name C37 or name O11 or name O12 or name O13 or name O14 or name O21 \ or name O22 or name O31 or name O32 or name P )))) selection = (chain 'C' and (resid 117 through 756 or (resid 802 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name O11 or name O12 or name O13 or name O14 or name O21 or \ name O22 or name O31 or name O32 or name P or name C210)) or (resid 803 and (nam \ e N or name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or na \ me C2 or name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or \ name C27 or name C28 or name C29 or name C3 or name C31 or name C32 or name C33 \ or name C34 or name C35 or name C36 or name C37 or name C38 or name O11 or name \ O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name O32 or \ name P )) or (resid 804 and (name N or name C1 or name C11 or name C12 or name C \ 13 or name C14 or name C15 or name C2 or name C21 or name C22 or name C23 or nam \ e C24 or name C25 or name C26 or name C27 or name C3 or name C31 or name C32 or \ name C33 or name O11 or name O12 or name O13 or name O14 or name O21 or name O22 \ or name O31 or name O32 or name P )) or (resid 805 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name C37 or name C38 or name O11 or name O12 or name O13 or \ name O14 or name O21 or name O22 or name O31 or name O32 or name P or name C210) \ ) or (resid 806 and (name N or name C1 or name C11 or name C12 or name C13 or na \ me C14 or name C15 or name C2 or name C21 or name C22 or name C23 or name C24 or \ name C25 or name C26 or name C27 or name C3 or name C31 or name C32 or name C33 \ or name C34 or name O11 or name O12 or name O13 or name O14 or name O21 or name \ O22 or name O31 or name O32 or name P )) or (resid 807 and (name N or name C1 o \ r name C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C2 \ 1 or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or nam \ e C28 or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or \ name C36 or name C37 or name O11 or name O12 or name O13 or name O14 or name O21 \ or name O22 or name O31 or name O32 or name P )))) selection = (chain 'D' and (resid 117 through 756 or (resid 802 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name O11 or name O12 or name O13 or name O14 or name O21 or \ name O22 or name O31 or name O32 or name P or name C210)) or (resid 803 and (nam \ e N or name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or na \ me C2 or name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or \ name C27 or name C28 or name C29 or name C3 or name C31 or name C32 or name C33 \ or name C34 or name C35 or name C36 or name C37 or name C38 or name O11 or name \ O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name O32 or \ name P )) or (resid 804 and (name N or name C1 or name C11 or name C12 or name C \ 13 or name C14 or name C15 or name C2 or name C21 or name C22 or name C23 or nam \ e C24 or name C25 or name C26 or name C27 or name C3 or name C31 or name C32 or \ name C33 or name O11 or name O12 or name O13 or name O14 or name O21 or name O22 \ or name O31 or name O32 or name P )) or (resid 805 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name C37 or name C38 or name O11 or name O12 or name O13 or \ name O14 or name O21 or name O22 or name O31 or name O32 or name P or name C210) \ ) or (resid 806 and (name N or name C1 or name C11 or name C12 or name C13 or na \ me C14 or name C15 or name C2 or name C21 or name C22 or name C23 or name C24 or \ name C25 or name C26 or name C27 or name C3 or name C31 or name C32 or name C33 \ or name C34 or name O11 or name O12 or name O13 or name O14 or name O21 or name \ O22 or name O31 or name O32 or name P )) or (resid 807 and (name N or name C1 o \ r name C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C2 \ 1 or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or nam \ e C28 or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or \ name C36 or name C37 or name O11 or name O12 or name O13 or name O14 or name O21 \ or name O22 or name O31 or name O32 or name P )))) } 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=0.00 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: 1.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.800 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 43.140 Find NCS groups from input model: 1.380 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 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 : 0.001 0.037 22226 Z= 0.071 Angle : 0.385 7.989 29830 Z= 0.190 Chirality : 0.032 0.119 3233 Planarity : 0.002 0.030 3600 Dihedral : 13.139 121.958 8793 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.54 % Allowed : 3.79 % Favored : 95.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.17), residues: 2484 helix: 1.20 (0.13), residues: 1556 sheet: 3.44 (0.63), residues: 64 loop : -1.31 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 739 HIS 0.002 0.000 HIS C 301 PHE 0.004 0.001 PHE D 377 TYR 0.006 0.001 TYR D 208 ARG 0.002 0.000 ARG D 363 Details of bonding type rmsd hydrogen bonds : bond 0.24984 ( 1124) hydrogen bonds : angle 6.43805 ( 3324) SS BOND : bond 0.00074 ( 4) SS BOND : angle 0.49181 ( 8) covalent geometry : bond 0.00141 (22222) covalent geometry : angle 0.38458 (29822) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 460 time to evaluate : 2.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 LYS cc_start: 0.7128 (mppt) cc_final: 0.6923 (mppt) REVERT: A 346 GLN cc_start: 0.8610 (mt0) cc_final: 0.7975 (mt0) REVERT: A 351 MET cc_start: 0.9254 (mtp) cc_final: 0.9013 (mtp) REVERT: A 514 GLN cc_start: 0.5620 (mm-40) cc_final: 0.5380 (tt0) REVERT: A 562 MET cc_start: 0.8987 (mmt) cc_final: 0.8652 (mmt) REVERT: B 253 LYS cc_start: 0.7125 (mppt) cc_final: 0.6922 (mppt) REVERT: B 346 GLN cc_start: 0.8626 (mt0) cc_final: 0.7990 (mt0) REVERT: B 351 MET cc_start: 0.9247 (mtp) cc_final: 0.9003 (mtp) REVERT: B 562 MET cc_start: 0.9015 (mmt) cc_final: 0.8728 (mmt) REVERT: B 680 THR cc_start: 0.8279 (p) cc_final: 0.8048 (m) REVERT: C 346 GLN cc_start: 0.8631 (mt0) cc_final: 0.7984 (mt0) REVERT: C 351 MET cc_start: 0.9252 (mtp) cc_final: 0.9010 (mtp) REVERT: C 562 MET cc_start: 0.9012 (mmt) cc_final: 0.8730 (mmt) REVERT: C 680 THR cc_start: 0.8274 (p) cc_final: 0.8054 (m) REVERT: D 346 GLN cc_start: 0.8630 (mt0) cc_final: 0.7996 (mt0) REVERT: D 351 MET cc_start: 0.9253 (mtp) cc_final: 0.9014 (mtp) REVERT: D 562 MET cc_start: 0.8992 (mmt) cc_final: 0.8687 (mmt) REVERT: D 680 THR cc_start: 0.8287 (p) cc_final: 0.8071 (m) outliers start: 12 outliers final: 4 residues processed: 468 average time/residue: 1.4489 time to fit residues: 763.8350 Evaluate side-chains 313 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 309 time to evaluate : 2.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain D residue 535 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 1.9990 chunk 187 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 126 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 chunk 194 optimal weight: 0.9980 chunk 75 optimal weight: 6.9990 chunk 118 optimal weight: 2.9990 chunk 144 optimal weight: 0.9980 chunk 225 optimal weight: 4.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 ASN A 205 ASN A 279 GLN A 580 GLN A 645 GLN B 182 ASN B 279 GLN B 570 GLN B 580 GLN B 645 GLN B 647 ASN B 695 GLN C 182 ASN C 279 GLN C 580 GLN C 645 GLN C 695 GLN D 182 ASN D 279 GLN D 580 GLN D 645 GLN D 695 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.161179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.125856 restraints weight = 22797.286| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.72 r_work: 0.3279 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3146 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3143 r_free = 0.3143 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| r_final: 0.3143 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 22226 Z= 0.193 Angle : 0.642 11.563 29830 Z= 0.320 Chirality : 0.041 0.147 3233 Planarity : 0.004 0.037 3600 Dihedral : 16.704 132.643 3893 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 3.20 % Allowed : 10.06 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.17), residues: 2484 helix: 1.28 (0.12), residues: 1604 sheet: 3.12 (0.65), residues: 64 loop : -1.53 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 692 HIS 0.007 0.001 HIS B 301 PHE 0.016 0.002 PHE A 526 TYR 0.019 0.003 TYR A 321 ARG 0.003 0.001 ARG C 698 Details of bonding type rmsd hydrogen bonds : bond 0.04934 ( 1124) hydrogen bonds : angle 4.25150 ( 3324) SS BOND : bond 0.00011 ( 4) SS BOND : angle 1.33789 ( 8) covalent geometry : bond 0.00461 (22222) covalent geometry : angle 0.64168 (29822) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 331 time to evaluate : 2.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 MET cc_start: 0.6768 (mmm) cc_final: 0.6187 (mmm) REVERT: A 185 GLU cc_start: 0.7662 (mm-30) cc_final: 0.7336 (mm-30) REVERT: A 351 MET cc_start: 0.9291 (mtp) cc_final: 0.9083 (mtp) REVERT: A 378 THR cc_start: 0.9240 (OUTLIER) cc_final: 0.8816 (t) REVERT: A 562 MET cc_start: 0.9251 (mmt) cc_final: 0.8843 (mmt) REVERT: A 738 LYS cc_start: 0.8385 (pttt) cc_final: 0.8055 (ptpp) REVERT: A 740 THR cc_start: 0.8003 (m) cc_final: 0.7711 (p) REVERT: A 747 SER cc_start: 0.8253 (p) cc_final: 0.8045 (t) REVERT: B 159 MET cc_start: 0.6639 (mmm) cc_final: 0.5876 (mmm) REVERT: B 185 GLU cc_start: 0.7655 (mm-30) cc_final: 0.7273 (mm-30) REVERT: B 351 MET cc_start: 0.9270 (mtp) cc_final: 0.9063 (mtp) REVERT: B 378 THR cc_start: 0.9247 (OUTLIER) cc_final: 0.8813 (t) REVERT: B 514 GLN cc_start: 0.7258 (OUTLIER) cc_final: 0.6478 (mm-40) REVERT: B 562 MET cc_start: 0.9257 (mmt) cc_final: 0.8802 (mmt) REVERT: B 738 LYS cc_start: 0.8479 (pttt) cc_final: 0.8108 (ptpp) REVERT: B 740 THR cc_start: 0.8015 (OUTLIER) cc_final: 0.7704 (p) REVERT: C 159 MET cc_start: 0.6808 (mmm) cc_final: 0.5881 (mmm) REVERT: C 185 GLU cc_start: 0.7645 (mm-30) cc_final: 0.7228 (mm-30) REVERT: C 351 MET cc_start: 0.9266 (mtp) cc_final: 0.9056 (mtp) REVERT: C 378 THR cc_start: 0.9242 (OUTLIER) cc_final: 0.8954 (t) REVERT: C 514 GLN cc_start: 0.7250 (OUTLIER) cc_final: 0.6471 (mm-40) REVERT: C 562 MET cc_start: 0.9266 (mmt) cc_final: 0.8806 (mmt) REVERT: C 738 LYS cc_start: 0.8461 (pttt) cc_final: 0.8102 (ptpp) REVERT: C 740 THR cc_start: 0.8057 (m) cc_final: 0.7756 (p) REVERT: D 159 MET cc_start: 0.6671 (mmm) cc_final: 0.5902 (mmm) REVERT: D 185 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7261 (mm-30) REVERT: D 346 GLN cc_start: 0.9105 (mt0) cc_final: 0.8429 (mt0) REVERT: D 351 MET cc_start: 0.9263 (mtp) cc_final: 0.9051 (mtp) REVERT: D 378 THR cc_start: 0.9250 (OUTLIER) cc_final: 0.8819 (t) REVERT: D 514 GLN cc_start: 0.7257 (OUTLIER) cc_final: 0.6526 (mm-40) REVERT: D 562 MET cc_start: 0.9268 (mmt) cc_final: 0.8804 (mmt) REVERT: D 738 LYS cc_start: 0.8466 (pttt) cc_final: 0.8108 (ptpp) REVERT: D 740 THR cc_start: 0.8019 (OUTLIER) cc_final: 0.7705 (p) outliers start: 71 outliers final: 22 residues processed: 388 average time/residue: 1.4902 time to fit residues: 648.0118 Evaluate side-chains 314 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 283 time to evaluate : 2.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 611 LYS Chi-restraints excluded: chain A residue 621 SER Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 514 GLN Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 611 LYS Chi-restraints excluded: chain B residue 621 SER Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 514 GLN Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 611 LYS Chi-restraints excluded: chain C residue 621 SER Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 378 THR Chi-restraints excluded: chain D residue 514 GLN Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 611 LYS Chi-restraints excluded: chain D residue 621 SER Chi-restraints excluded: chain D residue 723 VAL Chi-restraints excluded: chain D residue 740 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 115 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 222 optimal weight: 0.9990 chunk 193 optimal weight: 2.9990 chunk 220 optimal weight: 4.9990 chunk 151 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 chunk 201 optimal weight: 0.8980 chunk 182 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 647 ASN A 695 GLN ** B 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 570 GLN ** C 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.159162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.124246 restraints weight = 22806.061| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.70 r_work: 0.3266 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3113 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3113 r_free = 0.3113 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3113 r_free = 0.3113 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3113 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 22226 Z= 0.156 Angle : 0.584 11.448 29830 Z= 0.290 Chirality : 0.039 0.145 3233 Planarity : 0.004 0.028 3600 Dihedral : 16.678 129.150 3893 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.70 % Allowed : 11.46 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.16), residues: 2484 helix: 1.32 (0.12), residues: 1604 sheet: 3.12 (0.65), residues: 64 loop : -1.57 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 380 HIS 0.006 0.001 HIS A 301 PHE 0.013 0.002 PHE C 193 TYR 0.016 0.002 TYR B 208 ARG 0.002 0.000 ARG C 567 Details of bonding type rmsd hydrogen bonds : bond 0.04202 ( 1124) hydrogen bonds : angle 4.06366 ( 3324) SS BOND : bond 0.00021 ( 4) SS BOND : angle 1.24885 ( 8) covalent geometry : bond 0.00372 (22222) covalent geometry : angle 0.58363 (29822) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 316 time to evaluate : 2.489 Fit side-chains REVERT: A 159 MET cc_start: 0.6875 (mmm) cc_final: 0.6335 (mmm) REVERT: A 185 GLU cc_start: 0.7598 (mm-30) cc_final: 0.7193 (mm-30) REVERT: A 188 ARG cc_start: 0.7582 (OUTLIER) cc_final: 0.7354 (mtm-85) REVERT: A 280 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7944 (tp) REVERT: A 378 THR cc_start: 0.9296 (OUTLIER) cc_final: 0.9016 (t) REVERT: A 562 MET cc_start: 0.9254 (mmt) cc_final: 0.8816 (mmt) REVERT: A 619 CYS cc_start: 0.6449 (p) cc_final: 0.6221 (p) REVERT: A 686 LYS cc_start: 0.8814 (OUTLIER) cc_final: 0.8466 (ptpp) REVERT: A 738 LYS cc_start: 0.8256 (pttt) cc_final: 0.7837 (ptpp) REVERT: A 740 THR cc_start: 0.7978 (m) cc_final: 0.7613 (p) REVERT: A 747 SER cc_start: 0.8142 (p) cc_final: 0.7872 (t) REVERT: B 159 MET cc_start: 0.6796 (mmm) cc_final: 0.6169 (mmm) REVERT: B 185 GLU cc_start: 0.7600 (mm-30) cc_final: 0.7196 (mm-30) REVERT: B 280 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7971 (tp) REVERT: B 378 THR cc_start: 0.9257 (OUTLIER) cc_final: 0.8975 (t) REVERT: B 535 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8202 (tt) REVERT: B 562 MET cc_start: 0.9245 (mmt) cc_final: 0.8839 (mmt) REVERT: B 619 CYS cc_start: 0.6651 (p) cc_final: 0.6394 (p) REVERT: B 686 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8518 (ptpp) REVERT: B 738 LYS cc_start: 0.8273 (pttt) cc_final: 0.7873 (ptpp) REVERT: B 740 THR cc_start: 0.8089 (OUTLIER) cc_final: 0.7699 (p) REVERT: C 156 ASP cc_start: 0.5850 (t70) cc_final: 0.5567 (OUTLIER) REVERT: C 159 MET cc_start: 0.6930 (mmm) cc_final: 0.6291 (mmm) REVERT: C 185 GLU cc_start: 0.7539 (mm-30) cc_final: 0.7115 (mm-30) REVERT: C 283 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7568 (mt-10) REVERT: C 378 THR cc_start: 0.9259 (OUTLIER) cc_final: 0.8972 (t) REVERT: C 535 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8197 (tt) REVERT: C 562 MET cc_start: 0.9263 (mmt) cc_final: 0.8851 (mmt) REVERT: C 619 CYS cc_start: 0.6531 (p) cc_final: 0.6285 (p) REVERT: C 686 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8460 (ptpp) REVERT: C 717 MET cc_start: 0.5723 (ttm) cc_final: 0.5514 (ttt) REVERT: C 738 LYS cc_start: 0.8282 (pttt) cc_final: 0.7864 (ptpp) REVERT: C 740 THR cc_start: 0.7970 (OUTLIER) cc_final: 0.7584 (p) REVERT: C 743 LYS cc_start: 0.8506 (ptpp) cc_final: 0.8279 (ptpp) REVERT: D 159 MET cc_start: 0.6810 (mmm) cc_final: 0.6183 (mmm) REVERT: D 185 GLU cc_start: 0.7671 (mm-30) cc_final: 0.7269 (mm-30) REVERT: D 280 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7955 (tp) REVERT: D 346 GLN cc_start: 0.9068 (mt0) cc_final: 0.8504 (mt0) REVERT: D 378 THR cc_start: 0.9263 (OUTLIER) cc_final: 0.8979 (t) REVERT: D 562 MET cc_start: 0.9259 (mmt) cc_final: 0.8823 (mmt) REVERT: D 619 CYS cc_start: 0.6652 (p) cc_final: 0.6386 (p) REVERT: D 686 LYS cc_start: 0.8807 (OUTLIER) cc_final: 0.8474 (ptpp) REVERT: D 738 LYS cc_start: 0.8272 (pttt) cc_final: 0.7875 (ptpp) REVERT: D 740 THR cc_start: 0.8087 (m) cc_final: 0.7711 (p) REVERT: D 743 LYS cc_start: 0.8464 (ptpp) cc_final: 0.8237 (ptpp) outliers start: 82 outliers final: 23 residues processed: 377 average time/residue: 1.5782 time to fit residues: 668.2408 Evaluate side-chains 336 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 297 time to evaluate : 2.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 621 SER Chi-restraints excluded: chain A residue 686 LYS Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 576 SER Chi-restraints excluded: chain B residue 621 SER Chi-restraints excluded: chain B residue 686 LYS Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 621 SER Chi-restraints excluded: chain C residue 686 LYS Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 378 THR Chi-restraints excluded: chain D residue 411 THR Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 576 SER Chi-restraints excluded: chain D residue 621 SER Chi-restraints excluded: chain D residue 686 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 2 optimal weight: 0.8980 chunk 188 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 169 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 127 optimal weight: 0.4980 chunk 100 optimal weight: 10.0000 chunk 148 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 137 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN ** A 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 750 ASN ** B 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 750 ASN C 279 GLN ** C 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 750 ASN ** D 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 750 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.160798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.126201 restraints weight = 23247.015| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 1.71 r_work: 0.3292 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3169 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3169 r_free = 0.3169 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3169 r_free = 0.3169 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| r_final: 0.3169 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22226 Z= 0.121 Angle : 0.545 10.955 29830 Z= 0.272 Chirality : 0.037 0.143 3233 Planarity : 0.003 0.027 3600 Dihedral : 16.310 118.769 3893 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.30 % Allowed : 14.35 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.17), residues: 2484 helix: 1.44 (0.12), residues: 1620 sheet: 3.41 (0.66), residues: 64 loop : -1.50 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 739 HIS 0.005 0.001 HIS A 301 PHE 0.012 0.001 PHE D 193 TYR 0.015 0.002 TYR D 208 ARG 0.002 0.000 ARG B 225 Details of bonding type rmsd hydrogen bonds : bond 0.03654 ( 1124) hydrogen bonds : angle 3.93159 ( 3324) SS BOND : bond 0.00029 ( 4) SS BOND : angle 1.05087 ( 8) covalent geometry : bond 0.00278 (22222) covalent geometry : angle 0.54493 (29822) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 318 time to evaluate : 2.466 Fit side-chains REVERT: A 159 MET cc_start: 0.6902 (mmm) cc_final: 0.6429 (mmm) REVERT: A 185 GLU cc_start: 0.7623 (mm-30) cc_final: 0.7266 (mm-30) REVERT: A 351 MET cc_start: 0.9226 (mtp) cc_final: 0.9009 (mtp) REVERT: A 378 THR cc_start: 0.9288 (OUTLIER) cc_final: 0.9001 (t) REVERT: A 488 MET cc_start: 0.6792 (mmt) cc_final: 0.6224 (mtm) REVERT: A 562 MET cc_start: 0.9230 (mmt) cc_final: 0.8806 (mmt) REVERT: A 619 CYS cc_start: 0.6651 (p) cc_final: 0.6355 (p) REVERT: A 686 LYS cc_start: 0.8856 (OUTLIER) cc_final: 0.8463 (ptpp) REVERT: A 738 LYS cc_start: 0.8246 (pttt) cc_final: 0.7931 (pttm) REVERT: A 740 THR cc_start: 0.8084 (m) cc_final: 0.7827 (p) REVERT: A 747 SER cc_start: 0.8110 (p) cc_final: 0.7787 (t) REVERT: B 159 MET cc_start: 0.6941 (mmm) cc_final: 0.6370 (mmm) REVERT: B 185 GLU cc_start: 0.7614 (mm-30) cc_final: 0.7262 (mm-30) REVERT: B 351 MET cc_start: 0.9219 (mtp) cc_final: 0.9004 (mtp) REVERT: B 488 MET cc_start: 0.6827 (mmt) cc_final: 0.6272 (mtm) REVERT: B 562 MET cc_start: 0.9225 (mmt) cc_final: 0.8873 (mmt) REVERT: B 619 CYS cc_start: 0.6684 (p) cc_final: 0.6377 (p) REVERT: B 686 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8447 (ptpp) REVERT: B 738 LYS cc_start: 0.8295 (pttt) cc_final: 0.7872 (ptpp) REVERT: B 740 THR cc_start: 0.8177 (m) cc_final: 0.7866 (p) REVERT: C 159 MET cc_start: 0.7051 (mmm) cc_final: 0.6373 (mmm) REVERT: C 185 GLU cc_start: 0.7460 (mm-30) cc_final: 0.7138 (mm-30) REVERT: C 283 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7582 (mt-10) REVERT: C 488 MET cc_start: 0.6841 (mmt) cc_final: 0.6263 (mtm) REVERT: C 562 MET cc_start: 0.9238 (mmt) cc_final: 0.8840 (mmt) REVERT: C 619 CYS cc_start: 0.6657 (p) cc_final: 0.6394 (p) REVERT: C 686 LYS cc_start: 0.8852 (OUTLIER) cc_final: 0.8449 (ptpp) REVERT: C 738 LYS cc_start: 0.8297 (pttt) cc_final: 0.7881 (ptpp) REVERT: C 740 THR cc_start: 0.8185 (m) cc_final: 0.7877 (p) REVERT: C 743 LYS cc_start: 0.8436 (ptpp) cc_final: 0.8183 (ptpp) REVERT: D 159 MET cc_start: 0.6867 (mmm) cc_final: 0.6325 (mmm) REVERT: D 185 GLU cc_start: 0.7596 (mm-30) cc_final: 0.7252 (mm-30) REVERT: D 283 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7501 (mt-10) REVERT: D 346 GLN cc_start: 0.9053 (mt0) cc_final: 0.8407 (mt0) REVERT: D 488 MET cc_start: 0.6832 (mmt) cc_final: 0.6255 (mtm) REVERT: D 562 MET cc_start: 0.9244 (mmt) cc_final: 0.8857 (mmt) REVERT: D 619 CYS cc_start: 0.6627 (p) cc_final: 0.6354 (p) REVERT: D 686 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.8458 (ptpp) REVERT: D 738 LYS cc_start: 0.8308 (pttt) cc_final: 0.7892 (ptpp) REVERT: D 740 THR cc_start: 0.8176 (OUTLIER) cc_final: 0.7870 (p) REVERT: D 743 LYS cc_start: 0.8433 (ptpp) cc_final: 0.8182 (ptpp) outliers start: 51 outliers final: 17 residues processed: 361 average time/residue: 1.5615 time to fit residues: 629.2337 Evaluate side-chains 318 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 293 time to evaluate : 2.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 686 LYS Chi-restraints excluded: chain A residue 743 LYS Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 576 SER Chi-restraints excluded: chain B residue 686 LYS Chi-restraints excluded: chain B residue 743 LYS Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 418 GLU Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 686 LYS Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 576 SER Chi-restraints excluded: chain D residue 686 LYS Chi-restraints excluded: chain D residue 740 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 23 optimal weight: 0.7980 chunk 45 optimal weight: 0.5980 chunk 179 optimal weight: 0.6980 chunk 180 optimal weight: 2.9990 chunk 137 optimal weight: 0.2980 chunk 112 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 169 optimal weight: 1.9990 chunk 157 optimal weight: 5.9990 chunk 165 optimal weight: 0.8980 chunk 162 optimal weight: 9.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN A 452 ASN A 750 ASN B 279 GLN B 452 ASN B 750 ASN C 279 GLN C 452 ASN C 750 ASN D 279 GLN ** D 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 750 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.161944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.127677 restraints weight = 23202.537| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.68 r_work: 0.3313 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3183 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3182 r_free = 0.3182 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| r_final: 0.3182 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22226 Z= 0.111 Angle : 0.533 10.799 29830 Z= 0.265 Chirality : 0.037 0.142 3233 Planarity : 0.003 0.027 3600 Dihedral : 15.957 118.664 3885 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.03 % Allowed : 15.07 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.17), residues: 2484 helix: 1.57 (0.12), residues: 1620 sheet: 3.49 (0.66), residues: 64 loop : -1.47 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 710 HIS 0.005 0.001 HIS A 301 PHE 0.012 0.001 PHE C 506 TYR 0.013 0.001 TYR C 208 ARG 0.002 0.000 ARG B 337 Details of bonding type rmsd hydrogen bonds : bond 0.03445 ( 1124) hydrogen bonds : angle 3.82481 ( 3324) SS BOND : bond 0.00053 ( 4) SS BOND : angle 1.03643 ( 8) covalent geometry : bond 0.00252 (22222) covalent geometry : angle 0.53313 (29822) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 319 time to evaluate : 2.343 Fit side-chains REVERT: A 159 MET cc_start: 0.6902 (mmm) cc_final: 0.6448 (mmm) REVERT: A 185 GLU cc_start: 0.7588 (mm-30) cc_final: 0.7280 (mm-30) REVERT: A 283 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7512 (mt-10) REVERT: A 378 THR cc_start: 0.9317 (OUTLIER) cc_final: 0.9030 (t) REVERT: A 488 MET cc_start: 0.6673 (mmt) cc_final: 0.6187 (mtm) REVERT: A 562 MET cc_start: 0.9231 (mmt) cc_final: 0.8790 (mmt) REVERT: A 618 ASP cc_start: 0.7329 (m-30) cc_final: 0.7006 (m-30) REVERT: A 619 CYS cc_start: 0.6585 (p) cc_final: 0.6295 (p) REVERT: A 686 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8484 (ptpp) REVERT: A 738 LYS cc_start: 0.8196 (pttt) cc_final: 0.7856 (pttm) REVERT: A 740 THR cc_start: 0.7994 (m) cc_final: 0.7655 (p) REVERT: A 747 SER cc_start: 0.8071 (p) cc_final: 0.7733 (t) REVERT: B 159 MET cc_start: 0.6936 (mmm) cc_final: 0.6415 (mmm) REVERT: B 185 GLU cc_start: 0.7568 (mm-30) cc_final: 0.7251 (mm-30) REVERT: B 283 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7515 (mt-10) REVERT: B 488 MET cc_start: 0.6694 (mmt) cc_final: 0.6221 (mtm) REVERT: B 562 MET cc_start: 0.9220 (mmt) cc_final: 0.8865 (mmt) REVERT: B 618 ASP cc_start: 0.7357 (m-30) cc_final: 0.7039 (m-30) REVERT: B 619 CYS cc_start: 0.6606 (p) cc_final: 0.6315 (p) REVERT: B 738 LYS cc_start: 0.8261 (pttt) cc_final: 0.7889 (pttm) REVERT: B 740 THR cc_start: 0.8064 (m) cc_final: 0.7702 (p) REVERT: C 159 MET cc_start: 0.7030 (mmm) cc_final: 0.6363 (mmm) REVERT: C 185 GLU cc_start: 0.7475 (mm-30) cc_final: 0.7206 (mm-30) REVERT: C 283 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7554 (mt-10) REVERT: C 488 MET cc_start: 0.6610 (mmt) cc_final: 0.6140 (mtm) REVERT: C 562 MET cc_start: 0.9237 (mmt) cc_final: 0.8833 (mmt) REVERT: C 618 ASP cc_start: 0.7350 (m-30) cc_final: 0.7028 (m-30) REVERT: C 619 CYS cc_start: 0.6662 (p) cc_final: 0.6390 (p) REVERT: C 738 LYS cc_start: 0.8273 (pttt) cc_final: 0.7828 (ptpp) REVERT: C 740 THR cc_start: 0.8108 (m) cc_final: 0.7745 (p) REVERT: C 743 LYS cc_start: 0.8409 (ptpp) cc_final: 0.8121 (ptpp) REVERT: D 159 MET cc_start: 0.6849 (mmm) cc_final: 0.6349 (mmm) REVERT: D 185 GLU cc_start: 0.7538 (mm-30) cc_final: 0.7233 (mm-30) REVERT: D 283 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7470 (mt-10) REVERT: D 346 GLN cc_start: 0.9042 (mt0) cc_final: 0.8363 (mt0) REVERT: D 488 MET cc_start: 0.6690 (mmt) cc_final: 0.6203 (mtm) REVERT: D 514 GLN cc_start: 0.7156 (OUTLIER) cc_final: 0.6494 (mm-40) REVERT: D 562 MET cc_start: 0.9237 (mmt) cc_final: 0.8831 (mmt) REVERT: D 618 ASP cc_start: 0.7350 (m-30) cc_final: 0.7027 (m-30) REVERT: D 619 CYS cc_start: 0.6632 (p) cc_final: 0.6358 (p) REVERT: D 738 LYS cc_start: 0.8292 (pttt) cc_final: 0.7837 (ptpp) REVERT: D 740 THR cc_start: 0.8103 (OUTLIER) cc_final: 0.7739 (p) REVERT: D 743 LYS cc_start: 0.8398 (ptpp) cc_final: 0.8110 (ptpp) outliers start: 45 outliers final: 20 residues processed: 345 average time/residue: 1.5780 time to fit residues: 606.4351 Evaluate side-chains 330 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 302 time to evaluate : 2.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 686 LYS Chi-restraints excluded: chain A residue 743 LYS Chi-restraints excluded: chain B residue 283 GLU Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 576 SER Chi-restraints excluded: chain B residue 736 GLU Chi-restraints excluded: chain B residue 743 LYS Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 736 GLU Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 411 THR Chi-restraints excluded: chain D residue 514 GLN Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 576 SER Chi-restraints excluded: chain D residue 740 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 156 optimal weight: 0.7980 chunk 234 optimal weight: 20.0000 chunk 41 optimal weight: 3.9990 chunk 124 optimal weight: 10.0000 chunk 154 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 chunk 98 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 205 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN A 750 ASN B 182 ASN B 279 GLN B 750 ASN C 279 GLN C 750 ASN D 182 ASN D 279 GLN ** D 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 750 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.157754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.123345 restraints weight = 22929.488| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.66 r_work: 0.3254 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3132 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| r_final: 0.3132 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 22226 Z= 0.170 Angle : 0.616 12.148 29830 Z= 0.304 Chirality : 0.040 0.148 3233 Planarity : 0.004 0.027 3600 Dihedral : 16.300 116.242 3885 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.75 % Allowed : 14.76 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.16), residues: 2484 helix: 1.32 (0.12), residues: 1644 sheet: 3.10 (0.65), residues: 64 loop : -1.37 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 710 HIS 0.007 0.001 HIS A 301 PHE 0.013 0.002 PHE D 506 TYR 0.015 0.002 TYR A 208 ARG 0.003 0.000 ARG C 337 Details of bonding type rmsd hydrogen bonds : bond 0.03969 ( 1124) hydrogen bonds : angle 3.95743 ( 3324) SS BOND : bond 0.00043 ( 4) SS BOND : angle 1.22820 ( 8) covalent geometry : bond 0.00412 (22222) covalent geometry : angle 0.61548 (29822) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 320 time to evaluate : 2.364 Fit side-chains REVERT: A 159 MET cc_start: 0.6949 (mmm) cc_final: 0.6288 (mmm) REVERT: A 185 GLU cc_start: 0.7525 (mm-30) cc_final: 0.7292 (mm-30) REVERT: A 263 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7856 (pt0) REVERT: A 283 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7535 (mt-10) REVERT: A 351 MET cc_start: 0.9222 (mtp) cc_final: 0.9022 (mtp) REVERT: A 378 THR cc_start: 0.9346 (OUTLIER) cc_final: 0.9067 (t) REVERT: A 488 MET cc_start: 0.6899 (mmt) cc_final: 0.6346 (mtm) REVERT: A 562 MET cc_start: 0.9244 (mmt) cc_final: 0.8733 (mmt) REVERT: A 618 ASP cc_start: 0.7402 (m-30) cc_final: 0.7096 (m-30) REVERT: A 619 CYS cc_start: 0.6769 (p) cc_final: 0.6476 (p) REVERT: A 686 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8539 (ptpp) REVERT: A 738 LYS cc_start: 0.8326 (pttt) cc_final: 0.7974 (pttm) REVERT: A 740 THR cc_start: 0.8233 (OUTLIER) cc_final: 0.7988 (p) REVERT: A 747 SER cc_start: 0.8166 (p) cc_final: 0.7882 (t) REVERT: B 159 MET cc_start: 0.6872 (mmm) cc_final: 0.6159 (mmm) REVERT: B 185 GLU cc_start: 0.7526 (mm-30) cc_final: 0.7296 (mm-30) REVERT: B 283 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7536 (mt-10) REVERT: B 488 MET cc_start: 0.6845 (mmt) cc_final: 0.6294 (mtm) REVERT: B 514 GLN cc_start: 0.7214 (OUTLIER) cc_final: 0.6569 (mm-40) REVERT: B 562 MET cc_start: 0.9254 (mmt) cc_final: 0.8821 (mmt) REVERT: B 618 ASP cc_start: 0.7427 (m-30) cc_final: 0.7123 (m-30) REVERT: B 619 CYS cc_start: 0.6795 (p) cc_final: 0.6503 (p) REVERT: B 738 LYS cc_start: 0.8348 (pttt) cc_final: 0.7988 (pttm) REVERT: B 740 THR cc_start: 0.8194 (OUTLIER) cc_final: 0.7908 (p) REVERT: C 159 MET cc_start: 0.7026 (mmm) cc_final: 0.6135 (mmm) REVERT: C 185 GLU cc_start: 0.7478 (mm-30) cc_final: 0.7255 (mm-30) REVERT: C 283 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7560 (mt-10) REVERT: C 488 MET cc_start: 0.6851 (mmt) cc_final: 0.6317 (mtm) REVERT: C 514 GLN cc_start: 0.7205 (OUTLIER) cc_final: 0.6556 (mm-40) REVERT: C 562 MET cc_start: 0.9259 (mmt) cc_final: 0.8893 (mmt) REVERT: C 618 ASP cc_start: 0.7420 (m-30) cc_final: 0.7110 (m-30) REVERT: C 619 CYS cc_start: 0.6546 (p) cc_final: 0.6280 (p) REVERT: C 738 LYS cc_start: 0.8333 (pttt) cc_final: 0.7981 (pttm) REVERT: C 740 THR cc_start: 0.8197 (OUTLIER) cc_final: 0.7907 (p) REVERT: D 159 MET cc_start: 0.7010 (mmm) cc_final: 0.6200 (mmm) REVERT: D 185 GLU cc_start: 0.7511 (mm-30) cc_final: 0.7290 (mm-30) REVERT: D 283 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7503 (mt-10) REVERT: D 346 GLN cc_start: 0.9066 (mt0) cc_final: 0.8857 (mt0) REVERT: D 488 MET cc_start: 0.6920 (mmt) cc_final: 0.6369 (mtm) REVERT: D 514 GLN cc_start: 0.7203 (OUTLIER) cc_final: 0.6573 (mm-40) REVERT: D 562 MET cc_start: 0.9260 (mmt) cc_final: 0.8801 (mmt) REVERT: D 618 ASP cc_start: 0.7438 (m-30) cc_final: 0.7116 (m-30) REVERT: D 619 CYS cc_start: 0.6576 (p) cc_final: 0.6309 (p) REVERT: D 738 LYS cc_start: 0.8345 (pttt) cc_final: 0.7976 (pttm) REVERT: D 740 THR cc_start: 0.8198 (OUTLIER) cc_final: 0.7908 (p) outliers start: 61 outliers final: 19 residues processed: 360 average time/residue: 1.5411 time to fit residues: 620.5812 Evaluate side-chains 334 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 301 time to evaluate : 2.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 686 LYS Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain B residue 283 GLU Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 514 GLN Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 576 SER Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 743 LYS Chi-restraints excluded: chain C residue 282 MET Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 514 GLN Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 411 THR Chi-restraints excluded: chain D residue 514 GLN Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 576 SER Chi-restraints excluded: chain D residue 740 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 155 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 114 optimal weight: 0.9980 chunk 183 optimal weight: 0.9990 chunk 135 optimal weight: 5.9990 chunk 132 optimal weight: 0.9990 chunk 237 optimal weight: 0.8980 chunk 117 optimal weight: 3.9990 chunk 167 optimal weight: 0.0980 chunk 86 optimal weight: 2.9990 chunk 242 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN B 279 GLN B 750 ASN C 182 ASN C 279 GLN C 750 ASN D 452 ASN D 750 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.159994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.125825 restraints weight = 23006.398| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.67 r_work: 0.3285 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3157 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| r_final: 0.3157 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22226 Z= 0.121 Angle : 0.562 11.363 29830 Z= 0.278 Chirality : 0.037 0.143 3233 Planarity : 0.003 0.027 3600 Dihedral : 16.075 118.601 3885 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.62 % Allowed : 15.30 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.17), residues: 2484 helix: 1.53 (0.12), residues: 1616 sheet: 3.25 (0.65), residues: 64 loop : -1.48 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 710 HIS 0.006 0.001 HIS A 301 PHE 0.015 0.001 PHE D 506 TYR 0.014 0.002 TYR C 208 ARG 0.002 0.000 ARG C 337 Details of bonding type rmsd hydrogen bonds : bond 0.03523 ( 1124) hydrogen bonds : angle 3.84889 ( 3324) SS BOND : bond 0.00051 ( 4) SS BOND : angle 1.11673 ( 8) covalent geometry : bond 0.00281 (22222) covalent geometry : angle 0.56220 (29822) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 310 time to evaluate : 2.162 Fit side-chains REVERT: A 156 ASP cc_start: 0.5345 (t0) cc_final: 0.5064 (OUTLIER) REVERT: A 159 MET cc_start: 0.6915 (mmm) cc_final: 0.6456 (mmm) REVERT: A 185 GLU cc_start: 0.7443 (mm-30) cc_final: 0.7165 (mm-30) REVERT: A 283 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7545 (mt-10) REVERT: A 351 MET cc_start: 0.9217 (mtp) cc_final: 0.9014 (mtp) REVERT: A 378 THR cc_start: 0.9326 (OUTLIER) cc_final: 0.8916 (t) REVERT: A 488 MET cc_start: 0.6667 (mmt) cc_final: 0.6182 (mtm) REVERT: A 562 MET cc_start: 0.9227 (mmt) cc_final: 0.8786 (mmt) REVERT: A 618 ASP cc_start: 0.7412 (m-30) cc_final: 0.7099 (m-30) REVERT: A 619 CYS cc_start: 0.6721 (p) cc_final: 0.6420 (p) REVERT: A 686 LYS cc_start: 0.8850 (OUTLIER) cc_final: 0.8475 (ptpp) REVERT: A 738 LYS cc_start: 0.8269 (pttt) cc_final: 0.7904 (pttm) REVERT: A 740 THR cc_start: 0.8074 (OUTLIER) cc_final: 0.7745 (p) REVERT: B 156 ASP cc_start: 0.5359 (t0) cc_final: 0.5080 (OUTLIER) REVERT: B 159 MET cc_start: 0.6852 (mmm) cc_final: 0.6143 (mmm) REVERT: B 185 GLU cc_start: 0.7423 (mm-30) cc_final: 0.7146 (mm-30) REVERT: B 263 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7689 (pt0) REVERT: B 283 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7442 (mt-10) REVERT: B 488 MET cc_start: 0.6689 (mmt) cc_final: 0.6220 (mtm) REVERT: B 562 MET cc_start: 0.9222 (mmt) cc_final: 0.8840 (mmt) REVERT: B 618 ASP cc_start: 0.7426 (m-30) cc_final: 0.7115 (m-30) REVERT: B 619 CYS cc_start: 0.6744 (p) cc_final: 0.6447 (p) REVERT: B 738 LYS cc_start: 0.8287 (pttt) cc_final: 0.7922 (pttm) REVERT: B 740 THR cc_start: 0.8114 (OUTLIER) cc_final: 0.7740 (p) REVERT: C 156 ASP cc_start: 0.5389 (t0) cc_final: 0.5110 (OUTLIER) REVERT: C 159 MET cc_start: 0.7028 (mmm) cc_final: 0.6167 (mmm) REVERT: C 185 GLU cc_start: 0.7359 (mm-30) cc_final: 0.7073 (mm-30) REVERT: C 263 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7818 (pt0) REVERT: C 283 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7569 (mt-10) REVERT: C 488 MET cc_start: 0.6640 (mmt) cc_final: 0.6181 (mtm) REVERT: C 562 MET cc_start: 0.9228 (mmt) cc_final: 0.8817 (mmt) REVERT: C 618 ASP cc_start: 0.7394 (m-30) cc_final: 0.7074 (m-30) REVERT: C 619 CYS cc_start: 0.6647 (p) cc_final: 0.6348 (p) REVERT: C 738 LYS cc_start: 0.8283 (pttt) cc_final: 0.7939 (pttm) REVERT: C 740 THR cc_start: 0.8146 (OUTLIER) cc_final: 0.7802 (p) REVERT: D 159 MET cc_start: 0.6941 (mmm) cc_final: 0.6167 (mmm) REVERT: D 185 GLU cc_start: 0.7404 (mm-30) cc_final: 0.7128 (mm-30) REVERT: D 263 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7828 (pt0) REVERT: D 283 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7509 (mt-10) REVERT: D 346 GLN cc_start: 0.9048 (mt0) cc_final: 0.8370 (mt0) REVERT: D 488 MET cc_start: 0.6700 (mmt) cc_final: 0.6209 (mtm) REVERT: D 514 GLN cc_start: 0.7216 (OUTLIER) cc_final: 0.6563 (mm-40) REVERT: D 562 MET cc_start: 0.9239 (mmt) cc_final: 0.8828 (mmt) REVERT: D 618 ASP cc_start: 0.7414 (m-30) cc_final: 0.7097 (m-30) REVERT: D 619 CYS cc_start: 0.6649 (p) cc_final: 0.6334 (p) REVERT: D 738 LYS cc_start: 0.8307 (pttt) cc_final: 0.7944 (pttm) REVERT: D 740 THR cc_start: 0.8160 (OUTLIER) cc_final: 0.7800 (p) outliers start: 58 outliers final: 29 residues processed: 349 average time/residue: 1.4298 time to fit residues: 560.0004 Evaluate side-chains 341 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 301 time to evaluate : 2.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 686 LYS Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 282 MET Chi-restraints excluded: chain B residue 283 GLU Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 576 SER Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 743 LYS Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 282 MET Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain D residue 263 GLU Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 411 THR Chi-restraints excluded: chain D residue 498 SER Chi-restraints excluded: chain D residue 514 GLN Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 576 SER Chi-restraints excluded: chain D residue 740 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 150 optimal weight: 0.0470 chunk 12 optimal weight: 0.0020 chunk 130 optimal weight: 0.4980 chunk 56 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 230 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 147 optimal weight: 0.3980 chunk 102 optimal weight: 0.8980 overall best weight: 0.3686 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN A 523 HIS A 750 ASN B 279 GLN B 430 HIS B 750 ASN C 279 GLN C 750 ASN D 279 GLN D 750 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.163614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.129778 restraints weight = 23246.089| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 1.68 r_work: 0.3339 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3213 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| r_final: 0.3213 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 22226 Z= 0.100 Angle : 0.526 10.618 29830 Z= 0.261 Chirality : 0.036 0.142 3233 Planarity : 0.003 0.029 3600 Dihedral : 15.677 119.061 3885 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.30 % Allowed : 15.57 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.17), residues: 2484 helix: 1.73 (0.12), residues: 1616 sheet: 3.48 (0.66), residues: 64 loop : -1.44 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 710 HIS 0.004 0.001 HIS C 301 PHE 0.014 0.001 PHE C 377 TYR 0.012 0.001 TYR D 208 ARG 0.002 0.000 ARG D 416 Details of bonding type rmsd hydrogen bonds : bond 0.03149 ( 1124) hydrogen bonds : angle 3.72193 ( 3324) SS BOND : bond 0.00056 ( 4) SS BOND : angle 1.01831 ( 8) covalent geometry : bond 0.00219 (22222) covalent geometry : angle 0.52568 (29822) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 336 time to evaluate : 2.184 Fit side-chains REVERT: A 159 MET cc_start: 0.6818 (mmm) cc_final: 0.6286 (mmm) REVERT: A 185 GLU cc_start: 0.7360 (mm-30) cc_final: 0.7148 (mm-30) REVERT: A 283 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7548 (mt-10) REVERT: A 351 MET cc_start: 0.9207 (mtp) cc_final: 0.8984 (mtp) REVERT: A 378 THR cc_start: 0.9313 (OUTLIER) cc_final: 0.8921 (t) REVERT: A 488 MET cc_start: 0.6660 (mmt) cc_final: 0.6130 (mtm) REVERT: A 562 MET cc_start: 0.9159 (mmt) cc_final: 0.8781 (mmt) REVERT: A 618 ASP cc_start: 0.7342 (m-30) cc_final: 0.7024 (m-30) REVERT: A 619 CYS cc_start: 0.6619 (p) cc_final: 0.6328 (p) REVERT: A 686 LYS cc_start: 0.8859 (OUTLIER) cc_final: 0.8125 (mttp) REVERT: A 738 LYS cc_start: 0.8233 (pttt) cc_final: 0.7869 (pttm) REVERT: A 740 THR cc_start: 0.8103 (OUTLIER) cc_final: 0.7801 (p) REVERT: B 156 ASP cc_start: 0.5337 (t0) cc_final: 0.5055 (OUTLIER) REVERT: B 159 MET cc_start: 0.6833 (mmm) cc_final: 0.6238 (mmm) REVERT: B 185 GLU cc_start: 0.7382 (mm-30) cc_final: 0.7177 (mm-30) REVERT: B 263 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7580 (pt0) REVERT: B 283 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7523 (mt-10) REVERT: B 312 THR cc_start: 0.8655 (m) cc_final: 0.8437 (m) REVERT: B 488 MET cc_start: 0.6681 (mmt) cc_final: 0.6162 (mtm) REVERT: B 562 MET cc_start: 0.9163 (mmt) cc_final: 0.8675 (mmt) REVERT: B 618 ASP cc_start: 0.7345 (m-30) cc_final: 0.7028 (m-30) REVERT: B 619 CYS cc_start: 0.6626 (p) cc_final: 0.6337 (p) REVERT: B 686 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8083 (mttp) REVERT: B 738 LYS cc_start: 0.8256 (pttt) cc_final: 0.7883 (pttm) REVERT: B 740 THR cc_start: 0.8055 (OUTLIER) cc_final: 0.7695 (p) REVERT: C 156 ASP cc_start: 0.5338 (t0) cc_final: 0.5046 (OUTLIER) REVERT: C 159 MET cc_start: 0.6965 (mmm) cc_final: 0.6345 (mmm) REVERT: C 185 GLU cc_start: 0.7238 (mm-30) cc_final: 0.6970 (mm-30) REVERT: C 283 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7523 (mt-10) REVERT: C 488 MET cc_start: 0.6549 (mmt) cc_final: 0.6077 (mtm) REVERT: C 562 MET cc_start: 0.9187 (mmt) cc_final: 0.8814 (mmt) REVERT: C 618 ASP cc_start: 0.7334 (m-30) cc_final: 0.7025 (m-30) REVERT: C 619 CYS cc_start: 0.6590 (p) cc_final: 0.6297 (p) REVERT: C 686 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.8070 (mttp) REVERT: C 738 LYS cc_start: 0.8252 (pttt) cc_final: 0.7884 (pttm) REVERT: C 740 THR cc_start: 0.8097 (OUTLIER) cc_final: 0.7752 (p) REVERT: D 159 MET cc_start: 0.6914 (mmm) cc_final: 0.6356 (mmm) REVERT: D 283 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7473 (mt-10) REVERT: D 346 GLN cc_start: 0.9040 (mt0) cc_final: 0.8325 (mt0) REVERT: D 488 MET cc_start: 0.6691 (mmt) cc_final: 0.6169 (mtm) REVERT: D 514 GLN cc_start: 0.7129 (tt0) cc_final: 0.6490 (mm-40) REVERT: D 562 MET cc_start: 0.9191 (mmt) cc_final: 0.8843 (mmt) REVERT: D 618 ASP cc_start: 0.7331 (m-30) cc_final: 0.7018 (m-30) REVERT: D 619 CYS cc_start: 0.6558 (p) cc_final: 0.6255 (p) REVERT: D 686 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8056 (mttp) REVERT: D 738 LYS cc_start: 0.8260 (pttt) cc_final: 0.7896 (pttm) REVERT: D 740 THR cc_start: 0.8116 (OUTLIER) cc_final: 0.7763 (p) outliers start: 51 outliers final: 24 residues processed: 370 average time/residue: 1.5266 time to fit residues: 637.7341 Evaluate side-chains 345 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 309 time to evaluate : 2.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 686 LYS Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 282 MET Chi-restraints excluded: chain B residue 283 GLU Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 576 SER Chi-restraints excluded: chain B residue 686 LYS Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 611 LYS Chi-restraints excluded: chain C residue 686 LYS Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain C residue 743 LYS Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 411 THR Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 576 SER Chi-restraints excluded: chain D residue 686 LYS Chi-restraints excluded: chain D residue 740 THR Chi-restraints excluded: chain D residue 743 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 220 optimal weight: 1.9990 chunk 135 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 145 optimal weight: 4.9990 chunk 201 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 chunk 189 optimal weight: 7.9990 chunk 242 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 ASN A 279 GLN A 750 ASN B 205 ASN B 279 GLN B 750 ASN C 205 ASN C 279 GLN C 750 ASN D 205 ASN D 279 GLN D 750 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.155303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.121003 restraints weight = 23148.984| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.65 r_work: 0.3226 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3101 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3101 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.3608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 22226 Z= 0.221 Angle : 0.694 13.591 29830 Z= 0.340 Chirality : 0.043 0.178 3233 Planarity : 0.004 0.039 3600 Dihedral : 16.581 118.539 3885 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.39 % Allowed : 16.20 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.16), residues: 2484 helix: 1.28 (0.12), residues: 1644 sheet: 2.83 (0.64), residues: 64 loop : -1.38 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 710 HIS 0.008 0.001 HIS A 301 PHE 0.026 0.002 PHE B 377 TYR 0.017 0.002 TYR D 208 ARG 0.005 0.001 ARG A 337 Details of bonding type rmsd hydrogen bonds : bond 0.04317 ( 1124) hydrogen bonds : angle 4.06046 ( 3324) SS BOND : bond 0.00021 ( 4) SS BOND : angle 1.29198 ( 8) covalent geometry : bond 0.00538 (22222) covalent geometry : angle 0.69376 (29822) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 313 time to evaluate : 2.591 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 159 MET cc_start: 0.7054 (mmm) cc_final: 0.6379 (mmm) REVERT: A 185 GLU cc_start: 0.7449 (mm-30) cc_final: 0.7222 (mm-30) REVERT: A 283 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7544 (mt-10) REVERT: A 411 THR cc_start: 0.7855 (OUTLIER) cc_final: 0.7531 (p) REVERT: A 488 MET cc_start: 0.6857 (mmt) cc_final: 0.6358 (mtm) REVERT: A 562 MET cc_start: 0.9244 (mmt) cc_final: 0.8914 (mmt) REVERT: A 618 ASP cc_start: 0.7483 (m-30) cc_final: 0.7148 (m-30) REVERT: A 619 CYS cc_start: 0.6543 (p) cc_final: 0.6287 (p) REVERT: A 686 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8506 (ptpp) REVERT: A 738 LYS cc_start: 0.8359 (pttt) cc_final: 0.7978 (pttm) REVERT: A 740 THR cc_start: 0.8146 (OUTLIER) cc_final: 0.7920 (p) REVERT: B 159 MET cc_start: 0.6902 (mmm) cc_final: 0.6271 (mmm) REVERT: B 185 GLU cc_start: 0.7428 (mm-30) cc_final: 0.7195 (mm-30) REVERT: B 263 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7927 (pt0) REVERT: B 283 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7542 (mt-10) REVERT: B 488 MET cc_start: 0.6885 (mmt) cc_final: 0.6393 (mtm) REVERT: B 514 GLN cc_start: 0.7235 (OUTLIER) cc_final: 0.6576 (mm-40) REVERT: B 562 MET cc_start: 0.9236 (mmt) cc_final: 0.8903 (mmt) REVERT: B 618 ASP cc_start: 0.7580 (m-30) cc_final: 0.7238 (m-30) REVERT: B 619 CYS cc_start: 0.6576 (p) cc_final: 0.6315 (p) REVERT: B 686 LYS cc_start: 0.8773 (OUTLIER) cc_final: 0.8063 (mttp) REVERT: B 738 LYS cc_start: 0.8391 (pttt) cc_final: 0.8018 (pttm) REVERT: B 740 THR cc_start: 0.8218 (OUTLIER) cc_final: 0.7939 (p) REVERT: C 159 MET cc_start: 0.7032 (mmm) cc_final: 0.6126 (mmm) REVERT: C 185 GLU cc_start: 0.7377 (mm-30) cc_final: 0.7142 (mm-30) REVERT: C 283 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7560 (mt-10) REVERT: C 488 MET cc_start: 0.6840 (mmt) cc_final: 0.6367 (mtm) REVERT: C 514 GLN cc_start: 0.7220 (OUTLIER) cc_final: 0.6568 (mm-40) REVERT: C 562 MET cc_start: 0.9246 (mmt) cc_final: 0.8903 (mmt) REVERT: C 618 ASP cc_start: 0.7458 (m-30) cc_final: 0.7161 (m-30) REVERT: C 682 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8097 (tt0) REVERT: C 686 LYS cc_start: 0.8774 (OUTLIER) cc_final: 0.8069 (mttp) REVERT: C 738 LYS cc_start: 0.8360 (pttt) cc_final: 0.7991 (pttm) REVERT: C 740 THR cc_start: 0.8213 (OUTLIER) cc_final: 0.7937 (p) REVERT: D 159 MET cc_start: 0.6911 (mmm) cc_final: 0.6207 (mmm) REVERT: D 283 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7536 (mt-10) REVERT: D 488 MET cc_start: 0.6874 (mmt) cc_final: 0.6366 (mtm) REVERT: D 514 GLN cc_start: 0.7229 (OUTLIER) cc_final: 0.6598 (mm-40) REVERT: D 562 MET cc_start: 0.9239 (mmt) cc_final: 0.8925 (mmt) REVERT: D 618 ASP cc_start: 0.7461 (m-30) cc_final: 0.7166 (m-30) REVERT: D 682 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8131 (tt0) REVERT: D 686 LYS cc_start: 0.8794 (OUTLIER) cc_final: 0.8087 (mttp) REVERT: D 738 LYS cc_start: 0.8367 (pttt) cc_final: 0.8000 (pttm) REVERT: D 740 THR cc_start: 0.8219 (OUTLIER) cc_final: 0.7943 (p) outliers start: 53 outliers final: 25 residues processed: 349 average time/residue: 1.5659 time to fit residues: 611.1019 Evaluate side-chains 349 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 305 time to evaluate : 2.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 686 LYS Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 282 MET Chi-restraints excluded: chain B residue 283 GLU Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 514 GLN Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 576 SER Chi-restraints excluded: chain B residue 686 LYS Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain C residue 282 MET Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 418 GLU Chi-restraints excluded: chain C residue 514 GLN Chi-restraints excluded: chain C residue 519 ASP Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 682 GLU Chi-restraints excluded: chain C residue 686 LYS Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain C residue 743 LYS Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 411 THR Chi-restraints excluded: chain D residue 514 GLN Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 576 SER Chi-restraints excluded: chain D residue 682 GLU Chi-restraints excluded: chain D residue 686 LYS Chi-restraints excluded: chain D residue 740 THR Chi-restraints excluded: chain D residue 743 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 56 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 95 optimal weight: 4.9990 chunk 215 optimal weight: 1.9990 chunk 190 optimal weight: 2.9990 chunk 130 optimal weight: 0.7980 chunk 170 optimal weight: 0.6980 chunk 93 optimal weight: 0.6980 chunk 79 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN A 750 ASN B 279 GLN B 750 ASN C 279 GLN C 750 ASN D 750 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.159656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.125608 restraints weight = 23238.054| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.67 r_work: 0.3283 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3154 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| r_final: 0.3154 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22226 Z= 0.125 Angle : 0.590 11.889 29830 Z= 0.292 Chirality : 0.038 0.147 3233 Planarity : 0.003 0.033 3600 Dihedral : 16.097 119.446 3885 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.71 % Allowed : 17.19 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.17), residues: 2484 helix: 1.42 (0.12), residues: 1644 sheet: 3.00 (0.65), residues: 64 loop : -1.30 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 710 HIS 0.005 0.001 HIS A 301 PHE 0.017 0.001 PHE C 506 TYR 0.020 0.002 TYR C 208 ARG 0.003 0.000 ARG B 337 Details of bonding type rmsd hydrogen bonds : bond 0.03570 ( 1124) hydrogen bonds : angle 3.88149 ( 3324) SS BOND : bond 0.00044 ( 4) SS BOND : angle 1.10277 ( 8) covalent geometry : bond 0.00289 (22222) covalent geometry : angle 0.58945 (29822) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 327 time to evaluate : 2.234 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 159 MET cc_start: 0.6983 (mmm) cc_final: 0.6159 (mmm) REVERT: A 185 GLU cc_start: 0.7372 (mm-30) cc_final: 0.7150 (mm-30) REVERT: A 283 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7503 (mt-10) REVERT: A 488 MET cc_start: 0.6675 (mmt) cc_final: 0.6194 (mtm) REVERT: A 562 MET cc_start: 0.9238 (mmt) cc_final: 0.8811 (mmt) REVERT: A 618 ASP cc_start: 0.7419 (m-30) cc_final: 0.7093 (m-30) REVERT: A 619 CYS cc_start: 0.6690 (p) cc_final: 0.6365 (p) REVERT: A 686 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8430 (ptpp) REVERT: A 738 LYS cc_start: 0.8281 (pttt) cc_final: 0.7908 (pttm) REVERT: A 740 THR cc_start: 0.8069 (OUTLIER) cc_final: 0.7799 (p) REVERT: B 159 MET cc_start: 0.7014 (mmm) cc_final: 0.6303 (mmm) REVERT: B 185 GLU cc_start: 0.7369 (mm-30) cc_final: 0.7164 (mm-30) REVERT: B 263 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7773 (pt0) REVERT: B 283 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7519 (mt-10) REVERT: B 488 MET cc_start: 0.6699 (mmt) cc_final: 0.6234 (mtm) REVERT: B 562 MET cc_start: 0.9233 (mmt) cc_final: 0.8870 (mmt) REVERT: B 618 ASP cc_start: 0.7488 (m-30) cc_final: 0.7167 (m-30) REVERT: B 619 CYS cc_start: 0.6713 (p) cc_final: 0.6391 (p) REVERT: B 686 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8021 (mttp) REVERT: B 738 LYS cc_start: 0.8310 (pttt) cc_final: 0.7922 (pttm) REVERT: B 740 THR cc_start: 0.8095 (OUTLIER) cc_final: 0.7741 (p) REVERT: C 159 MET cc_start: 0.7003 (mmm) cc_final: 0.6181 (mmm) REVERT: C 185 GLU cc_start: 0.7308 (mm-30) cc_final: 0.7106 (mm-30) REVERT: C 283 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7579 (mt-10) REVERT: C 488 MET cc_start: 0.6719 (mmt) cc_final: 0.6275 (mtm) REVERT: C 562 MET cc_start: 0.9240 (mmt) cc_final: 0.8855 (mmt) REVERT: C 618 ASP cc_start: 0.7420 (m-30) cc_final: 0.7126 (m-30) REVERT: C 686 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8021 (mttp) REVERT: C 738 LYS cc_start: 0.8315 (pttt) cc_final: 0.7939 (pttm) REVERT: C 740 THR cc_start: 0.8101 (OUTLIER) cc_final: 0.7739 (p) REVERT: D 159 MET cc_start: 0.7012 (mmm) cc_final: 0.6229 (mmm) REVERT: D 283 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7543 (mt-10) REVERT: D 488 MET cc_start: 0.6705 (mmt) cc_final: 0.6224 (mtm) REVERT: D 514 GLN cc_start: 0.7186 (tt0) cc_final: 0.6568 (mm-40) REVERT: D 562 MET cc_start: 0.9229 (mmt) cc_final: 0.8817 (mmt) REVERT: D 618 ASP cc_start: 0.7440 (m-30) cc_final: 0.7142 (m-30) REVERT: D 686 LYS cc_start: 0.8763 (OUTLIER) cc_final: 0.8038 (mttp) REVERT: D 738 LYS cc_start: 0.8334 (pttt) cc_final: 0.7952 (pttm) REVERT: D 740 THR cc_start: 0.8121 (OUTLIER) cc_final: 0.7760 (p) outliers start: 38 outliers final: 21 residues processed: 353 average time/residue: 1.5109 time to fit residues: 597.4514 Evaluate side-chains 349 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 315 time to evaluate : 2.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 686 LYS Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 282 MET Chi-restraints excluded: chain B residue 283 GLU Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 576 SER Chi-restraints excluded: chain B residue 686 LYS Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain C residue 282 MET Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 611 LYS Chi-restraints excluded: chain C residue 686 LYS Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 411 THR Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 576 SER Chi-restraints excluded: chain D residue 686 LYS Chi-restraints excluded: chain D residue 740 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 172 optimal weight: 3.9990 chunk 185 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 191 optimal weight: 3.9990 chunk 196 optimal weight: 0.8980 chunk 65 optimal weight: 7.9990 chunk 225 optimal weight: 3.9990 chunk 229 optimal weight: 0.7980 chunk 123 optimal weight: 4.9990 chunk 142 optimal weight: 0.5980 chunk 171 optimal weight: 0.9980 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 279 GLN A 750 ASN B 279 GLN B 750 ASN C 279 GLN C 430 HIS C 750 ASN D 750 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.159597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.125564 restraints weight = 23197.109| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.66 r_work: 0.3283 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3156 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3156 r_free = 0.3156 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3156 r_free = 0.3156 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| r_final: 0.3156 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 22226 Z= 0.129 Angle : 0.601 11.941 29830 Z= 0.297 Chirality : 0.038 0.194 3233 Planarity : 0.003 0.034 3600 Dihedral : 15.973 117.235 3885 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.62 % Allowed : 16.92 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.17), residues: 2484 helix: 1.46 (0.12), residues: 1644 sheet: 3.03 (0.64), residues: 64 loop : -1.35 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B 710 HIS 0.006 0.001 HIS A 301 PHE 0.017 0.001 PHE C 377 TYR 0.021 0.002 TYR C 208 ARG 0.003 0.000 ARG A 337 Details of bonding type rmsd hydrogen bonds : bond 0.03602 ( 1124) hydrogen bonds : angle 3.88536 ( 3324) SS BOND : bond 0.00040 ( 4) SS BOND : angle 1.14643 ( 8) covalent geometry : bond 0.00307 (22222) covalent geometry : angle 0.60119 (29822) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20502.68 seconds wall clock time: 353 minutes 57.17 seconds (21237.17 seconds total)