Starting phenix.real_space_refine on Thu Jun 19 02:34:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gka_40181/06_2025/8gka_40181.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gka_40181/06_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_40181/06_2025/8gka_40181.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gka_40181/06_2025/8gka_40181.map" model { file = "/net/cci-nas-00/data/ceres_data/8gka_40181/06_2025/8gka_40181.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gka_40181/06_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-5710/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: 13.26, per 1000 atoms: 0.61 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: 5.09 Conformation dependent library (CDL) restraints added in 2.7 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: 1.87 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: 6.59 Time building geometry restraints manager: 6.13 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: 1.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.840 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 47.680 Find NCS groups from input model: 1.570 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.990 ------------------------------------------------------------------------------- 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 : 2.491 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: 1.5604 time to fit residues: 820.8673 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 : 2.421 ------------------------------------------------------------------------------- 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 = 22797.289| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.72 r_work: 0.3278 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3151 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 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 = 0.3148 r_free = 0.3148 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| r_final: 0.3148 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 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 : 2.377 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: 0.6818 (mmm) cc_final: 0.6237 (mmm) REVERT: A 185 GLU cc_start: 0.7664 (mm-30) cc_final: 0.7347 (mm-30) REVERT: A 351 MET cc_start: 0.9300 (mtp) cc_final: 0.9089 (mtp) REVERT: A 378 THR cc_start: 0.9252 (OUTLIER) cc_final: 0.8825 (t) REVERT: A 562 MET cc_start: 0.9245 (mmt) cc_final: 0.8841 (mmt) REVERT: A 738 LYS cc_start: 0.8387 (pttt) cc_final: 0.8081 (ptpp) REVERT: A 740 THR cc_start: 0.8010 (m) cc_final: 0.7728 (p) REVERT: A 747 SER cc_start: 0.8247 (p) cc_final: 0.8043 (t) REVERT: B 159 MET cc_start: 0.6685 (mmm) cc_final: 0.5924 (mmm) REVERT: B 185 GLU cc_start: 0.7659 (mm-30) cc_final: 0.7287 (mm-30) REVERT: B 351 MET cc_start: 0.9282 (mtp) cc_final: 0.9071 (mtp) REVERT: B 378 THR cc_start: 0.9257 (OUTLIER) cc_final: 0.8817 (t) REVERT: B 514 GLN cc_start: 0.7311 (OUTLIER) cc_final: 0.6546 (mm-40) REVERT: B 562 MET cc_start: 0.9253 (mmt) cc_final: 0.8800 (mmt) REVERT: B 738 LYS cc_start: 0.8484 (pttt) cc_final: 0.8139 (ptpp) REVERT: B 740 THR cc_start: 0.8024 (OUTLIER) cc_final: 0.7722 (p) REVERT: C 159 MET cc_start: 0.6852 (mmm) cc_final: 0.5925 (mmm) REVERT: C 185 GLU cc_start: 0.7645 (mm-30) cc_final: 0.7239 (mm-30) REVERT: C 351 MET cc_start: 0.9276 (mtp) cc_final: 0.9063 (mtp) REVERT: C 378 THR cc_start: 0.9253 (OUTLIER) cc_final: 0.8961 (t) REVERT: C 514 GLN cc_start: 0.7303 (OUTLIER) cc_final: 0.6540 (mm-40) REVERT: C 562 MET cc_start: 0.9263 (mmt) cc_final: 0.8806 (mmt) REVERT: C 738 LYS cc_start: 0.8462 (pttt) cc_final: 0.8130 (ptpp) REVERT: C 740 THR cc_start: 0.8066 (m) cc_final: 0.7776 (p) REVERT: D 159 MET cc_start: 0.6720 (mmm) cc_final: 0.5950 (mmm) REVERT: D 185 GLU cc_start: 0.7667 (mm-30) cc_final: 0.7275 (mm-30) REVERT: D 346 GLN cc_start: 0.9109 (mt0) cc_final: 0.8440 (mt0) REVERT: D 351 MET cc_start: 0.9274 (mtp) cc_final: 0.9060 (mtp) REVERT: D 378 THR cc_start: 0.9260 (OUTLIER) cc_final: 0.8823 (t) REVERT: D 514 GLN cc_start: 0.7305 (OUTLIER) cc_final: 0.6592 (mm-40) REVERT: D 562 MET cc_start: 0.9264 (mmt) cc_final: 0.8804 (mmt) REVERT: D 738 LYS cc_start: 0.8469 (pttt) cc_final: 0.8137 (ptpp) REVERT: D 740 THR cc_start: 0.8027 (OUTLIER) cc_final: 0.7726 (p) outliers start: 71 outliers final: 22 residues processed: 388 average time/residue: 1.7417 time to fit residues: 762.2585 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 : 2.321 ------------------------------------------------------------------------------- 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: 1.9990 chunk 220 optimal weight: 4.9990 chunk 151 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 201 optimal weight: 0.8980 chunk 182 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.3838 r_free = 0.3838 target = 0.160519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.125686 restraints weight = 22856.665| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.71 r_work: 0.3283 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3158 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3158 r_free = 0.3158 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3158 r_free = 0.3158 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3158 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 22226 Z= 0.139 Angle : 0.560 11.166 29830 Z= 0.278 Chirality : 0.038 0.142 3233 Planarity : 0.003 0.026 3600 Dihedral : 16.519 127.258 3893 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.47 % Allowed : 11.64 % Favored : 84.88 % 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: 0.77 (0.17), residues: 2484 helix: 1.36 (0.12), residues: 1612 sheet: 3.25 (0.66), residues: 64 loop : -1.49 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 380 HIS 0.006 0.001 HIS A 301 PHE 0.013 0.001 PHE C 193 TYR 0.015 0.002 TYR B 208 ARG 0.002 0.000 ARG B 416 Details of bonding type rmsd hydrogen bonds : bond 0.04080 ( 1124) hydrogen bonds : angle 4.01412 ( 3324) SS BOND : bond 0.00031 ( 4) SS BOND : angle 1.18133 ( 8) covalent geometry : bond 0.00327 (22222) covalent geometry : angle 0.55952 (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 392 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 315 time to evaluate : 2.509 Fit side-chains revert: symmetry clash REVERT: A 159 MET cc_start: 0.6811 (mmm) cc_final: 0.6275 (mmm) REVERT: A 185 GLU cc_start: 0.7556 (mm-30) cc_final: 0.7150 (mm-30) REVERT: A 253 LYS cc_start: 0.7260 (mppt) cc_final: 0.6982 (mppt) REVERT: A 280 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7986 (tp) REVERT: A 351 MET cc_start: 0.9280 (mtp) cc_final: 0.9063 (mtp) REVERT: A 378 THR cc_start: 0.9271 (OUTLIER) cc_final: 0.8994 (t) REVERT: A 562 MET cc_start: 0.9251 (mmt) cc_final: 0.8815 (mmt) REVERT: A 619 CYS cc_start: 0.6454 (p) cc_final: 0.6226 (p) REVERT: A 686 LYS cc_start: 0.8809 (OUTLIER) cc_final: 0.8445 (ptpp) REVERT: A 717 MET cc_start: 0.5629 (ttm) cc_final: 0.5425 (ttt) REVERT: A 738 LYS cc_start: 0.8323 (pttt) cc_final: 0.7809 (ptpp) REVERT: A 740 THR cc_start: 0.8020 (m) cc_final: 0.7664 (p) REVERT: A 747 SER cc_start: 0.8107 (p) cc_final: 0.7841 (t) REVERT: B 159 MET cc_start: 0.6835 (mmm) cc_final: 0.6175 (mmm) REVERT: B 185 GLU cc_start: 0.7639 (mm-30) cc_final: 0.7233 (mm-30) REVERT: B 253 LYS cc_start: 0.7242 (mppt) cc_final: 0.6967 (mppt) REVERT: B 351 MET cc_start: 0.9267 (mtp) cc_final: 0.9052 (mtp) REVERT: B 378 THR cc_start: 0.9255 (OUTLIER) cc_final: 0.8964 (t) REVERT: B 535 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8189 (tt) REVERT: B 562 MET cc_start: 0.9234 (mmt) cc_final: 0.8883 (mmt) REVERT: B 619 CYS cc_start: 0.6646 (p) cc_final: 0.6392 (p) REVERT: B 686 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8436 (ptpp) REVERT: B 738 LYS cc_start: 0.8374 (pttt) cc_final: 0.7853 (ptpp) REVERT: B 740 THR cc_start: 0.8090 (m) cc_final: 0.7693 (p) REVERT: B 743 LYS cc_start: 0.8458 (ptpp) cc_final: 0.8231 (ptpp) REVERT: C 159 MET cc_start: 0.6937 (mmm) cc_final: 0.6229 (mmm) REVERT: C 185 GLU cc_start: 0.7500 (mm-30) cc_final: 0.7086 (mm-30) REVERT: C 283 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7589 (mt-10) REVERT: C 351 MET cc_start: 0.9266 (mtp) cc_final: 0.9047 (mtp) REVERT: C 378 THR cc_start: 0.9255 (OUTLIER) cc_final: 0.8975 (t) REVERT: C 535 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8175 (tt) REVERT: C 562 MET cc_start: 0.9248 (mmt) cc_final: 0.8838 (mmt) REVERT: C 619 CYS cc_start: 0.6536 (p) cc_final: 0.6288 (p) REVERT: C 686 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.8435 (ptpp) REVERT: C 738 LYS cc_start: 0.8362 (pttt) cc_final: 0.7851 (ptpp) REVERT: C 740 THR cc_start: 0.8003 (OUTLIER) cc_final: 0.7630 (p) REVERT: C 743 LYS cc_start: 0.8455 (ptpp) cc_final: 0.8221 (ptpp) REVERT: D 159 MET cc_start: 0.6855 (mmm) cc_final: 0.6195 (mmm) REVERT: D 185 GLU cc_start: 0.7639 (mm-30) cc_final: 0.7256 (mm-30) REVERT: D 346 GLN cc_start: 0.9072 (mt0) cc_final: 0.8492 (mt0) REVERT: D 351 MET cc_start: 0.9259 (mtp) cc_final: 0.9048 (mtp) REVERT: D 378 THR cc_start: 0.9262 (OUTLIER) cc_final: 0.8971 (t) REVERT: D 562 MET cc_start: 0.9248 (mmt) cc_final: 0.8848 (mmt) REVERT: D 619 CYS cc_start: 0.6657 (p) cc_final: 0.6374 (p) REVERT: D 686 LYS cc_start: 0.8815 (OUTLIER) cc_final: 0.8474 (ptpp) REVERT: D 738 LYS cc_start: 0.8373 (pttt) cc_final: 0.7858 (ptpp) REVERT: D 740 THR cc_start: 0.8126 (m) cc_final: 0.7751 (p) REVERT: D 743 LYS cc_start: 0.8448 (ptpp) cc_final: 0.8215 (ptpp) outliers start: 77 outliers final: 22 residues processed: 374 average time/residue: 1.6299 time to fit residues: 684.0414 Evaluate side-chains 326 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 291 time to evaluate : 2.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 548 LEU Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 611 LYS Chi-restraints excluded: chain A residue 621 SER Chi-restraints excluded: chain A residue 686 LYS Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 378 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 611 LYS Chi-restraints excluded: chain B residue 621 SER Chi-restraints excluded: chain B residue 686 LYS 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 535 LEU 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 621 SER Chi-restraints excluded: chain C residue 686 LYS Chi-restraints excluded: chain C residue 740 THR 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 548 LEU Chi-restraints excluded: chain D residue 576 SER Chi-restraints excluded: chain D residue 611 LYS 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: 2.9990 chunk 188 optimal weight: 1.9990 chunk 76 optimal weight: 0.0670 chunk 169 optimal weight: 4.9990 chunk 4 optimal weight: 10.0000 chunk 127 optimal weight: 0.1980 chunk 100 optimal weight: 5.9990 chunk 148 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 137 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 overall best weight: 0.6320 ------------------------------------------------------------------------------- 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 B 750 ASN C 279 GLN C 452 ASN C 750 ASN ** D 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 750 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.162258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.127262 restraints weight = 23294.155| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 1.75 r_work: 0.3305 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3172 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3172 r_free = 0.3172 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 = 0.3172 r_free = 0.3172 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| r_final: 0.3172 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 22226 Z= 0.110 Angle : 0.529 10.937 29830 Z= 0.263 Chirality : 0.037 0.143 3233 Planarity : 0.003 0.026 3600 Dihedral : 16.102 118.879 3889 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.17 % Allowed : 13.76 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.53 (0.12), residues: 1620 sheet: 3.54 (0.66), residues: 64 loop : -1.49 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 710 HIS 0.005 0.001 HIS C 301 PHE 0.013 0.001 PHE A 193 TYR 0.014 0.001 TYR D 208 ARG 0.002 0.000 ARG A 416 Details of bonding type rmsd hydrogen bonds : bond 0.03529 ( 1124) hydrogen bonds : angle 3.87520 ( 3324) SS BOND : bond 0.00034 ( 4) SS BOND : angle 0.99673 ( 8) covalent geometry : bond 0.00249 (22222) covalent geometry : angle 0.52873 (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: 48 poor density : 321 time to evaluate : 2.341 Fit side-chains REVERT: A 185 GLU cc_start: 0.7567 (mm-30) cc_final: 0.7192 (mm-30) REVERT: A 378 THR cc_start: 0.9278 (OUTLIER) cc_final: 0.9002 (t) REVERT: A 488 MET cc_start: 0.6617 (mmt) cc_final: 0.6125 (mtm) REVERT: A 562 MET cc_start: 0.9221 (mmt) cc_final: 0.8773 (mmt) REVERT: A 619 CYS cc_start: 0.6511 (p) cc_final: 0.6235 (p) REVERT: A 686 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8358 (ptpp) REVERT: A 738 LYS cc_start: 0.8248 (pttt) cc_final: 0.7857 (pttm) REVERT: A 740 THR cc_start: 0.7980 (m) cc_final: 0.7655 (p) REVERT: A 747 SER cc_start: 0.8078 (p) cc_final: 0.7746 (t) REVERT: B 159 MET cc_start: 0.6781 (mmm) cc_final: 0.6340 (mmm) REVERT: B 185 GLU cc_start: 0.7530 (mm-30) cc_final: 0.7202 (mm-30) REVERT: B 378 THR cc_start: 0.9258 (OUTLIER) cc_final: 0.8985 (t) REVERT: B 488 MET cc_start: 0.6586 (mmt) cc_final: 0.6088 (mtm) REVERT: B 562 MET cc_start: 0.9221 (mmt) cc_final: 0.8854 (mmt) REVERT: B 619 CYS cc_start: 0.6555 (p) cc_final: 0.6276 (p) REVERT: B 686 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8420 (ptpp) REVERT: B 738 LYS cc_start: 0.8260 (pttt) cc_final: 0.7826 (ptpp) REVERT: B 740 THR cc_start: 0.8087 (m) cc_final: 0.7753 (p) REVERT: B 743 LYS cc_start: 0.8410 (ptpp) cc_final: 0.8125 (ptpp) REVERT: C 159 MET cc_start: 0.6935 (mmm) cc_final: 0.6270 (mmm) REVERT: C 185 GLU cc_start: 0.7352 (mm-30) cc_final: 0.6993 (mm-30) REVERT: C 283 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7568 (mt-10) REVERT: C 378 THR cc_start: 0.9260 (OUTLIER) cc_final: 0.8990 (t) REVERT: C 488 MET cc_start: 0.6584 (mmt) cc_final: 0.6072 (mtm) REVERT: C 562 MET cc_start: 0.9237 (mmt) cc_final: 0.8840 (mmt) REVERT: C 619 CYS cc_start: 0.6552 (p) cc_final: 0.6291 (p) REVERT: C 686 LYS cc_start: 0.8856 (OUTLIER) cc_final: 0.8443 (ptpp) REVERT: C 738 LYS cc_start: 0.8248 (pttt) cc_final: 0.7818 (ptpp) REVERT: C 740 THR cc_start: 0.8100 (m) cc_final: 0.7768 (p) REVERT: C 743 LYS cc_start: 0.8394 (ptpp) cc_final: 0.8123 (ptpp) REVERT: D 159 MET cc_start: 0.6682 (mmm) cc_final: 0.6141 (mmm) REVERT: D 185 GLU cc_start: 0.7504 (mm-30) cc_final: 0.7176 (mm-30) REVERT: D 283 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7485 (mt-10) REVERT: D 346 GLN cc_start: 0.9052 (mt0) cc_final: 0.8394 (mt0) REVERT: D 378 THR cc_start: 0.9266 (OUTLIER) cc_final: 0.8995 (t) REVERT: D 488 MET cc_start: 0.6588 (mmt) cc_final: 0.6075 (mtm) REVERT: D 562 MET cc_start: 0.9238 (mmt) cc_final: 0.8832 (mmt) REVERT: D 619 CYS cc_start: 0.6506 (p) cc_final: 0.6236 (p) REVERT: D 686 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8438 (ptpp) REVERT: D 738 LYS cc_start: 0.8265 (pttt) cc_final: 0.7833 (ptpp) REVERT: D 740 THR cc_start: 0.8091 (m) cc_final: 0.7761 (p) REVERT: D 743 LYS cc_start: 0.8403 (ptpp) cc_final: 0.8114 (ptpp) outliers start: 48 outliers final: 19 residues processed: 360 average time/residue: 1.5850 time to fit residues: 637.4836 Evaluate side-chains 327 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 298 time to evaluate : 2.288 ------------------------------------------------------------------------------- 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 535 LEU 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 378 THR Chi-restraints excluded: chain B residue 411 THR 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 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 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 378 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 23 optimal weight: 0.5980 chunk 45 optimal weight: 3.9990 chunk 179 optimal weight: 0.7980 chunk 180 optimal weight: 0.5980 chunk 137 optimal weight: 0.2980 chunk 112 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 169 optimal weight: 0.6980 chunk 157 optimal weight: 5.9990 chunk 165 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 750 ASN C 279 GLN 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.162592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.128314 restraints weight = 23227.286| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.70 r_work: 0.3320 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3191 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3191 r_free = 0.3191 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3191 r_free = 0.3191 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| r_final: 0.3191 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 22226 Z= 0.109 Angle : 0.525 10.646 29830 Z= 0.261 Chirality : 0.037 0.142 3233 Planarity : 0.003 0.026 3600 Dihedral : 15.887 118.323 3885 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.44 % Allowed : 14.76 % Favored : 82.81 % 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: 1.09 (0.17), residues: 2484 helix: 1.63 (0.12), residues: 1620 sheet: 3.55 (0.66), residues: 64 loop : -1.47 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 710 HIS 0.005 0.001 HIS D 301 PHE 0.013 0.001 PHE B 377 TYR 0.013 0.001 TYR C 208 ARG 0.002 0.000 ARG A 337 Details of bonding type rmsd hydrogen bonds : bond 0.03410 ( 1124) hydrogen bonds : angle 3.79424 ( 3324) SS BOND : bond 0.00053 ( 4) SS BOND : angle 1.02563 ( 8) covalent geometry : bond 0.00247 (22222) covalent geometry : angle 0.52484 (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 370 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 316 time to evaluate : 2.366 Fit side-chains REVERT: A 185 GLU cc_start: 0.7499 (mm-30) cc_final: 0.7242 (mm-30) REVERT: A 283 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7533 (mt-10) REVERT: A 312 THR cc_start: 0.8688 (m) cc_final: 0.8481 (m) REVERT: A 351 MET cc_start: 0.9216 (mtp) cc_final: 0.9002 (mtp) REVERT: A 378 THR cc_start: 0.9286 (OUTLIER) cc_final: 0.8998 (t) REVERT: A 488 MET cc_start: 0.6659 (mmt) cc_final: 0.6178 (mtm) REVERT: A 562 MET cc_start: 0.9217 (mmt) cc_final: 0.8750 (mmt) REVERT: A 618 ASP cc_start: 0.7300 (m-30) cc_final: 0.6982 (m-30) REVERT: A 619 CYS cc_start: 0.6565 (p) cc_final: 0.6291 (p) REVERT: A 686 LYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8483 (ptpp) REVERT: A 738 LYS cc_start: 0.8240 (pttt) cc_final: 0.7881 (pttm) REVERT: A 740 THR cc_start: 0.8024 (m) cc_final: 0.7673 (p) REVERT: A 747 SER cc_start: 0.8067 (p) cc_final: 0.7731 (t) REVERT: B 159 MET cc_start: 0.6872 (mmm) cc_final: 0.6631 (mmm) REVERT: B 185 GLU cc_start: 0.7505 (mm-30) cc_final: 0.7252 (mm-30) REVERT: B 283 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7538 (mt-10) REVERT: B 351 MET cc_start: 0.9206 (mtp) cc_final: 0.8981 (mtp) REVERT: B 378 THR cc_start: 0.9266 (OUTLIER) cc_final: 0.8988 (t) REVERT: B 488 MET cc_start: 0.6601 (mmt) cc_final: 0.6100 (mtm) REVERT: B 562 MET cc_start: 0.9209 (mmt) cc_final: 0.8821 (mmt) REVERT: B 618 ASP cc_start: 0.7343 (m-30) cc_final: 0.7023 (m-30) REVERT: B 619 CYS cc_start: 0.6616 (p) cc_final: 0.6342 (p) REVERT: B 738 LYS cc_start: 0.8252 (pttt) cc_final: 0.7807 (ptpp) REVERT: B 740 THR cc_start: 0.8097 (OUTLIER) cc_final: 0.7699 (p) REVERT: B 743 LYS cc_start: 0.8393 (ptpp) cc_final: 0.8099 (ptpp) REVERT: C 159 MET cc_start: 0.6986 (mmm) cc_final: 0.6342 (mmm) REVERT: C 185 GLU cc_start: 0.7464 (mm-30) cc_final: 0.7193 (mm-30) REVERT: C 283 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7559 (mt-10) REVERT: C 351 MET cc_start: 0.9201 (mtp) cc_final: 0.8972 (mtp) REVERT: C 378 THR cc_start: 0.9268 (OUTLIER) cc_final: 0.8993 (t) REVERT: C 488 MET cc_start: 0.6598 (mmt) cc_final: 0.6096 (mtm) REVERT: C 562 MET cc_start: 0.9227 (mmt) cc_final: 0.8813 (mmt) REVERT: C 618 ASP cc_start: 0.7330 (m-30) cc_final: 0.7002 (m-30) REVERT: C 619 CYS cc_start: 0.6648 (p) cc_final: 0.6379 (p) REVERT: C 738 LYS cc_start: 0.8247 (pttt) cc_final: 0.7813 (ptpp) REVERT: C 740 THR cc_start: 0.8051 (m) cc_final: 0.7654 (p) REVERT: C 743 LYS cc_start: 0.8393 (ptpp) cc_final: 0.8093 (ptpp) REVERT: D 159 MET cc_start: 0.6832 (mmm) cc_final: 0.6322 (mmm) REVERT: D 185 GLU cc_start: 0.7488 (mm-30) cc_final: 0.7239 (mm-30) REVERT: D 283 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7484 (mt-10) REVERT: D 346 GLN cc_start: 0.9044 (mt0) cc_final: 0.8354 (mt0) REVERT: D 378 THR cc_start: 0.9272 (OUTLIER) cc_final: 0.8995 (t) REVERT: D 488 MET cc_start: 0.6674 (mmt) cc_final: 0.6172 (mtm) REVERT: D 514 GLN cc_start: 0.7146 (tt0) cc_final: 0.6484 (mm-40) REVERT: D 562 MET cc_start: 0.9231 (mmt) cc_final: 0.8820 (mmt) REVERT: D 618 ASP cc_start: 0.7341 (m-30) cc_final: 0.7016 (m-30) REVERT: D 619 CYS cc_start: 0.6647 (p) cc_final: 0.6369 (p) REVERT: D 738 LYS cc_start: 0.8265 (pttt) cc_final: 0.7824 (ptpp) REVERT: D 740 THR cc_start: 0.8051 (m) cc_final: 0.7653 (p) REVERT: D 743 LYS cc_start: 0.8386 (ptpp) cc_final: 0.8085 (ptpp) outliers start: 54 outliers final: 24 residues processed: 350 average time/residue: 1.6897 time to fit residues: 657.3659 Evaluate side-chains 327 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 293 time to evaluate : 2.242 ------------------------------------------------------------------------------- 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 548 LEU Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 611 LYS Chi-restraints excluded: chain A residue 686 LYS Chi-restraints excluded: chain A residue 736 GLU 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 378 THR 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 611 LYS Chi-restraints excluded: chain B residue 736 GLU 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 548 LEU Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 611 LYS 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 378 THR 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 611 LYS Chi-restraints excluded: chain D residue 736 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 156 optimal weight: 0.9980 chunk 234 optimal weight: 10.0000 chunk 41 optimal weight: 4.9990 chunk 124 optimal weight: 10.0000 chunk 154 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 205 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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 279 GLN B 750 ASN C 279 GLN C 750 ASN ** D 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 750 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.157559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.122988 restraints weight = 22902.796| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 1.68 r_work: 0.3250 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3121 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| r_final: 0.3121 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.3366 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= 0.177 Angle : 0.626 12.544 29830 Z= 0.308 Chirality : 0.040 0.150 3233 Planarity : 0.004 0.029 3600 Dihedral : 16.336 116.461 3885 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.48 % Allowed : 15.52 % Favored : 81.99 % 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: 0.83 (0.16), residues: 2484 helix: 1.32 (0.12), residues: 1648 sheet: 3.20 (0.65), residues: 64 loop : -1.38 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 710 HIS 0.007 0.001 HIS D 301 PHE 0.013 0.002 PHE A 526 TYR 0.015 0.002 TYR C 208 ARG 0.003 0.000 ARG D 698 Details of bonding type rmsd hydrogen bonds : bond 0.04024 ( 1124) hydrogen bonds : angle 3.98803 ( 3324) SS BOND : bond 0.00040 ( 4) SS BOND : angle 1.23427 ( 8) covalent geometry : bond 0.00425 (22222) covalent geometry : angle 0.62547 (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 373 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 318 time to evaluate : 2.439 Fit side-chains REVERT: A 185 GLU cc_start: 0.7532 (mm-30) cc_final: 0.7229 (mm-30) REVERT: A 283 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7501 (mt-10) REVERT: A 351 MET cc_start: 0.9223 (mtp) cc_final: 0.9019 (mtp) REVERT: A 378 THR cc_start: 0.9314 (OUTLIER) cc_final: 0.9034 (t) REVERT: A 488 MET cc_start: 0.6861 (mmt) cc_final: 0.6309 (mtm) REVERT: A 562 MET cc_start: 0.9248 (mmt) cc_final: 0.8829 (mmt) REVERT: A 618 ASP cc_start: 0.7418 (m-30) cc_final: 0.7101 (m-30) REVERT: A 619 CYS cc_start: 0.6575 (p) cc_final: 0.6305 (p) REVERT: A 686 LYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8516 (ptpp) REVERT: A 738 LYS cc_start: 0.8315 (pttt) cc_final: 0.7943 (pttm) REVERT: A 740 THR cc_start: 0.8104 (m) cc_final: 0.7808 (p) REVERT: A 747 SER cc_start: 0.8200 (p) cc_final: 0.7923 (t) REVERT: B 159 MET cc_start: 0.6883 (mmm) cc_final: 0.6149 (mmm) REVERT: B 185 GLU cc_start: 0.7531 (mm-30) cc_final: 0.7283 (mm-30) REVERT: B 283 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7497 (mt-10) REVERT: B 351 MET cc_start: 0.9218 (mtp) cc_final: 0.9016 (mtp) REVERT: B 488 MET cc_start: 0.6886 (mmt) cc_final: 0.6347 (mtm) REVERT: B 514 GLN cc_start: 0.7152 (OUTLIER) cc_final: 0.6491 (mm-40) REVERT: B 562 MET cc_start: 0.9246 (mmt) cc_final: 0.8791 (mmt) REVERT: B 618 ASP cc_start: 0.7430 (m-30) cc_final: 0.7121 (m-30) REVERT: B 619 CYS cc_start: 0.6591 (p) cc_final: 0.6326 (p) REVERT: B 738 LYS cc_start: 0.8366 (pttt) cc_final: 0.7969 (pttm) REVERT: B 740 THR cc_start: 0.8182 (OUTLIER) cc_final: 0.7883 (p) REVERT: C 159 MET cc_start: 0.6993 (mmm) cc_final: 0.6104 (mmm) REVERT: C 185 GLU cc_start: 0.7482 (mm-30) cc_final: 0.7235 (mm-30) REVERT: C 283 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7522 (mt-10) REVERT: C 488 MET cc_start: 0.6805 (mmt) cc_final: 0.6271 (mtm) REVERT: C 514 GLN cc_start: 0.7094 (OUTLIER) cc_final: 0.6414 (mm-40) REVERT: C 562 MET cc_start: 0.9247 (mmt) cc_final: 0.8763 (mmt) REVERT: C 618 ASP cc_start: 0.7414 (m-30) cc_final: 0.7100 (m-30) REVERT: C 619 CYS cc_start: 0.6520 (p) cc_final: 0.6251 (p) REVERT: C 738 LYS cc_start: 0.8348 (pttt) cc_final: 0.7885 (ptpp) REVERT: C 740 THR cc_start: 0.8200 (OUTLIER) cc_final: 0.7903 (p) REVERT: D 159 MET cc_start: 0.6925 (mmm) cc_final: 0.6246 (mmm) REVERT: D 185 GLU cc_start: 0.7512 (mm-30) cc_final: 0.7269 (mm-30) REVERT: D 283 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7481 (mt-10) REVERT: D 346 GLN cc_start: 0.9062 (mt0) cc_final: 0.8842 (mt0) REVERT: D 447 PHE cc_start: 0.8748 (m-80) cc_final: 0.8547 (m-10) REVERT: D 488 MET cc_start: 0.6885 (mmt) cc_final: 0.6333 (mtm) REVERT: D 514 GLN cc_start: 0.7154 (OUTLIER) cc_final: 0.6500 (mm-40) REVERT: D 562 MET cc_start: 0.9264 (mmt) cc_final: 0.8793 (mmt) REVERT: D 618 ASP cc_start: 0.7420 (m-30) cc_final: 0.7105 (m-30) REVERT: D 619 CYS cc_start: 0.6553 (p) cc_final: 0.6282 (p) REVERT: D 738 LYS cc_start: 0.8346 (pttt) cc_final: 0.7882 (ptpp) REVERT: D 740 THR cc_start: 0.8194 (OUTLIER) cc_final: 0.7894 (p) outliers start: 55 outliers final: 18 residues processed: 355 average time/residue: 1.9010 time to fit residues: 754.3613 Evaluate side-chains 333 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 303 time to evaluate : 2.288 ------------------------------------------------------------------------------- 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 498 SER 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 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 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: 3.9990 chunk 114 optimal weight: 0.7980 chunk 183 optimal weight: 0.9980 chunk 135 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 chunk 237 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 167 optimal weight: 0.6980 chunk 86 optimal weight: 0.9990 chunk 242 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN B 182 ASN B 279 GLN C 279 GLN C 750 ASN D 279 GLN ** D 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.159492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.125209 restraints weight = 23004.408| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.67 r_work: 0.3278 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- 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: 26 | |-----------------------------------------------------------------------------| |-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: 24 | |-----------------------------------------------------------------------------| r_final: 0.3154 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.3317 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= 0.126 Angle : 0.567 11.434 29830 Z= 0.281 Chirality : 0.038 0.144 3233 Planarity : 0.003 0.028 3600 Dihedral : 16.122 118.121 3885 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % 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: 0.92 (0.17), residues: 2484 helix: 1.47 (0.12), residues: 1620 sheet: 3.18 (0.65), residues: 64 loop : -1.43 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 710 HIS 0.006 0.001 HIS B 301 PHE 0.015 0.001 PHE B 506 TYR 0.014 0.002 TYR B 208 ARG 0.002 0.000 ARG C 337 Details of bonding type rmsd hydrogen bonds : bond 0.03578 ( 1124) hydrogen bonds : angle 3.87356 ( 3324) SS BOND : bond 0.00047 ( 4) SS BOND : angle 1.13598 ( 8) covalent geometry : bond 0.00294 (22222) covalent geometry : angle 0.56641 (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 372 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 314 time to evaluate : 2.485 Fit side-chains REVERT: A 156 ASP cc_start: 0.5392 (t0) cc_final: 0.5123 (OUTLIER) REVERT: A 185 GLU cc_start: 0.7434 (mm-30) cc_final: 0.7163 (mm-30) REVERT: A 263 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7862 (pt0) REVERT: A 283 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7552 (mt-10) REVERT: A 378 THR cc_start: 0.9333 (OUTLIER) cc_final: 0.9072 (t) REVERT: A 488 MET cc_start: 0.6837 (mmt) cc_final: 0.6277 (mtm) REVERT: A 562 MET cc_start: 0.9233 (mmt) cc_final: 0.8788 (mmt) REVERT: A 618 ASP cc_start: 0.7407 (m-30) cc_final: 0.7099 (m-30) REVERT: A 619 CYS cc_start: 0.6719 (p) cc_final: 0.6425 (p) REVERT: A 686 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8483 (ptpp) REVERT: A 738 LYS cc_start: 0.8262 (pttt) cc_final: 0.7913 (pttm) REVERT: A 740 THR cc_start: 0.8199 (OUTLIER) cc_final: 0.7867 (p) REVERT: A 747 SER cc_start: 0.8131 (p) cc_final: 0.7774 (t) REVERT: B 156 ASP cc_start: 0.5362 (t0) cc_final: 0.5093 (OUTLIER) REVERT: B 159 MET cc_start: 0.6863 (mmm) cc_final: 0.6024 (mmm) REVERT: B 185 GLU cc_start: 0.7409 (mm-30) cc_final: 0.7141 (mm-30) REVERT: B 263 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7795 (pt0) REVERT: B 283 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7539 (mt-10) REVERT: B 488 MET cc_start: 0.6708 (mmt) cc_final: 0.6234 (mtm) REVERT: B 562 MET cc_start: 0.9221 (mmt) cc_final: 0.8853 (mmt) REVERT: B 618 ASP cc_start: 0.7443 (m-30) cc_final: 0.7133 (m-30) REVERT: B 619 CYS cc_start: 0.6746 (p) cc_final: 0.6449 (p) REVERT: B 686 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8045 (mttp) REVERT: B 738 LYS cc_start: 0.8287 (pttt) cc_final: 0.7922 (pttm) REVERT: B 740 THR cc_start: 0.8144 (OUTLIER) cc_final: 0.7796 (p) REVERT: C 156 ASP cc_start: 0.5387 (t0) cc_final: 0.5115 (OUTLIER) REVERT: C 159 MET cc_start: 0.7033 (mmm) cc_final: 0.6162 (mmm) REVERT: C 185 GLU cc_start: 0.7410 (mm-30) cc_final: 0.7194 (mm-30) REVERT: C 263 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7839 (pt0) REVERT: C 283 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7565 (mt-10) REVERT: C 488 MET cc_start: 0.6670 (mmt) cc_final: 0.6195 (mtm) REVERT: C 562 MET cc_start: 0.9230 (mmt) cc_final: 0.8821 (mmt) REVERT: C 618 ASP cc_start: 0.7427 (m-30) cc_final: 0.7109 (m-30) REVERT: C 619 CYS cc_start: 0.6673 (p) cc_final: 0.6371 (p) REVERT: C 686 LYS cc_start: 0.8777 (OUTLIER) cc_final: 0.8008 (mttp) REVERT: C 738 LYS cc_start: 0.8288 (pttt) cc_final: 0.7939 (pttm) REVERT: C 740 THR cc_start: 0.8170 (m) cc_final: 0.7818 (p) REVERT: D 159 MET cc_start: 0.6933 (mmm) cc_final: 0.6127 (mmm) REVERT: D 185 GLU cc_start: 0.7390 (mm-30) cc_final: 0.7123 (mm-30) REVERT: D 263 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7862 (pt0) REVERT: D 283 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7519 (mt-10) REVERT: D 346 GLN cc_start: 0.9046 (mt0) cc_final: 0.8776 (mt0) REVERT: D 488 MET cc_start: 0.6732 (mmt) cc_final: 0.6250 (mtm) REVERT: D 514 GLN cc_start: 0.7230 (OUTLIER) cc_final: 0.6587 (mm-40) REVERT: D 562 MET cc_start: 0.9244 (mmt) cc_final: 0.8831 (mmt) REVERT: D 618 ASP cc_start: 0.7424 (m-30) cc_final: 0.7101 (m-30) REVERT: D 619 CYS cc_start: 0.6528 (p) cc_final: 0.6252 (p) REVERT: D 686 LYS cc_start: 0.8784 (OUTLIER) cc_final: 0.8051 (mttp) REVERT: D 738 LYS cc_start: 0.8296 (pttt) cc_final: 0.7943 (pttm) REVERT: D 740 THR cc_start: 0.8168 (OUTLIER) cc_final: 0.7811 (p) outliers start: 58 outliers final: 27 residues processed: 358 average time/residue: 1.5497 time to fit residues: 621.4126 Evaluate side-chains 342 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 301 time to evaluate : 2.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 GLU 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 A residue 743 LYS 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 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 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 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 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 514 GLN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 150 optimal weight: 0.6980 chunk 12 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 56 optimal weight: 0.5980 chunk 121 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 230 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 147 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- 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 182 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 = 0.3812 r_free = 0.3812 target = 0.158161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.123852 restraints weight = 23120.758| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.67 r_work: 0.3260 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3138 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| r_final: 0.3138 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 22226 Z= 0.148 Angle : 0.598 11.771 29830 Z= 0.295 Chirality : 0.039 0.145 3233 Planarity : 0.003 0.031 3600 Dihedral : 16.220 116.346 3885 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.57 % Allowed : 14.94 % 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: 0.88 (0.17), residues: 2484 helix: 1.35 (0.12), residues: 1644 sheet: 3.09 (0.65), residues: 64 loop : -1.31 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 710 HIS 0.006 0.001 HIS A 301 PHE 0.016 0.001 PHE B 506 TYR 0.014 0.002 TYR C 208 ARG 0.003 0.000 ARG B 337 Details of bonding type rmsd hydrogen bonds : bond 0.03760 ( 1124) hydrogen bonds : angle 3.91714 ( 3324) SS BOND : bond 0.00038 ( 4) SS BOND : angle 1.19368 ( 8) covalent geometry : bond 0.00353 (22222) covalent geometry : angle 0.59762 (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 385 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 328 time to evaluate : 2.497 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 156 ASP cc_start: 0.5345 (t0) cc_final: 0.5067 (OUTLIER) REVERT: A 185 GLU cc_start: 0.7403 (mm-30) cc_final: 0.7143 (mm-30) REVERT: A 263 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7798 (pt0) REVERT: A 283 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7541 (mt-10) REVERT: A 378 THR cc_start: 0.9324 (OUTLIER) cc_final: 0.8883 (t) REVERT: A 488 MET cc_start: 0.6758 (mmt) cc_final: 0.6197 (mtm) REVERT: A 562 MET cc_start: 0.9234 (mmt) cc_final: 0.8841 (mmt) REVERT: A 618 ASP cc_start: 0.7411 (m-30) cc_final: 0.7093 (m-30) REVERT: A 619 CYS cc_start: 0.6550 (p) cc_final: 0.6277 (p) REVERT: A 686 LYS cc_start: 0.8828 (OUTLIER) cc_final: 0.8487 (ptpp) REVERT: A 738 LYS cc_start: 0.8313 (pttt) cc_final: 0.7936 (pttm) REVERT: A 740 THR cc_start: 0.8216 (OUTLIER) cc_final: 0.7959 (p) REVERT: A 747 SER cc_start: 0.8145 (p) cc_final: 0.7944 (p) REVERT: B 156 ASP cc_start: 0.5368 (t0) cc_final: 0.5099 (OUTLIER) REVERT: B 159 MET cc_start: 0.6880 (mmm) cc_final: 0.6176 (mmm) REVERT: B 185 GLU cc_start: 0.7398 (mm-30) cc_final: 0.7135 (mm-30) REVERT: B 263 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7855 (pt0) REVERT: B 283 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7522 (mt-10) REVERT: B 488 MET cc_start: 0.6695 (mmt) cc_final: 0.6218 (mtm) REVERT: B 562 MET cc_start: 0.9234 (mmt) cc_final: 0.8802 (mmt) REVERT: B 618 ASP cc_start: 0.7450 (m-30) cc_final: 0.7134 (m-30) REVERT: B 619 CYS cc_start: 0.6572 (p) cc_final: 0.6301 (p) REVERT: B 686 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8169 (mttp) REVERT: B 738 LYS cc_start: 0.8354 (pttt) cc_final: 0.7973 (pttm) REVERT: B 740 THR cc_start: 0.8169 (OUTLIER) cc_final: 0.7878 (p) REVERT: C 156 ASP cc_start: 0.5397 (t0) cc_final: 0.5122 (OUTLIER) REVERT: C 159 MET cc_start: 0.7025 (mmm) cc_final: 0.6111 (mmm) REVERT: C 185 GLU cc_start: 0.7281 (mm-30) cc_final: 0.7008 (mm-30) REVERT: C 263 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7841 (pt0) REVERT: C 283 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7530 (mt-10) REVERT: C 488 MET cc_start: 0.6721 (mmt) cc_final: 0.6183 (mtm) REVERT: C 562 MET cc_start: 0.9239 (mmt) cc_final: 0.8780 (mmt) REVERT: C 618 ASP cc_start: 0.7441 (m-30) cc_final: 0.7142 (m-30) REVERT: C 686 LYS cc_start: 0.8756 (OUTLIER) cc_final: 0.8014 (mttp) REVERT: C 738 LYS cc_start: 0.8329 (pttt) cc_final: 0.7958 (pttm) REVERT: C 740 THR cc_start: 0.8178 (OUTLIER) cc_final: 0.7879 (p) REVERT: D 159 MET cc_start: 0.6988 (mmm) cc_final: 0.6285 (mmm) REVERT: D 185 GLU cc_start: 0.7361 (mm-30) cc_final: 0.7157 (mm-30) REVERT: D 263 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7854 (pt0) REVERT: D 283 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7494 (mt-10) REVERT: D 346 GLN cc_start: 0.9052 (mt0) cc_final: 0.8385 (mt0) REVERT: D 488 MET cc_start: 0.6694 (mmt) cc_final: 0.6199 (mtm) REVERT: D 514 GLN cc_start: 0.7239 (OUTLIER) cc_final: 0.6602 (mm-40) REVERT: D 562 MET cc_start: 0.9251 (mmt) cc_final: 0.8785 (mmt) REVERT: D 618 ASP cc_start: 0.7442 (m-30) cc_final: 0.7141 (m-30) REVERT: D 686 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8120 (mttp) REVERT: D 738 LYS cc_start: 0.8337 (pttt) cc_final: 0.7960 (pttm) REVERT: D 740 THR cc_start: 0.8179 (OUTLIER) cc_final: 0.7879 (p) outliers start: 57 outliers final: 32 residues processed: 368 average time/residue: 1.5641 time to fit residues: 643.3224 Evaluate side-chains 360 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 313 time to evaluate : 2.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 263 GLU 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 519 ASP 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 A residue 743 LYS 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 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 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 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 C residue 740 THR Chi-restraints excluded: chain C residue 743 LYS 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 514 GLN 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: 4.9990 chunk 64 optimal weight: 2.9990 chunk 105 optimal weight: 0.6980 chunk 207 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 chunk 201 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 83 optimal weight: 0.0770 chunk 189 optimal weight: 7.9990 chunk 242 optimal weight: 0.8980 overall best weight: 0.7342 ------------------------------------------------------------------------------- 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 279 GLN D 452 ASN D 750 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.160213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.126069 restraints weight = 23227.677| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 1.68 r_work: 0.3290 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3163 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| r_final: 0.3163 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22226 Z= 0.119 Angle : 0.568 11.557 29830 Z= 0.281 Chirality : 0.037 0.142 3233 Planarity : 0.003 0.032 3600 Dihedral : 16.040 118.386 3885 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.08 % Allowed : 16.16 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.01 (0.17), residues: 2484 helix: 1.45 (0.12), residues: 1648 sheet: 3.11 (0.65), residues: 64 loop : -1.26 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 710 HIS 0.006 0.001 HIS A 301 PHE 0.017 0.001 PHE C 377 TYR 0.014 0.002 TYR B 208 ARG 0.003 0.000 ARG A 337 Details of bonding type rmsd hydrogen bonds : bond 0.03445 ( 1124) hydrogen bonds : angle 3.82995 ( 3324) SS BOND : bond 0.00050 ( 4) SS BOND : angle 1.10106 ( 8) covalent geometry : bond 0.00273 (22222) covalent geometry : angle 0.56762 (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 368 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 322 time to evaluate : 2.260 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 156 ASP cc_start: 0.5330 (t0) cc_final: 0.5061 (OUTLIER) REVERT: A 185 GLU cc_start: 0.7375 (mm-30) cc_final: 0.7169 (mm-30) REVERT: A 263 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7803 (pt0) REVERT: A 283 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7539 (mt-10) REVERT: A 378 THR cc_start: 0.9330 (OUTLIER) cc_final: 0.8930 (t) REVERT: A 488 MET cc_start: 0.6685 (mmt) cc_final: 0.6198 (mtm) REVERT: A 562 MET cc_start: 0.9222 (mmt) cc_final: 0.8788 (mmt) REVERT: A 618 ASP cc_start: 0.7446 (m-30) cc_final: 0.7130 (m-30) REVERT: A 619 CYS cc_start: 0.6668 (p) cc_final: 0.6351 (p) REVERT: A 738 LYS cc_start: 0.8255 (pttt) cc_final: 0.7896 (pttm) REVERT: A 740 THR cc_start: 0.8179 (OUTLIER) cc_final: 0.7840 (p) REVERT: B 156 ASP cc_start: 0.5349 (t0) cc_final: 0.5059 (OUTLIER) REVERT: B 159 MET cc_start: 0.6905 (mmm) cc_final: 0.6085 (mmm) REVERT: B 185 GLU cc_start: 0.7383 (mm-30) cc_final: 0.7121 (mm-30) REVERT: B 263 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7778 (pt0) REVERT: B 283 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7523 (mt-10) REVERT: B 488 MET cc_start: 0.6712 (mmt) cc_final: 0.6237 (mtm) REVERT: B 562 MET cc_start: 0.9213 (mmt) cc_final: 0.8853 (mmt) REVERT: B 618 ASP cc_start: 0.7468 (m-30) cc_final: 0.7162 (m-30) REVERT: B 619 CYS cc_start: 0.6699 (p) cc_final: 0.6383 (p) REVERT: B 686 LYS cc_start: 0.8848 (OUTLIER) cc_final: 0.8134 (mttp) REVERT: B 738 LYS cc_start: 0.8297 (pttt) cc_final: 0.7928 (pttm) REVERT: B 740 THR cc_start: 0.8101 (OUTLIER) cc_final: 0.7724 (p) REVERT: C 156 ASP cc_start: 0.5378 (t0) cc_final: 0.5079 (OUTLIER) REVERT: C 159 MET cc_start: 0.7083 (mmm) cc_final: 0.6210 (mmm) REVERT: C 185 GLU cc_start: 0.7260 (mm-30) cc_final: 0.7050 (mm-30) REVERT: C 263 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7714 (pt0) REVERT: C 283 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7569 (mt-10) REVERT: C 488 MET cc_start: 0.6646 (mmt) cc_final: 0.6185 (mtm) REVERT: C 562 MET cc_start: 0.9234 (mmt) cc_final: 0.8837 (mmt) REVERT: C 618 ASP cc_start: 0.7413 (m-30) cc_final: 0.7120 (m-30) REVERT: C 686 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8100 (mttp) REVERT: C 738 LYS cc_start: 0.8281 (pttt) cc_final: 0.7921 (pttm) REVERT: C 740 THR cc_start: 0.8111 (OUTLIER) cc_final: 0.7742 (p) REVERT: D 156 ASP cc_start: 0.5397 (t0) cc_final: 0.5127 (m-30) REVERT: D 159 MET cc_start: 0.7002 (mmm) cc_final: 0.6180 (mmm) REVERT: D 185 GLU cc_start: 0.7365 (mm-30) cc_final: 0.7103 (mm-30) REVERT: D 263 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7796 (pt0) REVERT: D 283 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7491 (mt-10) REVERT: D 346 GLN cc_start: 0.9043 (mt0) cc_final: 0.8371 (mt0) REVERT: D 488 MET cc_start: 0.6702 (mmt) cc_final: 0.6215 (mtm) REVERT: D 514 GLN cc_start: 0.7201 (OUTLIER) cc_final: 0.6539 (mm-40) REVERT: D 562 MET cc_start: 0.9232 (mmt) cc_final: 0.8825 (mmt) REVERT: D 618 ASP cc_start: 0.7416 (m-30) cc_final: 0.7119 (m-30) REVERT: D 686 LYS cc_start: 0.8855 (OUTLIER) cc_final: 0.8129 (mttp) REVERT: D 738 LYS cc_start: 0.8285 (pttt) cc_final: 0.7925 (pttm) REVERT: D 740 THR cc_start: 0.8113 (OUTLIER) cc_final: 0.7733 (p) outliers start: 46 outliers final: 26 residues processed: 353 average time/residue: 1.5329 time to fit residues: 605.1880 Evaluate side-chains 352 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 312 time to evaluate : 2.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 263 GLU 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 740 THR Chi-restraints excluded: chain A residue 743 LYS 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 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 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 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 514 GLN 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 56 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 215 optimal weight: 0.9990 chunk 190 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 170 optimal weight: 0.8980 chunk 93 optimal weight: 0.9980 chunk 79 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 279 GLN D 750 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.159840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.125631 restraints weight = 23232.146| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 1.68 r_work: 0.3284 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3155 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3155 r_free = 0.3155 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 = 0.3155 r_free = 0.3155 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| r_final: 0.3155 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3441 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= 0.126 Angle : 0.581 11.854 29830 Z= 0.287 Chirality : 0.038 0.148 3233 Planarity : 0.003 0.034 3600 Dihedral : 15.966 117.266 3885 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.85 % Allowed : 16.61 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.17), residues: 2484 helix: 1.47 (0.12), residues: 1644 sheet: 3.04 (0.65), residues: 64 loop : -1.32 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 710 HIS 0.006 0.001 HIS A 301 PHE 0.015 0.001 PHE B 506 TYR 0.014 0.002 TYR D 208 ARG 0.003 0.000 ARG C 337 Details of bonding type rmsd hydrogen bonds : bond 0.03554 ( 1124) hydrogen bonds : angle 3.85468 ( 3324) SS BOND : bond 0.00044 ( 4) SS BOND : angle 1.12201 ( 8) covalent geometry : bond 0.00296 (22222) covalent geometry : angle 0.58107 (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 357 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 316 time to evaluate : 2.392 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 156 ASP cc_start: 0.5325 (t0) cc_final: 0.5054 (OUTLIER) REVERT: A 185 GLU cc_start: 0.7363 (mm-30) cc_final: 0.7155 (mm-30) REVERT: A 263 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7815 (pt0) REVERT: A 283 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7540 (mt-10) REVERT: A 378 THR cc_start: 0.9321 (OUTLIER) cc_final: 0.9085 (t) REVERT: A 488 MET cc_start: 0.6674 (mmt) cc_final: 0.6196 (mtm) REVERT: A 562 MET cc_start: 0.9236 (mmt) cc_final: 0.8801 (mmt) REVERT: A 618 ASP cc_start: 0.7427 (m-30) cc_final: 0.7104 (m-30) REVERT: A 619 CYS cc_start: 0.6683 (p) cc_final: 0.6364 (p) REVERT: A 738 LYS cc_start: 0.8295 (pttt) cc_final: 0.7931 (pttm) REVERT: A 740 THR cc_start: 0.8181 (OUTLIER) cc_final: 0.7881 (p) REVERT: B 156 ASP cc_start: 0.5354 (t0) cc_final: 0.5058 (OUTLIER) REVERT: B 159 MET cc_start: 0.6937 (mmm) cc_final: 0.6096 (mmm) REVERT: B 185 GLU cc_start: 0.7377 (mm-30) cc_final: 0.7173 (mm-30) REVERT: B 263 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7692 (pt0) REVERT: B 283 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7547 (mt-10) REVERT: B 488 MET cc_start: 0.6693 (mmt) cc_final: 0.6223 (mtm) REVERT: B 562 MET cc_start: 0.9223 (mmt) cc_final: 0.8799 (mmt) REVERT: B 618 ASP cc_start: 0.7493 (m-30) cc_final: 0.7167 (m-30) REVERT: B 619 CYS cc_start: 0.6732 (p) cc_final: 0.6416 (p) REVERT: B 686 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.8137 (mttp) REVERT: B 738 LYS cc_start: 0.8320 (pttt) cc_final: 0.7951 (pttm) REVERT: B 740 THR cc_start: 0.8137 (OUTLIER) cc_final: 0.7818 (p) REVERT: C 156 ASP cc_start: 0.5387 (t0) cc_final: 0.5083 (OUTLIER) REVERT: C 159 MET cc_start: 0.7080 (mmm) cc_final: 0.6206 (mmm) REVERT: C 185 GLU cc_start: 0.7333 (mm-30) cc_final: 0.7124 (mm-30) REVERT: C 263 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7789 (pt0) REVERT: C 283 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7533 (mt-10) REVERT: C 488 MET cc_start: 0.6634 (mmt) cc_final: 0.6173 (mtm) REVERT: C 562 MET cc_start: 0.9228 (mmt) cc_final: 0.8820 (mmt) REVERT: C 618 ASP cc_start: 0.7423 (m-30) cc_final: 0.7129 (m-30) REVERT: C 686 LYS cc_start: 0.8886 (OUTLIER) cc_final: 0.8119 (mttp) REVERT: C 738 LYS cc_start: 0.8317 (pttt) cc_final: 0.7956 (pttm) REVERT: C 740 THR cc_start: 0.8154 (OUTLIER) cc_final: 0.7836 (p) REVERT: D 156 ASP cc_start: 0.5404 (t0) cc_final: 0.5127 (m-30) REVERT: D 159 MET cc_start: 0.6994 (mmm) cc_final: 0.6177 (mmm) REVERT: D 185 GLU cc_start: 0.7341 (mm-30) cc_final: 0.7138 (mm-30) REVERT: D 263 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7772 (pt0) REVERT: D 283 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7512 (mt-10) REVERT: D 346 GLN cc_start: 0.9052 (mt0) cc_final: 0.8349 (mt0) REVERT: D 488 MET cc_start: 0.6703 (mmt) cc_final: 0.6218 (mtm) REVERT: D 514 GLN cc_start: 0.7202 (OUTLIER) cc_final: 0.6540 (mm-40) REVERT: D 562 MET cc_start: 0.9238 (mmt) cc_final: 0.8815 (mmt) REVERT: D 618 ASP cc_start: 0.7428 (m-30) cc_final: 0.7134 (m-30) REVERT: D 686 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8127 (mttp) REVERT: D 738 LYS cc_start: 0.8331 (pttt) cc_final: 0.7967 (pttm) REVERT: D 740 THR cc_start: 0.8151 (OUTLIER) cc_final: 0.7828 (p) outliers start: 41 outliers final: 28 residues processed: 346 average time/residue: 1.5390 time to fit residues: 596.6211 Evaluate side-chains 354 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 312 time to evaluate : 2.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 263 GLU 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 740 THR Chi-restraints excluded: chain A residue 743 LYS 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 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 418 GLU 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 686 LYS Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain D residue 131 CYS 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 514 GLN 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: 7.9990 chunk 185 optimal weight: 4.9990 chunk 82 optimal weight: 0.7980 chunk 191 optimal weight: 2.9990 chunk 196 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 225 optimal weight: 3.9990 chunk 229 optimal weight: 0.6980 chunk 123 optimal weight: 0.8980 chunk 142 optimal weight: 0.6980 chunk 171 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN A 750 ASN B 750 ASN C 279 GLN C 750 ASN D 750 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.160304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.126175 restraints weight = 23242.119| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 1.68 r_work: 0.3291 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3164 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| r_final: 0.3164 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22226 Z= 0.122 Angle : 0.578 11.618 29830 Z= 0.285 Chirality : 0.038 0.152 3233 Planarity : 0.003 0.032 3600 Dihedral : 15.882 117.770 3885 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.08 % Allowed : 16.47 % 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: 1.02 (0.17), residues: 2484 helix: 1.57 (0.12), residues: 1620 sheet: 3.08 (0.65), residues: 64 loop : -1.44 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 710 HIS 0.006 0.001 HIS C 301 PHE 0.015 0.001 PHE D 377 TYR 0.015 0.002 TYR A 208 ARG 0.004 0.000 ARG B 337 Details of bonding type rmsd hydrogen bonds : bond 0.03499 ( 1124) hydrogen bonds : angle 3.85360 ( 3324) SS BOND : bond 0.00048 ( 4) SS BOND : angle 1.09048 ( 8) covalent geometry : bond 0.00285 (22222) covalent geometry : angle 0.57822 (29822) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22553.40 seconds wall clock time: 389 minutes 22.23 seconds (23362.23 seconds total)