Starting phenix.real_space_refine on Sat Jul 4 16:07:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8gka_40181/07_2026/8gka_40181.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gka_40181/07_2026/8gka_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 { model { file = "/net/cci-nas-00/data/ceres_data/8gka_40181/07_2026/8gka_40181.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gka_40181/07_2026/8gka_40181.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8gka_40181/07_2026/8gka_40181.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8gka_40181/07_2026/8gka_40181.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gka_40181/07_2026/8gka_40181.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gka_40181/07_2026/8gka_40181.map" } resolution = 2.55 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: 4.32, per 1000 atoms: 0.20 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: 1.69 Conformation dependent library (CDL) restraints added in 749.0 milliseconds 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: 0.56 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: 2.97 Time building geometry restraints manager: 2.29 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: 12913 24.39 - 48.78: 363 48.78 - 73.18: 87 73.18 - 97.57: 14 97.57 - 121.96: 6 Dihedral angle restraints: 13383 sinusoidal: 6023 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 13380 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: 0.020 Extract box with map and model: 0.460 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 17.060 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 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 : 12.093 121.958 8595 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (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 ARG 0.002 0.000 ARG D 363 TYR 0.006 0.001 TYR D 208 PHE 0.004 0.001 PHE D 377 TRP 0.010 0.001 TRP C 739 HIS 0.002 0.000 HIS C 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00141 / 0.07 (22222) covalent geometry : angle 0.38458 / 0.19 (29822) SS BOND : bond 0.00074 / 0.04 ( 4) SS BOND : angle 0.49181 / 0.34 ( 8) hydrogen bonds : bond 0.24984 / 16.75 ( 1124) hydrogen bonds : angle 6.43805 / 4.57 ( 3324) *********************** 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 : 0.727 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: 0.6241 time to fit residues: 329.8211 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 : 0.529 ------------------------------------------------------------------------------- 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 216 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 0.9980 chunk 227 optimal weight: 8.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 247 optimal weight: 7.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 7.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3844 r_free = 0.3844 target = 0.161112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.125758 restraints weight = 22880.432| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 1.72 r_work: 0.3280 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3146 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3143 r_free = 0.3143 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (11 function evaluations) r_final: 0.3143 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 22226 Z= 0.191 Angle : 0.636 11.410 29830 Z= 0.318 Chirality : 0.041 0.146 3233 Planarity : 0.004 0.038 3600 Dihedral : 15.507 133.119 3695 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.25 % Allowed : 10.29 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.17), residues: 2484 helix: 1.30 (0.12), residues: 1604 sheet: 3.25 (0.66), residues: 64 loop : -1.54 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 698 TYR 0.019 0.003 TYR A 321 PHE 0.015 0.002 PHE A 526 TRP 0.012 0.002 TRP A 692 HIS 0.007 0.001 HIS C 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.19 (22222) covalent geometry : angle 0.63566 / 0.32 (29822) SS BOND : bond 0.00011 / 0.01 ( 4) SS BOND : angle 1.33560 / 0.95 ( 8) hydrogen bonds : bond 0.05057 / 3.35 ( 1124) hydrogen bonds : angle 4.24336 / 3.08 ( 3324) *********************** 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 405 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 333 time to evaluate : 0.798 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: 0.6614 (mmm) cc_final: 0.6021 (mmm) REVERT: A 185 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7328 (mm-30) REVERT: A 378 THR cc_start: 0.9223 (OUTLIER) cc_final: 0.8915 (t) REVERT: A 562 MET cc_start: 0.9254 (mmt) cc_final: 0.8847 (mmt) REVERT: A 738 LYS cc_start: 0.8461 (pttt) cc_final: 0.8099 (ptpp) REVERT: A 740 THR cc_start: 0.8047 (m) cc_final: 0.7771 (p) REVERT: A 747 SER cc_start: 0.8248 (p) cc_final: 0.8039 (t) REVERT: B 159 MET cc_start: 0.6607 (mmm) cc_final: 0.5851 (mmm) REVERT: B 185 GLU cc_start: 0.7654 (mm-30) cc_final: 0.7315 (mm-30) REVERT: B 378 THR cc_start: 0.9210 (OUTLIER) cc_final: 0.8926 (t) REVERT: B 514 GLN cc_start: 0.7246 (OUTLIER) cc_final: 0.6474 (mm-40) REVERT: B 562 MET cc_start: 0.9257 (mmt) cc_final: 0.8798 (mmt) REVERT: B 738 LYS cc_start: 0.8476 (pttt) cc_final: 0.8102 (ptpp) REVERT: B 740 THR cc_start: 0.8060 (OUTLIER) cc_final: 0.7767 (p) REVERT: C 159 MET cc_start: 0.6779 (mmm) cc_final: 0.5861 (mmm) REVERT: C 185 GLU cc_start: 0.7643 (mm-30) cc_final: 0.7222 (mm-30) REVERT: C 378 THR cc_start: 0.9208 (OUTLIER) cc_final: 0.8924 (t) REVERT: C 514 GLN cc_start: 0.7228 (OUTLIER) cc_final: 0.6457 (mm-40) REVERT: C 562 MET cc_start: 0.9268 (mmt) cc_final: 0.8801 (mmt) REVERT: C 738 LYS cc_start: 0.8463 (pttt) cc_final: 0.8098 (ptpp) REVERT: C 740 THR cc_start: 0.8071 (m) cc_final: 0.7779 (p) REVERT: D 159 MET cc_start: 0.6641 (mmm) cc_final: 0.5884 (mmm) REVERT: D 185 GLU cc_start: 0.7661 (mm-30) cc_final: 0.7323 (mm-30) REVERT: D 346 GLN cc_start: 0.9096 (mt0) cc_final: 0.8410 (mt0) REVERT: D 378 THR cc_start: 0.9214 (OUTLIER) cc_final: 0.8930 (t) REVERT: D 514 GLN cc_start: 0.7241 (OUTLIER) cc_final: 0.6518 (mm-40) REVERT: D 562 MET cc_start: 0.9267 (mmt) cc_final: 0.8801 (mmt) REVERT: D 738 LYS cc_start: 0.8467 (pttt) cc_final: 0.8105 (ptpp) REVERT: D 740 THR cc_start: 0.8062 (OUTLIER) cc_final: 0.7766 (p) outliers start: 72 outliers final: 20 residues processed: 391 average time/residue: 0.6371 time to fit residues: 280.3867 Evaluate side-chains 314 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 285 time to evaluate : 0.711 ------------------------------------------------------------------------------- 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 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 740 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 3.9990 chunk 200 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 201 optimal weight: 0.8980 chunk 34 optimal weight: 0.3980 chunk 188 optimal weight: 3.9990 chunk 234 optimal weight: 6.9990 chunk 158 optimal weight: 0.0030 chunk 88 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 84 optimal weight: 0.6980 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 430 HIS A 452 ASN A 695 GLN B 430 HIS B 452 ASN B 570 GLN C 430 HIS C 452 ASN D 430 HIS D 452 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.163672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.128758 restraints weight = 23166.322| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.75 r_work: 0.3326 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3200 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3200 r_free = 0.3200 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3200 r_free = 0.3200 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3200 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2686 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= 0.108 Angle : 0.517 10.716 29830 Z= 0.258 Chirality : 0.036 0.140 3233 Planarity : 0.003 0.024 3600 Dihedral : 15.031 122.534 3695 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.75 % Allowed : 12.32 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.17), residues: 2484 helix: 1.50 (0.12), residues: 1616 sheet: 3.47 (0.66), residues: 64 loop : -1.43 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 225 TYR 0.014 0.002 TYR D 208 PHE 0.014 0.001 PHE C 193 TRP 0.009 0.001 TRP D 380 HIS 0.006 0.001 HIS D 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (22222) covalent geometry : angle 0.51704 / 0.26 (29822) SS BOND : bond 0.00036 / 0.02 ( 4) SS BOND : angle 1.02173 / 0.73 ( 8) hydrogen bonds : bond 0.03801 / 2.52 ( 1124) hydrogen bonds : angle 3.92008 / 2.85 ( 3324) *********************** 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 377 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 316 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 GLU cc_start: 0.7642 (mm-30) cc_final: 0.7213 (mm-30) REVERT: A 378 THR cc_start: 0.9223 (OUTLIER) cc_final: 0.8941 (t) REVERT: A 562 MET cc_start: 0.9244 (mmt) cc_final: 0.8800 (mmt) REVERT: A 686 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8331 (ptpp) REVERT: A 738 LYS cc_start: 0.8235 (pttt) cc_final: 0.7850 (ptpp) REVERT: A 740 THR cc_start: 0.8037 (m) cc_final: 0.7636 (p) REVERT: A 743 LYS cc_start: 0.8412 (ptpp) cc_final: 0.8169 (ptpp) REVERT: A 747 SER cc_start: 0.8049 (p) cc_final: 0.7787 (t) REVERT: B 159 MET cc_start: 0.6809 (mmm) cc_final: 0.6386 (mmm) REVERT: B 185 GLU cc_start: 0.7643 (mm-30) cc_final: 0.7253 (mm-30) REVERT: B 378 THR cc_start: 0.9211 (OUTLIER) cc_final: 0.8910 (t) REVERT: B 562 MET cc_start: 0.9220 (mmt) cc_final: 0.8883 (mmt) REVERT: B 686 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.8320 (ptpp) REVERT: B 738 LYS cc_start: 0.8263 (pttt) cc_final: 0.7798 (ptpp) REVERT: B 740 THR cc_start: 0.8044 (m) cc_final: 0.7640 (p) REVERT: B 743 LYS cc_start: 0.8445 (ptpp) cc_final: 0.8222 (ptpp) REVERT: C 159 MET cc_start: 0.6811 (mmm) cc_final: 0.6401 (mmm) REVERT: C 185 GLU cc_start: 0.7591 (mm-30) cc_final: 0.7174 (mm-30) REVERT: C 283 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7644 (mt-10) REVERT: C 378 THR cc_start: 0.9203 (OUTLIER) cc_final: 0.8908 (t) REVERT: C 562 MET cc_start: 0.9244 (mmt) cc_final: 0.8852 (mmt) REVERT: C 619 CYS cc_start: 0.6656 (p) cc_final: 0.6375 (p) REVERT: C 686 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8319 (ptpp) REVERT: C 738 LYS cc_start: 0.8229 (pttt) cc_final: 0.7851 (ptpp) REVERT: C 740 THR cc_start: 0.7927 (m) cc_final: 0.7542 (p) REVERT: C 743 LYS cc_start: 0.8450 (ptpp) cc_final: 0.8220 (ptpp) REVERT: D 159 MET cc_start: 0.6829 (mmm) cc_final: 0.6401 (mmm) REVERT: D 185 GLU cc_start: 0.7639 (mm-30) cc_final: 0.7248 (mm-30) REVERT: D 346 GLN cc_start: 0.9057 (mt0) cc_final: 0.8407 (mt0) REVERT: D 378 THR cc_start: 0.9216 (OUTLIER) cc_final: 0.8930 (t) REVERT: D 562 MET cc_start: 0.9251 (mmt) cc_final: 0.8857 (mmt) REVERT: D 619 CYS cc_start: 0.6637 (p) cc_final: 0.6354 (p) REVERT: D 686 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8357 (ptpp) REVERT: D 738 LYS cc_start: 0.8267 (pttt) cc_final: 0.7809 (ptpp) REVERT: D 740 THR cc_start: 0.8055 (m) cc_final: 0.7663 (p) REVERT: D 743 LYS cc_start: 0.8440 (ptpp) cc_final: 0.8211 (ptpp) outliers start: 61 outliers final: 20 residues processed: 366 average time/residue: 0.6193 time to fit residues: 254.9414 Evaluate side-chains 326 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 297 time to evaluate : 0.698 ------------------------------------------------------------------------------- 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 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 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 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 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 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 24 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 101 optimal weight: 0.6980 chunk 106 optimal weight: 6.9990 chunk 59 optimal weight: 0.1980 chunk 164 optimal weight: 3.9990 chunk 189 optimal weight: 0.0070 chunk 226 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 163 optimal weight: 0.7980 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 279 GLN A 647 ASN A 750 ASN B 279 GLN C 279 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.164222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.129506 restraints weight = 23256.868| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 1.75 r_work: 0.3338 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3180 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3180 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 22226 Z= 0.103 Angle : 0.513 10.304 29830 Z= 0.255 Chirality : 0.036 0.143 3233 Planarity : 0.003 0.024 3600 Dihedral : 14.662 118.704 3687 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.48 % Allowed : 13.54 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.17), residues: 2484 helix: 1.64 (0.13), residues: 1620 sheet: 3.63 (0.66), residues: 64 loop : -1.45 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 188 TYR 0.012 0.001 TYR C 208 PHE 0.014 0.001 PHE A 193 TRP 0.013 0.001 TRP A 710 HIS 0.005 0.001 HIS C 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 (22222) covalent geometry : angle 0.51263 / 0.25 (29822) SS BOND : bond 0.00045 / 0.02 ( 4) SS BOND : angle 0.95341 / 0.68 ( 8) hydrogen bonds : bond 0.03445 / 2.26 ( 1124) hydrogen bonds : angle 3.81653 / 2.78 ( 3324) *********************** 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 379 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 324 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 GLU cc_start: 0.7467 (mm-30) cc_final: 0.7080 (mm-30) REVERT: A 378 THR cc_start: 0.9200 (OUTLIER) cc_final: 0.8902 (t) REVERT: A 488 MET cc_start: 0.6608 (mmt) cc_final: 0.6113 (mtm) REVERT: A 562 MET cc_start: 0.9185 (mmt) cc_final: 0.8771 (mmt) REVERT: A 686 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8374 (ptpp) REVERT: A 738 LYS cc_start: 0.8318 (pttt) cc_final: 0.7796 (ptpp) REVERT: A 740 THR cc_start: 0.8063 (m) cc_final: 0.7738 (p) REVERT: A 743 LYS cc_start: 0.8350 (ptpp) cc_final: 0.8066 (ptpp) REVERT: B 159 MET cc_start: 0.6768 (mmm) cc_final: 0.6411 (mmm) REVERT: B 185 GLU cc_start: 0.7497 (mm-30) cc_final: 0.7117 (mm-30) REVERT: B 378 THR cc_start: 0.9183 (OUTLIER) cc_final: 0.8892 (t) REVERT: B 562 MET cc_start: 0.9178 (mmt) cc_final: 0.8812 (mmt) REVERT: B 686 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8333 (ptpp) REVERT: B 738 LYS cc_start: 0.8336 (pttt) cc_final: 0.7803 (ptpp) REVERT: B 740 THR cc_start: 0.8055 (m) cc_final: 0.7737 (p) REVERT: B 743 LYS cc_start: 0.8353 (ptpp) cc_final: 0.8060 (ptpp) REVERT: C 159 MET cc_start: 0.6828 (mmm) cc_final: 0.6334 (mmm) REVERT: C 185 GLU cc_start: 0.7316 (mm-30) cc_final: 0.6956 (mm-30) REVERT: C 283 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7573 (mt-10) REVERT: C 378 THR cc_start: 0.9159 (OUTLIER) cc_final: 0.8865 (t) REVERT: C 562 MET cc_start: 0.9202 (mmt) cc_final: 0.8841 (mmt) REVERT: C 619 CYS cc_start: 0.6612 (p) cc_final: 0.6341 (p) REVERT: C 686 LYS cc_start: 0.8746 (OUTLIER) cc_final: 0.8342 (ptpp) REVERT: C 738 LYS cc_start: 0.8314 (pttt) cc_final: 0.7795 (ptpp) REVERT: C 740 THR cc_start: 0.8074 (m) cc_final: 0.7762 (p) REVERT: C 743 LYS cc_start: 0.8355 (ptpp) cc_final: 0.8053 (ptpp) REVERT: D 159 MET cc_start: 0.6731 (mmm) cc_final: 0.6435 (mmm) REVERT: D 185 GLU cc_start: 0.7474 (mm-30) cc_final: 0.7152 (mm-30) REVERT: D 283 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7508 (mt-10) REVERT: D 346 GLN cc_start: 0.9043 (mt0) cc_final: 0.8372 (mt0) REVERT: D 378 THR cc_start: 0.9180 (OUTLIER) cc_final: 0.8891 (t) REVERT: D 562 MET cc_start: 0.9204 (mmt) cc_final: 0.8826 (mmt) REVERT: D 619 CYS cc_start: 0.6592 (p) cc_final: 0.6317 (p) REVERT: D 686 LYS cc_start: 0.8758 (OUTLIER) cc_final: 0.8353 (ptpp) REVERT: D 738 LYS cc_start: 0.8329 (pttt) cc_final: 0.7802 (ptpp) REVERT: D 740 THR cc_start: 0.8058 (m) cc_final: 0.7745 (p) REVERT: D 743 LYS cc_start: 0.8340 (ptpp) cc_final: 0.8041 (ptpp) outliers start: 55 outliers final: 20 residues processed: 360 average time/residue: 0.6351 time to fit residues: 256.4946 Evaluate side-chains 328 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 298 time to evaluate : 0.679 ------------------------------------------------------------------------------- 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 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 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 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 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 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 411 THR Chi-restraints excluded: chain D residue 548 LEU 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 222 optimal weight: 0.9990 chunk 63 optimal weight: 5.9990 chunk 162 optimal weight: 9.9990 chunk 67 optimal weight: 0.9980 chunk 161 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 165 optimal weight: 5.9990 chunk 168 optimal weight: 5.9990 chunk 179 optimal weight: 0.9990 chunk 117 optimal weight: 6.9990 chunk 123 optimal weight: 0.8980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 279 GLN B 279 GLN C 279 GLN D 279 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.160097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.125428 restraints weight = 23061.916| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.69 r_work: 0.3282 rms_B_bonded: 2.52 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: 0.3150 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3150 r_free = 0.3150 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 = 0.3150 r_free = 0.3150 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3150 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 22226 Z= 0.142 Angle : 0.569 11.400 29830 Z= 0.282 Chirality : 0.038 0.143 3233 Planarity : 0.003 0.025 3600 Dihedral : 14.883 115.879 3687 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.75 % Allowed : 14.49 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.17), residues: 2484 helix: 1.53 (0.12), residues: 1620 sheet: 3.35 (0.64), residues: 64 loop : -1.48 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 188 TYR 0.013 0.002 TYR A 208 PHE 0.010 0.001 PHE A 526 TRP 0.011 0.001 TRP B 380 HIS 0.006 0.001 HIS B 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 (22222) covalent geometry : angle 0.56891 / 0.28 (29822) SS BOND : bond 0.00034 / 0.02 ( 4) SS BOND : angle 1.11225 / 0.78 ( 8) hydrogen bonds : bond 0.03793 / 2.50 ( 1124) hydrogen bonds : angle 3.89558 / 2.84 ( 3324) *********************** 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 374 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 313 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 185 GLU cc_start: 0.7396 (mm-30) cc_final: 0.7147 (mm-30) REVERT: A 283 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7548 (mt-10) REVERT: A 378 THR cc_start: 0.9200 (OUTLIER) cc_final: 0.8922 (t) REVERT: A 488 MET cc_start: 0.6643 (mmt) cc_final: 0.6169 (mtm) REVERT: A 562 MET cc_start: 0.9243 (mmt) cc_final: 0.8738 (mmt) REVERT: A 686 LYS cc_start: 0.8874 (OUTLIER) cc_final: 0.8502 (ptpp) REVERT: A 738 LYS cc_start: 0.8294 (pttt) cc_final: 0.7852 (ptpp) REVERT: A 740 THR cc_start: 0.8114 (m) cc_final: 0.7757 (p) REVERT: A 743 LYS cc_start: 0.8413 (ptpp) cc_final: 0.8127 (ptpp) REVERT: B 159 MET cc_start: 0.6815 (mmm) cc_final: 0.6315 (mmm) REVERT: B 185 GLU cc_start: 0.7525 (mm-30) cc_final: 0.7267 (mm-30) REVERT: B 283 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7556 (mt-10) REVERT: B 378 THR cc_start: 0.9185 (OUTLIER) cc_final: 0.8906 (t) REVERT: B 488 MET cc_start: 0.6681 (mmt) cc_final: 0.6211 (mtm) REVERT: B 562 MET cc_start: 0.9232 (mmt) cc_final: 0.8851 (mmt) REVERT: B 738 LYS cc_start: 0.8319 (pttt) cc_final: 0.7876 (ptpp) REVERT: B 740 THR cc_start: 0.8152 (m) cc_final: 0.7791 (p) REVERT: B 743 LYS cc_start: 0.8411 (ptpp) cc_final: 0.8139 (ptpp) REVERT: C 159 MET cc_start: 0.6865 (mmm) cc_final: 0.6091 (mmm) REVERT: C 185 GLU cc_start: 0.7495 (mm-30) cc_final: 0.7161 (mm-30) REVERT: C 283 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7551 (mt-10) REVERT: C 378 THR cc_start: 0.9187 (OUTLIER) cc_final: 0.8911 (t) REVERT: C 488 MET cc_start: 0.6690 (mmt) cc_final: 0.6200 (mtm) REVERT: C 562 MET cc_start: 0.9240 (mmt) cc_final: 0.8816 (mmt) REVERT: C 618 ASP cc_start: 0.7358 (m-30) cc_final: 0.7034 (m-30) REVERT: C 619 CYS cc_start: 0.6593 (p) cc_final: 0.6351 (p) REVERT: C 738 LYS cc_start: 0.8310 (pttt) cc_final: 0.7877 (ptpp) REVERT: C 740 THR cc_start: 0.8155 (m) cc_final: 0.7799 (p) REVERT: C 743 LYS cc_start: 0.8415 (ptpp) cc_final: 0.8143 (ptpp) REVERT: D 159 MET cc_start: 0.6815 (mmm) cc_final: 0.6268 (mmm) REVERT: D 185 GLU cc_start: 0.7505 (mm-30) cc_final: 0.7253 (mm-30) REVERT: D 283 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7514 (mt-10) REVERT: D 346 GLN cc_start: 0.9068 (mt0) cc_final: 0.8397 (mt0) REVERT: D 378 THR cc_start: 0.9189 (OUTLIER) cc_final: 0.8913 (t) REVERT: D 488 MET cc_start: 0.6653 (mmt) cc_final: 0.6174 (mtm) REVERT: D 514 GLN cc_start: 0.7128 (tt0) cc_final: 0.6456 (mm-40) REVERT: D 562 MET cc_start: 0.9244 (mmt) cc_final: 0.8774 (mmt) REVERT: D 618 ASP cc_start: 0.7366 (m-30) cc_final: 0.7041 (m-30) REVERT: D 619 CYS cc_start: 0.6561 (p) cc_final: 0.6313 (p) REVERT: D 738 LYS cc_start: 0.8322 (pttt) cc_final: 0.7885 (ptpp) REVERT: D 740 THR cc_start: 0.8156 (m) cc_final: 0.7807 (p) REVERT: D 743 LYS cc_start: 0.8402 (ptpp) cc_final: 0.8129 (ptpp) outliers start: 61 outliers final: 22 residues processed: 352 average time/residue: 0.6589 time to fit residues: 259.2169 Evaluate side-chains 328 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 297 time to evaluate : 0.633 ------------------------------------------------------------------------------- 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 418 GLU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 621 SER Chi-restraints excluded: chain A residue 686 LYS Chi-restraints excluded: chain B residue 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 418 GLU Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 576 SER Chi-restraints excluded: chain B residue 621 SER Chi-restraints excluded: chain 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 611 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 411 THR Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 576 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 5 optimal weight: 3.9990 chunk 202 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 101 optimal weight: 0.5980 chunk 56 optimal weight: 0.5980 chunk 79 optimal weight: 0.0670 chunk 20 optimal weight: 0.6980 chunk 160 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 220 optimal weight: 7.9990 overall best weight: 0.5920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 750 ASN B 750 ASN C 279 GLN C 750 ASN D 750 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.162230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.127926 restraints weight = 23172.286| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.70 r_work: 0.3316 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3189 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3189 r_free = 0.3189 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 = 0.3189 r_free = 0.3189 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3189 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 22226 Z= 0.109 Angle : 0.534 10.969 29830 Z= 0.265 Chirality : 0.037 0.142 3233 Planarity : 0.003 0.026 3600 Dihedral : 14.653 118.663 3687 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.85 % Allowed : 15.43 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.17), residues: 2484 helix: 1.66 (0.12), residues: 1620 sheet: 3.51 (0.65), residues: 64 loop : -1.49 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 337 TYR 0.013 0.001 TYR A 208 PHE 0.012 0.001 PHE A 377 TRP 0.015 0.001 TRP A 710 HIS 0.005 0.001 HIS C 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (22222) covalent geometry : angle 0.53380 / 0.26 (29822) SS BOND : bond 0.00046 / 0.02 ( 4) SS BOND : angle 1.01700 / 0.72 ( 8) hydrogen bonds : bond 0.03391 / 2.24 ( 1124) hydrogen bonds : angle 3.77570 / 2.74 ( 3324) *********************** 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 354 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 313 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 156 ASP cc_start: 0.5389 (t0) cc_final: 0.5060 (m-30) REVERT: A 185 GLU cc_start: 0.7420 (mm-30) cc_final: 0.7179 (mm-30) REVERT: A 283 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7524 (mt-10) REVERT: A 378 THR cc_start: 0.9208 (OUTLIER) cc_final: 0.8914 (t) REVERT: A 488 MET cc_start: 0.6647 (mmt) cc_final: 0.6161 (mtm) REVERT: A 562 MET cc_start: 0.9202 (mmt) cc_final: 0.8731 (mmt) REVERT: A 618 ASP cc_start: 0.7302 (m-30) cc_final: 0.6992 (m-30) REVERT: A 738 LYS cc_start: 0.8292 (pttt) cc_final: 0.7848 (ptpp) REVERT: A 740 THR cc_start: 0.8095 (m) cc_final: 0.7725 (p) REVERT: B 159 MET cc_start: 0.6893 (mmm) cc_final: 0.6326 (mmm) REVERT: B 185 GLU cc_start: 0.7486 (mm-30) cc_final: 0.7247 (mm-30) REVERT: B 283 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7548 (mt-10) REVERT: B 488 MET cc_start: 0.6678 (mmt) cc_final: 0.6190 (mtm) REVERT: B 562 MET cc_start: 0.9220 (mmt) cc_final: 0.8865 (mmt) REVERT: B 618 ASP cc_start: 0.7331 (m-30) cc_final: 0.7027 (m-30) REVERT: B 738 LYS cc_start: 0.8305 (pttt) cc_final: 0.7855 (ptpp) REVERT: B 740 THR cc_start: 0.8071 (m) cc_final: 0.7705 (p) REVERT: B 743 LYS cc_start: 0.8397 (ptpp) cc_final: 0.8105 (ptpp) REVERT: C 159 MET cc_start: 0.6927 (mmm) cc_final: 0.6386 (mmm) REVERT: C 185 GLU cc_start: 0.7336 (mm-30) cc_final: 0.7072 (mm-30) REVERT: C 283 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7558 (mt-10) REVERT: C 488 MET cc_start: 0.6703 (mmt) cc_final: 0.6206 (mtm) REVERT: C 562 MET cc_start: 0.9226 (mmt) cc_final: 0.8824 (mmt) REVERT: C 618 ASP cc_start: 0.7335 (m-30) cc_final: 0.7021 (m-30) REVERT: C 619 CYS cc_start: 0.6766 (p) cc_final: 0.6500 (p) REVERT: C 738 LYS cc_start: 0.8283 (pttt) cc_final: 0.7846 (ptpp) REVERT: C 740 THR cc_start: 0.8086 (m) cc_final: 0.7735 (p) REVERT: C 743 LYS cc_start: 0.8396 (ptpp) cc_final: 0.8098 (ptpp) REVERT: D 159 MET cc_start: 0.6865 (mmm) cc_final: 0.6367 (mmm) REVERT: D 185 GLU cc_start: 0.7473 (mm-30) cc_final: 0.7232 (mm-30) REVERT: D 283 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7507 (mt-10) REVERT: D 346 GLN cc_start: 0.9042 (mt0) cc_final: 0.8348 (mt0) REVERT: D 488 MET cc_start: 0.6675 (mmt) cc_final: 0.6171 (mtm) REVERT: D 514 GLN cc_start: 0.7145 (tt0) cc_final: 0.6486 (mm-40) REVERT: D 562 MET cc_start: 0.9234 (mmt) cc_final: 0.8815 (mmt) REVERT: D 618 ASP cc_start: 0.7354 (m-30) cc_final: 0.7039 (m-30) REVERT: D 619 CYS cc_start: 0.6728 (p) cc_final: 0.6456 (p) REVERT: D 738 LYS cc_start: 0.8303 (pttt) cc_final: 0.7857 (ptpp) REVERT: D 740 THR cc_start: 0.8074 (m) cc_final: 0.7721 (p) REVERT: D 743 LYS cc_start: 0.8390 (ptpp) cc_final: 0.8095 (ptpp) outliers start: 41 outliers final: 19 residues processed: 343 average time/residue: 0.6642 time to fit residues: 255.1219 Evaluate side-chains 321 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 297 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 621 SER 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 621 SER Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 611 LYS Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 411 THR Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 576 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 245 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 chunk 102 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 157 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 147 optimal weight: 0.7980 chunk 119 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 200 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3847 r_free = 0.3847 target = 0.161432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.127160 restraints weight = 23185.989| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 1.68 r_work: 0.3304 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3174 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3174 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22226 Z= 0.119 Angle : 0.549 11.336 29830 Z= 0.272 Chirality : 0.037 0.153 3233 Planarity : 0.003 0.026 3600 Dihedral : 14.621 117.573 3687 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.12 % Allowed : 15.48 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.17), residues: 2484 helix: 1.67 (0.12), residues: 1616 sheet: 3.41 (0.65), residues: 64 loop : -1.49 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 337 TYR 0.013 0.002 TYR D 208 PHE 0.011 0.001 PHE C 377 TRP 0.020 0.002 TRP A 710 HIS 0.006 0.001 HIS A 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (22222) covalent geometry : angle 0.54838 / 0.27 (29822) SS BOND : bond 0.00045 / 0.02 ( 4) SS BOND : angle 1.04868 / 0.74 ( 8) hydrogen bonds : bond 0.03477 / 2.29 ( 1124) hydrogen bonds : angle 3.79335 / 2.75 ( 3324) *********************** 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 356 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 309 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 156 ASP cc_start: 0.5365 (t0) cc_final: 0.5062 (OUTLIER) REVERT: A 159 MET cc_start: 0.6567 (mmm) cc_final: 0.6060 (mmm) REVERT: A 185 GLU cc_start: 0.7447 (mm-30) cc_final: 0.7176 (mm-30) REVERT: A 283 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7555 (mt-10) REVERT: A 378 THR cc_start: 0.9212 (OUTLIER) cc_final: 0.8927 (t) REVERT: A 488 MET cc_start: 0.6691 (mmt) cc_final: 0.6211 (mtm) REVERT: A 562 MET cc_start: 0.9226 (mmt) cc_final: 0.8755 (mmt) REVERT: A 611 LYS cc_start: 0.8168 (ttpt) cc_final: 0.7847 (ptmt) REVERT: A 618 ASP cc_start: 0.7324 (m-30) cc_final: 0.7018 (m-30) REVERT: A 738 LYS cc_start: 0.8268 (pttt) cc_final: 0.7908 (pttm) REVERT: A 740 THR cc_start: 0.8132 (m) cc_final: 0.7791 (p) REVERT: B 159 MET cc_start: 0.6924 (mmm) cc_final: 0.6382 (mmm) REVERT: B 185 GLU cc_start: 0.7479 (mm-30) cc_final: 0.7194 (mm-30) REVERT: B 283 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7555 (mt-10) REVERT: B 488 MET cc_start: 0.6714 (mmt) cc_final: 0.6238 (mtm) REVERT: B 562 MET cc_start: 0.9227 (mmt) cc_final: 0.8852 (mmt) REVERT: B 611 LYS cc_start: 0.8171 (ttpt) cc_final: 0.7856 (ptmt) REVERT: B 618 ASP cc_start: 0.7389 (m-30) cc_final: 0.7089 (m-30) REVERT: B 738 LYS cc_start: 0.8287 (pttt) cc_final: 0.7925 (pttm) REVERT: B 740 THR cc_start: 0.8111 (m) cc_final: 0.7763 (p) REVERT: B 743 LYS cc_start: 0.8443 (ptpp) cc_final: 0.8153 (ptpp) REVERT: C 159 MET cc_start: 0.7075 (mmm) cc_final: 0.6183 (mmm) REVERT: C 185 GLU cc_start: 0.7343 (mm-30) cc_final: 0.7103 (mm-30) REVERT: C 283 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7579 (mt-10) REVERT: C 488 MET cc_start: 0.6733 (mmt) cc_final: 0.6250 (mtm) REVERT: C 562 MET cc_start: 0.9233 (mmt) cc_final: 0.8827 (mmt) REVERT: C 618 ASP cc_start: 0.7353 (m-30) cc_final: 0.7039 (m-30) REVERT: C 619 CYS cc_start: 0.6770 (p) cc_final: 0.6483 (p) REVERT: C 738 LYS cc_start: 0.8271 (pttt) cc_final: 0.7921 (pttm) REVERT: C 740 THR cc_start: 0.8126 (m) cc_final: 0.7789 (p) REVERT: C 743 LYS cc_start: 0.8451 (ptpp) cc_final: 0.8159 (ptpp) REVERT: D 159 MET cc_start: 0.6888 (mmm) cc_final: 0.6300 (mmm) REVERT: D 185 GLU cc_start: 0.7460 (mm-30) cc_final: 0.7176 (mm-30) REVERT: D 283 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7544 (mt-10) REVERT: D 346 GLN cc_start: 0.9053 (mt0) cc_final: 0.8372 (mt0) REVERT: D 488 MET cc_start: 0.6695 (mmt) cc_final: 0.6207 (mtm) REVERT: D 514 GLN cc_start: 0.7124 (OUTLIER) cc_final: 0.6482 (mm-40) REVERT: D 562 MET cc_start: 0.9235 (mmt) cc_final: 0.8807 (mmt) REVERT: D 618 ASP cc_start: 0.7366 (m-30) cc_final: 0.7052 (m-30) REVERT: D 619 CYS cc_start: 0.6753 (p) cc_final: 0.6459 (p) REVERT: D 738 LYS cc_start: 0.8291 (pttt) cc_final: 0.7932 (pttm) REVERT: D 740 THR cc_start: 0.8119 (m) cc_final: 0.7780 (p) REVERT: D 743 LYS cc_start: 0.8444 (ptpp) cc_final: 0.8152 (ptpp) outliers start: 47 outliers final: 32 residues processed: 343 average time/residue: 0.6513 time to fit residues: 250.3150 Evaluate side-chains 335 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 298 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 621 SER 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 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 621 SER Chi-restraints excluded: chain B residue 736 GLU Chi-restraints excluded: chain C residue 131 CYS 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 611 LYS Chi-restraints excluded: chain C residue 736 GLU Chi-restraints excluded: chain D residue 131 CYS 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 736 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 64 optimal weight: 0.8980 chunk 161 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 242 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 168 optimal weight: 0.9990 chunk 159 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 279 GLN A 750 ASN B 205 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.159389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.125022 restraints weight = 23063.825| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.68 r_work: 0.3277 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3150 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3150 r_free = 0.3150 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 = 0.3150 r_free = 0.3150 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3150 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 22226 Z= 0.141 Angle : 0.588 11.783 29830 Z= 0.290 Chirality : 0.039 0.150 3233 Planarity : 0.003 0.028 3600 Dihedral : 14.812 115.816 3687 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.12 % Allowed : 15.88 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.17), residues: 2484 helix: 1.57 (0.12), residues: 1624 sheet: 3.31 (0.64), residues: 64 loop : -1.47 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 337 TYR 0.014 0.002 TYR A 208 PHE 0.016 0.001 PHE C 377 TRP 0.024 0.002 TRP D 710 HIS 0.006 0.001 HIS B 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (22222) covalent geometry : angle 0.58778 / 0.29 (29822) SS BOND : bond 0.00038 / 0.02 ( 4) SS BOND : angle 1.10963 / 0.79 ( 8) hydrogen bonds : bond 0.03665 / 2.42 ( 1124) hydrogen bonds : angle 3.85758 / 2.80 ( 3324) *********************** 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 372 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 325 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 ASP cc_start: 0.5598 (t0) cc_final: 0.5273 (OUTLIER) REVERT: A 185 GLU cc_start: 0.7442 (mm-30) cc_final: 0.7218 (mm-30) REVERT: A 263 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7723 (pt0) REVERT: A 283 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7504 (mt-10) REVERT: A 378 THR cc_start: 0.9176 (OUTLIER) cc_final: 0.8901 (t) REVERT: A 488 MET cc_start: 0.6650 (mmt) cc_final: 0.6164 (mtm) REVERT: A 562 MET cc_start: 0.9234 (mmt) cc_final: 0.8711 (mmt) REVERT: A 618 ASP cc_start: 0.7463 (m-30) cc_final: 0.7160 (m-30) REVERT: A 686 LYS cc_start: 0.8875 (ptpp) cc_final: 0.8125 (mttp) REVERT: A 738 LYS cc_start: 0.8293 (pttt) cc_final: 0.7906 (pttm) REVERT: A 740 THR cc_start: 0.8142 (m) cc_final: 0.7805 (p) REVERT: B 156 ASP cc_start: 0.5609 (t0) cc_final: 0.5283 (OUTLIER) REVERT: B 159 MET cc_start: 0.6945 (mmm) cc_final: 0.6192 (mmm) REVERT: B 185 GLU cc_start: 0.7426 (mm-30) cc_final: 0.7196 (mm-30) REVERT: B 263 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7696 (pt0) REVERT: B 283 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7514 (mt-10) REVERT: B 488 MET cc_start: 0.6705 (mmt) cc_final: 0.6234 (mtm) REVERT: B 562 MET cc_start: 0.9237 (mmt) cc_final: 0.8857 (mmt) REVERT: B 618 ASP cc_start: 0.7402 (m-30) cc_final: 0.7098 (m-30) REVERT: B 686 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.8167 (mttp) REVERT: B 738 LYS cc_start: 0.8316 (pttt) cc_final: 0.7848 (ptpp) REVERT: B 740 THR cc_start: 0.8125 (m) cc_final: 0.7773 (p) REVERT: C 159 MET cc_start: 0.6984 (mmm) cc_final: 0.6054 (mmm) REVERT: C 185 GLU cc_start: 0.7273 (mm-30) cc_final: 0.7040 (mm-30) REVERT: C 263 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7822 (pt0) REVERT: C 283 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7505 (mt-10) REVERT: C 488 MET cc_start: 0.6698 (mmt) cc_final: 0.6209 (mtm) REVERT: C 562 MET cc_start: 0.9234 (mmt) cc_final: 0.8764 (mmt) REVERT: C 618 ASP cc_start: 0.7397 (m-30) cc_final: 0.7100 (m-30) REVERT: C 686 LYS cc_start: 0.8855 (OUTLIER) cc_final: 0.8152 (mttp) REVERT: C 738 LYS cc_start: 0.8296 (pttt) cc_final: 0.7846 (ptpp) REVERT: C 740 THR cc_start: 0.8144 (OUTLIER) cc_final: 0.7804 (p) REVERT: D 159 MET cc_start: 0.6935 (mmm) cc_final: 0.6161 (mmm) REVERT: D 185 GLU cc_start: 0.7402 (mm-30) cc_final: 0.7173 (mm-30) REVERT: D 263 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7711 (pt0) REVERT: D 283 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7490 (mt-10) REVERT: D 346 GLN cc_start: 0.9062 (mt0) cc_final: 0.8385 (mt0) REVERT: D 488 MET cc_start: 0.6701 (mmt) cc_final: 0.6214 (mtm) REVERT: D 514 GLN cc_start: 0.7125 (OUTLIER) cc_final: 0.6467 (mm-40) REVERT: D 562 MET cc_start: 0.9235 (mmt) cc_final: 0.8759 (mmt) REVERT: D 618 ASP cc_start: 0.7403 (m-30) cc_final: 0.7105 (m-30) REVERT: D 686 LYS cc_start: 0.8862 (OUTLIER) cc_final: 0.8155 (mttp) REVERT: D 738 LYS cc_start: 0.8312 (pttt) cc_final: 0.7852 (ptpp) REVERT: D 740 THR cc_start: 0.8135 (m) cc_final: 0.7784 (p) outliers start: 47 outliers final: 32 residues processed: 358 average time/residue: 0.6411 time to fit residues: 256.7119 Evaluate side-chains 349 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 305 time to evaluate : 0.717 ------------------------------------------------------------------------------- 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 548 LEU Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 621 SER Chi-restraints excluded: chain A residue 743 LYS Chi-restraints excluded: chain B residue 131 CYS 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 519 ASP Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 576 SER Chi-restraints excluded: chain B residue 621 SER Chi-restraints excluded: chain B residue 686 LYS Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 263 GLU 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 20 optimal weight: 0.5980 chunk 99 optimal weight: 4.9990 chunk 230 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 chunk 224 optimal weight: 0.3980 chunk 215 optimal weight: 0.7980 chunk 143 optimal weight: 0.0870 chunk 53 optimal weight: 2.9990 chunk 169 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 279 GLN B 279 GLN 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 = 0.3853 r_free = 0.3853 target = 0.161972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.127921 restraints weight = 23371.914| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 1.68 r_work: 0.3313 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3186 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3186 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 22226 Z= 0.109 Angle : 0.549 10.778 29830 Z= 0.274 Chirality : 0.037 0.144 3233 Planarity : 0.003 0.030 3600 Dihedral : 14.550 119.106 3687 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 1.62 % Allowed : 16.56 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.17), residues: 2484 helix: 1.69 (0.12), residues: 1620 sheet: 3.42 (0.66), residues: 64 loop : -1.45 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 337 TYR 0.014 0.001 TYR A 208 PHE 0.015 0.001 PHE B 377 TRP 0.031 0.002 TRP D 710 HIS 0.005 0.001 HIS A 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (22222) covalent geometry : angle 0.54915 / 0.27 (29822) SS BOND : bond 0.00043 / 0.02 ( 4) SS BOND : angle 1.01804 / 0.72 ( 8) hydrogen bonds : bond 0.03330 / 2.19 ( 1124) hydrogen bonds : angle 3.76816 / 2.74 ( 3324) *********************** 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 361 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 325 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 GLU cc_start: 0.7401 (mm-30) cc_final: 0.7181 (mm-30) REVERT: A 283 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7545 (mt-10) REVERT: A 378 THR cc_start: 0.9210 (OUTLIER) cc_final: 0.8931 (t) REVERT: A 488 MET cc_start: 0.6701 (mmt) cc_final: 0.6225 (mtm) REVERT: A 562 MET cc_start: 0.9218 (mmt) cc_final: 0.8751 (mmt) REVERT: A 618 ASP cc_start: 0.7443 (m-30) cc_final: 0.7143 (m-30) REVERT: A 686 LYS cc_start: 0.8862 (ptpp) cc_final: 0.8152 (mttp) REVERT: A 738 LYS cc_start: 0.8219 (pttt) cc_final: 0.7868 (pttm) REVERT: A 740 THR cc_start: 0.8050 (m) cc_final: 0.7693 (p) REVERT: B 159 MET cc_start: 0.6991 (mmm) cc_final: 0.6347 (mmm) REVERT: B 185 GLU cc_start: 0.7426 (mm-30) cc_final: 0.7201 (mm-30) REVERT: B 283 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7551 (mt-10) REVERT: B 488 MET cc_start: 0.6738 (mmt) cc_final: 0.6229 (mtm) REVERT: B 562 MET cc_start: 0.9216 (mmt) cc_final: 0.8724 (mmt) REVERT: B 618 ASP cc_start: 0.7457 (m-30) cc_final: 0.7161 (m-30) REVERT: B 686 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8155 (mttp) REVERT: B 738 LYS cc_start: 0.8245 (pttt) cc_final: 0.7786 (ptpp) REVERT: B 740 THR cc_start: 0.8068 (m) cc_final: 0.7714 (p) REVERT: C 159 MET cc_start: 0.7036 (mmm) cc_final: 0.6154 (mmm) REVERT: C 185 GLU cc_start: 0.7289 (mm-30) cc_final: 0.7071 (mm-30) REVERT: C 283 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7553 (mt-10) REVERT: C 488 MET cc_start: 0.6696 (mmt) cc_final: 0.6210 (mtm) REVERT: C 562 MET cc_start: 0.9220 (mmt) cc_final: 0.8820 (mmt) REVERT: C 618 ASP cc_start: 0.7385 (m-30) cc_final: 0.7088 (m-30) REVERT: C 686 LYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8153 (mttp) REVERT: C 738 LYS cc_start: 0.8221 (pttt) cc_final: 0.7775 (ptpp) REVERT: C 740 THR cc_start: 0.8114 (OUTLIER) cc_final: 0.7773 (p) REVERT: D 159 MET cc_start: 0.6988 (mmm) cc_final: 0.6436 (mmm) REVERT: D 185 GLU cc_start: 0.7391 (mm-30) cc_final: 0.7175 (mm-30) REVERT: D 283 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7522 (mt-10) REVERT: D 346 GLN cc_start: 0.9047 (mt0) cc_final: 0.8339 (mt0) REVERT: D 488 MET cc_start: 0.6734 (mmt) cc_final: 0.6205 (mtm) REVERT: D 562 MET cc_start: 0.9222 (mmt) cc_final: 0.8812 (mmt) REVERT: D 618 ASP cc_start: 0.7398 (m-30) cc_final: 0.7103 (m-30) REVERT: D 686 LYS cc_start: 0.8827 (OUTLIER) cc_final: 0.8140 (mttp) REVERT: D 738 LYS cc_start: 0.8240 (pttt) cc_final: 0.7789 (ptpp) REVERT: D 740 THR cc_start: 0.8109 (m) cc_final: 0.7761 (p) outliers start: 36 outliers final: 19 residues processed: 351 average time/residue: 0.6361 time to fit residues: 250.8457 Evaluate side-chains 341 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 313 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 621 SER 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 519 ASP Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 576 SER Chi-restraints excluded: chain B residue 621 SER Chi-restraints excluded: chain B residue 686 LYS Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 686 LYS 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 548 LEU Chi-restraints excluded: chain D residue 576 SER Chi-restraints excluded: chain D residue 686 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 25 optimal weight: 3.9990 chunk 124 optimal weight: 10.0000 chunk 209 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 chunk 200 optimal weight: 2.9990 chunk 169 optimal weight: 3.9990 chunk 95 optimal weight: 0.6980 chunk 216 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 229 optimal weight: 0.0060 chunk 178 optimal weight: 0.7980 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 279 GLN A 750 ASN B 279 GLN B 750 ASN C 205 ASN C 279 GLN C 750 ASN D 205 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 = 0.3854 r_free = 0.3854 target = 0.162086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.128151 restraints weight = 23219.634| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.67 r_work: 0.3321 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3190 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3190 r_free = 0.3190 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3190 r_free = 0.3190 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3190 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22226 Z= 0.112 Angle : 0.558 11.286 29830 Z= 0.277 Chirality : 0.037 0.146 3233 Planarity : 0.003 0.033 3600 Dihedral : 14.416 117.982 3687 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.58 % Allowed : 17.42 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.17), residues: 2484 helix: 1.72 (0.12), residues: 1620 sheet: 3.37 (0.65), residues: 64 loop : -1.44 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 337 TYR 0.013 0.001 TYR D 208 PHE 0.014 0.001 PHE B 506 TRP 0.036 0.002 TRP D 710 HIS 0.005 0.001 HIS A 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (22222) covalent geometry : angle 0.55818 / 0.28 (29822) SS BOND : bond 0.00041 / 0.02 ( 4) SS BOND : angle 1.01471 / 0.72 ( 8) hydrogen bonds : bond 0.03358 / 2.20 ( 1124) hydrogen bonds : angle 3.76391 / 2.74 ( 3324) ********************** 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 362 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 327 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 GLU cc_start: 0.7332 (mm-30) cc_final: 0.7115 (mm-30) REVERT: A 263 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7669 (pt0) REVERT: A 283 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7553 (mt-10) REVERT: A 378 THR cc_start: 0.9203 (OUTLIER) cc_final: 0.8918 (t) REVERT: A 488 MET cc_start: 0.6663 (mmt) cc_final: 0.6138 (mtm) REVERT: A 562 MET cc_start: 0.9210 (mmt) cc_final: 0.8752 (mmt) REVERT: A 618 ASP cc_start: 0.7413 (m-30) cc_final: 0.7112 (m-30) REVERT: A 686 LYS cc_start: 0.8840 (ptpp) cc_final: 0.8159 (mttp) REVERT: A 738 LYS cc_start: 0.8241 (pttt) cc_final: 0.7887 (pttm) REVERT: A 740 THR cc_start: 0.8085 (m) cc_final: 0.7745 (p) REVERT: B 159 MET cc_start: 0.6947 (mmm) cc_final: 0.6315 (mmm) REVERT: B 185 GLU cc_start: 0.7350 (mm-30) cc_final: 0.7130 (mm-30) REVERT: B 263 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7593 (pt0) REVERT: B 283 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7554 (mt-10) REVERT: B 488 MET cc_start: 0.6682 (mmt) cc_final: 0.6157 (mtm) REVERT: B 562 MET cc_start: 0.9215 (mmt) cc_final: 0.8864 (mmt) REVERT: B 618 ASP cc_start: 0.7430 (m-30) cc_final: 0.7128 (m-30) REVERT: B 686 LYS cc_start: 0.8831 (ptpp) cc_final: 0.8107 (mttp) REVERT: B 738 LYS cc_start: 0.8258 (pttt) cc_final: 0.7880 (pttm) REVERT: B 740 THR cc_start: 0.8102 (m) cc_final: 0.7769 (p) REVERT: C 159 MET cc_start: 0.7005 (mmm) cc_final: 0.6159 (mmm) REVERT: C 185 GLU cc_start: 0.7246 (mm-30) cc_final: 0.7021 (mm-30) REVERT: C 283 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7565 (mt-10) REVERT: C 488 MET cc_start: 0.6708 (mmt) cc_final: 0.6189 (mtm) REVERT: C 562 MET cc_start: 0.9222 (mmt) cc_final: 0.8826 (mmt) REVERT: C 618 ASP cc_start: 0.7327 (m-30) cc_final: 0.7026 (m-30) REVERT: C 686 LYS cc_start: 0.8817 (ptpp) cc_final: 0.8085 (mttp) REVERT: C 738 LYS cc_start: 0.8208 (pttt) cc_final: 0.7862 (pttm) REVERT: C 740 THR cc_start: 0.8066 (OUTLIER) cc_final: 0.7748 (p) REVERT: D 159 MET cc_start: 0.6955 (mmm) cc_final: 0.6378 (mmm) REVERT: D 185 GLU cc_start: 0.7330 (mm-30) cc_final: 0.7116 (mm-30) REVERT: D 263 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7701 (pt0) REVERT: D 283 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7535 (mt-10) REVERT: D 346 GLN cc_start: 0.9043 (mt0) cc_final: 0.8346 (mt0) REVERT: D 418 GLU cc_start: 0.8328 (mt-10) cc_final: 0.8002 (pt0) REVERT: D 488 MET cc_start: 0.6708 (mmt) cc_final: 0.6187 (mtm) REVERT: D 562 MET cc_start: 0.9223 (mmt) cc_final: 0.8816 (mmt) REVERT: D 618 ASP cc_start: 0.7359 (m-30) cc_final: 0.7057 (m-30) REVERT: D 686 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8103 (mttp) REVERT: D 738 LYS cc_start: 0.8269 (pttt) cc_final: 0.7906 (pttm) REVERT: D 740 THR cc_start: 0.8107 (m) cc_final: 0.7778 (p) outliers start: 35 outliers final: 19 residues processed: 356 average time/residue: 0.6172 time to fit residues: 247.3111 Evaluate side-chains 351 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 322 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 621 SER Chi-restraints excluded: chain B residue 263 GLU 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 519 ASP Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 576 SER Chi-restraints excluded: chain B residue 621 SER Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain D residue 263 GLU Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 411 THR Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 576 SER Chi-restraints excluded: chain D residue 686 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 12 optimal weight: 1.9990 chunk 162 optimal weight: 0.9990 chunk 184 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 180 optimal weight: 0.9990 chunk 194 optimal weight: 5.9990 chunk 244 optimal weight: 5.9990 chunk 158 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 7.9990 chunk 138 optimal weight: 3.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3820 r_free = 0.3820 target = 0.158891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.124642 restraints weight = 23090.988| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.66 r_work: 0.3272 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3144 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3144 r_free = 0.3144 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3144 r_free = 0.3144 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3144 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 22226 Z= 0.149 Angle : 0.620 12.892 29830 Z= 0.306 Chirality : 0.039 0.199 3233 Planarity : 0.003 0.034 3600 Dihedral : 14.752 115.083 3687 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.81 % Allowed : 17.28 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.17), residues: 2484 helix: 1.45 (0.12), residues: 1648 sheet: 3.14 (0.64), residues: 64 loop : -1.28 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 337 TYR 0.016 0.002 TYR A 208 PHE 0.022 0.001 PHE A 377 TRP 0.040 0.002 TRP D 710 HIS 0.007 0.001 HIS D 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 (22222) covalent geometry : angle 0.62016 / 0.31 (29822) SS BOND : bond 0.00020 / 0.01 ( 4) SS BOND : angle 1.10463 / 0.78 ( 8) hydrogen bonds : bond 0.03781 / 2.48 ( 1124) hydrogen bonds : angle 3.89394 / 2.84 ( 3324) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8839.85 seconds wall clock time: 150 minutes 50.53 seconds (9050.53 seconds total)