Starting phenix.real_space_refine on Sun Aug 24 18:20:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gka_40181/08_2025/8gka_40181.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gka_40181/08_2025/8gka_40181.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8gka_40181/08_2025/8gka_40181.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gka_40181/08_2025/8gka_40181.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gka_40181/08_2025/8gka_40181.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gka_40181/08_2025/8gka_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-2.0-5787/lib/python3.9/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: 4.61, per 1000 atoms: 0.21 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: 1.87 Conformation dependent library (CDL) restraints added in 680.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.45 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: 3.61 Time building geometry restraints manager: 2.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3578 1.32 - 1.45: 5647 1.45 - 1.57: 12727 1.57 - 1.69: 66 1.69 - 1.81: 204 Bond restraints: 22222 Sorted by residual: bond pdb=" CA ASP C 151 " pdb=" CB ASP C 151 " ideal model delta sigma weight residual 1.530 1.544 -0.013 1.69e-02 3.50e+03 6.36e-01 bond pdb=" CA ASP B 151 " pdb=" CB ASP B 151 " ideal model delta sigma weight residual 1.530 1.544 -0.013 1.69e-02 3.50e+03 6.36e-01 bond pdb=" CA ASP A 151 " pdb=" CB ASP A 151 " ideal model delta sigma weight residual 1.530 1.543 -0.013 1.69e-02 3.50e+03 5.77e-01 bond pdb=" CA ASP D 151 " pdb=" CB ASP D 151 " ideal model delta sigma weight residual 1.530 1.543 -0.012 1.69e-02 3.50e+03 5.38e-01 bond pdb=" CB PRO C 510 " pdb=" CG PRO C 510 " ideal model delta sigma weight residual 1.492 1.529 -0.037 5.00e-02 4.00e+02 5.36e-01 ... (remaining 22217 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 29597 1.60 - 3.20: 176 3.20 - 4.79: 33 4.79 - 6.39: 8 6.39 - 7.99: 8 Bond angle restraints: 29822 Sorted by residual: angle pdb=" C HIS B 150 " pdb=" N ASP B 151 " pdb=" CA ASP B 151 " ideal model delta sigma weight residual 121.54 128.21 -6.67 1.91e+00 2.74e-01 1.22e+01 angle pdb=" C HIS C 150 " pdb=" N ASP C 151 " pdb=" CA ASP C 151 " ideal model delta sigma weight residual 121.54 128.20 -6.66 1.91e+00 2.74e-01 1.22e+01 angle pdb=" C HIS A 150 " pdb=" N ASP A 151 " pdb=" CA ASP A 151 " ideal model delta sigma weight residual 121.54 128.18 -6.64 1.91e+00 2.74e-01 1.21e+01 angle pdb=" C HIS D 150 " pdb=" N ASP D 151 " pdb=" CA ASP D 151 " ideal model delta sigma weight residual 121.54 128.17 -6.63 1.91e+00 2.74e-01 1.21e+01 angle pdb=" CA LEU D 608 " pdb=" CB LEU D 608 " pdb=" CG LEU D 608 " ideal model delta sigma weight residual 116.30 124.29 -7.99 3.50e+00 8.16e-02 5.21e+00 ... (remaining 29817 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.39: 12994 24.39 - 48.78: 433 48.78 - 73.18: 131 73.18 - 97.57: 17 97.57 - 121.96: 6 Dihedral angle restraints: 13581 sinusoidal: 6221 harmonic: 7360 Sorted by residual: dihedral pdb=" C27 POV B 803 " pdb=" C28 POV B 803 " pdb=" C29 POV B 803 " pdb="C210 POV B 803 " ideal model delta sinusoidal sigma weight residual 127.48 -110.56 -121.96 1 3.00e+01 1.11e-03 1.63e+01 dihedral pdb=" C27 POV A 809 " pdb=" C28 POV A 809 " pdb=" C29 POV A 809 " pdb="C210 POV A 809 " ideal model delta sinusoidal sigma weight residual 127.48 -116.73 -115.79 1 3.00e+01 1.11e-03 1.53e+01 dihedral pdb=" C3 POV B 808 " pdb=" C31 POV B 808 " pdb=" O31 POV B 808 " pdb=" C32 POV B 808 " ideal model delta sinusoidal sigma weight residual 172.61 -76.70 -110.69 1 3.00e+01 1.11e-03 1.44e+01 ... (remaining 13578 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 2038 0.024 - 0.047: 729 0.047 - 0.071: 342 0.071 - 0.095: 83 0.095 - 0.119: 41 Chirality restraints: 3233 Sorted by residual: chirality pdb=" CA ILE B 734 " pdb=" N ILE B 734 " pdb=" C ILE B 734 " pdb=" CB ILE B 734 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.51e-01 chirality pdb=" CA ILE A 734 " pdb=" N ILE A 734 " pdb=" C ILE A 734 " pdb=" CB ILE A 734 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.39e-01 chirality pdb=" CA ILE D 734 " pdb=" N ILE D 734 " pdb=" C ILE D 734 " pdb=" CB ILE D 734 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.35e-01 ... (remaining 3230 not shown) Planarity restraints: 3600 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 180 " 0.020 5.00e-02 4.00e+02 3.04e-02 1.48e+00 pdb=" N PRO C 181 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO C 181 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 181 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN D 180 " 0.020 5.00e-02 4.00e+02 3.04e-02 1.48e+00 pdb=" N PRO D 181 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO D 181 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO D 181 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 180 " -0.020 5.00e-02 4.00e+02 3.03e-02 1.47e+00 pdb=" N PRO A 181 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 181 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 181 " -0.017 5.00e-02 4.00e+02 ... (remaining 3597 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 5905 2.81 - 3.33: 21514 3.33 - 3.86: 35968 3.86 - 4.38: 44100 4.38 - 4.90: 74799 Nonbonded interactions: 182286 Sorted by model distance: nonbonded pdb=" O GLY B 638 " pdb="NA NA A 801 " model vdw 2.291 2.470 nonbonded pdb=" O GLY C 638 " pdb="NA NA A 801 " model vdw 2.292 2.470 nonbonded pdb=" O GLY A 638 " pdb="NA NA A 801 " model vdw 2.292 2.470 nonbonded pdb=" O GLY D 638 " pdb="NA NA A 801 " model vdw 2.293 2.470 nonbonded pdb=" NZ LYS C 589 " pdb=" O14 POV C 805 " model vdw 2.297 3.120 ... (remaining 182281 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 117 through 756 or (resid 802 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name O11 or name O12 or name O13 or name O14 or name O21 or \ name O22 or name O31 or name O32 or name P or name C210)) or (resid 803 and (nam \ e N or name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or na \ me C2 or name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or \ name C27 or name C28 or name C29 or name C3 or name C31 or name C32 or name C33 \ or name C34 or name C35 or name C36 or name C37 or name C38 or name O11 or name \ O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name O32 or \ name P )) or (resid 804 and (name N or name C1 or name C11 or name C12 or name C \ 13 or name C14 or name C15 or name C2 or name C21 or name C22 or name C23 or nam \ e C24 or name C25 or name C26 or name C27 or name C3 or name C31 or name C32 or \ name C33 or name O11 or name O12 or name O13 or name O14 or name O21 or name O22 \ or name O31 or name O32 or name P )) or resid 805 or (resid 806 and (name N or \ name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or name C2 o \ r name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C \ 27 or name C3 or name C31 or name C32 or name C33 or name C34 or name O11 or nam \ e O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name O32 or \ name P )) or resid 807)) selection = (chain 'B' and (resid 117 through 756 or (resid 802 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name O11 or name O12 or name O13 or name O14 or name O21 or \ name O22 or name O31 or name O32 or name P or name C210)) or (resid 803 and (nam \ e N or name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or na \ me C2 or name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or \ name C27 or name C28 or name C29 or name C3 or name C31 or name C32 or name C33 \ or name C34 or name C35 or name C36 or name C37 or name C38 or name O11 or name \ O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name O32 or \ name P )) or (resid 804 and (name N or name C1 or name C11 or name C12 or name C \ 13 or name C14 or name C15 or name C2 or name C21 or name C22 or name C23 or nam \ e C24 or name C25 or name C26 or name C27 or name C3 or name C31 or name C32 or \ name C33 or name O11 or name O12 or name O13 or name O14 or name O21 or name O22 \ or name O31 or name O32 or name P )) or (resid 805 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name C37 or name C38 or name O11 or name O12 or name O13 or \ name O14 or name O21 or name O22 or name O31 or name O32 or name P or name C210) \ ) or (resid 806 and (name N or name C1 or name C11 or name C12 or name C13 or na \ me C14 or name C15 or name C2 or name C21 or name C22 or name C23 or name C24 or \ name C25 or name C26 or name C27 or name C3 or name C31 or name C32 or name C33 \ or name C34 or name O11 or name O12 or name O13 or name O14 or name O21 or name \ O22 or name O31 or name O32 or name P )) or (resid 807 and (name N or name C1 o \ r name C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C2 \ 1 or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or nam \ e C28 or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or \ name C36 or name C37 or name O11 or name O12 or name O13 or name O14 or name O21 \ or name O22 or name O31 or name O32 or name P )))) selection = (chain 'C' and (resid 117 through 756 or (resid 802 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name O11 or name O12 or name O13 or name O14 or name O21 or \ name O22 or name O31 or name O32 or name P or name C210)) or (resid 803 and (nam \ e N or name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or na \ me C2 or name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or \ name C27 or name C28 or name C29 or name C3 or name C31 or name C32 or name C33 \ or name C34 or name C35 or name C36 or name C37 or name C38 or name O11 or name \ O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name O32 or \ name P )) or (resid 804 and (name N or name C1 or name C11 or name C12 or name C \ 13 or name C14 or name C15 or name C2 or name C21 or name C22 or name C23 or nam \ e C24 or name C25 or name C26 or name C27 or name C3 or name C31 or name C32 or \ name C33 or name O11 or name O12 or name O13 or name O14 or name O21 or name O22 \ or name O31 or name O32 or name P )) or (resid 805 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name C37 or name C38 or name O11 or name O12 or name O13 or \ name O14 or name O21 or name O22 or name O31 or name O32 or name P or name C210) \ ) or (resid 806 and (name N or name C1 or name C11 or name C12 or name C13 or na \ me C14 or name C15 or name C2 or name C21 or name C22 or name C23 or name C24 or \ name C25 or name C26 or name C27 or name C3 or name C31 or name C32 or name C33 \ or name C34 or name O11 or name O12 or name O13 or name O14 or name O21 or name \ O22 or name O31 or name O32 or name P )) or (resid 807 and (name N or name C1 o \ r name C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C2 \ 1 or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or nam \ e C28 or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or \ name C36 or name C37 or name O11 or name O12 or name O13 or name O14 or name O21 \ or name O22 or name O31 or name O32 or name P )))) selection = (chain 'D' and (resid 117 through 756 or (resid 802 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name O11 or name O12 or name O13 or name O14 or name O21 or \ name O22 or name O31 or name O32 or name P or name C210)) or (resid 803 and (nam \ e N or name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or na \ me C2 or name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or \ name C27 or name C28 or name C29 or name C3 or name C31 or name C32 or name C33 \ or name C34 or name C35 or name C36 or name C37 or name C38 or name O11 or name \ O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name O32 or \ name P )) or (resid 804 and (name N or name C1 or name C11 or name C12 or name C \ 13 or name C14 or name C15 or name C2 or name C21 or name C22 or name C23 or nam \ e C24 or name C25 or name C26 or name C27 or name C3 or name C31 or name C32 or \ name C33 or name O11 or name O12 or name O13 or name O14 or name O21 or name O22 \ or name O31 or name O32 or name P )) or (resid 805 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name C37 or name C38 or name O11 or name O12 or name O13 or \ name O14 or name O21 or name O22 or name O31 or name O32 or name P or name C210) \ ) or (resid 806 and (name N or name C1 or name C11 or name C12 or name C13 or na \ me C14 or name C15 or name C2 or name C21 or name C22 or name C23 or name C24 or \ name C25 or name C26 or name C27 or name C3 or name C31 or name C32 or name C33 \ or name C34 or name O11 or name O12 or name O13 or name O14 or name O21 or name \ O22 or name O31 or name O32 or name P )) or (resid 807 and (name N or name C1 o \ r name C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C2 \ 1 or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or nam \ e C28 or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or \ name C36 or name C37 or name O11 or name O12 or name O13 or name O14 or name O21 \ or name O22 or name O31 or name O32 or name P )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 17.690 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.037 22226 Z= 0.071 Angle : 0.385 7.989 29830 Z= 0.190 Chirality : 0.032 0.119 3233 Planarity : 0.002 0.030 3600 Dihedral : 13.139 121.958 8793 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.54 % Allowed : 3.79 % Favored : 95.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.61 (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 covalent geometry : bond 0.00141 (22222) covalent geometry : angle 0.38458 (29822) SS BOND : bond 0.00074 ( 4) SS BOND : angle 0.49181 ( 8) hydrogen bonds : bond 0.24984 ( 1124) hydrogen bonds : angle 6.43805 ( 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 : 0.816 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: 0.6171 time to fit residues: 324.6944 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 : 0.854 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 182 ASN A 205 ASN A 279 GLN A 580 GLN A 645 GLN B 182 ASN B 279 GLN B 570 GLN B 580 GLN B 645 GLN B 647 ASN B 695 GLN C 182 ASN C 279 GLN C 580 GLN C 645 GLN C 695 GLN D 182 ASN D 279 GLN D 580 GLN D 645 GLN D 695 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.161051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.125682 restraints weight = 22880.934| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.72 r_work: 0.3275 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.11 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: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3141 r_free = 0.3141 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| r_final: 0.3141 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 22226 Z= 0.191 Angle : 0.639 11.466 29830 Z= 0.318 Chirality : 0.041 0.145 3233 Planarity : 0.004 0.039 3600 Dihedral : 16.730 133.034 3893 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 3.43 % Allowed : 9.93 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.17), residues: 2484 helix: 1.28 (0.12), residues: 1604 sheet: 3.22 (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 693 TYR 0.018 0.003 TYR A 321 PHE 0.015 0.002 PHE A 526 TRP 0.013 0.002 TRP A 692 HIS 0.008 0.001 HIS B 301 Details of bonding type rmsd covalent geometry : bond 0.00450 (22222) covalent geometry : angle 0.63878 (29822) SS BOND : bond 0.00011 ( 4) SS BOND : angle 1.33891 ( 8) hydrogen bonds : bond 0.05004 ( 1124) hydrogen bonds : angle 4.23653 ( 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 409 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 333 time to evaluate : 0.926 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: 0.6805 (mmm) cc_final: 0.6232 (mmm) REVERT: A 185 GLU cc_start: 0.7677 (mm-30) cc_final: 0.7356 (mm-30) REVERT: A 378 THR cc_start: 0.9239 (OUTLIER) cc_final: 0.8933 (t) REVERT: A 562 MET cc_start: 0.9252 (mmt) cc_final: 0.8838 (mmt) REVERT: A 738 LYS cc_start: 0.8469 (pttt) cc_final: 0.8123 (ptpp) REVERT: A 740 THR cc_start: 0.8056 (m) cc_final: 0.7781 (p) REVERT: A 747 SER cc_start: 0.8256 (p) cc_final: 0.8044 (t) REVERT: B 159 MET cc_start: 0.6673 (mmm) cc_final: 0.5920 (mmm) REVERT: B 185 GLU cc_start: 0.7677 (mm-30) cc_final: 0.7346 (mm-30) REVERT: B 378 THR cc_start: 0.9239 (OUTLIER) cc_final: 0.8933 (t) REVERT: B 514 GLN cc_start: 0.7286 (OUTLIER) cc_final: 0.6525 (mm-40) REVERT: B 562 MET cc_start: 0.9257 (mmt) cc_final: 0.8795 (mmt) REVERT: B 738 LYS cc_start: 0.8480 (pttt) cc_final: 0.8123 (ptpp) REVERT: B 740 THR cc_start: 0.8066 (OUTLIER) cc_final: 0.7799 (p) REVERT: C 159 MET cc_start: 0.6842 (mmm) cc_final: 0.5925 (mmm) REVERT: C 185 GLU cc_start: 0.7665 (mm-30) cc_final: 0.7271 (mm-30) REVERT: C 378 THR cc_start: 0.9215 (OUTLIER) cc_final: 0.8927 (t) REVERT: C 514 GLN cc_start: 0.7277 (OUTLIER) cc_final: 0.6517 (mm-40) REVERT: C 562 MET cc_start: 0.9269 (mmt) cc_final: 0.8799 (mmt) REVERT: C 738 LYS cc_start: 0.8464 (pttt) cc_final: 0.8116 (ptpp) REVERT: C 740 THR cc_start: 0.8078 (m) cc_final: 0.7787 (p) REVERT: D 159 MET cc_start: 0.6705 (mmm) cc_final: 0.5948 (mmm) REVERT: D 185 GLU cc_start: 0.7688 (mm-30) cc_final: 0.7357 (mm-30) REVERT: D 346 GLN cc_start: 0.9103 (mt0) cc_final: 0.8410 (mt0) REVERT: D 378 THR cc_start: 0.9241 (OUTLIER) cc_final: 0.8933 (t) REVERT: D 514 GLN cc_start: 0.7280 (OUTLIER) cc_final: 0.6564 (mm-40) REVERT: D 562 MET cc_start: 0.9268 (mmt) cc_final: 0.8901 (mmt) REVERT: D 738 LYS cc_start: 0.8472 (pttt) cc_final: 0.8126 (ptpp) REVERT: D 740 THR cc_start: 0.8072 (OUTLIER) cc_final: 0.7777 (p) outliers start: 76 outliers final: 24 residues processed: 395 average time/residue: 0.6708 time to fit residues: 297.3478 Evaluate side-chains 319 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 286 time to evaluate : 0.821 ------------------------------------------------------------------------------- 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 A residue 723 VAL Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 514 GLN Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 611 LYS Chi-restraints excluded: chain B residue 621 SER Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 514 GLN Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 611 LYS Chi-restraints excluded: chain C residue 621 SER Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 378 THR Chi-restraints excluded: chain D residue 514 GLN Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 611 LYS Chi-restraints excluded: chain D residue 621 SER Chi-restraints excluded: chain D residue 723 VAL Chi-restraints excluded: chain D residue 740 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 3.9990 chunk 200 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 201 optimal weight: 0.7980 chunk 34 optimal weight: 0.1980 chunk 188 optimal weight: 3.9990 chunk 234 optimal weight: 6.9990 chunk 158 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 84 optimal weight: 0.0770 overall best weight: 0.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3871 r_free = 0.3871 target = 0.163482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.128538 restraints weight = 23150.218| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 1.75 r_work: 0.3318 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- 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: 22 | |-----------------------------------------------------------------------------| |-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: 25 | |-----------------------------------------------------------------------------| r_final: 0.3190 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 22226 Z= 0.108 Angle : 0.519 10.590 29830 Z= 0.259 Chirality : 0.036 0.140 3233 Planarity : 0.003 0.024 3600 Dihedral : 16.248 122.625 3893 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.80 % Allowed : 12.41 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.17), residues: 2484 helix: 1.47 (0.12), residues: 1616 sheet: 3.50 (0.66), residues: 64 loop : -1.40 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 188 TYR 0.014 0.002 TYR C 208 PHE 0.014 0.001 PHE C 193 TRP 0.010 0.001 TRP D 380 HIS 0.006 0.001 HIS C 301 Details of bonding type rmsd covalent geometry : bond 0.00240 (22222) covalent geometry : angle 0.51921 (29822) SS BOND : bond 0.00045 ( 4) SS BOND : angle 1.04072 ( 8) hydrogen bonds : bond 0.03826 ( 1124) hydrogen bonds : angle 3.92692 ( 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 375 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 313 time to evaluate : 0.562 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: 0.7643 (mm-30) cc_final: 0.7200 (mm-30) REVERT: A 378 THR cc_start: 0.9217 (OUTLIER) cc_final: 0.8924 (t) REVERT: A 562 MET cc_start: 0.9239 (mmt) cc_final: 0.8796 (mmt) REVERT: A 686 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8325 (ptpp) REVERT: A 738 LYS cc_start: 0.8228 (pttt) cc_final: 0.7841 (ptpp) REVERT: A 740 THR cc_start: 0.8037 (m) cc_final: 0.7637 (p) REVERT: A 743 LYS cc_start: 0.8401 (ptpp) cc_final: 0.8161 (ptpp) REVERT: A 747 SER cc_start: 0.8066 (p) cc_final: 0.7796 (t) REVERT: B 159 MET cc_start: 0.6741 (mmm) cc_final: 0.6314 (mmm) REVERT: B 185 GLU cc_start: 0.7647 (mm-30) cc_final: 0.7222 (mm-30) REVERT: B 188 ARG cc_start: 0.7582 (ttp-170) cc_final: 0.7374 (mtm-85) REVERT: B 378 THR cc_start: 0.9202 (OUTLIER) cc_final: 0.8908 (t) REVERT: B 562 MET cc_start: 0.9234 (mmt) cc_final: 0.8890 (mmt) REVERT: B 686 LYS cc_start: 0.8746 (OUTLIER) cc_final: 0.8319 (ptpp) REVERT: B 717 MET cc_start: 0.5545 (ttm) cc_final: 0.5339 (ttt) REVERT: B 738 LYS cc_start: 0.8263 (pttt) cc_final: 0.7789 (ptpp) REVERT: B 740 THR cc_start: 0.8043 (m) cc_final: 0.7640 (p) REVERT: B 743 LYS cc_start: 0.8470 (ptpp) cc_final: 0.8245 (ptpp) REVERT: C 159 MET cc_start: 0.6739 (mmm) cc_final: 0.6321 (mmm) REVERT: C 185 GLU cc_start: 0.7518 (mm-30) cc_final: 0.7101 (mm-30) REVERT: C 283 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7623 (mt-10) REVERT: C 378 THR cc_start: 0.9196 (OUTLIER) cc_final: 0.8907 (t) REVERT: C 562 MET cc_start: 0.9252 (mmt) cc_final: 0.8862 (mmt) REVERT: C 619 CYS cc_start: 0.6567 (p) cc_final: 0.6283 (p) REVERT: C 686 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.8318 (ptpp) REVERT: C 717 MET cc_start: 0.5556 (ttm) cc_final: 0.5350 (ttt) REVERT: C 738 LYS cc_start: 0.8231 (pttt) cc_final: 0.7845 (ptpp) REVERT: C 740 THR cc_start: 0.7926 (m) cc_final: 0.7531 (p) REVERT: C 743 LYS cc_start: 0.8456 (ptpp) cc_final: 0.8221 (ptpp) REVERT: D 159 MET cc_start: 0.6755 (mmm) cc_final: 0.6434 (mmm) REVERT: D 185 GLU cc_start: 0.7636 (mm-30) cc_final: 0.7208 (mm-30) REVERT: D 188 ARG cc_start: 0.7569 (ttp-170) cc_final: 0.7355 (mtm-85) REVERT: D 346 GLN cc_start: 0.9056 (mt0) cc_final: 0.8447 (mt0) REVERT: D 378 THR cc_start: 0.9209 (OUTLIER) cc_final: 0.8918 (t) REVERT: D 562 MET cc_start: 0.9244 (mmt) cc_final: 0.8847 (mmt) REVERT: D 619 CYS cc_start: 0.6530 (p) cc_final: 0.6255 (p) REVERT: D 686 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8350 (ptpp) REVERT: D 717 MET cc_start: 0.5546 (ttm) cc_final: 0.5344 (ttt) REVERT: D 738 LYS cc_start: 0.8266 (pttt) cc_final: 0.7799 (ptpp) REVERT: D 740 THR cc_start: 0.8055 (m) cc_final: 0.7665 (p) REVERT: D 743 LYS cc_start: 0.8449 (ptpp) cc_final: 0.8217 (ptpp) outliers start: 62 outliers final: 20 residues processed: 363 average time/residue: 0.6844 time to fit residues: 277.7801 Evaluate side-chains 321 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 292 time to evaluate : 0.622 ------------------------------------------------------------------------------- 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: 2.9990 chunk 31 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 chunk 106 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 164 optimal weight: 3.9990 chunk 189 optimal weight: 0.0000 chunk 226 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 163 optimal weight: 0.8980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3832 r_free = 0.3832 target = 0.160010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.125246 restraints weight = 23076.141| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.70 r_work: 0.3280 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3151 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| r_final: 0.3151 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 22226 Z= 0.141 Angle : 0.575 11.312 29830 Z= 0.284 Chirality : 0.039 0.146 3233 Planarity : 0.003 0.025 3600 Dihedral : 16.258 115.767 3885 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.66 % Allowed : 13.54 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.17), residues: 2484 helix: 1.44 (0.12), residues: 1620 sheet: 3.34 (0.65), residues: 64 loop : -1.50 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 698 TYR 0.014 0.002 TYR C 208 PHE 0.012 0.001 PHE A 193 TRP 0.011 0.002 TRP A 710 HIS 0.006 0.001 HIS C 301 Details of bonding type rmsd covalent geometry : bond 0.00333 (22222) covalent geometry : angle 0.57470 (29822) SS BOND : bond 0.00021 ( 4) SS BOND : angle 1.08643 ( 8) hydrogen bonds : bond 0.03879 ( 1124) hydrogen bonds : angle 3.96059 ( 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 373 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 314 time to evaluate : 0.864 Fit side-chains REVERT: A 185 GLU cc_start: 0.7594 (mm-30) cc_final: 0.7206 (mm-30) REVERT: A 378 THR cc_start: 0.9225 (OUTLIER) cc_final: 0.8942 (t) REVERT: A 488 MET cc_start: 0.6751 (mmt) cc_final: 0.6190 (mtm) REVERT: A 562 MET cc_start: 0.9228 (mmt) cc_final: 0.8767 (mmt) REVERT: A 619 CYS cc_start: 0.6585 (p) cc_final: 0.6293 (p) REVERT: A 686 LYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8484 (ptpp) REVERT: A 738 LYS cc_start: 0.8315 (pttt) cc_final: 0.7886 (ptpp) REVERT: A 740 THR cc_start: 0.8148 (m) cc_final: 0.7830 (p) REVERT: A 743 LYS cc_start: 0.8468 (ptpp) cc_final: 0.8189 (ptpp) REVERT: A 747 SER cc_start: 0.8206 (p) cc_final: 0.7875 (t) REVERT: B 159 MET cc_start: 0.6803 (mmm) cc_final: 0.6283 (mmm) REVERT: B 185 GLU cc_start: 0.7634 (mm-30) cc_final: 0.7255 (mm-30) REVERT: B 188 ARG cc_start: 0.7631 (ttp-170) cc_final: 0.7385 (mtm-85) REVERT: B 488 MET cc_start: 0.6782 (mmt) cc_final: 0.6224 (mtm) REVERT: B 562 MET cc_start: 0.9233 (mmt) cc_final: 0.8849 (mmt) REVERT: B 619 CYS cc_start: 0.6616 (p) cc_final: 0.6325 (p) REVERT: B 686 LYS cc_start: 0.8859 (OUTLIER) cc_final: 0.8453 (ptpp) REVERT: B 738 LYS cc_start: 0.8304 (pttt) cc_final: 0.7896 (ptpp) REVERT: B 740 THR cc_start: 0.8149 (m) cc_final: 0.7832 (p) REVERT: B 743 LYS cc_start: 0.8490 (ptpp) cc_final: 0.8206 (ptpp) REVERT: C 159 MET cc_start: 0.6804 (mmm) cc_final: 0.6131 (mmm) REVERT: C 185 GLU cc_start: 0.7578 (mm-30) cc_final: 0.7187 (mm-30) REVERT: C 283 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7568 (mt-10) REVERT: C 378 THR cc_start: 0.9173 (OUTLIER) cc_final: 0.8910 (t) REVERT: C 562 MET cc_start: 0.9230 (mmt) cc_final: 0.8804 (mmt) REVERT: C 619 CYS cc_start: 0.6638 (p) cc_final: 0.6364 (p) REVERT: C 686 LYS cc_start: 0.8870 (OUTLIER) cc_final: 0.8472 (ptpp) REVERT: C 738 LYS cc_start: 0.8310 (pttt) cc_final: 0.7886 (ptpp) REVERT: C 740 THR cc_start: 0.8163 (OUTLIER) cc_final: 0.7847 (p) REVERT: C 743 LYS cc_start: 0.8446 (ptpp) cc_final: 0.8188 (ptpp) REVERT: D 159 MET cc_start: 0.6723 (mmm) cc_final: 0.6119 (mmm) REVERT: D 185 GLU cc_start: 0.7615 (mm-30) cc_final: 0.7250 (mm-30) REVERT: D 188 ARG cc_start: 0.7627 (ttp-170) cc_final: 0.7376 (mtm-85) REVERT: D 283 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7533 (mt-10) REVERT: D 346 GLN cc_start: 0.9061 (mt0) cc_final: 0.8406 (mt0) REVERT: D 488 MET cc_start: 0.6784 (mmt) cc_final: 0.6212 (mtm) REVERT: D 514 GLN cc_start: 0.7093 (tt0) cc_final: 0.6438 (mm-40) REVERT: D 562 MET cc_start: 0.9235 (mmt) cc_final: 0.8820 (mmt) REVERT: D 619 CYS cc_start: 0.6619 (p) cc_final: 0.6337 (p) REVERT: D 686 LYS cc_start: 0.8872 (OUTLIER) cc_final: 0.8483 (ptpp) REVERT: D 738 LYS cc_start: 0.8296 (pttt) cc_final: 0.7896 (ptpp) REVERT: D 740 THR cc_start: 0.8149 (m) cc_final: 0.7836 (p) REVERT: D 743 LYS cc_start: 0.8484 (ptpp) cc_final: 0.8194 (ptpp) outliers start: 59 outliers final: 24 residues processed: 355 average time/residue: 0.7216 time to fit residues: 285.6924 Evaluate side-chains 329 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 296 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 MET 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 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 548 LEU Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 621 SER Chi-restraints excluded: chain C residue 686 LYS Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 411 THR Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 576 SER Chi-restraints excluded: chain D residue 621 SER Chi-restraints excluded: chain D residue 686 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 222 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 162 optimal weight: 8.9990 chunk 67 optimal weight: 0.8980 chunk 161 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 chunk 165 optimal weight: 10.0000 chunk 168 optimal weight: 1.9990 chunk 179 optimal weight: 0.9980 chunk 117 optimal weight: 0.7980 chunk 123 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN A 750 ASN B 750 ASN C 279 GLN C 750 ASN D 279 GLN D 750 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.158535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.123933 restraints weight = 22993.570| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.68 r_work: 0.3263 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3133 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3133 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 22226 Z= 0.155 Angle : 0.590 11.482 29830 Z= 0.292 Chirality : 0.039 0.146 3233 Planarity : 0.003 0.027 3600 Dihedral : 16.347 116.068 3885 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.84 % Allowed : 14.21 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.16), residues: 2484 helix: 1.39 (0.12), residues: 1616 sheet: 3.08 (0.65), residues: 64 loop : -1.53 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 188 TYR 0.014 0.002 TYR C 208 PHE 0.012 0.002 PHE D 506 TRP 0.016 0.002 TRP A 710 HIS 0.006 0.001 HIS A 301 Details of bonding type rmsd covalent geometry : bond 0.00370 (22222) covalent geometry : angle 0.58950 (29822) SS BOND : bond 0.00014 ( 4) SS BOND : angle 1.15550 ( 8) hydrogen bonds : bond 0.03909 ( 1124) hydrogen bonds : angle 3.95935 ( 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 379 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 316 time to evaluate : 0.578 Fit side-chains REVERT: A 185 GLU cc_start: 0.7530 (mm-30) cc_final: 0.7283 (mm-30) REVERT: A 283 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7449 (mt-10) REVERT: A 378 THR cc_start: 0.9244 (OUTLIER) cc_final: 0.8968 (t) REVERT: A 488 MET cc_start: 0.6852 (mmt) cc_final: 0.6301 (mtm) REVERT: A 562 MET cc_start: 0.9239 (mmt) cc_final: 0.8750 (mmt) REVERT: A 619 CYS cc_start: 0.6656 (p) cc_final: 0.6375 (p) REVERT: A 686 LYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8500 (ptpp) REVERT: A 738 LYS cc_start: 0.8318 (pttt) cc_final: 0.7885 (ptpp) REVERT: A 740 THR cc_start: 0.8163 (OUTLIER) cc_final: 0.7787 (p) REVERT: A 747 SER cc_start: 0.8152 (p) cc_final: 0.7929 (t) REVERT: B 159 MET cc_start: 0.6858 (mmm) cc_final: 0.6050 (mmm) REVERT: B 185 GLU cc_start: 0.7609 (mm-30) cc_final: 0.7299 (mm-30) REVERT: B 188 ARG cc_start: 0.7718 (ttp-170) cc_final: 0.7435 (mtm-85) REVERT: B 488 MET cc_start: 0.6809 (mmt) cc_final: 0.6259 (mtm) REVERT: B 562 MET cc_start: 0.9233 (mmt) cc_final: 0.8809 (mmt) REVERT: B 611 LYS cc_start: 0.8079 (OUTLIER) cc_final: 0.7772 (ptmt) REVERT: B 619 CYS cc_start: 0.6693 (p) cc_final: 0.6395 (p) REVERT: B 686 LYS cc_start: 0.8870 (OUTLIER) cc_final: 0.8507 (ptpp) REVERT: B 738 LYS cc_start: 0.8320 (pttt) cc_final: 0.7886 (ptpp) REVERT: B 740 THR cc_start: 0.8112 (OUTLIER) cc_final: 0.7731 (p) REVERT: B 743 LYS cc_start: 0.8503 (ptpp) cc_final: 0.8236 (ptpp) REVERT: C 159 MET cc_start: 0.6939 (mmm) cc_final: 0.6138 (mmm) REVERT: C 185 GLU cc_start: 0.7504 (mm-30) cc_final: 0.7261 (mm-30) REVERT: C 283 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7550 (mt-10) REVERT: C 488 MET cc_start: 0.6735 (mmt) cc_final: 0.6176 (mtm) REVERT: C 514 GLN cc_start: 0.7160 (OUTLIER) cc_final: 0.6493 (mm-40) REVERT: C 562 MET cc_start: 0.9247 (mmt) cc_final: 0.8799 (mmt) REVERT: C 619 CYS cc_start: 0.6669 (p) cc_final: 0.6383 (p) REVERT: C 686 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8519 (ptpp) REVERT: C 738 LYS cc_start: 0.8319 (pttt) cc_final: 0.7890 (ptpp) REVERT: C 740 THR cc_start: 0.8121 (OUTLIER) cc_final: 0.7757 (p) REVERT: C 743 LYS cc_start: 0.8500 (ptpp) cc_final: 0.8226 (ptpp) REVERT: D 159 MET cc_start: 0.6830 (mmm) cc_final: 0.6095 (mmm) REVERT: D 185 GLU cc_start: 0.7599 (mm-30) cc_final: 0.7303 (mm-30) REVERT: D 188 ARG cc_start: 0.7720 (ttp-170) cc_final: 0.7452 (mtm-85) REVERT: D 280 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7922 (tp) REVERT: D 283 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7508 (mt-10) REVERT: D 346 GLN cc_start: 0.9061 (mt0) cc_final: 0.8814 (mt0) REVERT: D 488 MET cc_start: 0.6869 (mmt) cc_final: 0.6318 (mtm) REVERT: D 514 GLN cc_start: 0.7150 (OUTLIER) cc_final: 0.6500 (mm-40) REVERT: D 562 MET cc_start: 0.9241 (mmt) cc_final: 0.8839 (mmt) REVERT: D 618 ASP cc_start: 0.7397 (m-30) cc_final: 0.7076 (m-30) REVERT: D 619 CYS cc_start: 0.6652 (p) cc_final: 0.6355 (p) REVERT: D 686 LYS cc_start: 0.8862 (OUTLIER) cc_final: 0.8499 (ptpp) REVERT: D 738 LYS cc_start: 0.8320 (pttt) cc_final: 0.7889 (ptpp) REVERT: D 740 THR cc_start: 0.8110 (OUTLIER) cc_final: 0.7747 (p) REVERT: D 743 LYS cc_start: 0.8494 (ptpp) cc_final: 0.8220 (ptpp) outliers start: 63 outliers final: 23 residues processed: 358 average time/residue: 0.7470 time to fit residues: 296.5866 Evaluate side-chains 341 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 302 time to evaluate : 0.873 ------------------------------------------------------------------------------- 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 A residue 740 THR 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 611 LYS Chi-restraints excluded: chain B residue 621 SER Chi-restraints excluded: chain B residue 686 LYS Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 418 GLU Chi-restraints excluded: chain C residue 514 GLN Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 621 SER Chi-restraints excluded: chain C residue 686 LYS Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 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 621 SER Chi-restraints excluded: chain D residue 686 LYS Chi-restraints excluded: chain D residue 740 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 5 optimal weight: 0.7980 chunk 202 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 160 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 220 optimal weight: 9.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN A 750 ASN B 279 GLN B 750 ASN C 279 GLN C 750 ASN D 279 GLN D 750 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.160084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.125747 restraints weight = 23118.309| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 1.68 r_work: 0.3286 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3162 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3162 r_free = 0.3162 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3162 r_free = 0.3162 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3162 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22226 Z= 0.125 Angle : 0.565 11.184 29830 Z= 0.280 Chirality : 0.038 0.144 3233 Planarity : 0.003 0.027 3600 Dihedral : 16.127 118.293 3885 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.26 % Allowed : 15.12 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.17), residues: 2484 helix: 1.50 (0.12), residues: 1620 sheet: 3.26 (0.66), residues: 64 loop : -1.53 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 337 TYR 0.014 0.002 TYR A 208 PHE 0.014 0.001 PHE C 506 TRP 0.021 0.002 TRP A 710 HIS 0.006 0.001 HIS C 301 Details of bonding type rmsd covalent geometry : bond 0.00292 (22222) covalent geometry : angle 0.56509 (29822) SS BOND : bond 0.00033 ( 4) SS BOND : angle 1.04968 ( 8) hydrogen bonds : bond 0.03559 ( 1124) hydrogen bonds : angle 3.85405 ( 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 364 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 314 time to evaluate : 0.838 Fit side-chains REVERT: A 185 GLU cc_start: 0.7481 (mm-30) cc_final: 0.7190 (mm-30) REVERT: A 280 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7906 (tp) REVERT: A 283 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7484 (mt-10) REVERT: A 378 THR cc_start: 0.9268 (OUTLIER) cc_final: 0.9005 (t) REVERT: A 488 MET cc_start: 0.6692 (mmt) cc_final: 0.6202 (mtm) REVERT: A 562 MET cc_start: 0.9224 (mmt) cc_final: 0.8786 (mmt) REVERT: A 618 ASP cc_start: 0.7354 (m-30) cc_final: 0.7036 (m-30) REVERT: A 619 CYS cc_start: 0.6643 (p) cc_final: 0.6345 (p) REVERT: A 686 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8486 (ptpp) REVERT: A 738 LYS cc_start: 0.8286 (pttt) cc_final: 0.7828 (ptpp) REVERT: A 740 THR cc_start: 0.8142 (m) cc_final: 0.7815 (p) REVERT: A 747 SER cc_start: 0.8158 (p) cc_final: 0.7813 (t) REVERT: B 156 ASP cc_start: 0.5369 (t0) cc_final: 0.5113 (m-30) REVERT: B 159 MET cc_start: 0.6898 (mmm) cc_final: 0.6304 (mmm) REVERT: B 185 GLU cc_start: 0.7567 (mm-30) cc_final: 0.7273 (mm-30) REVERT: B 488 MET cc_start: 0.6708 (mmt) cc_final: 0.6235 (mtm) REVERT: B 514 GLN cc_start: 0.7172 (OUTLIER) cc_final: 0.6499 (mm-40) REVERT: B 562 MET cc_start: 0.9229 (mmt) cc_final: 0.8864 (mmt) REVERT: B 611 LYS cc_start: 0.8094 (OUTLIER) cc_final: 0.7795 (ptmt) REVERT: B 618 ASP cc_start: 0.7420 (m-30) cc_final: 0.7111 (m-30) REVERT: B 619 CYS cc_start: 0.6671 (p) cc_final: 0.6374 (p) REVERT: B 738 LYS cc_start: 0.8303 (pttt) cc_final: 0.7865 (ptpp) REVERT: B 740 THR cc_start: 0.8137 (m) cc_final: 0.7806 (p) REVERT: C 159 MET cc_start: 0.6978 (mmm) cc_final: 0.6073 (mmm) REVERT: C 185 GLU cc_start: 0.7437 (mm-30) cc_final: 0.7213 (mm-30) REVERT: C 283 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7531 (mt-10) REVERT: C 488 MET cc_start: 0.6725 (mmt) cc_final: 0.6234 (mtm) REVERT: C 562 MET cc_start: 0.9222 (mmt) cc_final: 0.8830 (mmt) REVERT: C 618 ASP cc_start: 0.7360 (m-30) cc_final: 0.7043 (m-30) REVERT: C 619 CYS cc_start: 0.6665 (p) cc_final: 0.6377 (p) REVERT: C 738 LYS cc_start: 0.8296 (pttt) cc_final: 0.7861 (ptpp) REVERT: C 740 THR cc_start: 0.8149 (m) cc_final: 0.7822 (p) REVERT: D 159 MET cc_start: 0.6856 (mmm) cc_final: 0.6038 (mmm) REVERT: D 185 GLU cc_start: 0.7549 (mm-30) cc_final: 0.7219 (mm-30) REVERT: D 280 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7906 (tp) REVERT: D 283 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7487 (mt-10) REVERT: D 346 GLN cc_start: 0.9052 (mt0) cc_final: 0.8414 (mt0) REVERT: D 488 MET cc_start: 0.6720 (mmt) cc_final: 0.6226 (mtm) REVERT: D 514 GLN cc_start: 0.7185 (tt0) cc_final: 0.6546 (mm-40) REVERT: D 562 MET cc_start: 0.9228 (mmt) cc_final: 0.8832 (mmt) REVERT: D 618 ASP cc_start: 0.7373 (m-30) cc_final: 0.7056 (m-30) REVERT: D 619 CYS cc_start: 0.6655 (p) cc_final: 0.6359 (p) REVERT: D 738 LYS cc_start: 0.8303 (pttt) cc_final: 0.7863 (ptpp) REVERT: D 740 THR cc_start: 0.8136 (m) cc_final: 0.7808 (p) outliers start: 50 outliers final: 18 residues processed: 353 average time/residue: 0.6213 time to fit residues: 245.2048 Evaluate side-chains 319 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 292 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 686 LYS Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 514 GLN Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 576 SER Chi-restraints excluded: chain B residue 611 LYS Chi-restraints excluded: chain C residue 282 MET Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 418 GLU Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain D residue 280 LEU 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: 0.9980 chunk 5 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 chunk 102 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 157 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 147 optimal weight: 0.7980 chunk 119 optimal weight: 0.7980 chunk 23 optimal weight: 0.0270 chunk 200 optimal weight: 0.5980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN A 750 ASN B 279 GLN B 750 ASN C 279 GLN C 750 ASN D 279 GLN D 750 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.161618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.127538 restraints weight = 23169.160| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 1.67 r_work: 0.3311 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3182 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3182 r_free = 0.3182 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3182 r_free = 0.3182 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| r_final: 0.3182 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 22226 Z= 0.109 Angle : 0.540 10.924 29830 Z= 0.268 Chirality : 0.037 0.143 3233 Planarity : 0.003 0.026 3600 Dihedral : 15.859 118.445 3885 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.08 % Allowed : 15.97 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.17), residues: 2484 helix: 1.62 (0.12), residues: 1616 sheet: 3.41 (0.66), residues: 64 loop : -1.44 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 337 TYR 0.013 0.001 TYR C 208 PHE 0.014 0.001 PHE B 506 TRP 0.024 0.002 TRP C 710 HIS 0.005 0.001 HIS C 301 Details of bonding type rmsd covalent geometry : bond 0.00249 (22222) covalent geometry : angle 0.53955 (29822) SS BOND : bond 0.00065 ( 4) SS BOND : angle 1.01790 ( 8) hydrogen bonds : bond 0.03351 ( 1124) hydrogen bonds : angle 3.78555 ( 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 366 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 320 time to evaluate : 0.903 Fit side-chains REVERT: A 185 GLU cc_start: 0.7420 (mm-30) cc_final: 0.7151 (mm-30) REVERT: A 283 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7525 (mt-10) REVERT: A 378 THR cc_start: 0.9277 (OUTLIER) cc_final: 0.9009 (t) REVERT: A 488 MET cc_start: 0.6669 (mmt) cc_final: 0.6184 (mtm) REVERT: A 562 MET cc_start: 0.9212 (mmt) cc_final: 0.8771 (mmt) REVERT: A 618 ASP cc_start: 0.7402 (m-30) cc_final: 0.7095 (m-30) REVERT: A 619 CYS cc_start: 0.6701 (p) cc_final: 0.6400 (p) REVERT: A 738 LYS cc_start: 0.8255 (pttt) cc_final: 0.7903 (pttm) REVERT: A 740 THR cc_start: 0.8060 (OUTLIER) cc_final: 0.7668 (p) REVERT: A 747 SER cc_start: 0.8116 (p) cc_final: 0.7770 (t) REVERT: B 159 MET cc_start: 0.6980 (mmm) cc_final: 0.6423 (mmm) REVERT: B 185 GLU cc_start: 0.7520 (mm-30) cc_final: 0.7226 (mm-30) REVERT: B 188 ARG cc_start: 0.7622 (ttp-170) cc_final: 0.7357 (mtm-85) REVERT: B 263 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7702 (pt0) REVERT: B 488 MET cc_start: 0.6689 (mmt) cc_final: 0.6211 (mtm) REVERT: B 514 GLN cc_start: 0.7181 (OUTLIER) cc_final: 0.6511 (mm-40) REVERT: B 562 MET cc_start: 0.9210 (mmt) cc_final: 0.8858 (mmt) REVERT: B 611 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.7996 (ptmt) REVERT: B 618 ASP cc_start: 0.7413 (m-30) cc_final: 0.7109 (m-30) REVERT: B 619 CYS cc_start: 0.6701 (p) cc_final: 0.6401 (p) REVERT: B 738 LYS cc_start: 0.8282 (pttt) cc_final: 0.7922 (pttm) REVERT: B 740 THR cc_start: 0.8062 (m) cc_final: 0.7708 (p) REVERT: C 159 MET cc_start: 0.7099 (mmm) cc_final: 0.6190 (mmm) REVERT: C 185 GLU cc_start: 0.7362 (mm-30) cc_final: 0.7097 (mm-30) REVERT: C 263 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7625 (pt0) REVERT: C 283 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7570 (mt-10) REVERT: C 488 MET cc_start: 0.6705 (mmt) cc_final: 0.6211 (mtm) REVERT: C 562 MET cc_start: 0.9226 (mmt) cc_final: 0.8854 (mmt) REVERT: C 618 ASP cc_start: 0.7350 (m-30) cc_final: 0.7032 (m-30) REVERT: C 619 CYS cc_start: 0.6665 (p) cc_final: 0.6373 (p) REVERT: C 738 LYS cc_start: 0.8266 (pttt) cc_final: 0.7915 (pttm) REVERT: C 740 THR cc_start: 0.8074 (m) cc_final: 0.7722 (p) REVERT: D 159 MET cc_start: 0.6948 (mmm) cc_final: 0.6141 (mmm) REVERT: D 185 GLU cc_start: 0.7479 (mm-30) cc_final: 0.7190 (mm-30) REVERT: D 188 ARG cc_start: 0.7612 (ttp-170) cc_final: 0.7346 (mtm-85) REVERT: D 283 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7519 (mt-10) REVERT: D 346 GLN cc_start: 0.9046 (mt0) cc_final: 0.8344 (mt0) REVERT: D 488 MET cc_start: 0.6686 (mmt) cc_final: 0.6199 (mtm) REVERT: D 514 GLN cc_start: 0.7201 (OUTLIER) cc_final: 0.6548 (mm-40) REVERT: D 562 MET cc_start: 0.9227 (mmt) cc_final: 0.8833 (mmt) REVERT: D 618 ASP cc_start: 0.7358 (m-30) cc_final: 0.7041 (m-30) REVERT: D 619 CYS cc_start: 0.6662 (p) cc_final: 0.6359 (p) REVERT: D 738 LYS cc_start: 0.8277 (pttt) cc_final: 0.7922 (pttm) REVERT: D 740 THR cc_start: 0.8070 (m) cc_final: 0.7708 (p) outliers start: 46 outliers final: 20 residues processed: 355 average time/residue: 0.6717 time to fit residues: 266.8151 Evaluate side-chains 333 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 303 time to evaluate : 0.541 ------------------------------------------------------------------------------- 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 740 THR Chi-restraints excluded: chain A residue 743 LYS Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 514 GLN Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 576 SER Chi-restraints excluded: chain B residue 611 LYS Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 282 MET Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 576 SER 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 64 optimal weight: 3.9990 chunk 161 optimal weight: 6.9990 chunk 71 optimal weight: 0.0270 chunk 242 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 138 optimal weight: 0.4980 chunk 128 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 chunk 159 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 overall best weight: 1.2642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 ASN A 279 GLN A 750 ASN B 279 GLN B 750 ASN C 182 ASN C 279 GLN C 750 ASN D 182 ASN D 750 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.158497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.124223 restraints weight = 23067.079| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.67 r_work: 0.3266 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3137 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3137 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 22226 Z= 0.151 Angle : 0.607 12.417 29830 Z= 0.298 Chirality : 0.039 0.157 3233 Planarity : 0.003 0.029 3600 Dihedral : 16.096 116.220 3885 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.30 % Allowed : 15.39 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.17), residues: 2484 helix: 1.40 (0.12), residues: 1648 sheet: 3.14 (0.65), residues: 64 loop : -1.31 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 337 TYR 0.014 0.002 TYR A 208 PHE 0.023 0.002 PHE B 377 TRP 0.026 0.002 TRP D 710 HIS 0.007 0.001 HIS A 301 Details of bonding type rmsd covalent geometry : bond 0.00361 (22222) covalent geometry : angle 0.60693 (29822) SS BOND : bond 0.00051 ( 4) SS BOND : angle 1.13251 ( 8) hydrogen bonds : bond 0.03752 ( 1124) hydrogen bonds : angle 3.88377 ( 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 366 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 315 time to evaluate : 0.594 Fit side-chains REVERT: A 156 ASP cc_start: 0.5482 (t0) cc_final: 0.5146 (OUTLIER) REVERT: A 185 GLU cc_start: 0.7390 (mm-30) cc_final: 0.7159 (mm-30) REVERT: A 283 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7492 (mt-10) REVERT: A 371 ARG cc_start: 0.7894 (OUTLIER) cc_final: 0.7218 (ttm170) REVERT: A 378 THR cc_start: 0.9277 (OUTLIER) cc_final: 0.9020 (t) REVERT: A 488 MET cc_start: 0.6667 (mmt) cc_final: 0.6187 (mtm) REVERT: A 562 MET cc_start: 0.9239 (mmt) cc_final: 0.8738 (mmt) REVERT: A 618 ASP cc_start: 0.7454 (m-30) cc_final: 0.7152 (m-30) REVERT: A 619 CYS cc_start: 0.6685 (p) cc_final: 0.6384 (p) REVERT: A 738 LYS cc_start: 0.8311 (pttt) cc_final: 0.7928 (pttm) REVERT: A 740 THR cc_start: 0.8151 (OUTLIER) cc_final: 0.7833 (p) REVERT: A 747 SER cc_start: 0.8145 (p) cc_final: 0.7790 (t) REVERT: B 159 MET cc_start: 0.6985 (mmm) cc_final: 0.6188 (mmm) REVERT: B 185 GLU cc_start: 0.7539 (mm-30) cc_final: 0.7233 (mm-30) REVERT: B 263 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7772 (pt0) REVERT: B 488 MET cc_start: 0.6683 (mmt) cc_final: 0.6215 (mtm) REVERT: B 514 GLN cc_start: 0.7172 (OUTLIER) cc_final: 0.6496 (mm-40) REVERT: B 562 MET cc_start: 0.9243 (mmt) cc_final: 0.8813 (mmt) REVERT: B 618 ASP cc_start: 0.7470 (m-30) cc_final: 0.7169 (m-30) REVERT: B 619 CYS cc_start: 0.6700 (p) cc_final: 0.6399 (p) REVERT: B 738 LYS cc_start: 0.8334 (pttt) cc_final: 0.7946 (pttm) REVERT: B 740 THR cc_start: 0.8149 (OUTLIER) cc_final: 0.7835 (p) REVERT: C 156 ASP cc_start: 0.5633 (t0) cc_final: 0.5298 (OUTLIER) REVERT: C 159 MET cc_start: 0.6986 (mmm) cc_final: 0.6138 (mmm) REVERT: C 185 GLU cc_start: 0.7348 (mm-30) cc_final: 0.7131 (mm-30) REVERT: C 263 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7796 (pt0) REVERT: C 283 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7533 (mt-10) REVERT: C 371 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.7211 (ttm170) REVERT: C 488 MET cc_start: 0.6691 (mmt) cc_final: 0.6198 (mtm) REVERT: C 562 MET cc_start: 0.9239 (mmt) cc_final: 0.8787 (mmt) REVERT: C 618 ASP cc_start: 0.7393 (m-30) cc_final: 0.7080 (m-30) REVERT: C 619 CYS cc_start: 0.6729 (p) cc_final: 0.6429 (p) REVERT: C 738 LYS cc_start: 0.8316 (pttt) cc_final: 0.7939 (pttm) REVERT: C 740 THR cc_start: 0.8156 (OUTLIER) cc_final: 0.7847 (p) REVERT: D 156 ASP cc_start: 0.5595 (t0) cc_final: 0.5290 (OUTLIER) REVERT: D 159 MET cc_start: 0.6928 (mmm) cc_final: 0.6235 (mmm) REVERT: D 185 GLU cc_start: 0.7507 (mm-30) cc_final: 0.7208 (mm-30) REVERT: D 283 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7510 (mt-10) REVERT: D 346 GLN cc_start: 0.9057 (mt0) cc_final: 0.8801 (mt0) REVERT: D 488 MET cc_start: 0.6696 (mmt) cc_final: 0.6206 (mtm) REVERT: D 514 GLN cc_start: 0.7183 (OUTLIER) cc_final: 0.6529 (mm-40) REVERT: D 562 MET cc_start: 0.9246 (mmt) cc_final: 0.8781 (mmt) REVERT: D 618 ASP cc_start: 0.7421 (m-30) cc_final: 0.7110 (m-30) REVERT: D 619 CYS cc_start: 0.6714 (p) cc_final: 0.6404 (p) REVERT: D 738 LYS cc_start: 0.8323 (pttt) cc_final: 0.7941 (pttm) REVERT: D 740 THR cc_start: 0.8155 (OUTLIER) cc_final: 0.7838 (p) outliers start: 51 outliers final: 31 residues processed: 353 average time/residue: 0.7178 time to fit residues: 282.6943 Evaluate side-chains 350 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 308 time to evaluate : 0.729 ------------------------------------------------------------------------------- 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 371 ARG Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 519 ASP Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 743 LYS Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 282 MET Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 514 GLN 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 740 THR Chi-restraints excluded: chain B residue 743 LYS Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 282 MET Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 371 ARG 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 C residue 743 LYS Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 411 THR Chi-restraints excluded: chain D residue 514 GLN Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 576 SER Chi-restraints excluded: chain D residue 740 THR Chi-restraints excluded: chain D residue 743 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 20 optimal weight: 0.8980 chunk 99 optimal weight: 3.9990 chunk 230 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 224 optimal weight: 9.9990 chunk 215 optimal weight: 0.9980 chunk 143 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 169 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 750 ASN B 279 GLN B 750 ASN 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 = 0.3826 r_free = 0.3826 target = 0.159366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.125206 restraints weight = 23334.260| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.67 r_work: 0.3281 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3161 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3161 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.3406 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= 0.132 Angle : 0.587 11.553 29830 Z= 0.290 Chirality : 0.038 0.152 3233 Planarity : 0.003 0.032 3600 Dihedral : 16.047 117.423 3885 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.94 % Allowed : 16.65 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.17), residues: 2484 helix: 1.41 (0.12), residues: 1648 sheet: 3.05 (0.65), residues: 64 loop : -1.25 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 337 TYR 0.015 0.002 TYR C 208 PHE 0.022 0.001 PHE B 377 TRP 0.032 0.002 TRP D 710 HIS 0.006 0.001 HIS A 301 Details of bonding type rmsd covalent geometry : bond 0.00311 (22222) covalent geometry : angle 0.58677 (29822) SS BOND : bond 0.00052 ( 4) SS BOND : angle 1.09350 ( 8) hydrogen bonds : bond 0.03588 ( 1124) hydrogen bonds : angle 3.85275 ( 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 364 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 321 time to evaluate : 0.598 Fit side-chains REVERT: A 185 GLU cc_start: 0.7368 (mm-30) cc_final: 0.7158 (mm-30) REVERT: A 283 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7497 (mt-10) REVERT: A 488 MET cc_start: 0.6684 (mmt) cc_final: 0.6198 (mtm) REVERT: A 562 MET cc_start: 0.9231 (mmt) cc_final: 0.8791 (mmt) REVERT: A 618 ASP cc_start: 0.7450 (m-30) cc_final: 0.7145 (m-30) REVERT: A 619 CYS cc_start: 0.6672 (p) cc_final: 0.6367 (p) REVERT: A 686 LYS cc_start: 0.8730 (ptpp) cc_final: 0.8012 (mttp) REVERT: A 738 LYS cc_start: 0.8275 (pttt) cc_final: 0.7903 (pttm) REVERT: A 740 THR cc_start: 0.8097 (OUTLIER) cc_final: 0.7729 (p) REVERT: A 747 SER cc_start: 0.8138 (p) cc_final: 0.7792 (t) REVERT: B 156 ASP cc_start: 0.5236 (t0) cc_final: 0.5029 (m-30) REVERT: B 159 MET cc_start: 0.6863 (mmm) cc_final: 0.6102 (mmm) REVERT: B 185 GLU cc_start: 0.7426 (mm-30) cc_final: 0.7192 (mm-30) REVERT: B 263 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7725 (pt0) REVERT: B 371 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.7138 (ttm170) REVERT: B 488 MET cc_start: 0.6706 (mmt) cc_final: 0.6233 (mtm) REVERT: B 514 GLN cc_start: 0.7206 (OUTLIER) cc_final: 0.6539 (mm-40) REVERT: B 562 MET cc_start: 0.9232 (mmt) cc_final: 0.8867 (mmt) REVERT: B 618 ASP cc_start: 0.7465 (m-30) cc_final: 0.7161 (m-30) REVERT: B 619 CYS cc_start: 0.6747 (p) cc_final: 0.6442 (p) REVERT: B 686 LYS cc_start: 0.8735 (ptpp) cc_final: 0.8016 (mttp) REVERT: B 738 LYS cc_start: 0.8312 (pttt) cc_final: 0.7945 (pttm) REVERT: B 740 THR cc_start: 0.8097 (OUTLIER) cc_final: 0.7743 (p) REVERT: C 159 MET cc_start: 0.6995 (mmm) cc_final: 0.6029 (mmm) REVERT: C 185 GLU cc_start: 0.7334 (mm-30) cc_final: 0.7132 (mm-30) REVERT: C 263 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7723 (pt0) REVERT: C 283 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7549 (mt-10) REVERT: C 488 MET cc_start: 0.6698 (mmt) cc_final: 0.6202 (mtm) REVERT: C 562 MET cc_start: 0.9241 (mmt) cc_final: 0.8855 (mmt) REVERT: C 618 ASP cc_start: 0.7410 (m-30) cc_final: 0.7100 (m-30) REVERT: C 619 CYS cc_start: 0.6701 (p) cc_final: 0.6405 (p) REVERT: C 738 LYS cc_start: 0.8299 (pttt) cc_final: 0.7941 (pttm) REVERT: C 740 THR cc_start: 0.8107 (m) cc_final: 0.7751 (p) REVERT: D 159 MET cc_start: 0.6939 (mmm) cc_final: 0.6123 (mmm) REVERT: D 185 GLU cc_start: 0.7392 (mm-30) cc_final: 0.7161 (mm-30) REVERT: D 283 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7515 (mt-10) REVERT: D 346 GLN cc_start: 0.9054 (mt0) cc_final: 0.8769 (mt0) REVERT: D 371 ARG cc_start: 0.7781 (OUTLIER) cc_final: 0.7128 (ttm170) REVERT: D 488 MET cc_start: 0.6693 (mmt) cc_final: 0.6210 (mtm) REVERT: D 514 GLN cc_start: 0.7251 (OUTLIER) cc_final: 0.6613 (mm-40) REVERT: D 562 MET cc_start: 0.9233 (mmt) cc_final: 0.8828 (mmt) REVERT: D 618 ASP cc_start: 0.7455 (m-30) cc_final: 0.7150 (m-30) REVERT: D 619 CYS cc_start: 0.6685 (p) cc_final: 0.6374 (p) REVERT: D 738 LYS cc_start: 0.8302 (pttt) cc_final: 0.7942 (pttm) REVERT: D 740 THR cc_start: 0.8105 (m) cc_final: 0.7742 (p) outliers start: 43 outliers final: 25 residues processed: 354 average time/residue: 0.6449 time to fit residues: 255.1948 Evaluate side-chains 351 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 315 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 743 LYS Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 371 ARG Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 514 GLN Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 576 SER Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 743 LYS Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 282 MET Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 743 LYS Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 371 ARG 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 743 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 25 optimal weight: 2.9990 chunk 124 optimal weight: 10.0000 chunk 209 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 200 optimal weight: 0.6980 chunk 169 optimal weight: 0.9980 chunk 95 optimal weight: 4.9990 chunk 216 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 229 optimal weight: 0.9990 chunk 178 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.158865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.124709 restraints weight = 23143.535| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.67 r_work: 0.3272 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3151 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3151 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 22226 Z= 0.143 Angle : 0.605 12.014 29830 Z= 0.299 Chirality : 0.039 0.152 3233 Planarity : 0.003 0.033 3600 Dihedral : 16.073 116.621 3885 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 1.76 % Allowed : 16.47 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.17), residues: 2484 helix: 1.38 (0.12), residues: 1648 sheet: 2.96 (0.65), residues: 64 loop : -1.35 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 337 TYR 0.015 0.002 TYR C 208 PHE 0.017 0.001 PHE A 377 TRP 0.037 0.002 TRP D 710 HIS 0.006 0.001 HIS B 301 Details of bonding type rmsd covalent geometry : bond 0.00341 (22222) covalent geometry : angle 0.60516 (29822) SS BOND : bond 0.00048 ( 4) SS BOND : angle 1.13258 ( 8) hydrogen bonds : bond 0.03676 ( 1124) hydrogen bonds : angle 3.89584 ( 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 361 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 322 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 185 GLU cc_start: 0.7339 (mm-30) cc_final: 0.7124 (mm-30) REVERT: A 283 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7499 (mt-10) REVERT: A 488 MET cc_start: 0.6680 (mmt) cc_final: 0.6198 (mtm) REVERT: A 562 MET cc_start: 0.9235 (mmt) cc_final: 0.8786 (mmt) REVERT: A 618 ASP cc_start: 0.7462 (m-30) cc_final: 0.7151 (m-30) REVERT: A 619 CYS cc_start: 0.6734 (p) cc_final: 0.6417 (p) REVERT: A 686 LYS cc_start: 0.8854 (ptpp) cc_final: 0.8102 (mttp) REVERT: A 738 LYS cc_start: 0.8316 (pttt) cc_final: 0.7942 (pttm) REVERT: A 740 THR cc_start: 0.8143 (OUTLIER) cc_final: 0.7841 (p) REVERT: B 156 ASP cc_start: 0.5390 (t0) cc_final: 0.5129 (m-30) REVERT: B 159 MET cc_start: 0.6932 (mmm) cc_final: 0.6186 (mmm) REVERT: B 185 GLU cc_start: 0.7421 (mm-30) cc_final: 0.7184 (mm-30) REVERT: B 263 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7735 (pt0) REVERT: B 371 ARG cc_start: 0.7812 (OUTLIER) cc_final: 0.7146 (ttm170) REVERT: B 488 MET cc_start: 0.6719 (mmt) cc_final: 0.6251 (mtm) REVERT: B 514 GLN cc_start: 0.7203 (OUTLIER) cc_final: 0.6535 (mm-40) REVERT: B 562 MET cc_start: 0.9236 (mmt) cc_final: 0.8868 (mmt) REVERT: B 618 ASP cc_start: 0.7483 (m-30) cc_final: 0.7166 (m-30) REVERT: B 619 CYS cc_start: 0.6758 (p) cc_final: 0.6446 (p) REVERT: B 686 LYS cc_start: 0.8744 (ptpp) cc_final: 0.8115 (mttp) REVERT: B 738 LYS cc_start: 0.8333 (pttt) cc_final: 0.7950 (pttm) REVERT: B 740 THR cc_start: 0.8139 (OUTLIER) cc_final: 0.7838 (p) REVERT: C 159 MET cc_start: 0.6943 (mmm) cc_final: 0.6160 (mmm) REVERT: C 185 GLU cc_start: 0.7331 (mm-30) cc_final: 0.7123 (mm-30) REVERT: C 263 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7766 (pt0) REVERT: C 283 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7555 (mt-10) REVERT: C 488 MET cc_start: 0.6717 (mmt) cc_final: 0.6224 (mtm) REVERT: C 562 MET cc_start: 0.9235 (mmt) cc_final: 0.8795 (mmt) REVERT: C 618 ASP cc_start: 0.7466 (m-30) cc_final: 0.7179 (m-30) REVERT: C 686 LYS cc_start: 0.8742 (ptpp) cc_final: 0.8108 (mttp) REVERT: C 738 LYS cc_start: 0.8320 (pttt) cc_final: 0.7944 (pttm) REVERT: C 740 THR cc_start: 0.8151 (OUTLIER) cc_final: 0.7854 (p) REVERT: D 159 MET cc_start: 0.6975 (mmm) cc_final: 0.6273 (mmm) REVERT: D 185 GLU cc_start: 0.7376 (mm-30) cc_final: 0.7146 (mm-30) REVERT: D 283 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7514 (mt-10) REVERT: D 346 GLN cc_start: 0.9051 (mt0) cc_final: 0.8768 (mt0) REVERT: D 371 ARG cc_start: 0.7854 (OUTLIER) cc_final: 0.7184 (ttm170) REVERT: D 488 MET cc_start: 0.6706 (mmt) cc_final: 0.6219 (mtm) REVERT: D 514 GLN cc_start: 0.7252 (OUTLIER) cc_final: 0.6615 (mm-40) REVERT: D 562 MET cc_start: 0.9242 (mmt) cc_final: 0.8830 (mmt) REVERT: D 618 ASP cc_start: 0.7486 (m-30) cc_final: 0.7197 (m-30) REVERT: D 686 LYS cc_start: 0.8737 (ptpp) cc_final: 0.8100 (mttp) REVERT: D 738 LYS cc_start: 0.8320 (pttt) cc_final: 0.7942 (pttm) REVERT: D 740 THR cc_start: 0.8145 (OUTLIER) cc_final: 0.7842 (p) outliers start: 39 outliers final: 25 residues processed: 353 average time/residue: 0.6978 time to fit residues: 275.0815 Evaluate side-chains 353 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 315 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 743 LYS Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 371 ARG Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 514 GLN 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 740 THR Chi-restraints excluded: chain B residue 743 LYS Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 282 MET Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain C residue 743 LYS Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 371 ARG Chi-restraints excluded: chain D residue 411 THR Chi-restraints excluded: chain D residue 514 GLN Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 576 SER Chi-restraints excluded: chain D residue 740 THR Chi-restraints excluded: chain D residue 743 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 12 optimal weight: 0.5980 chunk 162 optimal weight: 0.9990 chunk 184 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 180 optimal weight: 0.5980 chunk 194 optimal weight: 1.9990 chunk 244 optimal weight: 5.9990 chunk 158 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 138 optimal weight: 0.3980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN A 523 HIS A 750 ASN B 279 GLN B 750 ASN C 279 GLN C 750 ASN D 750 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.160795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.126854 restraints weight = 23117.804| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 1.66 r_work: 0.3304 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- 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: 24 | |-----------------------------------------------------------------------------| |-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: 24 | |-----------------------------------------------------------------------------| r_final: 0.3174 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22226 Z= 0.118 Angle : 0.577 11.122 29830 Z= 0.285 Chirality : 0.038 0.155 3233 Planarity : 0.003 0.034 3600 Dihedral : 15.849 118.764 3885 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.90 % Allowed : 16.74 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.17), residues: 2484 helix: 1.49 (0.12), residues: 1644 sheet: 3.16 (0.65), residues: 64 loop : -1.34 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 337 TYR 0.014 0.001 TYR A 208 PHE 0.015 0.001 PHE B 506 TRP 0.043 0.002 TRP D 710 HIS 0.005 0.001 HIS A 301 Details of bonding type rmsd covalent geometry : bond 0.00272 (22222) covalent geometry : angle 0.57645 (29822) SS BOND : bond 0.00054 ( 4) SS BOND : angle 1.06404 ( 8) hydrogen bonds : bond 0.03435 ( 1124) hydrogen bonds : angle 3.83823 ( 3324) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9228.15 seconds wall clock time: 157 minutes 21.20 seconds (9441.20 seconds total)