Starting phenix.real_space_refine on Thu Jun 12 19:49:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eu8_28608/06_2025/8eu8_28608_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eu8_28608/06_2025/8eu8_28608.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8eu8_28608/06_2025/8eu8_28608.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eu8_28608/06_2025/8eu8_28608.map" model { file = "/net/cci-nas-00/data/ceres_data/8eu8_28608/06_2025/8eu8_28608_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eu8_28608/06_2025/8eu8_28608_neut.cif" } resolution = 3.73 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.031 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: 4 Type Number sf(0) Gaussians S 105 5.16 5 C 8856 2.51 5 N 2358 2.21 5 O 2862 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 75 residue(s): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 14181 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 4433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 564, 4433 Classifications: {'peptide': 564} Link IDs: {'PTRANS': 25, 'TRANS': 538} Chain breaks: 5 Chain: "B" Number of atoms: 4433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 564, 4433 Classifications: {'peptide': 564} Link IDs: {'PTRANS': 25, 'TRANS': 538} Chain breaks: 5 Chain: "C" Number of atoms: 4433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 564, 4433 Classifications: {'peptide': 564} Link IDs: {'PTRANS': 25, 'TRANS': 538} Chain breaks: 5 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 10.76, per 1000 atoms: 0.76 Number of scatterers: 14181 At special positions: 0 Unit cell: (130.68, 126.36, 120.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 105 16.00 O 2862 8.00 N 2358 7.00 C 8856 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.05 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 155 " distance=2.02 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.04 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.05 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.01 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.02 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS A 605 " distance=2.04 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.01 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 74 " distance=2.05 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.04 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 155 " distance=2.02 Simple disulfide: pdb=" SG CYS B 201 " - pdb=" SG CYS B 433 " distance=2.04 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.02 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.05 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.01 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.02 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS B 605 " distance=2.04 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.01 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.05 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.04 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 155 " distance=2.02 Simple disulfide: pdb=" SG CYS C 201 " - pdb=" SG CYS C 433 " distance=2.04 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.05 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.01 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.02 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS C 605 " distance=2.04 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.01 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 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A 801 " - " ASN A 158 " " NAG A 802 " - " ASN A 197 " " NAG A 803 " - " ASN A 234 " " NAG A 804 " - " ASN A 339 " " NAG A 805 " - " ASN A 362 " " NAG A 806 " - " ASN A 386 " " NAG A 807 " - " ASN A 448 " " NAG A 808 " - " ASN A 611 " " NAG A 809 " - " ASN A 618 " " NAG B 801 " - " ASN B 158 " " NAG B 802 " - " ASN B 197 " " NAG B 803 " - " ASN B 234 " " NAG B 804 " - " ASN B 339 " " NAG B 805 " - " ASN B 362 " " NAG B 806 " - " ASN B 386 " " NAG B 807 " - " ASN B 448 " " NAG B 808 " - " ASN B 611 " " NAG B 809 " - " ASN B 618 " " NAG C 801 " - " ASN C 158 " " NAG C 802 " - " ASN C 197 " " NAG C 803 " - " ASN C 234 " " NAG C 804 " - " ASN C 339 " " NAG C 805 " - " ASN C 362 " " NAG C 806 " - " ASN C 386 " " NAG C 807 " - " ASN C 448 " " NAG C 808 " - " ASN C 611 " " NAG C 809 " - " ASN C 618 " " NAG D 1 " - " ASN A 154 " " NAG E 1 " - " ASN A 241 " " NAG F 1 " - " ASN A 262 " " NAG G 1 " - " ASN A 276 " " NAG H 1 " - " ASN A 332 " " NAG I 1 " - " ASN A 392 " " NAG J 1 " - " ASN B 154 " " NAG K 1 " - " ASN B 241 " " NAG L 1 " - " ASN B 262 " " NAG M 1 " - " ASN B 276 " " NAG N 1 " - " ASN B 332 " " NAG O 1 " - " ASN B 392 " " NAG P 1 " - " ASN C 154 " " NAG Q 1 " - " ASN C 241 " " NAG R 1 " - " ASN C 262 " " NAG S 1 " - " ASN C 276 " " NAG T 1 " - " ASN C 332 " " NAG U 1 " - " ASN C 392 " Time building additional restraints: 4.95 Conformation dependent library (CDL) restraints added in 2.6 seconds 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3174 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 21 sheets defined 25.9% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.00 Creating SS restraints... Processing helix chain 'A' and resid 68 through 72 removed outlier: 3.706A pdb=" N THR A 71 " --> pdb=" O VAL A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 115 removed outlier: 4.218A pdb=" N ASP A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 335 through 351 removed outlier: 3.638A pdb=" N GLU A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LYS A 351 " --> pdb=" O ILE A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 475 through 483 removed outlier: 3.775A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 536 through 543 removed outlier: 4.180A pdb=" N GLN A 540 " --> pdb=" O THR A 536 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASN A 543 " --> pdb=" O VAL A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 596 removed outlier: 4.299A pdb=" N GLN A 575 " --> pdb=" O TRP A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 624 Processing helix chain 'A' and resid 627 through 636 Processing helix chain 'A' and resid 638 through 661 removed outlier: 3.703A pdb=" N ILE A 642 " --> pdb=" O TYR A 638 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR A 643 " --> pdb=" O THR A 639 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLY A 644 " --> pdb=" O GLN A 640 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU A 645 " --> pdb=" O ILE A 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 72 Processing helix chain 'B' and resid 98 through 115 removed outlier: 4.218A pdb=" N ASP B 102 " --> pdb=" O ASN B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 126 Processing helix chain 'B' and resid 195 through 198 Processing helix chain 'B' and resid 335 through 351 removed outlier: 3.638A pdb=" N GLU B 348 " --> pdb=" O LYS B 344 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LYS B 351 " --> pdb=" O ILE B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 373 Processing helix chain 'B' and resid 475 through 483 removed outlier: 3.775A pdb=" N TRP B 479 " --> pdb=" O MET B 475 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU B 482 " --> pdb=" O ASN B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 543 removed outlier: 4.180A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 596 removed outlier: 4.435A pdb=" N GLN B 575 " --> pdb=" O TRP B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 638 through 661 removed outlier: 3.702A pdb=" N ILE B 642 " --> pdb=" O TYR B 638 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR B 643 " --> pdb=" O THR B 639 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU B 645 " --> pdb=" O ILE B 641 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 72 Processing helix chain 'C' and resid 98 through 115 removed outlier: 4.218A pdb=" N ASP C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 335 through 351 removed outlier: 3.638A pdb=" N GLU C 348 " --> pdb=" O LYS C 344 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LYS C 351 " --> pdb=" O ILE C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 475 through 483 removed outlier: 3.776A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 534 Processing helix chain 'C' and resid 536 through 543 removed outlier: 4.180A pdb=" N GLN C 540 " --> pdb=" O THR C 536 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASN C 543 " --> pdb=" O VAL C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 596 removed outlier: 4.372A pdb=" N GLN C 575 " --> pdb=" O TRP C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 624 Processing helix chain 'C' and resid 627 through 636 Processing helix chain 'C' and resid 638 through 661 removed outlier: 3.702A pdb=" N ILE C 642 " --> pdb=" O TYR C 638 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TYR C 643 " --> pdb=" O THR C 639 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLY C 644 " --> pdb=" O GLN C 640 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU C 645 " --> pdb=" O ILE C 641 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.458A pdb=" N VAL A 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N VAL A 38 " --> pdb=" O THR A 606 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N THR A 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N TYR A 40 " --> pdb=" O CYS A 604 " (cutoff:3.500A) removed outlier: 8.390A pdb=" N CYS A 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.023A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.537A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 167 through 175 removed outlier: 10.285A pdb=" N GLU A 150 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 11.883A pdb=" N VAL A 136 " --> pdb=" O GLU A 150 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N MET A 152 " --> pdb=" O ALA A 134 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA A 134 " --> pdb=" O MET A 152 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.660A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 284 through 308 removed outlier: 3.939A pdb=" N ASP A 321A" --> pdb=" O THR A 303 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N LYS A 305 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N THR A 320 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N VAL A 307 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N TYR A 318 " --> pdb=" O VAL A 307 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 316 through 322 current: chain 'A' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 381 through 385 current: chain 'A' and resid 465 through 470 Processing sheet with id=AA8, first strand: chain 'B' and resid 494 through 499 removed outlier: 5.457A pdb=" N VAL B 608 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N VAL B 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N THR B 606 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N TYR B 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.390A pdb=" N CYS B 604 " --> pdb=" O TYR B 40 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 45 through 47 removed outlier: 4.022A pdb=" N ILE B 225 " --> pdb=" O VAL B 245 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 75 through 76 Processing sheet with id=AB2, first strand: chain 'B' and resid 91 through 94 removed outlier: 3.536A pdb=" N GLU B 91 " --> pdb=" O CYS B 239 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 167 through 175 removed outlier: 10.285A pdb=" N GLU B 150 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 11.883A pdb=" N VAL B 136 " --> pdb=" O GLU B 150 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N MET B 152 " --> pdb=" O ALA B 134 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA B 134 " --> pdb=" O MET B 152 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 202 through 203 removed outlier: 6.660A pdb=" N THR B 202 " --> pdb=" O TYR B 435 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 259 through 261 current: chain 'B' and resid 284 through 308 removed outlier: 3.939A pdb=" N ASP B 321A" --> pdb=" O THR B 303 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N LYS B 305 " --> pdb=" O THR B 320 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N THR B 320 " --> pdb=" O LYS B 305 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N VAL B 307 " --> pdb=" O TYR B 318 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N TYR B 318 " --> pdb=" O VAL B 307 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 316 through 322 current: chain 'B' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 381 through 385 current: chain 'B' and resid 465 through 470 Processing sheet with id=AB6, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.459A pdb=" N VAL C 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N VAL C 38 " --> pdb=" O THR C 606 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N THR C 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N TYR C 40 " --> pdb=" O CYS C 604 " (cutoff:3.500A) removed outlier: 8.389A pdb=" N CYS C 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.026A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 75 through 76 Processing sheet with id=AB9, first strand: chain 'C' and resid 91 through 94 removed outlier: 3.537A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 167 through 175 removed outlier: 10.285A pdb=" N GLU C 150 " --> pdb=" O VAL C 136 " (cutoff:3.500A) removed outlier: 11.884A pdb=" N VAL C 136 " --> pdb=" O GLU C 150 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N MET C 152 " --> pdb=" O ALA C 134 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA C 134 " --> pdb=" O MET C 152 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 202 through 203 removed outlier: 6.660A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 259 through 261 current: chain 'C' and resid 284 through 308 removed outlier: 3.939A pdb=" N ASP C 321A" --> pdb=" O THR C 303 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N LYS C 305 " --> pdb=" O THR C 320 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N THR C 320 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N VAL C 307 " --> pdb=" O TYR C 318 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N TYR C 318 " --> pdb=" O VAL C 307 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 316 through 322 current: chain 'C' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 381 through 385 current: chain 'C' and resid 465 through 470 391 hydrogen bonds defined for protein. 1092 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: 8.83 Time building geometry restraints manager: 5.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4158 1.34 - 1.46: 2182 1.46 - 1.58: 7970 1.58 - 1.70: 0 1.70 - 1.82: 138 Bond restraints: 14448 Sorted by residual: bond pdb=" C4 NAG U 1 " pdb=" O4 NAG U 1 " ideal model delta sigma weight residual 1.409 1.488 -0.079 2.00e-02 2.50e+03 1.57e+01 bond pdb=" C4 NAG I 1 " pdb=" O4 NAG I 1 " ideal model delta sigma weight residual 1.409 1.488 -0.079 2.00e-02 2.50e+03 1.56e+01 bond pdb=" C4 NAG O 1 " pdb=" O4 NAG O 1 " ideal model delta sigma weight residual 1.409 1.487 -0.078 2.00e-02 2.50e+03 1.53e+01 bond pdb=" C4 NAG G 1 " pdb=" O4 NAG G 1 " ideal model delta sigma weight residual 1.409 1.486 -0.077 2.00e-02 2.50e+03 1.50e+01 bond pdb=" C4 NAG S 1 " pdb=" O4 NAG S 1 " ideal model delta sigma weight residual 1.409 1.486 -0.077 2.00e-02 2.50e+03 1.49e+01 ... (remaining 14443 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 10821 1.34 - 2.69: 6052 2.69 - 4.03: 2254 4.03 - 5.37: 401 5.37 - 6.72: 104 Bond angle restraints: 19632 Sorted by residual: angle pdb=" C ASP A 78 " pdb=" CA ASP A 78 " pdb=" CB ASP A 78 " ideal model delta sigma weight residual 111.20 116.25 -5.05 7.10e-01 1.98e+00 5.05e+01 angle pdb=" C ASP C 78 " pdb=" CA ASP C 78 " pdb=" CB ASP C 78 " ideal model delta sigma weight residual 111.20 115.14 -3.94 7.10e-01 1.98e+00 3.08e+01 angle pdb=" CA ASN B 234 " pdb=" CB ASN B 234 " pdb=" CG ASN B 234 " ideal model delta sigma weight residual 112.60 118.14 -5.54 1.00e+00 1.00e+00 3.07e+01 angle pdb=" C ASP B 78 " pdb=" CA ASP B 78 " pdb=" CB ASP B 78 " ideal model delta sigma weight residual 111.20 115.14 -3.94 7.10e-01 1.98e+00 3.07e+01 angle pdb=" CA ASN A 234 " pdb=" CB ASN A 234 " pdb=" CG ASN A 234 " ideal model delta sigma weight residual 112.60 118.14 -5.54 1.00e+00 1.00e+00 3.07e+01 ... (remaining 19627 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 8856 17.68 - 35.36: 523 35.36 - 53.03: 151 53.03 - 70.71: 23 70.71 - 88.39: 14 Dihedral angle restraints: 9567 sinusoidal: 4668 harmonic: 4899 Sorted by residual: dihedral pdb=" CB CYS B 228 " pdb=" SG CYS B 228 " pdb=" SG CYS B 239 " pdb=" CB CYS B 239 " ideal model delta sinusoidal sigma weight residual -86.00 -144.72 58.72 1 1.00e+01 1.00e-02 4.62e+01 dihedral pdb=" CB CYS C 228 " pdb=" SG CYS C 228 " pdb=" SG CYS C 239 " pdb=" CB CYS C 239 " ideal model delta sinusoidal sigma weight residual -86.00 -144.72 58.72 1 1.00e+01 1.00e-02 4.62e+01 dihedral pdb=" CB CYS A 228 " pdb=" SG CYS A 228 " pdb=" SG CYS A 239 " pdb=" CB CYS A 239 " ideal model delta sinusoidal sigma weight residual -86.00 -144.72 58.72 1 1.00e+01 1.00e-02 4.62e+01 ... (remaining 9564 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1147 0.068 - 0.136: 800 0.136 - 0.204: 337 0.204 - 0.272: 116 0.272 - 0.339: 18 Chirality restraints: 2418 Sorted by residual: chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 9.90e+01 chirality pdb=" C1 NAG T 2 " pdb=" O4 NAG T 1 " pdb=" C2 NAG T 2 " pdb=" O5 NAG T 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 9.86e+01 chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 9.80e+01 ... (remaining 2415 not shown) Planarity restraints: 2466 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 618 " 0.192 2.00e-02 2.50e+03 1.81e-01 4.08e+02 pdb=" CG ASN B 618 " -0.075 2.00e-02 2.50e+03 pdb=" OD1 ASN B 618 " -0.091 2.00e-02 2.50e+03 pdb=" ND2 ASN B 618 " -0.250 2.00e-02 2.50e+03 pdb=" C1 NAG B 809 " 0.224 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 618 " 0.192 2.00e-02 2.50e+03 1.81e-01 4.08e+02 pdb=" CG ASN C 618 " -0.075 2.00e-02 2.50e+03 pdb=" OD1 ASN C 618 " -0.091 2.00e-02 2.50e+03 pdb=" ND2 ASN C 618 " -0.250 2.00e-02 2.50e+03 pdb=" C1 NAG C 809 " 0.224 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 618 " 0.192 2.00e-02 2.50e+03 1.81e-01 4.08e+02 pdb=" CG ASN A 618 " -0.075 2.00e-02 2.50e+03 pdb=" OD1 ASN A 618 " -0.091 2.00e-02 2.50e+03 pdb=" ND2 ASN A 618 " -0.250 2.00e-02 2.50e+03 pdb=" C1 NAG A 809 " 0.224 2.00e-02 2.50e+03 ... (remaining 2463 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.38: 12 2.38 - 3.01: 7162 3.01 - 3.64: 19015 3.64 - 4.27: 30204 4.27 - 4.90: 47392 Nonbonded interactions: 103785 Sorted by model distance: nonbonded pdb=" O CYS A 196 " pdb=" CB GLU B 162 " model vdw 1.755 3.440 nonbonded pdb=" CB GLU A 162 " pdb=" O CYS C 196 " model vdw 1.760 3.440 nonbonded pdb=" O CYS B 196 " pdb=" CB GLU C 162 " model vdw 1.762 3.440 nonbonded pdb=" O CYS A 196 " pdb=" CG GLU B 162 " model vdw 2.083 3.440 nonbonded pdb=" CG GLU A 162 " pdb=" O CYS C 196 " model vdw 2.086 3.440 ... (remaining 103780 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' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 86.440 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: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 45.720 Find NCS groups from input model: 1.100 Set up NCS constraints: 0.130 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:4.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 139.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 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 : 0.014 0.261 14547 Z= 0.809 Angle : 1.894 19.222 19893 Z= 1.202 Chirality : 0.105 0.339 2418 Planarity : 0.013 0.083 2421 Dihedral : 12.696 88.387 6285 Min Nonbonded Distance : 1.755 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 0.47 % Allowed : 5.67 % Favored : 93.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.18), residues: 1656 helix: -0.84 (0.23), residues: 351 sheet: 1.08 (0.26), residues: 345 loop : -1.18 (0.17), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.129 0.030 TRP C 610 HIS 0.011 0.003 HIS C 216 PHE 0.082 0.017 PHE B 233 TYR 0.138 0.023 TYR C 361 ARG 0.007 0.001 ARG A 585 Details of bonding type rmsd link_NAG-ASN : bond 0.06780 ( 45) link_NAG-ASN : angle 6.12498 ( 135) link_BETA1-4 : bond 0.02967 ( 18) link_BETA1-4 : angle 5.99643 ( 54) hydrogen bonds : bond 0.18548 ( 391) hydrogen bonds : angle 6.92144 ( 1092) SS BOND : bond 0.01350 ( 36) SS BOND : angle 1.77325 ( 72) covalent geometry : bond 0.01396 (14448) covalent geometry : angle 1.80780 (19632) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 530 time to evaluate : 1.618 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.7290 (m100) cc_final: 0.6999 (m100) REVERT: A 42 VAL cc_start: 0.8247 (t) cc_final: 0.7761 (p) REVERT: A 46 LYS cc_start: 0.7871 (mmmt) cc_final: 0.7599 (mmmt) REVERT: A 49 LYS cc_start: 0.7763 (OUTLIER) cc_final: 0.7531 (pttm) REVERT: A 53 PHE cc_start: 0.7594 (p90) cc_final: 0.7051 (p90) REVERT: A 69 TRP cc_start: 0.7276 (m-90) cc_final: 0.6158 (m-90) REVERT: A 88 ASN cc_start: 0.7939 (m110) cc_final: 0.7720 (m-40) REVERT: A 98 ASN cc_start: 0.7823 (t0) cc_final: 0.7613 (t0) REVERT: A 99 ASP cc_start: 0.7534 (m-30) cc_final: 0.7216 (m-30) REVERT: A 102 ASP cc_start: 0.7739 (t70) cc_final: 0.7330 (t0) REVERT: A 104 MET cc_start: 0.7962 (ttt) cc_final: 0.7677 (ttm) REVERT: A 106 GLU cc_start: 0.7565 (tp30) cc_final: 0.7285 (tp30) REVERT: A 113 ASP cc_start: 0.7394 (t0) cc_final: 0.6915 (t0) REVERT: A 117 LYS cc_start: 0.8521 (ttmm) cc_final: 0.8109 (ttmm) REVERT: A 150 GLU cc_start: 0.7636 (tp30) cc_final: 0.7335 (tp30) REVERT: A 166 LYS cc_start: 0.7868 (mmmt) cc_final: 0.7456 (mmmt) REVERT: A 199 SER cc_start: 0.7809 (m) cc_final: 0.7487 (t) REVERT: A 223 TYR cc_start: 0.8157 (m-80) cc_final: 0.7881 (m-80) REVERT: A 245 VAL cc_start: 0.8674 (t) cc_final: 0.8407 (p) REVERT: A 258 GLN cc_start: 0.8253 (mt0) cc_final: 0.8039 (mt0) REVERT: A 264 SER cc_start: 0.8165 (m) cc_final: 0.7541 (p) REVERT: A 269 GLU cc_start: 0.8100 (tt0) cc_final: 0.7872 (tt0) REVERT: A 301 ASN cc_start: 0.7705 (t0) cc_final: 0.7502 (t0) REVERT: A 302 ASN cc_start: 0.8568 (m-40) cc_final: 0.8235 (m110) REVERT: A 321 ASP cc_start: 0.7174 (t0) cc_final: 0.6958 (t0) REVERT: A 327 LYS cc_start: 0.7954 (tptp) cc_final: 0.7727 (tptp) REVERT: A 343 GLN cc_start: 0.7618 (tt0) cc_final: 0.7304 (tt0) REVERT: A 414 ILE cc_start: 0.8354 (tp) cc_final: 0.8150 (tp) REVERT: A 420 ILE cc_start: 0.8425 (mt) cc_final: 0.8145 (mm) REVERT: A 421 LYS cc_start: 0.8622 (mtpt) cc_final: 0.8402 (mtpp) REVERT: A 468 PHE cc_start: 0.7650 (m-80) cc_final: 0.7325 (m-10) REVERT: A 482 GLU cc_start: 0.7523 (mm-30) cc_final: 0.6721 (mm-30) REVERT: A 487 LYS cc_start: 0.8294 (tttt) cc_final: 0.7599 (tttt) REVERT: A 500 ARG cc_start: 0.6917 (mtp85) cc_final: 0.6595 (mtp180) REVERT: A 535 MET cc_start: 0.7066 (tpp) cc_final: 0.6564 (tpp) REVERT: A 646 LEU cc_start: 0.8210 (mt) cc_final: 0.7915 (mm) REVERT: A 647 GLU cc_start: 0.7608 (tm-30) cc_final: 0.7189 (tm-30) REVERT: A 656 ASN cc_start: 0.7821 (t0) cc_final: 0.7404 (t0) REVERT: B 35 TRP cc_start: 0.7254 (m100) cc_final: 0.6543 (m100) REVERT: B 42 VAL cc_start: 0.8349 (t) cc_final: 0.7856 (p) REVERT: B 47 GLU cc_start: 0.7200 (tt0) cc_final: 0.6836 (tt0) REVERT: B 50 THR cc_start: 0.8438 (m) cc_final: 0.8200 (p) REVERT: B 93 PHE cc_start: 0.8012 (m-80) cc_final: 0.7795 (m-80) REVERT: B 97 LYS cc_start: 0.8181 (tppt) cc_final: 0.7401 (tppt) REVERT: B 103 GLN cc_start: 0.7882 (tp40) cc_final: 0.7497 (tm-30) REVERT: B 104 MET cc_start: 0.7794 (ttt) cc_final: 0.7385 (ttm) REVERT: B 106 GLU cc_start: 0.7353 (tp30) cc_final: 0.6876 (tp30) REVERT: B 113 ASP cc_start: 0.7412 (t0) cc_final: 0.6736 (t70) REVERT: B 169 LYS cc_start: 0.8007 (tttp) cc_final: 0.7711 (tttp) REVERT: B 205 CYS cc_start: 0.5873 (m) cc_final: 0.5639 (m) REVERT: B 234 ASN cc_start: 0.7538 (t0) cc_final: 0.7208 (t0) REVERT: B 245 VAL cc_start: 0.8574 (t) cc_final: 0.8341 (p) REVERT: B 293 GLU cc_start: 0.7572 (tt0) cc_final: 0.7081 (tt0) REVERT: B 301 ASN cc_start: 0.7762 (t0) cc_final: 0.7483 (t0) REVERT: B 302 ASN cc_start: 0.8556 (m-40) cc_final: 0.8273 (m110) REVERT: B 420 ILE cc_start: 0.8463 (mt) cc_final: 0.8197 (mm) REVERT: B 427 TRP cc_start: 0.7633 (m-90) cc_final: 0.7404 (m-10) REVERT: B 432 ARG cc_start: 0.6973 (mtt90) cc_final: 0.6640 (mtt90) REVERT: B 447 SER cc_start: 0.8286 (m) cc_final: 0.7955 (p) REVERT: B 487 LYS cc_start: 0.8200 (tttt) cc_final: 0.7378 (tttt) REVERT: B 490 LYS cc_start: 0.7892 (ttpt) cc_final: 0.7561 (ttpt) REVERT: B 535 MET cc_start: 0.6940 (tpp) cc_final: 0.6570 (tpp) REVERT: B 536 THR cc_start: 0.8410 (t) cc_final: 0.8152 (p) REVERT: B 591 GLN cc_start: 0.8312 (tt0) cc_final: 0.8018 (tt0) REVERT: B 634 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7945 (mt-10) REVERT: B 640 GLN cc_start: 0.8945 (tp40) cc_final: 0.8340 (tp-100) REVERT: B 650 GLN cc_start: 0.7970 (tp40) cc_final: 0.7342 (tp40) REVERT: B 652 GLN cc_start: 0.7629 (tm-30) cc_final: 0.7336 (tm-30) REVERT: B 656 ASN cc_start: 0.7755 (t0) cc_final: 0.7374 (t0) REVERT: B 657 GLU cc_start: 0.7484 (tp30) cc_final: 0.7184 (tp30) REVERT: C 35 TRP cc_start: 0.7293 (m100) cc_final: 0.7083 (m100) REVERT: C 42 VAL cc_start: 0.8318 (t) cc_final: 0.7899 (p) REVERT: C 47 GLU cc_start: 0.7290 (tt0) cc_final: 0.6905 (tt0) REVERT: C 53 PHE cc_start: 0.7586 (p90) cc_final: 0.7369 (p90) REVERT: C 86 LEU cc_start: 0.8563 (mp) cc_final: 0.8318 (mm) REVERT: C 92 ASN cc_start: 0.7736 (p0) cc_final: 0.7319 (p0) REVERT: C 102 ASP cc_start: 0.7708 (t70) cc_final: 0.7381 (t0) REVERT: C 103 GLN cc_start: 0.8056 (tp40) cc_final: 0.7609 (tm-30) REVERT: C 104 MET cc_start: 0.7848 (ttt) cc_final: 0.7611 (ttp) REVERT: C 113 ASP cc_start: 0.7405 (t0) cc_final: 0.7127 (t70) REVERT: C 164 ARG cc_start: 0.7040 (ttp80) cc_final: 0.6810 (ttp-170) REVERT: C 171 TYR cc_start: 0.7769 (p90) cc_final: 0.7494 (p90) REVERT: C 223 TYR cc_start: 0.7925 (m-80) cc_final: 0.7529 (m-80) REVERT: C 258 GLN cc_start: 0.8412 (mt0) cc_final: 0.8204 (mt0) REVERT: C 273 ARG cc_start: 0.7803 (mtt90) cc_final: 0.7549 (mtt-85) REVERT: C 279 ASN cc_start: 0.8223 (t0) cc_final: 0.7685 (t0) REVERT: C 301 ASN cc_start: 0.7790 (t0) cc_final: 0.7469 (t0) REVERT: C 327 LYS cc_start: 0.8016 (tptp) cc_final: 0.7811 (tptp) REVERT: C 414 ILE cc_start: 0.8473 (tp) cc_final: 0.8252 (tp) REVERT: C 420 ILE cc_start: 0.8516 (mt) cc_final: 0.8249 (mm) REVERT: C 427 TRP cc_start: 0.7676 (m-90) cc_final: 0.7280 (m-10) REVERT: C 443 ILE cc_start: 0.7757 (mt) cc_final: 0.7532 (mm) REVERT: C 447 SER cc_start: 0.8388 (m) cc_final: 0.8131 (p) REVERT: C 484 TYR cc_start: 0.8467 (p90) cc_final: 0.8036 (p90) REVERT: C 487 LYS cc_start: 0.8148 (tttt) cc_final: 0.7158 (tttt) REVERT: C 500 ARG cc_start: 0.6921 (mtp85) cc_final: 0.6640 (mtp180) REVERT: C 575 GLN cc_start: 0.7852 (mm-40) cc_final: 0.7517 (mm-40) REVERT: C 634 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7833 (mt-10) REVERT: C 640 GLN cc_start: 0.9048 (tp40) cc_final: 0.8531 (tp-100) REVERT: C 647 GLU cc_start: 0.7639 (tm-30) cc_final: 0.7421 (tp30) REVERT: C 656 ASN cc_start: 0.7762 (t0) cc_final: 0.7477 (t0) REVERT: C 657 GLU cc_start: 0.7607 (tp30) cc_final: 0.6905 (tp30) outliers start: 7 outliers final: 2 residues processed: 533 average time/residue: 0.3275 time to fit residues: 245.6141 Evaluate side-chains 437 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 434 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LYS Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain C residue 49 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 0.6980 chunk 127 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 43 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 131 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 80 optimal weight: 0.5980 chunk 98 optimal weight: 0.9980 chunk 152 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN A 229 ASN A 315 GLN A 350 GLN A 363 GLN A 374 HIS A 575 GLN A 630 GLN B 88 ASN B 114 GLN B 315 GLN B 374 HIS B 575 GLN B 630 GLN B 658 GLN C 229 ASN C 315 GLN C 328 GLN C 350 GLN C 363 GLN C 463 ASN C 478 ASN C 630 GLN C 658 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.124738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.103853 restraints weight = 21356.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.107984 restraints weight = 11708.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.110819 restraints weight = 7800.769| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 14547 Z= 0.153 Angle : 0.787 9.302 19893 Z= 0.386 Chirality : 0.051 0.317 2418 Planarity : 0.004 0.051 2421 Dihedral : 8.563 59.488 3126 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.23 % Favored : 97.71 % Rotamer: Outliers : 2.60 % Allowed : 10.00 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.19), residues: 1656 helix: 0.65 (0.26), residues: 375 sheet: 1.30 (0.25), residues: 339 loop : -1.10 (0.18), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 628 HIS 0.003 0.001 HIS B 216 PHE 0.022 0.002 PHE C 53 TYR 0.022 0.001 TYR C 191 ARG 0.006 0.001 ARG A 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00468 ( 45) link_NAG-ASN : angle 3.34550 ( 135) link_BETA1-4 : bond 0.00971 ( 18) link_BETA1-4 : angle 3.25621 ( 54) hydrogen bonds : bond 0.04870 ( 391) hydrogen bonds : angle 4.72132 ( 1092) SS BOND : bond 0.00320 ( 36) SS BOND : angle 1.96407 ( 72) covalent geometry : bond 0.00335 (14448) covalent geometry : angle 0.71257 (19632) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 454 time to evaluate : 1.381 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 PHE cc_start: 0.7472 (p90) cc_final: 0.7072 (p90) REVERT: A 69 TRP cc_start: 0.7103 (m-90) cc_final: 0.6146 (m-90) REVERT: A 88 ASN cc_start: 0.8022 (m110) cc_final: 0.7821 (m-40) REVERT: A 96 TRP cc_start: 0.8090 (m100) cc_final: 0.7322 (m100) REVERT: A 102 ASP cc_start: 0.7569 (t70) cc_final: 0.7180 (t0) REVERT: A 104 MET cc_start: 0.8058 (ttt) cc_final: 0.7688 (ttt) REVERT: A 106 GLU cc_start: 0.7524 (tp30) cc_final: 0.7203 (tp30) REVERT: A 113 ASP cc_start: 0.7534 (t0) cc_final: 0.7200 (t0) REVERT: A 165 ASP cc_start: 0.7016 (t0) cc_final: 0.6795 (t0) REVERT: A 166 LYS cc_start: 0.7806 (mmmt) cc_final: 0.7550 (mmmt) REVERT: A 198 THR cc_start: 0.8307 (t) cc_final: 0.8047 (t) REVERT: A 264 SER cc_start: 0.8265 (m) cc_final: 0.7676 (p) REVERT: A 269 GLU cc_start: 0.8045 (tt0) cc_final: 0.7787 (tt0) REVERT: A 344 LYS cc_start: 0.8245 (ttmm) cc_final: 0.7998 (ttmm) REVERT: A 374 HIS cc_start: 0.8443 (OUTLIER) cc_final: 0.8099 (t-170) REVERT: A 420 ILE cc_start: 0.8352 (mt) cc_final: 0.8129 (mm) REVERT: A 468 PHE cc_start: 0.7601 (m-80) cc_final: 0.7368 (m-10) REVERT: A 482 GLU cc_start: 0.7633 (mm-30) cc_final: 0.6828 (mm-30) REVERT: A 535 MET cc_start: 0.6956 (tpp) cc_final: 0.6541 (tpp) REVERT: A 647 GLU cc_start: 0.7509 (tm-30) cc_final: 0.7306 (tm-30) REVERT: A 656 ASN cc_start: 0.7792 (t0) cc_final: 0.7357 (t0) REVERT: B 44 VAL cc_start: 0.8951 (p) cc_final: 0.8610 (m) REVERT: B 50 THR cc_start: 0.8498 (m) cc_final: 0.8265 (m) REVERT: B 53 PHE cc_start: 0.7179 (p90) cc_final: 0.6849 (p90) REVERT: B 82 GLN cc_start: 0.7201 (tp40) cc_final: 0.6730 (tp40) REVERT: B 97 LYS cc_start: 0.7957 (tppt) cc_final: 0.7242 (tppt) REVERT: B 104 MET cc_start: 0.7864 (ttt) cc_final: 0.7556 (ttt) REVERT: B 106 GLU cc_start: 0.7356 (tp30) cc_final: 0.6609 (tp30) REVERT: B 113 ASP cc_start: 0.7595 (t0) cc_final: 0.7076 (t70) REVERT: B 202 THR cc_start: 0.8269 (p) cc_final: 0.7986 (p) REVERT: B 234 ASN cc_start: 0.7474 (t0) cc_final: 0.7121 (t0) REVERT: B 245 VAL cc_start: 0.8453 (OUTLIER) cc_final: 0.8249 (p) REVERT: B 268 LYS cc_start: 0.8498 (pptt) cc_final: 0.8248 (pptt) REVERT: B 280 ASN cc_start: 0.8012 (p0) cc_final: 0.7671 (p0) REVERT: B 297 THR cc_start: 0.8675 (t) cc_final: 0.8435 (p) REVERT: B 432 ARG cc_start: 0.6888 (mtt90) cc_final: 0.6531 (mtt90) REVERT: B 447 SER cc_start: 0.8292 (m) cc_final: 0.7972 (p) REVERT: B 487 LYS cc_start: 0.8194 (tttt) cc_final: 0.7666 (tttt) REVERT: B 490 LYS cc_start: 0.7754 (ttpt) cc_final: 0.7526 (ttpt) REVERT: B 535 MET cc_start: 0.6878 (tpp) cc_final: 0.6621 (tpp) REVERT: B 538 THR cc_start: 0.8207 (p) cc_final: 0.7968 (m) REVERT: B 590 GLN cc_start: 0.8127 (mm-40) cc_final: 0.7892 (mm-40) REVERT: B 656 ASN cc_start: 0.7624 (t0) cc_final: 0.7275 (t0) REVERT: B 657 GLU cc_start: 0.7448 (tp30) cc_final: 0.7213 (tp30) REVERT: C 82 GLN cc_start: 0.7178 (tp40) cc_final: 0.6645 (tp40) REVERT: C 92 ASN cc_start: 0.7605 (p0) cc_final: 0.7284 (p0) REVERT: C 106 GLU cc_start: 0.7337 (tp30) cc_final: 0.6975 (tp30) REVERT: C 121 LYS cc_start: 0.8698 (mttt) cc_final: 0.8315 (mttm) REVERT: C 150 GLU cc_start: 0.7322 (tp30) cc_final: 0.7117 (tp30) REVERT: C 166 LYS cc_start: 0.7910 (mmmt) cc_final: 0.7577 (mmmt) REVERT: C 171 TYR cc_start: 0.7953 (p90) cc_final: 0.7572 (p90) REVERT: C 223 TYR cc_start: 0.8094 (m-80) cc_final: 0.7875 (m-10) REVERT: C 302 ASN cc_start: 0.8625 (m-40) cc_final: 0.8400 (m110) REVERT: C 347 ILE cc_start: 0.8481 (tp) cc_final: 0.8248 (mt) REVERT: C 395 TYR cc_start: 0.7410 (t80) cc_final: 0.7119 (t80) REVERT: C 427 TRP cc_start: 0.7733 (m-90) cc_final: 0.7523 (m-10) REVERT: C 434 MET cc_start: 0.7087 (ttm) cc_final: 0.6789 (ttp) REVERT: C 447 SER cc_start: 0.8408 (m) cc_final: 0.8182 (p) REVERT: C 482 GLU cc_start: 0.7727 (mm-30) cc_final: 0.7315 (mm-30) REVERT: C 656 ASN cc_start: 0.7818 (t0) cc_final: 0.7445 (t0) REVERT: C 657 GLU cc_start: 0.7509 (tp30) cc_final: 0.6789 (tp30) outliers start: 39 outliers final: 19 residues processed: 472 average time/residue: 0.2854 time to fit residues: 189.1496 Evaluate side-chains 438 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 417 time to evaluate : 1.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 628 TRP Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 576 LEU Chi-restraints excluded: chain C residue 628 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 31 optimal weight: 0.9990 chunk 100 optimal weight: 6.9990 chunk 166 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 156 optimal weight: 4.9990 chunk 29 optimal weight: 0.0470 chunk 75 optimal weight: 2.9990 chunk 129 optimal weight: 0.0060 chunk 53 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS A 302 ASN A 315 GLN A 363 GLN A 374 HIS B 229 ASN B 302 ASN B 363 GLN B 374 HIS C 72 HIS C 114 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.124548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.103828 restraints weight = 21675.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.107962 restraints weight = 11935.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.110750 restraints weight = 7968.576| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 14547 Z= 0.133 Angle : 0.718 9.026 19893 Z= 0.351 Chirality : 0.048 0.320 2418 Planarity : 0.004 0.051 2421 Dihedral : 7.962 59.611 3122 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.73 % Allowed : 14.33 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.20), residues: 1656 helix: 1.09 (0.27), residues: 369 sheet: 1.18 (0.24), residues: 375 loop : -0.91 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 35 HIS 0.007 0.001 HIS B 374 PHE 0.026 0.002 PHE C 53 TYR 0.017 0.001 TYR A 191 ARG 0.005 0.000 ARG B 456 Details of bonding type rmsd link_NAG-ASN : bond 0.00444 ( 45) link_NAG-ASN : angle 2.86763 ( 135) link_BETA1-4 : bond 0.00956 ( 18) link_BETA1-4 : angle 2.98422 ( 54) hydrogen bonds : bond 0.04180 ( 391) hydrogen bonds : angle 4.47589 ( 1092) SS BOND : bond 0.00445 ( 36) SS BOND : angle 2.46631 ( 72) covalent geometry : bond 0.00297 (14448) covalent geometry : angle 0.64702 (19632) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 436 time to evaluate : 1.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 PHE cc_start: 0.7397 (p90) cc_final: 0.6969 (p90) REVERT: A 67 ASN cc_start: 0.7331 (t0) cc_final: 0.7114 (t0) REVERT: A 69 TRP cc_start: 0.7078 (m-90) cc_final: 0.6457 (m-90) REVERT: A 104 MET cc_start: 0.8035 (ttt) cc_final: 0.7795 (ttt) REVERT: A 106 GLU cc_start: 0.7491 (tp30) cc_final: 0.7252 (tp30) REVERT: A 117 LYS cc_start: 0.8487 (ttmm) cc_final: 0.8030 (ttmm) REVERT: A 150 GLU cc_start: 0.7463 (tp30) cc_final: 0.7116 (tp30) REVERT: A 165 ASP cc_start: 0.6953 (t0) cc_final: 0.6746 (t0) REVERT: A 166 LYS cc_start: 0.7764 (mmmt) cc_final: 0.7528 (mmmt) REVERT: A 178 ASP cc_start: 0.7817 (OUTLIER) cc_final: 0.7410 (t70) REVERT: A 198 THR cc_start: 0.8182 (t) cc_final: 0.7938 (t) REVERT: A 202 THR cc_start: 0.8139 (p) cc_final: 0.7878 (p) REVERT: A 223 TYR cc_start: 0.8227 (m-80) cc_final: 0.7753 (m-80) REVERT: A 264 SER cc_start: 0.8273 (m) cc_final: 0.7657 (p) REVERT: A 269 GLU cc_start: 0.7974 (tt0) cc_final: 0.7688 (tt0) REVERT: A 273 ARG cc_start: 0.8177 (mtt-85) cc_final: 0.7939 (mtt-85) REVERT: A 321 ASP cc_start: 0.7393 (t0) cc_final: 0.7144 (t70) REVERT: A 348 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7473 (mm-30) REVERT: A 447 SER cc_start: 0.8575 (m) cc_final: 0.8075 (p) REVERT: A 468 PHE cc_start: 0.7757 (m-80) cc_final: 0.7496 (m-10) REVERT: A 482 GLU cc_start: 0.7514 (mm-30) cc_final: 0.6710 (mm-30) REVERT: A 535 MET cc_start: 0.7102 (tpp) cc_final: 0.6625 (tpp) REVERT: A 647 GLU cc_start: 0.7495 (tm-30) cc_final: 0.7225 (tm-30) REVERT: A 654 GLU cc_start: 0.7897 (tp30) cc_final: 0.7620 (tp30) REVERT: A 656 ASN cc_start: 0.7851 (t0) cc_final: 0.7458 (t0) REVERT: B 44 VAL cc_start: 0.8980 (p) cc_final: 0.8662 (m) REVERT: B 53 PHE cc_start: 0.7249 (p90) cc_final: 0.6944 (p90) REVERT: B 69 TRP cc_start: 0.6873 (m-90) cc_final: 0.6379 (m-90) REVERT: B 104 MET cc_start: 0.7766 (ttt) cc_final: 0.7542 (ttt) REVERT: B 106 GLU cc_start: 0.7283 (tp30) cc_final: 0.6901 (tp30) REVERT: B 113 ASP cc_start: 0.7479 (t0) cc_final: 0.6613 (t70) REVERT: B 161 THR cc_start: 0.7569 (m) cc_final: 0.7350 (m) REVERT: B 202 THR cc_start: 0.8303 (p) cc_final: 0.8090 (p) REVERT: B 215 ILE cc_start: 0.8357 (mm) cc_final: 0.8120 (mm) REVERT: B 234 ASN cc_start: 0.7395 (t0) cc_final: 0.7090 (t0) REVERT: B 280 ASN cc_start: 0.8032 (p0) cc_final: 0.7644 (p0) REVERT: B 297 THR cc_start: 0.8686 (t) cc_final: 0.8278 (p) REVERT: B 321 ASP cc_start: 0.7493 (t0) cc_final: 0.7197 (t70) REVERT: B 446 ARG cc_start: 0.7605 (mtp85) cc_final: 0.7352 (mtp85) REVERT: B 447 SER cc_start: 0.8213 (m) cc_final: 0.7929 (p) REVERT: B 456 ARG cc_start: 0.7806 (OUTLIER) cc_final: 0.7358 (mtp85) REVERT: B 482 GLU cc_start: 0.7341 (mm-30) cc_final: 0.7094 (mm-30) REVERT: B 490 LYS cc_start: 0.7816 (ttpt) cc_final: 0.7601 (ttpt) REVERT: B 535 MET cc_start: 0.6970 (tpp) cc_final: 0.6650 (tpp) REVERT: B 656 ASN cc_start: 0.7646 (t0) cc_final: 0.7305 (t0) REVERT: B 657 GLU cc_start: 0.7446 (tp30) cc_final: 0.6880 (tp30) REVERT: C 53 PHE cc_start: 0.7325 (p90) cc_final: 0.7098 (p90) REVERT: C 93 PHE cc_start: 0.7661 (m-80) cc_final: 0.7323 (m-10) REVERT: C 96 TRP cc_start: 0.7631 (m-90) cc_final: 0.6864 (m100) REVERT: C 106 GLU cc_start: 0.7311 (tp30) cc_final: 0.7026 (tp30) REVERT: C 116 LEU cc_start: 0.7964 (mt) cc_final: 0.7593 (mp) REVERT: C 150 GLU cc_start: 0.7330 (tp30) cc_final: 0.7099 (tp30) REVERT: C 166 LYS cc_start: 0.7913 (mmmt) cc_final: 0.7622 (mmmt) REVERT: C 171 TYR cc_start: 0.7899 (p90) cc_final: 0.7533 (p90) REVERT: C 195 ASN cc_start: 0.7428 (p0) cc_final: 0.6703 (p0) REVERT: C 252 ARG cc_start: 0.8566 (mtt-85) cc_final: 0.8366 (mtt180) REVERT: C 301 ASN cc_start: 0.8087 (t0) cc_final: 0.7865 (t0) REVERT: C 302 ASN cc_start: 0.8631 (m-40) cc_final: 0.8393 (m-40) REVERT: C 417 GLN cc_start: 0.7866 (pt0) cc_final: 0.7392 (mt0) REVERT: C 427 TRP cc_start: 0.7636 (m-90) cc_final: 0.7367 (m-10) REVERT: C 482 GLU cc_start: 0.7619 (mm-30) cc_final: 0.7269 (mm-30) REVERT: C 626 MET cc_start: 0.7820 (OUTLIER) cc_final: 0.7436 (mtt) REVERT: C 656 ASN cc_start: 0.7904 (t0) cc_final: 0.7499 (t0) REVERT: C 657 GLU cc_start: 0.7523 (tp30) cc_final: 0.6827 (tp30) outliers start: 56 outliers final: 20 residues processed: 469 average time/residue: 0.3054 time to fit residues: 198.5404 Evaluate side-chains 437 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 414 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 456 ARG Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain C residue 576 LEU Chi-restraints excluded: chain C residue 626 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 58 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 142 optimal weight: 3.9990 chunk 3 optimal weight: 0.4980 chunk 125 optimal weight: 0.6980 chunk 71 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN B 105 HIS B 302 ASN B 363 GLN B 374 HIS B 625 ASN ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.122239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.101442 restraints weight = 21725.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.105493 restraints weight = 12114.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.108202 restraints weight = 8162.590| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 14547 Z= 0.245 Angle : 0.756 10.959 19893 Z= 0.373 Chirality : 0.051 0.415 2418 Planarity : 0.005 0.056 2421 Dihedral : 8.012 56.731 3122 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 4.07 % Allowed : 16.67 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.20), residues: 1656 helix: 1.02 (0.27), residues: 372 sheet: 1.21 (0.25), residues: 375 loop : -1.05 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 35 HIS 0.008 0.002 HIS B 216 PHE 0.025 0.003 PHE C 53 TYR 0.021 0.002 TYR A 638 ARG 0.004 0.000 ARG B 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00490 ( 45) link_NAG-ASN : angle 2.78636 ( 135) link_BETA1-4 : bond 0.00807 ( 18) link_BETA1-4 : angle 2.90059 ( 54) hydrogen bonds : bond 0.04765 ( 391) hydrogen bonds : angle 4.57065 ( 1092) SS BOND : bond 0.00603 ( 36) SS BOND : angle 2.82799 ( 72) covalent geometry : bond 0.00565 (14448) covalent geometry : angle 0.68786 (19632) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 442 time to evaluate : 1.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ASN cc_start: 0.7374 (t0) cc_final: 0.7124 (t0) REVERT: A 69 TRP cc_start: 0.7106 (m-90) cc_final: 0.6540 (m-90) REVERT: A 91 GLU cc_start: 0.6705 (mm-30) cc_final: 0.6464 (mm-30) REVERT: A 117 LYS cc_start: 0.8499 (ttmm) cc_final: 0.8088 (ttmm) REVERT: A 150 GLU cc_start: 0.7429 (tp30) cc_final: 0.7068 (tp30) REVERT: A 166 LYS cc_start: 0.7852 (mmmt) cc_final: 0.7575 (mmmt) REVERT: A 246 GLN cc_start: 0.7772 (tp40) cc_final: 0.7371 (tp40) REVERT: A 264 SER cc_start: 0.8284 (m) cc_final: 0.7668 (p) REVERT: A 321 ASP cc_start: 0.7410 (t0) cc_final: 0.7172 (t70) REVERT: A 447 SER cc_start: 0.8527 (m) cc_final: 0.7980 (p) REVERT: A 468 PHE cc_start: 0.7877 (m-80) cc_final: 0.7606 (m-10) REVERT: A 477 ASP cc_start: 0.7565 (m-30) cc_final: 0.7294 (m-30) REVERT: A 482 GLU cc_start: 0.7544 (mm-30) cc_final: 0.6743 (mm-30) REVERT: A 535 MET cc_start: 0.6910 (tpp) cc_final: 0.6607 (tpp) REVERT: A 647 GLU cc_start: 0.7591 (tm-30) cc_final: 0.7260 (tm-30) REVERT: A 654 GLU cc_start: 0.7900 (tp30) cc_final: 0.7623 (tp30) REVERT: A 656 ASN cc_start: 0.7896 (t0) cc_final: 0.7506 (t0) REVERT: B 44 VAL cc_start: 0.9037 (p) cc_final: 0.8747 (m) REVERT: B 53 PHE cc_start: 0.7255 (p90) cc_final: 0.7050 (p90) REVERT: B 104 MET cc_start: 0.7835 (ttt) cc_final: 0.7575 (ttt) REVERT: B 106 GLU cc_start: 0.7331 (tp30) cc_final: 0.6949 (tp30) REVERT: B 113 ASP cc_start: 0.7388 (t0) cc_final: 0.6859 (t0) REVERT: B 161 THR cc_start: 0.7653 (m) cc_final: 0.7389 (m) REVERT: B 205 CYS cc_start: 0.5683 (m) cc_final: 0.5399 (m) REVERT: B 245 VAL cc_start: 0.8696 (t) cc_final: 0.8472 (p) REVERT: B 268 LYS cc_start: 0.8504 (pptt) cc_final: 0.8221 (pptt) REVERT: B 273 ARG cc_start: 0.8116 (mtt-85) cc_final: 0.7915 (mtt-85) REVERT: B 280 ASN cc_start: 0.8037 (p0) cc_final: 0.7658 (p0) REVERT: B 297 THR cc_start: 0.8676 (t) cc_final: 0.8290 (p) REVERT: B 321 ASP cc_start: 0.7533 (t0) cc_final: 0.7242 (t70) REVERT: B 432 ARG cc_start: 0.6361 (mtt90) cc_final: 0.5955 (mtt90) REVERT: B 446 ARG cc_start: 0.7609 (mtp85) cc_final: 0.7274 (mtt90) REVERT: B 447 SER cc_start: 0.8246 (m) cc_final: 0.8004 (p) REVERT: B 490 LYS cc_start: 0.7784 (ttpt) cc_final: 0.7582 (ttpt) REVERT: B 535 MET cc_start: 0.6924 (tpp) cc_final: 0.6669 (tpp) REVERT: B 656 ASN cc_start: 0.7722 (t0) cc_final: 0.7434 (t0) REVERT: B 657 GLU cc_start: 0.7468 (tp30) cc_final: 0.6929 (tp30) REVERT: C 53 PHE cc_start: 0.7313 (p90) cc_final: 0.6946 (p90) REVERT: C 93 PHE cc_start: 0.7891 (m-80) cc_final: 0.7636 (m-10) REVERT: C 106 GLU cc_start: 0.7372 (tp30) cc_final: 0.7044 (tp30) REVERT: C 150 GLU cc_start: 0.7365 (tp30) cc_final: 0.7076 (tp30) REVERT: C 166 LYS cc_start: 0.7989 (mmmt) cc_final: 0.7632 (mmmt) REVERT: C 171 TYR cc_start: 0.7913 (p90) cc_final: 0.7525 (p90) REVERT: C 417 GLN cc_start: 0.7919 (pt0) cc_final: 0.7386 (mt0) REVERT: C 427 TRP cc_start: 0.7644 (m-90) cc_final: 0.7209 (m-10) REVERT: C 482 GLU cc_start: 0.7660 (mm-30) cc_final: 0.7264 (mm-30) REVERT: C 530 MET cc_start: 0.8801 (mmm) cc_final: 0.8311 (mmm) REVERT: C 577 GLN cc_start: 0.7256 (tm-30) cc_final: 0.6971 (tm-30) REVERT: C 626 MET cc_start: 0.7884 (OUTLIER) cc_final: 0.7497 (mtt) REVERT: C 656 ASN cc_start: 0.7876 (t0) cc_final: 0.7520 (t0) REVERT: C 657 GLU cc_start: 0.7535 (tp30) cc_final: 0.6874 (tp30) outliers start: 61 outliers final: 39 residues processed: 474 average time/residue: 0.2858 time to fit residues: 190.4718 Evaluate side-chains 458 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 418 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 328 GLN Chi-restraints excluded: chain A residue 417 GLN Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 344 LYS Chi-restraints excluded: chain B residue 417 GLN Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 119 CYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 576 LEU Chi-restraints excluded: chain C residue 626 MET Chi-restraints excluded: chain C residue 628 TRP Chi-restraints excluded: chain C residue 629 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 83 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 22 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 59 optimal weight: 0.0770 chunk 108 optimal weight: 0.1980 chunk 84 optimal weight: 5.9990 chunk 134 optimal weight: 0.0270 overall best weight: 0.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 363 GLN B 302 ASN B 363 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.124346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.103579 restraints weight = 21947.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.107686 restraints weight = 12182.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.110448 restraints weight = 8166.538| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 14547 Z= 0.123 Angle : 0.679 11.062 19893 Z= 0.335 Chirality : 0.047 0.305 2418 Planarity : 0.004 0.052 2421 Dihedral : 7.660 55.242 3122 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.60 % Allowed : 18.27 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.20), residues: 1656 helix: 1.21 (0.27), residues: 375 sheet: 1.06 (0.26), residues: 363 loop : -1.00 (0.20), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP B 610 HIS 0.006 0.001 HIS A 374 PHE 0.023 0.002 PHE C 53 TYR 0.027 0.001 TYR A 638 ARG 0.008 0.000 ARG A 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00364 ( 45) link_NAG-ASN : angle 2.49739 ( 135) link_BETA1-4 : bond 0.00913 ( 18) link_BETA1-4 : angle 2.76650 ( 54) hydrogen bonds : bond 0.03855 ( 391) hydrogen bonds : angle 4.42052 ( 1092) SS BOND : bond 0.00621 ( 36) SS BOND : angle 2.63563 ( 72) covalent geometry : bond 0.00278 (14448) covalent geometry : angle 0.61481 (19632) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 435 time to evaluate : 1.600 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: symmetry clash revert: symmetry clash REVERT: A 67 ASN cc_start: 0.7330 (t0) cc_final: 0.7014 (t0) REVERT: A 69 TRP cc_start: 0.7011 (m-90) cc_final: 0.6675 (m-90) REVERT: A 104 MET cc_start: 0.8149 (ttt) cc_final: 0.7810 (ttt) REVERT: A 117 LYS cc_start: 0.8406 (ttmm) cc_final: 0.8004 (ttmm) REVERT: A 150 GLU cc_start: 0.7394 (tp30) cc_final: 0.6996 (tp30) REVERT: A 166 LYS cc_start: 0.7797 (mmmt) cc_final: 0.7488 (mmmt) REVERT: A 202 THR cc_start: 0.7903 (p) cc_final: 0.7694 (p) REVERT: A 223 TYR cc_start: 0.8148 (m-80) cc_final: 0.7882 (m-80) REVERT: A 264 SER cc_start: 0.8302 (m) cc_final: 0.7702 (p) REVERT: A 344 LYS cc_start: 0.8082 (ttmm) cc_final: 0.7841 (ttmm) REVERT: A 468 PHE cc_start: 0.7905 (m-80) cc_final: 0.7561 (m-10) REVERT: A 477 ASP cc_start: 0.7508 (m-30) cc_final: 0.7270 (m-30) REVERT: A 482 GLU cc_start: 0.7509 (mm-30) cc_final: 0.6663 (mm-30) REVERT: A 535 MET cc_start: 0.7043 (tpp) cc_final: 0.6755 (tpp) REVERT: A 647 GLU cc_start: 0.7551 (tm-30) cc_final: 0.7210 (tm-30) REVERT: A 654 GLU cc_start: 0.7886 (tp30) cc_final: 0.7618 (tp30) REVERT: A 656 ASN cc_start: 0.7909 (t0) cc_final: 0.7505 (t0) REVERT: B 44 VAL cc_start: 0.9005 (p) cc_final: 0.8701 (m) REVERT: B 53 PHE cc_start: 0.7067 (p90) cc_final: 0.6816 (p90) REVERT: B 69 TRP cc_start: 0.6796 (m-90) cc_final: 0.6325 (m-90) REVERT: B 104 MET cc_start: 0.7790 (ttt) cc_final: 0.7564 (ttt) REVERT: B 106 GLU cc_start: 0.7315 (tp30) cc_final: 0.6976 (tp30) REVERT: B 113 ASP cc_start: 0.7362 (t0) cc_final: 0.6677 (t0) REVERT: B 161 THR cc_start: 0.7853 (m) cc_final: 0.7602 (m) REVERT: B 280 ASN cc_start: 0.7988 (p0) cc_final: 0.7572 (p0) REVERT: B 297 THR cc_start: 0.8665 (t) cc_final: 0.8328 (p) REVERT: B 417 GLN cc_start: 0.7770 (pt0) cc_final: 0.7540 (mt0) REVERT: B 432 ARG cc_start: 0.6328 (mtt90) cc_final: 0.5982 (mtt90) REVERT: B 446 ARG cc_start: 0.7598 (mtp85) cc_final: 0.7387 (mtp85) REVERT: B 447 SER cc_start: 0.8193 (m) cc_final: 0.7949 (p) REVERT: B 490 LYS cc_start: 0.7807 (ttpt) cc_final: 0.7587 (ttpt) REVERT: B 530 MET cc_start: 0.8724 (tpt) cc_final: 0.8356 (mmm) REVERT: B 656 ASN cc_start: 0.7722 (t0) cc_final: 0.7429 (t0) REVERT: B 657 GLU cc_start: 0.7423 (tp30) cc_final: 0.6906 (tp30) REVERT: C 53 PHE cc_start: 0.7118 (p90) cc_final: 0.6762 (p90) REVERT: C 93 PHE cc_start: 0.7751 (m-80) cc_final: 0.7535 (m-10) REVERT: C 103 GLN cc_start: 0.7891 (tp40) cc_final: 0.7338 (tm-30) REVERT: C 106 GLU cc_start: 0.7345 (tp30) cc_final: 0.7041 (tp30) REVERT: C 153 LYS cc_start: 0.7915 (mmtt) cc_final: 0.7581 (mmtm) REVERT: C 166 LYS cc_start: 0.7924 (mmmt) cc_final: 0.7589 (mmmt) REVERT: C 171 TYR cc_start: 0.7860 (p90) cc_final: 0.7474 (p90) REVERT: C 176 LYS cc_start: 0.8602 (ttmt) cc_final: 0.8305 (mtmt) REVERT: C 273 ARG cc_start: 0.8172 (mtt-85) cc_final: 0.7705 (mtt-85) REVERT: C 417 GLN cc_start: 0.7811 (OUTLIER) cc_final: 0.7506 (mt0) REVERT: C 427 TRP cc_start: 0.7585 (m-90) cc_final: 0.7180 (m-10) REVERT: C 482 GLU cc_start: 0.7631 (mm-30) cc_final: 0.7244 (mm-30) REVERT: C 529 THR cc_start: 0.8024 (m) cc_final: 0.7727 (m) REVERT: C 626 MET cc_start: 0.7851 (OUTLIER) cc_final: 0.7477 (mtt) REVERT: C 656 ASN cc_start: 0.7862 (t0) cc_final: 0.7514 (t0) REVERT: C 657 GLU cc_start: 0.7586 (tp30) cc_final: 0.6941 (tp30) outliers start: 54 outliers final: 33 residues processed: 464 average time/residue: 0.3332 time to fit residues: 220.2854 Evaluate side-chains 448 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 413 time to evaluate : 1.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 328 GLN Chi-restraints excluded: chain A residue 417 GLN Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 344 LYS Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 119 CYS Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 417 GLN Chi-restraints excluded: chain C residue 626 MET Chi-restraints excluded: chain C residue 628 TRP Chi-restraints excluded: chain C residue 629 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 154 optimal weight: 0.9990 chunk 143 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 149 optimal weight: 0.7980 chunk 137 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN B 302 ASN B 363 GLN C 105 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.122128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.101426 restraints weight = 22209.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.105486 restraints weight = 12347.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.108243 restraints weight = 8306.394| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.3602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 14547 Z= 0.150 Angle : 0.686 13.519 19893 Z= 0.335 Chirality : 0.046 0.245 2418 Planarity : 0.004 0.078 2421 Dihedral : 7.621 54.882 3122 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 4.53 % Allowed : 19.07 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.20), residues: 1656 helix: 1.32 (0.28), residues: 375 sheet: 1.25 (0.27), residues: 327 loop : -1.07 (0.19), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP C 35 HIS 0.005 0.001 HIS A 374 PHE 0.021 0.002 PHE C 53 TYR 0.024 0.002 TYR C 638 ARG 0.008 0.001 ARG B 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00355 ( 45) link_NAG-ASN : angle 2.42516 ( 135) link_BETA1-4 : bond 0.00818 ( 18) link_BETA1-4 : angle 2.71443 ( 54) hydrogen bonds : bond 0.03988 ( 391) hydrogen bonds : angle 4.49935 ( 1092) SS BOND : bond 0.00398 ( 36) SS BOND : angle 2.57841 ( 72) covalent geometry : bond 0.00347 (14448) covalent geometry : angle 0.62577 (19632) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 428 time to evaluate : 1.400 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: symmetry clash revert: symmetry clash REVERT: A 67 ASN cc_start: 0.7361 (t0) cc_final: 0.7049 (t0) REVERT: A 69 TRP cc_start: 0.7035 (m-90) cc_final: 0.6733 (m-90) REVERT: A 104 MET cc_start: 0.8145 (ttt) cc_final: 0.7778 (ttt) REVERT: A 117 LYS cc_start: 0.8411 (ttmm) cc_final: 0.8016 (ttmm) REVERT: A 136 VAL cc_start: 0.7603 (OUTLIER) cc_final: 0.7318 (p) REVERT: A 150 GLU cc_start: 0.7397 (tp30) cc_final: 0.7015 (tp30) REVERT: A 166 LYS cc_start: 0.7805 (mmmt) cc_final: 0.7519 (mmmt) REVERT: A 202 THR cc_start: 0.8105 (p) cc_final: 0.7878 (p) REVERT: A 264 SER cc_start: 0.8323 (m) cc_final: 0.7698 (p) REVERT: A 297 THR cc_start: 0.8690 (t) cc_final: 0.8448 (p) REVERT: A 344 LYS cc_start: 0.8134 (ttmm) cc_final: 0.7871 (ttmm) REVERT: A 417 GLN cc_start: 0.7820 (OUTLIER) cc_final: 0.7229 (mt0) REVERT: A 434 MET cc_start: 0.7100 (ttm) cc_final: 0.6896 (ttm) REVERT: A 447 SER cc_start: 0.8616 (m) cc_final: 0.7968 (p) REVERT: A 477 ASP cc_start: 0.7546 (m-30) cc_final: 0.7292 (m-30) REVERT: A 482 GLU cc_start: 0.7512 (mm-30) cc_final: 0.6703 (mm-30) REVERT: A 535 MET cc_start: 0.7018 (tpp) cc_final: 0.6810 (tpp) REVERT: A 647 GLU cc_start: 0.7593 (tm-30) cc_final: 0.7222 (tm-30) REVERT: A 654 GLU cc_start: 0.7879 (tp30) cc_final: 0.7615 (tp30) REVERT: A 656 ASN cc_start: 0.7898 (t0) cc_final: 0.7513 (t0) REVERT: B 44 VAL cc_start: 0.9030 (p) cc_final: 0.8782 (m) REVERT: B 53 PHE cc_start: 0.6936 (p90) cc_final: 0.6703 (p90) REVERT: B 69 TRP cc_start: 0.6852 (m-90) cc_final: 0.6403 (m-90) REVERT: B 104 MET cc_start: 0.7810 (ttt) cc_final: 0.7575 (ttt) REVERT: B 106 GLU cc_start: 0.7338 (tp30) cc_final: 0.6958 (tp30) REVERT: B 113 ASP cc_start: 0.7360 (t0) cc_final: 0.6599 (t0) REVERT: B 136 VAL cc_start: 0.7555 (OUTLIER) cc_final: 0.7299 (p) REVERT: B 161 THR cc_start: 0.7850 (m) cc_final: 0.7592 (m) REVERT: B 268 LYS cc_start: 0.8466 (pptt) cc_final: 0.8111 (pptt) REVERT: B 269 GLU cc_start: 0.7981 (tt0) cc_final: 0.6661 (tt0) REVERT: B 280 ASN cc_start: 0.8006 (p0) cc_final: 0.7581 (p0) REVERT: B 297 THR cc_start: 0.8690 (t) cc_final: 0.8376 (p) REVERT: B 432 ARG cc_start: 0.6455 (mtt90) cc_final: 0.6186 (mtt90) REVERT: B 475 MET cc_start: 0.8143 (tpp) cc_final: 0.7812 (tpp) REVERT: B 490 LYS cc_start: 0.7799 (ttpt) cc_final: 0.7588 (ttpt) REVERT: B 656 ASN cc_start: 0.7756 (t0) cc_final: 0.7465 (t0) REVERT: B 657 GLU cc_start: 0.7413 (tp30) cc_final: 0.6945 (tp30) REVERT: C 53 PHE cc_start: 0.7135 (p90) cc_final: 0.6782 (p90) REVERT: C 91 GLU cc_start: 0.6866 (mm-30) cc_final: 0.6609 (mm-30) REVERT: C 93 PHE cc_start: 0.7775 (m-80) cc_final: 0.7546 (m-10) REVERT: C 106 GLU cc_start: 0.7364 (tp30) cc_final: 0.7085 (tp30) REVERT: C 136 VAL cc_start: 0.7486 (OUTLIER) cc_final: 0.7141 (p) REVERT: C 166 LYS cc_start: 0.7961 (mmmt) cc_final: 0.7624 (mmmt) REVERT: C 171 TYR cc_start: 0.7850 (p90) cc_final: 0.7494 (p90) REVERT: C 176 LYS cc_start: 0.8567 (ttmt) cc_final: 0.8292 (mtmt) REVERT: C 202 THR cc_start: 0.8232 (p) cc_final: 0.7988 (p) REVERT: C 267 GLU cc_start: 0.6998 (tp30) cc_final: 0.6769 (tp30) REVERT: C 273 ARG cc_start: 0.8244 (mtt-85) cc_final: 0.7864 (mtt-85) REVERT: C 417 GLN cc_start: 0.7838 (OUTLIER) cc_final: 0.7506 (mt0) REVERT: C 427 TRP cc_start: 0.7596 (m-90) cc_final: 0.7152 (m-10) REVERT: C 482 GLU cc_start: 0.7625 (mm-30) cc_final: 0.7245 (mm-30) REVERT: C 529 THR cc_start: 0.8049 (m) cc_final: 0.7792 (m) REVERT: C 530 MET cc_start: 0.8571 (tpt) cc_final: 0.7908 (mmm) REVERT: C 540 GLN cc_start: 0.7568 (mp10) cc_final: 0.7324 (mp10) REVERT: C 626 MET cc_start: 0.7848 (OUTLIER) cc_final: 0.7459 (mtt) REVERT: C 656 ASN cc_start: 0.7891 (t0) cc_final: 0.7546 (t0) REVERT: C 657 GLU cc_start: 0.7576 (tp30) cc_final: 0.6948 (tp30) outliers start: 68 outliers final: 40 residues processed: 467 average time/residue: 0.2834 time to fit residues: 186.4852 Evaluate side-chains 457 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 411 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LYS Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 328 GLN Chi-restraints excluded: chain A residue 417 GLN Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 119 CYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 321 ASP Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 417 GLN Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 576 LEU Chi-restraints excluded: chain C residue 626 MET Chi-restraints excluded: chain C residue 628 TRP Chi-restraints excluded: chain C residue 629 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 81 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN B 302 ASN ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 315 GLN C 363 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.121017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.100443 restraints weight = 21932.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.104409 restraints weight = 12295.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.107098 restraints weight = 8291.980| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 14547 Z= 0.284 Angle : 0.766 13.819 19893 Z= 0.382 Chirality : 0.050 0.274 2418 Planarity : 0.005 0.075 2421 Dihedral : 7.906 56.641 3122 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 4.07 % Allowed : 20.13 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.20), residues: 1656 helix: 1.04 (0.27), residues: 378 sheet: 0.97 (0.28), residues: 339 loop : -1.27 (0.19), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP A 631 HIS 0.009 0.002 HIS B 216 PHE 0.020 0.002 PHE C 93 TYR 0.025 0.003 TYR C 638 ARG 0.008 0.001 ARG B 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00481 ( 45) link_NAG-ASN : angle 2.50588 ( 135) link_BETA1-4 : bond 0.00836 ( 18) link_BETA1-4 : angle 2.69166 ( 54) hydrogen bonds : bond 0.05081 ( 391) hydrogen bonds : angle 4.76219 ( 1092) SS BOND : bond 0.00630 ( 36) SS BOND : angle 2.97555 ( 72) covalent geometry : bond 0.00648 (14448) covalent geometry : angle 0.70589 (19632) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 460 time to evaluate : 1.498 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LYS cc_start: 0.8625 (OUTLIER) cc_final: 0.8360 (ptpt) REVERT: A 67 ASN cc_start: 0.7510 (t0) cc_final: 0.7183 (t0) REVERT: A 69 TRP cc_start: 0.7074 (m-90) cc_final: 0.6757 (m-90) REVERT: A 117 LYS cc_start: 0.8537 (ttmm) cc_final: 0.8146 (ttmm) REVERT: A 136 VAL cc_start: 0.7548 (OUTLIER) cc_final: 0.7248 (p) REVERT: A 150 GLU cc_start: 0.7434 (tp30) cc_final: 0.6921 (tp30) REVERT: A 202 THR cc_start: 0.8245 (p) cc_final: 0.8044 (p) REVERT: A 246 GLN cc_start: 0.7799 (tp40) cc_final: 0.7519 (tp40) REVERT: A 258 GLN cc_start: 0.8077 (mt0) cc_final: 0.7767 (mt0) REVERT: A 264 SER cc_start: 0.8307 (m) cc_final: 0.7661 (p) REVERT: A 447 SER cc_start: 0.8552 (m) cc_final: 0.7815 (p) REVERT: A 477 ASP cc_start: 0.7536 (m-30) cc_final: 0.7249 (m-30) REVERT: A 482 GLU cc_start: 0.7512 (mm-30) cc_final: 0.6755 (mm-30) REVERT: A 635 ILE cc_start: 0.8526 (tp) cc_final: 0.8156 (tt) REVERT: A 647 GLU cc_start: 0.7651 (tm-30) cc_final: 0.7241 (tm-30) REVERT: A 654 GLU cc_start: 0.7921 (tp30) cc_final: 0.7658 (tp30) REVERT: A 656 ASN cc_start: 0.7922 (t0) cc_final: 0.7530 (t0) REVERT: B 44 VAL cc_start: 0.9036 (p) cc_final: 0.8822 (m) REVERT: B 53 PHE cc_start: 0.7027 (p90) cc_final: 0.6826 (p90) REVERT: B 106 GLU cc_start: 0.7354 (tp30) cc_final: 0.7001 (tp30) REVERT: B 113 ASP cc_start: 0.7205 (t0) cc_final: 0.6290 (t0) REVERT: B 136 VAL cc_start: 0.7540 (OUTLIER) cc_final: 0.7193 (p) REVERT: B 150 GLU cc_start: 0.7570 (tp30) cc_final: 0.7109 (tp30) REVERT: B 161 THR cc_start: 0.7890 (m) cc_final: 0.7651 (m) REVERT: B 205 CYS cc_start: 0.5801 (m) cc_final: 0.5552 (m) REVERT: B 268 LYS cc_start: 0.8455 (pptt) cc_final: 0.8190 (pptt) REVERT: B 280 ASN cc_start: 0.8048 (p0) cc_final: 0.7645 (p0) REVERT: B 297 THR cc_start: 0.8695 (t) cc_final: 0.8338 (p) REVERT: B 432 ARG cc_start: 0.6449 (mtt90) cc_final: 0.6191 (mtt90) REVERT: B 475 MET cc_start: 0.8045 (tpp) cc_final: 0.7673 (tpp) REVERT: B 490 LYS cc_start: 0.7744 (ttpt) cc_final: 0.7532 (ttpt) REVERT: B 656 ASN cc_start: 0.7824 (t0) cc_final: 0.7555 (t0) REVERT: B 657 GLU cc_start: 0.7429 (tp30) cc_final: 0.6981 (tp30) REVERT: C 53 PHE cc_start: 0.7203 (p90) cc_final: 0.6931 (p90) REVERT: C 91 GLU cc_start: 0.6839 (mm-30) cc_final: 0.6582 (mm-30) REVERT: C 93 PHE cc_start: 0.7888 (m-80) cc_final: 0.7669 (m-10) REVERT: C 96 TRP cc_start: 0.8000 (m100) cc_final: 0.6903 (m100) REVERT: C 103 GLN cc_start: 0.7943 (tp-100) cc_final: 0.7324 (tm-30) REVERT: C 106 GLU cc_start: 0.7420 (tp30) cc_final: 0.7118 (tp30) REVERT: C 108 ILE cc_start: 0.7255 (mt) cc_final: 0.7047 (mm) REVERT: C 121 LYS cc_start: 0.8711 (mttt) cc_final: 0.8339 (mttm) REVERT: C 166 LYS cc_start: 0.8023 (mmmt) cc_final: 0.7632 (mmmt) REVERT: C 171 TYR cc_start: 0.7871 (p90) cc_final: 0.7434 (p90) REVERT: C 202 THR cc_start: 0.8308 (p) cc_final: 0.8077 (p) REVERT: C 272 ILE cc_start: 0.8398 (mp) cc_final: 0.8113 (mt) REVERT: C 273 ARG cc_start: 0.8231 (mtt-85) cc_final: 0.7774 (mtt-85) REVERT: C 309 ILE cc_start: 0.7346 (tp) cc_final: 0.7126 (mt) REVERT: C 348 GLU cc_start: 0.7522 (mm-30) cc_final: 0.7226 (mm-30) REVERT: C 417 GLN cc_start: 0.7917 (OUTLIER) cc_final: 0.7471 (mt0) REVERT: C 427 TRP cc_start: 0.7675 (m-90) cc_final: 0.7195 (m-10) REVERT: C 439 ILE cc_start: 0.8138 (mp) cc_final: 0.7936 (mm) REVERT: C 482 GLU cc_start: 0.7650 (mm-30) cc_final: 0.7292 (mm-30) REVERT: C 529 THR cc_start: 0.8089 (m) cc_final: 0.7802 (m) REVERT: C 577 GLN cc_start: 0.7331 (tm-30) cc_final: 0.6791 (tm-30) REVERT: C 626 MET cc_start: 0.7887 (OUTLIER) cc_final: 0.7558 (mtt) REVERT: C 656 ASN cc_start: 0.7920 (t0) cc_final: 0.7587 (t0) REVERT: C 657 GLU cc_start: 0.7589 (tp30) cc_final: 0.6971 (tp30) outliers start: 61 outliers final: 42 residues processed: 489 average time/residue: 0.2819 time to fit residues: 194.8425 Evaluate side-chains 489 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 442 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LYS Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 417 GLN Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 605 CYS Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 344 LYS Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 119 CYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 417 GLN Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 576 LEU Chi-restraints excluded: chain C residue 626 MET Chi-restraints excluded: chain C residue 628 TRP Chi-restraints excluded: chain C residue 629 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 37 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 157 optimal weight: 0.1980 chunk 106 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 154 optimal weight: 0.6980 chunk 156 optimal weight: 4.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN A 363 GLN B 302 ASN C 114 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.120585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.100146 restraints weight = 21889.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.104084 restraints weight = 12187.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.106903 restraints weight = 8230.731| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.3864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 14547 Z= 0.161 Angle : 0.690 11.646 19893 Z= 0.342 Chirality : 0.046 0.236 2418 Planarity : 0.005 0.068 2421 Dihedral : 7.652 55.105 3122 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.73 % Allowed : 21.60 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.20), residues: 1656 helix: 1.20 (0.27), residues: 378 sheet: 1.25 (0.30), residues: 303 loop : -1.25 (0.19), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 631 HIS 0.004 0.001 HIS A 374 PHE 0.019 0.002 PHE C 53 TYR 0.026 0.002 TYR C 638 ARG 0.010 0.001 ARG A 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00322 ( 45) link_NAG-ASN : angle 2.29869 ( 135) link_BETA1-4 : bond 0.00829 ( 18) link_BETA1-4 : angle 2.58759 ( 54) hydrogen bonds : bond 0.04220 ( 391) hydrogen bonds : angle 4.58923 ( 1092) SS BOND : bond 0.00489 ( 36) SS BOND : angle 2.49900 ( 72) covalent geometry : bond 0.00373 (14448) covalent geometry : angle 0.63608 (19632) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 449 time to evaluate : 1.533 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: symmetry clash REVERT: A 49 LYS cc_start: 0.8524 (OUTLIER) cc_final: 0.8286 (ptpt) REVERT: A 69 TRP cc_start: 0.6965 (m-90) cc_final: 0.6738 (m-90) REVERT: A 117 LYS cc_start: 0.8498 (ttmm) cc_final: 0.8099 (ttmm) REVERT: A 136 VAL cc_start: 0.7476 (OUTLIER) cc_final: 0.7168 (p) REVERT: A 150 GLU cc_start: 0.7389 (tp30) cc_final: 0.6736 (tp30) REVERT: A 176 LYS cc_start: 0.8622 (ttmt) cc_final: 0.8394 (ttmt) REVERT: A 264 SER cc_start: 0.8312 (m) cc_final: 0.7684 (p) REVERT: A 297 THR cc_start: 0.8721 (t) cc_final: 0.8443 (p) REVERT: A 321 ASP cc_start: 0.7232 (t70) cc_final: 0.6869 (t0) REVERT: A 344 LYS cc_start: 0.8122 (ttmm) cc_final: 0.7875 (ttmm) REVERT: A 482 GLU cc_start: 0.7498 (mm-30) cc_final: 0.6680 (mm-30) REVERT: A 631 TRP cc_start: 0.7891 (t-100) cc_final: 0.7172 (t-100) REVERT: A 635 ILE cc_start: 0.8384 (tp) cc_final: 0.7970 (tt) REVERT: A 647 GLU cc_start: 0.7583 (tm-30) cc_final: 0.7229 (tm-30) REVERT: A 654 GLU cc_start: 0.7914 (tp30) cc_final: 0.7699 (tp30) REVERT: A 656 ASN cc_start: 0.7893 (t0) cc_final: 0.7515 (t0) REVERT: B 35 TRP cc_start: 0.7787 (m-10) cc_final: 0.7271 (m-10) REVERT: B 44 VAL cc_start: 0.9023 (p) cc_final: 0.8821 (m) REVERT: B 53 PHE cc_start: 0.6994 (p90) cc_final: 0.6763 (p90) REVERT: B 69 TRP cc_start: 0.6906 (m-90) cc_final: 0.6491 (m-90) REVERT: B 106 GLU cc_start: 0.7325 (tp30) cc_final: 0.6918 (tp30) REVERT: B 113 ASP cc_start: 0.7253 (t0) cc_final: 0.6278 (t0) REVERT: B 136 VAL cc_start: 0.7496 (OUTLIER) cc_final: 0.7162 (p) REVERT: B 150 GLU cc_start: 0.7485 (tp30) cc_final: 0.7015 (tp30) REVERT: B 161 THR cc_start: 0.7882 (OUTLIER) cc_final: 0.7670 (m) REVERT: B 205 CYS cc_start: 0.5721 (m) cc_final: 0.5488 (m) REVERT: B 269 GLU cc_start: 0.7985 (tt0) cc_final: 0.7749 (tt0) REVERT: B 280 ASN cc_start: 0.8044 (p0) cc_final: 0.7650 (p0) REVERT: B 297 THR cc_start: 0.8703 (t) cc_final: 0.8397 (p) REVERT: B 308 ARG cc_start: 0.7731 (mmt-90) cc_final: 0.7508 (tpp80) REVERT: B 337 LYS cc_start: 0.8329 (OUTLIER) cc_final: 0.8073 (ttmm) REVERT: B 432 ARG cc_start: 0.6331 (mtt90) cc_final: 0.5911 (mtt90) REVERT: B 475 MET cc_start: 0.7949 (tpp) cc_final: 0.7578 (tpp) REVERT: B 492 GLU cc_start: 0.7415 (mt-10) cc_final: 0.7004 (mt-10) REVERT: B 530 MET cc_start: 0.8765 (tpt) cc_final: 0.8412 (mmm) REVERT: B 626 MET cc_start: 0.7462 (mtt) cc_final: 0.6618 (ttt) REVERT: B 656 ASN cc_start: 0.7811 (t0) cc_final: 0.7526 (t0) REVERT: B 657 GLU cc_start: 0.7400 (tp30) cc_final: 0.6948 (tp30) REVERT: C 53 PHE cc_start: 0.7138 (p90) cc_final: 0.6824 (p90) REVERT: C 91 GLU cc_start: 0.6786 (mm-30) cc_final: 0.6532 (mm-30) REVERT: C 93 PHE cc_start: 0.7814 (m-80) cc_final: 0.7589 (m-10) REVERT: C 96 TRP cc_start: 0.7892 (m100) cc_final: 0.6760 (m100) REVERT: C 103 GLN cc_start: 0.7909 (tp-100) cc_final: 0.7293 (tm-30) REVERT: C 106 GLU cc_start: 0.7354 (tp30) cc_final: 0.7095 (tp30) REVERT: C 121 LYS cc_start: 0.8697 (mttt) cc_final: 0.8332 (mttm) REVERT: C 136 VAL cc_start: 0.7380 (OUTLIER) cc_final: 0.6981 (p) REVERT: C 166 LYS cc_start: 0.7964 (mmmt) cc_final: 0.7604 (mmmt) REVERT: C 171 TYR cc_start: 0.7831 (p90) cc_final: 0.7453 (p90) REVERT: C 272 ILE cc_start: 0.8361 (mp) cc_final: 0.8055 (mt) REVERT: C 309 ILE cc_start: 0.7297 (tp) cc_final: 0.7078 (mt) REVERT: C 417 GLN cc_start: 0.7869 (OUTLIER) cc_final: 0.7589 (mt0) REVERT: C 427 TRP cc_start: 0.7696 (m-90) cc_final: 0.6880 (m-90) REVERT: C 482 GLU cc_start: 0.7603 (mm-30) cc_final: 0.7215 (mm-30) REVERT: C 529 THR cc_start: 0.8063 (m) cc_final: 0.7811 (m) REVERT: C 530 MET cc_start: 0.8471 (tpt) cc_final: 0.8069 (mmm) REVERT: C 577 GLN cc_start: 0.7210 (tm-30) cc_final: 0.6712 (tm-30) REVERT: C 626 MET cc_start: 0.7893 (OUTLIER) cc_final: 0.7542 (mtt) REVERT: C 656 ASN cc_start: 0.7877 (t0) cc_final: 0.7560 (t0) REVERT: C 657 GLU cc_start: 0.7574 (tp30) cc_final: 0.6943 (tp30) outliers start: 56 outliers final: 39 residues processed: 475 average time/residue: 0.2873 time to fit residues: 192.6251 Evaluate side-chains 481 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 434 time to evaluate : 1.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LYS Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 417 GLN Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain B residue 344 LYS Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 119 CYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 395 TYR Chi-restraints excluded: chain C residue 417 GLN Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 626 MET Chi-restraints excluded: chain C residue 628 TRP Chi-restraints excluded: chain C residue 629 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 116 optimal weight: 2.9990 chunk 111 optimal weight: 0.8980 chunk 165 optimal weight: 4.9990 chunk 143 optimal weight: 3.9990 chunk 25 optimal weight: 0.3980 chunk 27 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN A 363 GLN ** B 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 ASN B 315 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.119696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.099250 restraints weight = 21761.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.103253 restraints weight = 12145.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.105955 restraints weight = 8184.756| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.3946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 14547 Z= 0.200 Angle : 0.715 11.286 19893 Z= 0.356 Chirality : 0.047 0.250 2418 Planarity : 0.005 0.066 2421 Dihedral : 7.672 55.273 3122 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 4.00 % Allowed : 22.47 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.20), residues: 1656 helix: 1.20 (0.27), residues: 378 sheet: 0.92 (0.28), residues: 339 loop : -1.26 (0.19), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 35 HIS 0.006 0.002 HIS B 216 PHE 0.017 0.002 PHE C 53 TYR 0.025 0.002 TYR C 638 ARG 0.013 0.001 ARG A 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00381 ( 45) link_NAG-ASN : angle 2.30257 ( 135) link_BETA1-4 : bond 0.00819 ( 18) link_BETA1-4 : angle 2.56863 ( 54) hydrogen bonds : bond 0.04468 ( 391) hydrogen bonds : angle 4.62706 ( 1092) SS BOND : bond 0.00494 ( 36) SS BOND : angle 2.58026 ( 72) covalent geometry : bond 0.00465 (14448) covalent geometry : angle 0.66302 (19632) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 441 time to evaluate : 1.606 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: symmetry clash revert: symmetry clash REVERT: A 49 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.8235 (ptpt) REVERT: A 69 TRP cc_start: 0.6902 (m-90) cc_final: 0.6674 (m-90) REVERT: A 99 ASP cc_start: 0.7849 (m-30) cc_final: 0.7639 (m-30) REVERT: A 117 LYS cc_start: 0.8514 (ttmm) cc_final: 0.8140 (ttmm) REVERT: A 136 VAL cc_start: 0.7448 (OUTLIER) cc_final: 0.7102 (p) REVERT: A 150 GLU cc_start: 0.7385 (tp30) cc_final: 0.6677 (tp30) REVERT: A 176 LYS cc_start: 0.8628 (ttmt) cc_final: 0.8241 (ttmt) REVERT: A 264 SER cc_start: 0.8400 (m) cc_final: 0.7756 (p) REVERT: A 297 THR cc_start: 0.8720 (t) cc_final: 0.8446 (p) REVERT: A 321 ASP cc_start: 0.7278 (t70) cc_final: 0.6961 (t0) REVERT: A 344 LYS cc_start: 0.8134 (ttmm) cc_final: 0.7909 (ttmm) REVERT: A 434 MET cc_start: 0.7066 (ttp) cc_final: 0.6818 (ttm) REVERT: A 447 SER cc_start: 0.8511 (m) cc_final: 0.7941 (p) REVERT: A 482 GLU cc_start: 0.7517 (mm-30) cc_final: 0.6722 (mm-30) REVERT: A 530 MET cc_start: 0.8871 (tpt) cc_final: 0.8398 (tpt) REVERT: A 631 TRP cc_start: 0.7949 (t-100) cc_final: 0.7220 (t-100) REVERT: A 635 ILE cc_start: 0.8451 (tp) cc_final: 0.8036 (tt) REVERT: A 647 GLU cc_start: 0.7622 (tm-30) cc_final: 0.7226 (tm-30) REVERT: A 654 GLU cc_start: 0.7915 (tp30) cc_final: 0.7706 (tp30) REVERT: A 656 ASN cc_start: 0.7905 (t0) cc_final: 0.7523 (t0) REVERT: B 35 TRP cc_start: 0.7856 (m-10) cc_final: 0.7275 (m-10) REVERT: B 69 TRP cc_start: 0.6937 (m-90) cc_final: 0.6542 (m-90) REVERT: B 106 GLU cc_start: 0.7313 (tp30) cc_final: 0.6966 (tp30) REVERT: B 113 ASP cc_start: 0.7160 (t0) cc_final: 0.6170 (t0) REVERT: B 136 VAL cc_start: 0.7496 (OUTLIER) cc_final: 0.7155 (p) REVERT: B 150 GLU cc_start: 0.7507 (tp30) cc_final: 0.7002 (tp30) REVERT: B 161 THR cc_start: 0.7909 (OUTLIER) cc_final: 0.7698 (m) REVERT: B 205 CYS cc_start: 0.5777 (m) cc_final: 0.5534 (m) REVERT: B 269 GLU cc_start: 0.8017 (tt0) cc_final: 0.7724 (tt0) REVERT: B 280 ASN cc_start: 0.8082 (p0) cc_final: 0.7717 (p0) REVERT: B 297 THR cc_start: 0.8707 (t) cc_final: 0.8407 (p) REVERT: B 337 LYS cc_start: 0.8367 (OUTLIER) cc_final: 0.8108 (ttmm) REVERT: B 432 ARG cc_start: 0.6405 (mtt90) cc_final: 0.6133 (mtt90) REVERT: B 474 ASP cc_start: 0.7545 (t0) cc_final: 0.7248 (m-30) REVERT: B 475 MET cc_start: 0.7879 (tpp) cc_final: 0.7340 (tpp) REVERT: B 490 LYS cc_start: 0.7820 (ttpt) cc_final: 0.7602 (ttpt) REVERT: B 530 MET cc_start: 0.8795 (tpt) cc_final: 0.8460 (mmm) REVERT: B 656 ASN cc_start: 0.7824 (t0) cc_final: 0.7538 (t0) REVERT: B 657 GLU cc_start: 0.7407 (tp30) cc_final: 0.6955 (tp30) REVERT: C 47 GLU cc_start: 0.7404 (mm-30) cc_final: 0.7178 (mm-30) REVERT: C 53 PHE cc_start: 0.7172 (p90) cc_final: 0.6901 (p90) REVERT: C 93 PHE cc_start: 0.7862 (m-80) cc_final: 0.7644 (m-10) REVERT: C 96 TRP cc_start: 0.7896 (m100) cc_final: 0.6760 (m100) REVERT: C 103 GLN cc_start: 0.7877 (tp-100) cc_final: 0.7262 (tm-30) REVERT: C 106 GLU cc_start: 0.7346 (tp30) cc_final: 0.7071 (tp30) REVERT: C 121 LYS cc_start: 0.8724 (mttt) cc_final: 0.8316 (mttp) REVERT: C 136 VAL cc_start: 0.7348 (OUTLIER) cc_final: 0.6938 (p) REVERT: C 166 LYS cc_start: 0.7966 (mmmt) cc_final: 0.7646 (mmmt) REVERT: C 171 TYR cc_start: 0.7867 (p90) cc_final: 0.7471 (p90) REVERT: C 309 ILE cc_start: 0.7328 (tp) cc_final: 0.6959 (pt) REVERT: C 417 GLN cc_start: 0.7880 (OUTLIER) cc_final: 0.7540 (mt0) REVERT: C 427 TRP cc_start: 0.7756 (m-90) cc_final: 0.7046 (m-10) REVERT: C 482 GLU cc_start: 0.7619 (mm-30) cc_final: 0.7231 (mm-30) REVERT: C 529 THR cc_start: 0.8046 (m) cc_final: 0.7783 (m) REVERT: C 577 GLN cc_start: 0.7242 (tm-30) cc_final: 0.6719 (tm-30) REVERT: C 626 MET cc_start: 0.7884 (OUTLIER) cc_final: 0.7594 (mtt) REVERT: C 656 ASN cc_start: 0.7891 (t0) cc_final: 0.7592 (t0) REVERT: C 657 GLU cc_start: 0.7613 (tp30) cc_final: 0.7007 (tp30) outliers start: 60 outliers final: 44 residues processed: 470 average time/residue: 0.2849 time to fit residues: 189.4069 Evaluate side-chains 486 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 434 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LYS Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 417 GLN Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain B residue 344 LYS Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 119 CYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 344 LYS Chi-restraints excluded: chain C residue 395 TYR Chi-restraints excluded: chain C residue 417 GLN Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 626 MET Chi-restraints excluded: chain C residue 628 TRP Chi-restraints excluded: chain C residue 629 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 61 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 118 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 119 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 chunk 155 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 chunk 138 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN A 363 GLN ** B 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 ASN B 363 GLN C 114 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.122069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.101661 restraints weight = 21680.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.105687 restraints weight = 12091.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.108399 restraints weight = 8151.140| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 14547 Z= 0.145 Angle : 0.689 12.064 19893 Z= 0.343 Chirality : 0.046 0.231 2418 Planarity : 0.005 0.062 2421 Dihedral : 7.537 55.420 3122 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.13 % Allowed : 23.33 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.20), residues: 1656 helix: 1.32 (0.27), residues: 378 sheet: 0.87 (0.26), residues: 375 loop : -1.21 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 35 HIS 0.005 0.001 HIS A 374 PHE 0.018 0.002 PHE C 53 TYR 0.027 0.001 TYR C 638 ARG 0.011 0.001 ARG A 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00317 ( 45) link_NAG-ASN : angle 2.17359 ( 135) link_BETA1-4 : bond 0.00802 ( 18) link_BETA1-4 : angle 2.50274 ( 54) hydrogen bonds : bond 0.04016 ( 391) hydrogen bonds : angle 4.57938 ( 1092) SS BOND : bond 0.00375 ( 36) SS BOND : angle 2.50584 ( 72) covalent geometry : bond 0.00340 (14448) covalent geometry : angle 0.63874 (19632) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 445 time to evaluate : 1.497 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.8202 (ptpt) REVERT: A 69 TRP cc_start: 0.6884 (m-90) cc_final: 0.6654 (m-90) REVERT: A 99 ASP cc_start: 0.7851 (m-30) cc_final: 0.7447 (m-30) REVERT: A 117 LYS cc_start: 0.8533 (ttmm) cc_final: 0.8140 (ttmm) REVERT: A 150 GLU cc_start: 0.7353 (tp30) cc_final: 0.6684 (tp30) REVERT: A 176 LYS cc_start: 0.8602 (ttmt) cc_final: 0.8346 (ttmt) REVERT: A 245 VAL cc_start: 0.8719 (t) cc_final: 0.8373 (p) REVERT: A 264 SER cc_start: 0.8452 (m) cc_final: 0.7807 (p) REVERT: A 297 THR cc_start: 0.8706 (t) cc_final: 0.8457 (p) REVERT: A 321 ASP cc_start: 0.7266 (t70) cc_final: 0.6868 (t0) REVERT: A 344 LYS cc_start: 0.8131 (ttmm) cc_final: 0.7899 (ttmm) REVERT: A 434 MET cc_start: 0.6921 (ttp) cc_final: 0.6633 (ttm) REVERT: A 468 PHE cc_start: 0.8057 (m-80) cc_final: 0.7746 (m-10) REVERT: A 482 GLU cc_start: 0.7499 (mm-30) cc_final: 0.6684 (mm-30) REVERT: A 631 TRP cc_start: 0.7912 (t-100) cc_final: 0.7670 (t-100) REVERT: A 635 ILE cc_start: 0.8369 (tp) cc_final: 0.7955 (tt) REVERT: A 647 GLU cc_start: 0.7585 (tm-30) cc_final: 0.7217 (tm-30) REVERT: A 656 ASN cc_start: 0.7905 (t0) cc_final: 0.7542 (t0) REVERT: B 35 TRP cc_start: 0.7774 (m-10) cc_final: 0.7320 (m-10) REVERT: B 69 TRP cc_start: 0.6932 (m-90) cc_final: 0.6531 (m-90) REVERT: B 106 GLU cc_start: 0.7273 (tp30) cc_final: 0.6828 (tp30) REVERT: B 113 ASP cc_start: 0.7177 (t0) cc_final: 0.6126 (t0) REVERT: B 136 VAL cc_start: 0.7432 (OUTLIER) cc_final: 0.7073 (p) REVERT: B 150 GLU cc_start: 0.7446 (tp30) cc_final: 0.6918 (tp30) REVERT: B 161 THR cc_start: 0.7839 (OUTLIER) cc_final: 0.7599 (m) REVERT: B 205 CYS cc_start: 0.5739 (m) cc_final: 0.5503 (m) REVERT: B 246 GLN cc_start: 0.7779 (tp40) cc_final: 0.7295 (tp40) REVERT: B 269 GLU cc_start: 0.7943 (tt0) cc_final: 0.7734 (tt0) REVERT: B 280 ASN cc_start: 0.8023 (p0) cc_final: 0.7664 (p0) REVERT: B 297 THR cc_start: 0.8687 (t) cc_final: 0.8432 (p) REVERT: B 432 ARG cc_start: 0.6273 (mtt90) cc_final: 0.5993 (mtt90) REVERT: B 475 MET cc_start: 0.7906 (tpp) cc_final: 0.7451 (tpp) REVERT: B 500 ARG cc_start: 0.6902 (mmt180) cc_final: 0.6696 (mmt180) REVERT: B 530 MET cc_start: 0.8697 (tpt) cc_final: 0.8398 (mmm) REVERT: B 656 ASN cc_start: 0.7826 (t0) cc_final: 0.7538 (t0) REVERT: B 657 GLU cc_start: 0.7429 (tp30) cc_final: 0.6982 (tp30) REVERT: C 53 PHE cc_start: 0.7199 (p90) cc_final: 0.6860 (p90) REVERT: C 96 TRP cc_start: 0.7852 (m100) cc_final: 0.6771 (m100) REVERT: C 103 GLN cc_start: 0.7867 (tp-100) cc_final: 0.7250 (tm-30) REVERT: C 106 GLU cc_start: 0.7327 (tp30) cc_final: 0.7061 (tp30) REVERT: C 166 LYS cc_start: 0.8007 (mmmt) cc_final: 0.7657 (mmmt) REVERT: C 171 TYR cc_start: 0.7816 (p90) cc_final: 0.7408 (p90) REVERT: C 265 LEU cc_start: 0.8941 (mp) cc_final: 0.8738 (mm) REVERT: C 273 ARG cc_start: 0.8096 (mtt-85) cc_final: 0.7886 (mtt180) REVERT: C 308 ARG cc_start: 0.7697 (mmt90) cc_final: 0.7327 (tpt-90) REVERT: C 309 ILE cc_start: 0.7316 (tp) cc_final: 0.7017 (pt) REVERT: C 414 ILE cc_start: 0.8769 (tp) cc_final: 0.8502 (tt) REVERT: C 417 GLN cc_start: 0.7823 (OUTLIER) cc_final: 0.7516 (mt0) REVERT: C 427 TRP cc_start: 0.7737 (m-90) cc_final: 0.7038 (m-10) REVERT: C 439 ILE cc_start: 0.8171 (mp) cc_final: 0.7904 (mm) REVERT: C 482 GLU cc_start: 0.7611 (mm-30) cc_final: 0.7229 (mm-30) REVERT: C 530 MET cc_start: 0.8473 (tpt) cc_final: 0.8112 (tmm) REVERT: C 610 TRP cc_start: 0.8097 (t-100) cc_final: 0.7709 (t-100) REVERT: C 626 MET cc_start: 0.7859 (OUTLIER) cc_final: 0.7487 (mtt) REVERT: C 656 ASN cc_start: 0.7913 (t0) cc_final: 0.7590 (t0) REVERT: C 657 GLU cc_start: 0.7617 (tp30) cc_final: 0.7070 (tp30) outliers start: 47 outliers final: 35 residues processed: 468 average time/residue: 0.2975 time to fit residues: 195.2929 Evaluate side-chains 473 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 433 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LYS Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 417 GLN Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 119 CYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 417 GLN Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 626 MET Chi-restraints excluded: chain C residue 628 TRP Chi-restraints excluded: chain C residue 629 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 113 optimal weight: 0.6980 chunk 158 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 90 optimal weight: 0.6980 chunk 99 optimal weight: 0.0010 chunk 81 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 8 optimal weight: 0.4980 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN A 363 GLN B 33 ASN B 363 GLN C 114 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.122492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.102151 restraints weight = 21949.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.106187 restraints weight = 12171.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.108978 restraints weight = 8135.454| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.4197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 14547 Z= 0.129 Angle : 0.682 11.981 19893 Z= 0.339 Chirality : 0.045 0.226 2418 Planarity : 0.005 0.059 2421 Dihedral : 7.422 55.375 3122 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.87 % Allowed : 24.20 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.20), residues: 1656 helix: 1.43 (0.27), residues: 378 sheet: 1.17 (0.27), residues: 339 loop : -1.22 (0.20), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 614 HIS 0.005 0.001 HIS A 374 PHE 0.025 0.002 PHE C 93 TYR 0.026 0.001 TYR C 638 ARG 0.010 0.000 ARG A 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00305 ( 45) link_NAG-ASN : angle 2.11111 ( 135) link_BETA1-4 : bond 0.00796 ( 18) link_BETA1-4 : angle 2.47067 ( 54) hydrogen bonds : bond 0.03837 ( 391) hydrogen bonds : angle 4.56552 ( 1092) SS BOND : bond 0.00340 ( 36) SS BOND : angle 2.28866 ( 72) covalent geometry : bond 0.00302 (14448) covalent geometry : angle 0.63623 (19632) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5311.66 seconds wall clock time: 93 minutes 17.43 seconds (5597.43 seconds total)