Starting phenix.real_space_refine on Fri May 16 09:05:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eu8_28608/05_2025/8eu8_28608_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eu8_28608/05_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_28608/05_2025/8eu8_28608.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eu8_28608/05_2025/8eu8_28608.map" model { file = "/net/cci-nas-00/data/ceres_data/8eu8_28608/05_2025/8eu8_28608_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eu8_28608/05_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 9.14, per 1000 atoms: 0.64 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: 3.74 Conformation dependent library (CDL) restraints added in 1.8 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: 1.49 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: 4.47 Time building geometry restraints manager: 4.40 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: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 33.780 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.310 ------------------------------------------------------------------------------- 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 : 1.580 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: 0.2850 time to fit residues: 211.4619 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 : 1.415 ------------------------------------------------------------------------------- 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 = 37)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.103854 restraints weight = 21356.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.107983 restraints weight = 11708.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.110817 restraints weight = 7801.899| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 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 9.300 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 3.34559 ( 135) link_BETA1-4 : bond 0.00970 ( 18) link_BETA1-4 : angle 3.25626 ( 54) hydrogen bonds : bond 0.04870 ( 391) hydrogen bonds : angle 4.72134 ( 1092) SS BOND : bond 0.00320 ( 36) SS BOND : angle 1.96417 ( 72) covalent geometry : bond 0.00335 (14448) covalent geometry : angle 0.71258 (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 : 1.537 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 PHE cc_start: 0.7472 (p90) cc_final: 0.7071 (p90) REVERT: A 69 TRP cc_start: 0.7104 (m-90) cc_final: 0.6143 (m-90) REVERT: A 88 ASN cc_start: 0.8028 (m110) cc_final: 0.7827 (m-40) REVERT: A 96 TRP cc_start: 0.8096 (m100) cc_final: 0.7326 (m100) REVERT: A 102 ASP cc_start: 0.7573 (t70) cc_final: 0.7184 (t0) REVERT: A 104 MET cc_start: 0.8059 (ttt) cc_final: 0.7686 (ttt) REVERT: A 106 GLU cc_start: 0.7525 (tp30) cc_final: 0.7205 (tp30) REVERT: A 113 ASP cc_start: 0.7532 (t0) cc_final: 0.7197 (t0) REVERT: A 165 ASP cc_start: 0.7021 (t0) cc_final: 0.6800 (t0) REVERT: A 166 LYS cc_start: 0.7808 (mmmt) cc_final: 0.7549 (mmmt) REVERT: A 198 THR cc_start: 0.8306 (t) cc_final: 0.8046 (t) REVERT: A 264 SER cc_start: 0.8261 (m) cc_final: 0.7673 (p) REVERT: A 269 GLU cc_start: 0.8054 (tt0) cc_final: 0.7791 (tt0) REVERT: A 344 LYS cc_start: 0.8245 (ttmm) cc_final: 0.7997 (ttmm) REVERT: A 374 HIS cc_start: 0.8436 (OUTLIER) cc_final: 0.8092 (t-170) REVERT: A 420 ILE cc_start: 0.8354 (mt) cc_final: 0.8128 (mm) REVERT: A 468 PHE cc_start: 0.7601 (m-80) cc_final: 0.7367 (m-10) REVERT: A 482 GLU cc_start: 0.7639 (mm-30) cc_final: 0.6832 (mm-30) REVERT: A 535 MET cc_start: 0.6965 (tpp) cc_final: 0.6545 (tpp) REVERT: A 647 GLU cc_start: 0.7517 (tm-30) cc_final: 0.7309 (tm-30) REVERT: A 656 ASN cc_start: 0.7791 (t0) cc_final: 0.7356 (t0) REVERT: B 44 VAL cc_start: 0.8950 (p) cc_final: 0.8608 (m) REVERT: B 50 THR cc_start: 0.8497 (m) cc_final: 0.8264 (m) REVERT: B 53 PHE cc_start: 0.7178 (p90) cc_final: 0.6846 (p90) REVERT: B 82 GLN cc_start: 0.7208 (tp40) cc_final: 0.6734 (tp40) REVERT: B 97 LYS cc_start: 0.7961 (tppt) cc_final: 0.7242 (tppt) REVERT: B 104 MET cc_start: 0.7863 (ttt) cc_final: 0.7555 (ttt) REVERT: B 106 GLU cc_start: 0.7358 (tp30) cc_final: 0.6610 (tp30) REVERT: B 113 ASP cc_start: 0.7595 (t0) cc_final: 0.7072 (t70) REVERT: B 202 THR cc_start: 0.8267 (p) cc_final: 0.7984 (p) REVERT: B 234 ASN cc_start: 0.7471 (t0) cc_final: 0.7117 (t0) REVERT: B 245 VAL cc_start: 0.8452 (OUTLIER) cc_final: 0.8247 (p) REVERT: B 268 LYS cc_start: 0.8502 (pptt) cc_final: 0.8248 (pptt) REVERT: B 280 ASN cc_start: 0.8017 (p0) cc_final: 0.7674 (p0) REVERT: B 297 THR cc_start: 0.8673 (t) cc_final: 0.8434 (p) REVERT: B 432 ARG cc_start: 0.6895 (mtt90) cc_final: 0.6533 (mtt90) REVERT: B 447 SER cc_start: 0.8289 (m) cc_final: 0.7968 (p) REVERT: B 487 LYS cc_start: 0.8196 (tttt) cc_final: 0.7668 (tttt) REVERT: B 490 LYS cc_start: 0.7759 (ttpt) cc_final: 0.7527 (ttpt) REVERT: B 535 MET cc_start: 0.6887 (tpp) cc_final: 0.6625 (tpp) REVERT: B 538 THR cc_start: 0.8204 (p) cc_final: 0.7967 (m) REVERT: B 590 GLN cc_start: 0.8130 (mm-40) cc_final: 0.7895 (mm-40) REVERT: B 656 ASN cc_start: 0.7624 (t0) cc_final: 0.7275 (t0) REVERT: B 657 GLU cc_start: 0.7453 (tp30) cc_final: 0.7218 (tp30) REVERT: C 82 GLN cc_start: 0.7185 (tp40) cc_final: 0.6649 (tp40) REVERT: C 92 ASN cc_start: 0.7609 (p0) cc_final: 0.7286 (p0) REVERT: C 106 GLU cc_start: 0.7338 (tp30) cc_final: 0.6977 (tp30) REVERT: C 121 LYS cc_start: 0.8697 (mttt) cc_final: 0.8314 (mttm) REVERT: C 150 GLU cc_start: 0.7327 (tp30) cc_final: 0.7122 (tp30) REVERT: C 166 LYS cc_start: 0.7911 (mmmt) cc_final: 0.7575 (mmmt) REVERT: C 171 TYR cc_start: 0.7953 (p90) cc_final: 0.7570 (p90) REVERT: C 223 TYR cc_start: 0.8092 (m-80) cc_final: 0.7874 (m-10) REVERT: C 302 ASN cc_start: 0.8629 (m-40) cc_final: 0.8403 (m110) REVERT: C 347 ILE cc_start: 0.8478 (tp) cc_final: 0.8246 (mt) REVERT: C 395 TYR cc_start: 0.7412 (t80) cc_final: 0.7116 (t80) REVERT: C 427 TRP cc_start: 0.7736 (m-90) cc_final: 0.7521 (m-10) REVERT: C 434 MET cc_start: 0.7092 (ttm) cc_final: 0.6789 (ttp) REVERT: C 447 SER cc_start: 0.8405 (m) cc_final: 0.8179 (p) REVERT: C 482 GLU cc_start: 0.7731 (mm-30) cc_final: 0.7319 (mm-30) REVERT: C 656 ASN cc_start: 0.7818 (t0) cc_final: 0.7444 (t0) REVERT: C 657 GLU cc_start: 0.7516 (tp30) cc_final: 0.6793 (tp30) outliers start: 39 outliers final: 19 residues processed: 472 average time/residue: 0.2883 time to fit residues: 190.5689 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 : 1.437 ------------------------------------------------------------------------------- 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: 0.9980 chunk 100 optimal weight: 6.9990 chunk 166 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 chunk 156 optimal weight: 4.9990 chunk 29 optimal weight: 0.0470 chunk 75 optimal weight: 2.9990 chunk 129 optimal weight: 0.0020 chunk 53 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 overall best weight: 0.5286 ------------------------------------------------------------------------------- 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 = 0.3569 r_free = 0.3569 target = 0.124677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.103957 restraints weight = 21675.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.108082 restraints weight = 11929.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.110882 restraints weight = 7973.127| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 14547 Z= 0.131 Angle : 0.713 8.871 19893 Z= 0.349 Chirality : 0.048 0.302 2418 Planarity : 0.004 0.050 2421 Dihedral : 7.933 59.592 3122 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.80 % Allowed : 14.20 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.10 (0.27), residues: 369 sheet: 1.19 (0.24), residues: 375 loop : -0.90 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 35 HIS 0.007 0.001 HIS B 374 PHE 0.024 0.002 PHE C 53 TYR 0.018 0.001 TYR A 191 ARG 0.005 0.000 ARG B 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00411 ( 45) link_NAG-ASN : angle 2.85243 ( 135) link_BETA1-4 : bond 0.01060 ( 18) link_BETA1-4 : angle 3.02330 ( 54) hydrogen bonds : bond 0.04125 ( 391) hydrogen bonds : angle 4.46377 ( 1092) SS BOND : bond 0.00610 ( 36) SS BOND : angle 2.39399 ( 72) covalent geometry : bond 0.00291 (14448) covalent geometry : angle 0.64253 (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 494 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 437 time to evaluate : 1.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 PHE cc_start: 0.7391 (p90) cc_final: 0.6958 (p90) REVERT: A 67 ASN cc_start: 0.7307 (t0) cc_final: 0.7102 (t0) REVERT: A 69 TRP cc_start: 0.7074 (m-90) cc_final: 0.6483 (m-90) REVERT: A 104 MET cc_start: 0.8031 (ttt) cc_final: 0.7800 (ttt) REVERT: A 106 GLU cc_start: 0.7490 (tp30) cc_final: 0.7260 (tp30) REVERT: A 150 GLU cc_start: 0.7465 (tp30) cc_final: 0.7118 (tp30) REVERT: A 165 ASP cc_start: 0.6953 (t0) cc_final: 0.6745 (t0) REVERT: A 166 LYS cc_start: 0.7758 (mmmt) cc_final: 0.7526 (mmmt) REVERT: A 178 ASP cc_start: 0.7815 (OUTLIER) cc_final: 0.7394 (t70) REVERT: A 198 THR cc_start: 0.8171 (t) cc_final: 0.7899 (t) REVERT: A 202 THR cc_start: 0.8125 (p) cc_final: 0.7876 (p) REVERT: A 223 TYR cc_start: 0.8223 (m-80) cc_final: 0.7753 (m-80) REVERT: A 264 SER cc_start: 0.8273 (m) cc_final: 0.8044 (p) REVERT: A 321 ASP cc_start: 0.7391 (t0) cc_final: 0.7142 (t70) REVERT: A 420 ILE cc_start: 0.8338 (mt) cc_final: 0.8134 (mm) REVERT: A 447 SER cc_start: 0.8576 (m) cc_final: 0.8068 (p) REVERT: A 468 PHE cc_start: 0.7756 (m-80) cc_final: 0.7493 (m-10) REVERT: A 482 GLU cc_start: 0.7519 (mm-30) cc_final: 0.7275 (mm-30) REVERT: A 535 MET cc_start: 0.7105 (tpp) cc_final: 0.6626 (tpp) REVERT: A 647 GLU cc_start: 0.7491 (tm-30) cc_final: 0.7225 (tm-30) REVERT: A 654 GLU cc_start: 0.7899 (tp30) cc_final: 0.7624 (tp30) REVERT: A 656 ASN cc_start: 0.7853 (t0) cc_final: 0.7456 (t0) REVERT: B 44 VAL cc_start: 0.8978 (p) cc_final: 0.8661 (m) REVERT: B 53 PHE cc_start: 0.7235 (p90) cc_final: 0.6928 (p90) REVERT: B 69 TRP cc_start: 0.6872 (m-90) cc_final: 0.6368 (m-90) REVERT: B 104 MET cc_start: 0.7762 (ttt) cc_final: 0.7542 (ttt) REVERT: B 106 GLU cc_start: 0.7285 (tp30) cc_final: 0.6907 (tp30) REVERT: B 113 ASP cc_start: 0.7485 (t0) cc_final: 0.6626 (t70) REVERT: B 161 THR cc_start: 0.7571 (m) cc_final: 0.7353 (m) REVERT: B 202 THR cc_start: 0.8291 (p) cc_final: 0.8071 (p) REVERT: B 215 ILE cc_start: 0.8350 (mm) cc_final: 0.8112 (mm) REVERT: B 234 ASN cc_start: 0.7360 (t0) cc_final: 0.7058 (t0) REVERT: B 268 LYS cc_start: 0.8463 (pptt) cc_final: 0.8211 (pptt) REVERT: B 280 ASN cc_start: 0.8033 (p0) cc_final: 0.7636 (p0) REVERT: B 297 THR cc_start: 0.8681 (t) cc_final: 0.8277 (p) REVERT: B 321 ASP cc_start: 0.7505 (t0) cc_final: 0.7204 (t70) REVERT: B 446 ARG cc_start: 0.7600 (mtp85) cc_final: 0.7345 (mtp85) REVERT: B 447 SER cc_start: 0.8213 (m) cc_final: 0.7930 (p) REVERT: B 482 GLU cc_start: 0.7344 (mm-30) cc_final: 0.7097 (mm-30) REVERT: B 490 LYS cc_start: 0.7818 (ttpt) cc_final: 0.7600 (ttpt) REVERT: B 535 MET cc_start: 0.6987 (tpp) cc_final: 0.6660 (tpp) REVERT: B 656 ASN cc_start: 0.7644 (t0) cc_final: 0.7301 (t0) REVERT: B 657 GLU cc_start: 0.7447 (tp30) cc_final: 0.6875 (tp30) REVERT: C 53 PHE cc_start: 0.7317 (p90) cc_final: 0.7084 (p90) REVERT: C 93 PHE cc_start: 0.7650 (m-80) cc_final: 0.7361 (m-10) REVERT: C 96 TRP cc_start: 0.7615 (m-90) cc_final: 0.6796 (m100) REVERT: C 106 GLU cc_start: 0.7310 (tp30) cc_final: 0.7027 (tp30) REVERT: C 116 LEU cc_start: 0.7955 (mt) cc_final: 0.7649 (mp) REVERT: C 150 GLU cc_start: 0.7339 (tp30) cc_final: 0.7101 (tp30) REVERT: C 166 LYS cc_start: 0.7914 (mmmt) cc_final: 0.7616 (mmmt) REVERT: C 171 TYR cc_start: 0.7898 (p90) cc_final: 0.7533 (p90) REVERT: C 195 ASN cc_start: 0.7433 (p0) cc_final: 0.6714 (p0) REVERT: C 301 ASN cc_start: 0.8063 (t0) cc_final: 0.7847 (t0) REVERT: C 302 ASN cc_start: 0.8630 (m-40) cc_final: 0.8389 (m-40) REVERT: C 417 GLN cc_start: 0.7866 (pt0) cc_final: 0.7400 (mt0) REVERT: C 427 TRP cc_start: 0.7639 (m-90) cc_final: 0.7371 (m-10) REVERT: C 482 GLU cc_start: 0.7623 (mm-30) cc_final: 0.7271 (mm-30) REVERT: C 626 MET cc_start: 0.7826 (OUTLIER) cc_final: 0.7443 (mtt) REVERT: C 656 ASN cc_start: 0.7904 (t0) cc_final: 0.7493 (t0) REVERT: C 657 GLU cc_start: 0.7526 (tp30) cc_final: 0.6827 (tp30) outliers start: 57 outliers final: 22 residues processed: 470 average time/residue: 0.2844 time to fit residues: 185.4527 Evaluate side-chains 438 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 414 time to evaluate : 1.358 ------------------------------------------------------------------------------- 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 496 VAL Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 616 ASN 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 323 ILE 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: 2.9990 chunk 89 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 3 optimal weight: 0.0570 chunk 125 optimal weight: 0.5980 chunk 71 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 overall best weight: 1.7304 ------------------------------------------------------------------------------- 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 374 HIS B 625 ASN ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.121367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.100748 restraints weight = 21717.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.104744 restraints weight = 12119.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.107451 restraints weight = 8176.542| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 14547 Z= 0.256 Angle : 0.771 11.002 19893 Z= 0.383 Chirality : 0.053 0.536 2418 Planarity : 0.005 0.064 2421 Dihedral : 8.076 57.417 3122 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 4.40 % Allowed : 16.53 % Favored : 79.07 % 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: -0.20 (0.20), residues: 1656 helix: 0.89 (0.27), residues: 378 sheet: 1.23 (0.27), residues: 339 loop : -1.13 (0.19), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP B 35 HIS 0.010 0.003 HIS B 216 PHE 0.025 0.003 PHE C 53 TYR 0.022 0.002 TYR A 638 ARG 0.011 0.001 ARG A 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00565 ( 45) link_NAG-ASN : angle 2.86729 ( 135) link_BETA1-4 : bond 0.00865 ( 18) link_BETA1-4 : angle 2.86533 ( 54) hydrogen bonds : bond 0.05040 ( 391) hydrogen bonds : angle 4.64193 ( 1092) SS BOND : bond 0.00586 ( 36) SS BOND : angle 2.86857 ( 72) covalent geometry : bond 0.00591 (14448) covalent geometry : angle 0.70268 (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 517 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 451 time to evaluate : 1.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ASN cc_start: 0.7364 (t0) cc_final: 0.7130 (t0) REVERT: A 69 TRP cc_start: 0.7128 (m-90) cc_final: 0.6573 (m-90) REVERT: A 91 GLU cc_start: 0.6689 (mm-30) cc_final: 0.6486 (mm-30) REVERT: A 117 LYS cc_start: 0.8491 (ttmm) cc_final: 0.8078 (ttmm) REVERT: A 150 GLU cc_start: 0.7428 (tp30) cc_final: 0.7018 (tp30) REVERT: A 166 LYS cc_start: 0.7853 (mmmt) cc_final: 0.7567 (mmmt) REVERT: A 246 GLN cc_start: 0.7791 (tp40) cc_final: 0.7385 (tp40) REVERT: A 264 SER cc_start: 0.8257 (m) cc_final: 0.7648 (p) REVERT: A 308 ARG cc_start: 0.7809 (tpp80) cc_final: 0.7588 (tpp80) REVERT: A 321 ASP cc_start: 0.7425 (t0) cc_final: 0.7189 (t70) REVERT: A 468 PHE cc_start: 0.7936 (m-80) cc_final: 0.7598 (m-10) REVERT: A 477 ASP cc_start: 0.7523 (m-30) cc_final: 0.7259 (m-30) REVERT: A 482 GLU cc_start: 0.7543 (mm-30) cc_final: 0.6761 (mm-30) REVERT: A 535 MET cc_start: 0.6896 (tpp) cc_final: 0.6601 (tpp) REVERT: A 647 GLU cc_start: 0.7615 (tm-30) cc_final: 0.7218 (tm-30) REVERT: A 654 GLU cc_start: 0.7905 (tp30) cc_final: 0.7618 (tp30) REVERT: A 656 ASN cc_start: 0.7909 (t0) cc_final: 0.7519 (t0) REVERT: B 44 VAL cc_start: 0.9038 (p) cc_final: 0.8758 (m) REVERT: B 53 PHE cc_start: 0.7258 (p90) cc_final: 0.7040 (p90) REVERT: B 104 MET cc_start: 0.7832 (ttt) cc_final: 0.7553 (ttt) REVERT: B 106 GLU cc_start: 0.7340 (tp30) cc_final: 0.6967 (tp30) REVERT: B 113 ASP cc_start: 0.7330 (t0) cc_final: 0.6568 (t0) REVERT: B 161 THR cc_start: 0.7678 (m) cc_final: 0.7416 (m) REVERT: B 205 CYS cc_start: 0.5742 (m) cc_final: 0.5464 (m) REVERT: B 245 VAL cc_start: 0.8711 (t) cc_final: 0.8500 (p) REVERT: B 268 LYS cc_start: 0.8487 (pptt) cc_final: 0.8215 (pptt) REVERT: B 273 ARG cc_start: 0.8112 (mtt-85) cc_final: 0.7905 (mtt-85) REVERT: B 280 ASN cc_start: 0.8048 (p0) cc_final: 0.7665 (p0) REVERT: B 297 THR cc_start: 0.8690 (t) cc_final: 0.8293 (p) REVERT: B 321 ASP cc_start: 0.7556 (t0) cc_final: 0.7257 (t70) REVERT: B 432 ARG cc_start: 0.6411 (mtt90) cc_final: 0.6060 (mtt90) REVERT: B 447 SER cc_start: 0.8216 (m) cc_final: 0.7999 (p) REVERT: B 482 GLU cc_start: 0.7324 (mm-30) cc_final: 0.7101 (mm-30) REVERT: B 490 LYS cc_start: 0.7746 (ttpt) cc_final: 0.7543 (ttpt) REVERT: B 656 ASN cc_start: 0.7761 (t0) cc_final: 0.7478 (t0) REVERT: B 657 GLU cc_start: 0.7472 (tp30) cc_final: 0.6947 (tp30) REVERT: C 53 PHE cc_start: 0.7319 (p90) cc_final: 0.6969 (p90) REVERT: C 72 HIS cc_start: 0.6677 (OUTLIER) cc_final: 0.6421 (t70) REVERT: C 93 PHE cc_start: 0.7899 (m-80) cc_final: 0.7624 (m-10) REVERT: C 106 GLU cc_start: 0.7379 (tp30) cc_final: 0.7045 (tp30) REVERT: C 150 GLU cc_start: 0.7319 (tp30) cc_final: 0.6978 (tp30) REVERT: C 166 LYS cc_start: 0.8025 (mmmt) cc_final: 0.7638 (mmmt) REVERT: C 171 TYR cc_start: 0.7930 (p90) cc_final: 0.7562 (p90) REVERT: C 273 ARG cc_start: 0.8119 (mtt-85) cc_final: 0.7756 (mtt-85) REVERT: C 302 ASN cc_start: 0.8508 (m-40) cc_final: 0.8304 (m-40) REVERT: C 417 GLN cc_start: 0.7946 (pt0) cc_final: 0.7457 (mt0) REVERT: C 427 TRP cc_start: 0.7660 (m-90) cc_final: 0.7265 (m-10) REVERT: C 475 MET cc_start: 0.7879 (tpp) cc_final: 0.7615 (tpp) REVERT: C 482 GLU cc_start: 0.7682 (mm-30) cc_final: 0.7320 (mm-30) REVERT: C 529 THR cc_start: 0.7981 (m) cc_final: 0.7672 (m) REVERT: C 530 MET cc_start: 0.8868 (mmm) cc_final: 0.8389 (mmm) REVERT: C 577 GLN cc_start: 0.7299 (tm-30) cc_final: 0.6760 (tm-30) REVERT: C 626 MET cc_start: 0.7868 (OUTLIER) cc_final: 0.7495 (mtt) REVERT: C 656 ASN cc_start: 0.7894 (t0) cc_final: 0.7547 (t0) REVERT: C 657 GLU cc_start: 0.7607 (tp30) cc_final: 0.6957 (tp30) outliers start: 66 outliers final: 37 residues processed: 486 average time/residue: 0.2805 time to fit residues: 191.6073 Evaluate side-chains 468 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 429 time to evaluate : 1.427 ------------------------------------------------------------------------------- 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 199 SER 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 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 75 VAL 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 199 SER Chi-restraints excluded: chain B residue 290 THR 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 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 72 HIS 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: 7.9990 chunk 10 optimal weight: 1.9990 chunk 50 optimal weight: 0.3980 chunk 22 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 59 optimal weight: 6.9990 chunk 108 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 363 GLN B 114 GLN B 302 ASN C 105 HIS ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.121487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.100887 restraints weight = 22042.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.104958 restraints weight = 12231.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.107710 restraints weight = 8209.893| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 14547 Z= 0.168 Angle : 0.715 12.111 19893 Z= 0.354 Chirality : 0.048 0.318 2418 Planarity : 0.004 0.060 2421 Dihedral : 7.789 55.080 3122 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 4.53 % Allowed : 18.53 % Favored : 76.93 % 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: -0.13 (0.20), residues: 1656 helix: 1.17 (0.27), residues: 375 sheet: 1.06 (0.27), residues: 339 loop : -1.09 (0.19), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP C 35 HIS 0.004 0.001 HIS C 374 PHE 0.022 0.002 PHE C 53 TYR 0.025 0.002 TYR A 638 ARG 0.005 0.000 ARG A 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00365 ( 45) link_NAG-ASN : angle 2.54377 ( 135) link_BETA1-4 : bond 0.00923 ( 18) link_BETA1-4 : angle 2.78496 ( 54) hydrogen bonds : bond 0.04319 ( 391) hydrogen bonds : angle 4.51564 ( 1092) SS BOND : bond 0.00566 ( 36) SS BOND : angle 2.87349 ( 72) covalent geometry : bond 0.00391 (14448) covalent geometry : angle 0.64960 (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 519 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 451 time to evaluate : 1.609 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 67 ASN cc_start: 0.7427 (t0) cc_final: 0.7119 (t0) REVERT: A 69 TRP cc_start: 0.7069 (m-90) cc_final: 0.6650 (m-90) REVERT: A 104 MET cc_start: 0.8146 (ttt) cc_final: 0.7900 (ttt) REVERT: A 117 LYS cc_start: 0.8421 (ttmm) cc_final: 0.8030 (ttmm) REVERT: A 150 GLU cc_start: 0.7389 (tp30) cc_final: 0.6953 (tp30) REVERT: A 166 LYS cc_start: 0.7835 (mmmt) cc_final: 0.7566 (mmmt) REVERT: A 202 THR cc_start: 0.8035 (p) cc_final: 0.7808 (p) REVERT: A 246 GLN cc_start: 0.7791 (tp40) cc_final: 0.7394 (tp40) REVERT: A 258 GLN cc_start: 0.8068 (mt0) cc_final: 0.7770 (mt0) REVERT: A 264 SER cc_start: 0.8298 (m) cc_final: 0.7719 (p) REVERT: A 468 PHE cc_start: 0.7899 (m-80) cc_final: 0.7616 (m-10) REVERT: A 477 ASP cc_start: 0.7507 (m-30) cc_final: 0.7283 (m-30) REVERT: A 482 GLU cc_start: 0.7510 (mm-30) cc_final: 0.6746 (mm-30) REVERT: A 535 MET cc_start: 0.6938 (tpp) cc_final: 0.6700 (tpp) REVERT: A 647 GLU cc_start: 0.7591 (tm-30) cc_final: 0.7232 (tm-30) REVERT: A 656 ASN cc_start: 0.7901 (t0) cc_final: 0.7526 (t0) REVERT: B 44 VAL cc_start: 0.9028 (p) cc_final: 0.8768 (m) REVERT: B 53 PHE cc_start: 0.7071 (p90) cc_final: 0.6847 (p90) REVERT: B 106 GLU cc_start: 0.7336 (tp30) cc_final: 0.6970 (tp30) REVERT: B 113 ASP cc_start: 0.7345 (t0) cc_final: 0.6619 (t0) REVERT: B 136 VAL cc_start: 0.7599 (OUTLIER) cc_final: 0.7318 (p) REVERT: B 150 GLU cc_start: 0.7586 (tp30) cc_final: 0.7190 (tp30) REVERT: B 161 THR cc_start: 0.7829 (m) cc_final: 0.7569 (m) REVERT: B 205 CYS cc_start: 0.5700 (m) cc_final: 0.5446 (m) REVERT: B 280 ASN cc_start: 0.8022 (p0) cc_final: 0.7601 (p0) REVERT: B 297 THR cc_start: 0.8656 (t) cc_final: 0.8315 (p) REVERT: B 321 ASP cc_start: 0.7552 (t0) cc_final: 0.7343 (t70) REVERT: B 432 ARG cc_start: 0.6448 (mtt90) cc_final: 0.6142 (mtt90) REVERT: B 447 SER cc_start: 0.8185 (m) cc_final: 0.7963 (p) REVERT: B 490 LYS cc_start: 0.7797 (ttpt) cc_final: 0.7566 (ttpt) REVERT: B 656 ASN cc_start: 0.7762 (t0) cc_final: 0.7482 (t0) REVERT: B 657 GLU cc_start: 0.7437 (tp30) cc_final: 0.6936 (tp30) REVERT: C 53 PHE cc_start: 0.7133 (p90) cc_final: 0.6852 (p90) REVERT: C 72 HIS cc_start: 0.6705 (OUTLIER) cc_final: 0.6411 (t70) REVERT: C 91 GLU cc_start: 0.6916 (mm-30) cc_final: 0.6682 (mm-30) REVERT: C 93 PHE cc_start: 0.7791 (m-80) cc_final: 0.7531 (m-10) REVERT: C 103 GLN cc_start: 0.7922 (tp40) cc_final: 0.7352 (tm-30) REVERT: C 106 GLU cc_start: 0.7337 (tp30) cc_final: 0.7060 (tp30) REVERT: C 150 GLU cc_start: 0.7319 (tp30) cc_final: 0.6922 (tp30) REVERT: C 153 LYS cc_start: 0.7914 (mmtt) cc_final: 0.7590 (mmtm) REVERT: C 166 LYS cc_start: 0.7980 (mmmt) cc_final: 0.7634 (mmmt) REVERT: C 171 TYR cc_start: 0.7910 (p90) cc_final: 0.7513 (p90) REVERT: C 273 ARG cc_start: 0.8167 (mtt-85) cc_final: 0.7729 (mtt-85) REVERT: C 302 ASN cc_start: 0.8494 (m-40) cc_final: 0.8283 (m110) REVERT: C 417 GLN cc_start: 0.7874 (OUTLIER) cc_final: 0.7553 (mt0) REVERT: C 427 TRP cc_start: 0.7639 (m-90) cc_final: 0.7207 (m-10) REVERT: C 475 MET cc_start: 0.7850 (tpp) cc_final: 0.7629 (tpp) REVERT: C 482 GLU cc_start: 0.7655 (mm-30) cc_final: 0.7307 (mm-30) REVERT: C 529 THR cc_start: 0.8043 (m) cc_final: 0.7753 (m) REVERT: C 530 MET cc_start: 0.8779 (mmm) cc_final: 0.8515 (tpp) REVERT: C 577 GLN cc_start: 0.7245 (tm-30) cc_final: 0.6669 (tm-30) REVERT: C 626 MET cc_start: 0.7875 (OUTLIER) cc_final: 0.7561 (mtt) REVERT: C 656 ASN cc_start: 0.7875 (t0) cc_final: 0.7543 (t0) REVERT: C 657 GLU cc_start: 0.7589 (tp30) cc_final: 0.6957 (tp30) outliers start: 68 outliers final: 46 residues processed: 488 average time/residue: 0.2926 time to fit residues: 200.3281 Evaluate side-chains 490 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 440 time to evaluate : 1.503 ------------------------------------------------------------------------------- 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 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 A residue 629 LEU 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 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 182 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 213 ILE 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 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 72 HIS 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 120 VAL Chi-restraints excluded: chain C residue 182 LEU 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 323 ILE Chi-restraints excluded: chain C residue 347 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 154 optimal weight: 0.6980 chunk 143 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 76 optimal weight: 0.0470 chunk 48 optimal weight: 0.6980 chunk 8 optimal weight: 0.0050 chunk 149 optimal weight: 4.9990 chunk 137 optimal weight: 0.9990 chunk 85 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 overall best weight: 0.4492 ------------------------------------------------------------------------------- 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 114 GLN B 302 ASN B 363 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.122945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.102265 restraints weight = 22137.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.106398 restraints weight = 12240.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.109075 restraints weight = 8184.015| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.3701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 14547 Z= 0.123 Angle : 0.662 12.697 19893 Z= 0.326 Chirality : 0.046 0.243 2418 Planarity : 0.004 0.059 2421 Dihedral : 7.584 54.796 3122 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 4.93 % Allowed : 19.07 % Favored : 76.00 % 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: -0.10 (0.20), residues: 1656 helix: 1.33 (0.27), residues: 378 sheet: 1.03 (0.27), residues: 339 loop : -1.13 (0.19), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP C 35 HIS 0.004 0.001 HIS A 374 PHE 0.020 0.001 PHE C 53 TYR 0.024 0.001 TYR C 638 ARG 0.010 0.001 ARG B 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00313 ( 45) link_NAG-ASN : angle 2.35066 ( 135) link_BETA1-4 : bond 0.00916 ( 18) link_BETA1-4 : angle 2.67266 ( 54) hydrogen bonds : bond 0.03790 ( 391) hydrogen bonds : angle 4.48821 ( 1092) SS BOND : bond 0.00359 ( 36) SS BOND : angle 2.43552 ( 72) covalent geometry : bond 0.00280 (14448) covalent geometry : angle 0.60423 (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 513 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 439 time to evaluate : 1.404 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 67 ASN cc_start: 0.7380 (t0) cc_final: 0.7062 (t0) REVERT: A 69 TRP cc_start: 0.6953 (m-90) cc_final: 0.6709 (m-90) REVERT: A 104 MET cc_start: 0.8079 (ttt) cc_final: 0.7784 (ttt) REVERT: A 117 LYS cc_start: 0.8423 (ttmm) cc_final: 0.8027 (ttmm) REVERT: A 121 LYS cc_start: 0.8479 (mttm) cc_final: 0.8255 (mtpp) REVERT: A 136 VAL cc_start: 0.7577 (OUTLIER) cc_final: 0.7285 (p) REVERT: A 150 GLU cc_start: 0.7392 (tp30) cc_final: 0.6916 (tp30) REVERT: A 166 LYS cc_start: 0.7797 (mmmt) cc_final: 0.7507 (mmmt) REVERT: A 245 VAL cc_start: 0.8695 (t) cc_final: 0.8348 (p) REVERT: A 246 GLN cc_start: 0.7829 (tp40) cc_final: 0.7476 (tp40) REVERT: A 264 SER cc_start: 0.8329 (m) cc_final: 0.7705 (p) REVERT: A 297 THR cc_start: 0.8694 (t) cc_final: 0.8444 (p) REVERT: A 308 ARG cc_start: 0.7823 (tpp80) cc_final: 0.7560 (tpp80) REVERT: A 344 LYS cc_start: 0.8148 (ttmm) cc_final: 0.7829 (ttmm) REVERT: A 417 GLN cc_start: 0.7780 (OUTLIER) cc_final: 0.7193 (mt0) REVERT: A 420 ILE cc_start: 0.8482 (mt) cc_final: 0.8212 (mm) REVERT: A 477 ASP cc_start: 0.7450 (m-30) cc_final: 0.7206 (m-30) REVERT: A 482 GLU cc_start: 0.7516 (mm-30) cc_final: 0.6683 (mm-30) REVERT: A 535 MET cc_start: 0.7033 (tpp) cc_final: 0.6832 (tpp) REVERT: A 631 TRP cc_start: 0.7990 (t-100) cc_final: 0.7776 (t-100) REVERT: A 647 GLU cc_start: 0.7569 (tm-30) cc_final: 0.7199 (tm-30) REVERT: A 656 ASN cc_start: 0.7829 (t0) cc_final: 0.7476 (t0) REVERT: B 35 TRP cc_start: 0.7744 (m-10) cc_final: 0.7377 (m-10) REVERT: B 44 VAL cc_start: 0.9039 (p) cc_final: 0.8796 (m) REVERT: B 69 TRP cc_start: 0.6831 (m-90) cc_final: 0.6365 (m-90) REVERT: B 93 PHE cc_start: 0.7419 (m-10) cc_final: 0.7180 (m-80) REVERT: B 106 GLU cc_start: 0.7327 (tp30) cc_final: 0.6952 (tp30) REVERT: B 113 ASP cc_start: 0.7322 (t0) cc_final: 0.6491 (t0) REVERT: B 150 GLU cc_start: 0.7553 (tp30) cc_final: 0.7164 (tp30) REVERT: B 161 THR cc_start: 0.7828 (m) cc_final: 0.7587 (m) REVERT: B 251 ILE cc_start: 0.8325 (mm) cc_final: 0.7886 (mm) REVERT: B 268 LYS cc_start: 0.8427 (pptt) cc_final: 0.8127 (pptt) REVERT: B 280 ASN cc_start: 0.8003 (p0) cc_final: 0.7585 (p0) REVERT: B 297 THR cc_start: 0.8670 (t) cc_final: 0.8417 (p) REVERT: B 321 ASP cc_start: 0.7546 (t0) cc_final: 0.7296 (t70) REVERT: B 432 ARG cc_start: 0.6384 (mtt90) cc_final: 0.6012 (mtt90) REVERT: B 490 LYS cc_start: 0.7802 (ttpt) cc_final: 0.7585 (ttpt) REVERT: B 530 MET cc_start: 0.8846 (mmm) cc_final: 0.8642 (tpp) REVERT: B 656 ASN cc_start: 0.7769 (t0) cc_final: 0.7494 (t0) REVERT: B 657 GLU cc_start: 0.7429 (tp30) cc_final: 0.6953 (tp30) REVERT: C 53 PHE cc_start: 0.7098 (p90) cc_final: 0.6772 (p90) REVERT: C 72 HIS cc_start: 0.6768 (OUTLIER) cc_final: 0.6418 (t70) REVERT: C 91 GLU cc_start: 0.6879 (mm-30) cc_final: 0.6635 (mm-30) REVERT: C 93 PHE cc_start: 0.7728 (m-80) cc_final: 0.7479 (m-10) REVERT: C 103 GLN cc_start: 0.7853 (tp40) cc_final: 0.7285 (tm-30) REVERT: C 106 GLU cc_start: 0.7308 (tp30) cc_final: 0.7049 (tp30) REVERT: C 136 VAL cc_start: 0.7403 (OUTLIER) cc_final: 0.7011 (p) REVERT: C 150 GLU cc_start: 0.7318 (tp30) cc_final: 0.6675 (tp30) REVERT: C 166 LYS cc_start: 0.7926 (mmmt) cc_final: 0.7593 (mmmt) REVERT: C 171 TYR cc_start: 0.7864 (p90) cc_final: 0.7477 (p90) REVERT: C 176 LYS cc_start: 0.8595 (ttmt) cc_final: 0.8253 (ttpt) REVERT: C 202 THR cc_start: 0.8135 (p) cc_final: 0.7876 (p) REVERT: C 265 LEU cc_start: 0.8944 (mp) cc_final: 0.8692 (mm) REVERT: C 267 GLU cc_start: 0.7012 (tp30) cc_final: 0.6757 (tp30) REVERT: C 273 ARG cc_start: 0.8246 (mtt-85) cc_final: 0.7836 (mtt-85) REVERT: C 302 ASN cc_start: 0.8508 (m-40) cc_final: 0.8236 (m110) REVERT: C 417 GLN cc_start: 0.7815 (OUTLIER) cc_final: 0.7521 (mt0) REVERT: C 427 TRP cc_start: 0.7590 (m-90) cc_final: 0.7127 (m-10) REVERT: C 482 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7225 (mm-30) REVERT: C 529 THR cc_start: 0.8024 (m) cc_final: 0.7760 (m) REVERT: C 626 MET cc_start: 0.7871 (OUTLIER) cc_final: 0.7547 (mtt) REVERT: C 656 ASN cc_start: 0.7862 (t0) cc_final: 0.7530 (t0) REVERT: C 657 GLU cc_start: 0.7571 (tp30) cc_final: 0.6955 (tp30) outliers start: 74 outliers final: 45 residues processed: 481 average time/residue: 0.2707 time to fit residues: 183.7371 Evaluate side-chains 480 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 429 time to evaluate : 1.472 ------------------------------------------------------------------------------- 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 167 GLU 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 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 A residue 455 THR Chi-restraints excluded: chain A residue 642 ILE 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 138 THR Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 213 ILE 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 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 B residue 595 ILE Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 72 HIS 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 182 LEU 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 323 ILE Chi-restraints excluded: chain C residue 395 TYR Chi-restraints excluded: chain C residue 417 GLN Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 496 VAL 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: 0.8980 chunk 124 optimal weight: 1.9990 chunk 146 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 153 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.120711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.100058 restraints weight = 21920.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.104075 restraints weight = 12247.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.106875 restraints weight = 8236.513| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 14547 Z= 0.209 Angle : 0.710 13.174 19893 Z= 0.352 Chirality : 0.048 0.253 2418 Planarity : 0.004 0.064 2421 Dihedral : 7.691 55.145 3122 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 4.00 % Allowed : 20.87 % Favored : 75.13 % 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: -0.20 (0.20), residues: 1656 helix: 1.31 (0.27), residues: 378 sheet: 0.98 (0.28), residues: 339 loop : -1.23 (0.19), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP C 35 HIS 0.005 0.002 HIS A 216 PHE 0.018 0.002 PHE C 53 TYR 0.022 0.002 TYR C 638 ARG 0.007 0.001 ARG B 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00408 ( 45) link_NAG-ASN : angle 2.35666 ( 135) link_BETA1-4 : bond 0.00829 ( 18) link_BETA1-4 : angle 2.64202 ( 54) hydrogen bonds : bond 0.04452 ( 391) hydrogen bonds : angle 4.60096 ( 1092) SS BOND : bond 0.00507 ( 36) SS BOND : angle 2.80079 ( 72) covalent geometry : bond 0.00482 (14448) covalent geometry : angle 0.65191 (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 522 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 462 time to evaluate : 1.573 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: A 67 ASN cc_start: 0.7447 (t0) cc_final: 0.7139 (t0) REVERT: A 69 TRP cc_start: 0.6968 (m-90) cc_final: 0.6730 (m-90) REVERT: A 117 LYS cc_start: 0.8454 (ttmm) cc_final: 0.8078 (ttmm) REVERT: A 136 VAL cc_start: 0.7500 (OUTLIER) cc_final: 0.7191 (p) REVERT: A 150 GLU cc_start: 0.7417 (tp30) cc_final: 0.6857 (tp30) REVERT: A 166 LYS cc_start: 0.7828 (mmmt) cc_final: 0.7617 (mmmt) REVERT: A 176 LYS cc_start: 0.8594 (ttmt) cc_final: 0.8384 (ttmt) REVERT: A 246 GLN cc_start: 0.7847 (tp40) cc_final: 0.7495 (tp40) REVERT: A 258 GLN cc_start: 0.8106 (mt0) cc_final: 0.7768 (mt0) REVERT: A 264 SER cc_start: 0.8303 (m) cc_final: 0.7680 (p) REVERT: A 297 THR cc_start: 0.8720 (t) cc_final: 0.8459 (p) REVERT: A 417 GLN cc_start: 0.7830 (OUTLIER) cc_final: 0.7257 (mt0) REVERT: A 477 ASP cc_start: 0.7455 (m-30) cc_final: 0.7232 (m-30) REVERT: A 482 GLU cc_start: 0.7524 (mm-30) cc_final: 0.6730 (mm-30) REVERT: A 631 TRP cc_start: 0.8113 (t-100) cc_final: 0.7807 (t-100) REVERT: A 635 ILE cc_start: 0.8454 (tp) cc_final: 0.8099 (tt) REVERT: A 647 GLU cc_start: 0.7616 (tm-30) cc_final: 0.7191 (tm-30) REVERT: A 656 ASN cc_start: 0.7894 (t0) cc_final: 0.7526 (t0) REVERT: B 35 TRP cc_start: 0.7854 (m-10) cc_final: 0.7483 (m-10) REVERT: B 44 VAL cc_start: 0.9040 (p) cc_final: 0.8816 (m) REVERT: B 69 TRP cc_start: 0.6934 (m-90) cc_final: 0.6475 (m-90) REVERT: B 106 GLU cc_start: 0.7339 (tp30) cc_final: 0.6948 (tp30) REVERT: B 113 ASP cc_start: 0.7243 (t0) cc_final: 0.6230 (t0) REVERT: B 136 VAL cc_start: 0.7527 (OUTLIER) cc_final: 0.7167 (p) REVERT: B 150 GLU cc_start: 0.7567 (tp30) cc_final: 0.7114 (tp30) REVERT: B 161 THR cc_start: 0.7914 (OUTLIER) cc_final: 0.7649 (m) REVERT: B 205 CYS cc_start: 0.5747 (m) cc_final: 0.5502 (m) REVERT: B 246 GLN cc_start: 0.7783 (tp40) cc_final: 0.7310 (tp40) REVERT: B 268 LYS cc_start: 0.8425 (pptt) cc_final: 0.8130 (pptt) REVERT: B 280 ASN cc_start: 0.8053 (p0) cc_final: 0.7641 (p0) REVERT: B 297 THR cc_start: 0.8746 (t) cc_final: 0.8396 (p) REVERT: B 321 ASP cc_start: 0.7570 (t0) cc_final: 0.7313 (t70) REVERT: B 432 ARG cc_start: 0.6445 (mtt90) cc_final: 0.6166 (mtt90) REVERT: B 490 LYS cc_start: 0.7792 (ttpt) cc_final: 0.7590 (ttpt) REVERT: B 530 MET cc_start: 0.8884 (mmm) cc_final: 0.8620 (tpp) REVERT: B 656 ASN cc_start: 0.7826 (t0) cc_final: 0.7545 (t0) REVERT: B 657 GLU cc_start: 0.7424 (tp30) cc_final: 0.6963 (tp30) REVERT: C 35 TRP cc_start: 0.7490 (m-10) cc_final: 0.7248 (m-10) REVERT: C 53 PHE cc_start: 0.7148 (p90) cc_final: 0.6830 (p90) REVERT: C 72 HIS cc_start: 0.6759 (OUTLIER) cc_final: 0.6413 (t70) REVERT: C 91 GLU cc_start: 0.6841 (mm-30) cc_final: 0.6578 (mm-30) REVERT: C 106 GLU cc_start: 0.7375 (tp30) cc_final: 0.7090 (tp30) REVERT: C 121 LYS cc_start: 0.8705 (mttt) cc_final: 0.8323 (mttm) REVERT: C 150 GLU cc_start: 0.7330 (tp30) cc_final: 0.6799 (tp30) REVERT: C 166 LYS cc_start: 0.7978 (mmmt) cc_final: 0.7628 (mmmt) REVERT: C 171 TYR cc_start: 0.7873 (p90) cc_final: 0.7496 (p90) REVERT: C 273 ARG cc_start: 0.8239 (mtt-85) cc_final: 0.7891 (mtt-85) REVERT: C 302 ASN cc_start: 0.8471 (m-40) cc_final: 0.8264 (m110) REVERT: C 417 GLN cc_start: 0.7889 (OUTLIER) cc_final: 0.7560 (mt0) REVERT: C 427 TRP cc_start: 0.7679 (m-90) cc_final: 0.7086 (m-10) REVERT: C 439 ILE cc_start: 0.8120 (mp) cc_final: 0.7888 (mm) REVERT: C 482 GLU cc_start: 0.7692 (mm-30) cc_final: 0.7233 (mm-30) REVERT: C 529 THR cc_start: 0.8045 (m) cc_final: 0.7804 (m) REVERT: C 540 GLN cc_start: 0.7639 (mp10) cc_final: 0.7325 (mp10) REVERT: C 626 MET cc_start: 0.7872 (OUTLIER) cc_final: 0.7585 (mtt) REVERT: C 656 ASN cc_start: 0.7892 (t0) cc_final: 0.7576 (t0) REVERT: C 657 GLU cc_start: 0.7584 (tp30) cc_final: 0.6979 (tp30) outliers start: 60 outliers final: 38 residues processed: 491 average time/residue: 0.2743 time to fit residues: 189.8213 Evaluate side-chains 494 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 449 time to evaluate : 1.415 ------------------------------------------------------------------------------- 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 119 CYS Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 167 GLU 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 271 VAL Chi-restraints excluded: chain A residue 283 ILE 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 642 ILE 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 213 ILE 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 C residue 49 LYS Chi-restraints excluded: chain C residue 72 HIS 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 182 LEU Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 290 THR 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 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: 2.9990 chunk 17 optimal weight: 0.9990 chunk 157 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 chunk 18 optimal weight: 0.1980 chunk 16 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 154 optimal weight: 1.9990 chunk 156 optimal weight: 0.7980 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 315 GLN C 363 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.122919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.102295 restraints weight = 21793.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.106358 restraints weight = 12137.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.109075 restraints weight = 8167.219| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.3936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 14547 Z= 0.166 Angle : 0.687 11.870 19893 Z= 0.340 Chirality : 0.046 0.237 2418 Planarity : 0.004 0.062 2421 Dihedral : 7.570 54.933 3122 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 4.20 % Allowed : 21.40 % Favored : 74.40 % 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: 1.37 (0.27), residues: 378 sheet: 0.93 (0.26), residues: 369 loop : -1.25 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP C 35 HIS 0.004 0.001 HIS A 216 PHE 0.017 0.002 PHE C 53 TYR 0.025 0.002 TYR A 638 ARG 0.007 0.000 ARG B 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00339 ( 45) link_NAG-ASN : angle 2.23923 ( 135) link_BETA1-4 : bond 0.00803 ( 18) link_BETA1-4 : angle 2.57231 ( 54) hydrogen bonds : bond 0.04142 ( 391) hydrogen bonds : angle 4.55161 ( 1092) SS BOND : bond 0.00464 ( 36) SS BOND : angle 2.49420 ( 72) covalent geometry : bond 0.00387 (14448) covalent geometry : angle 0.63409 (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 509 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 446 time to evaluate : 1.417 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: A 67 ASN cc_start: 0.7440 (t0) cc_final: 0.7153 (t0) REVERT: A 69 TRP cc_start: 0.6943 (m-90) cc_final: 0.6688 (m-90) REVERT: A 117 LYS cc_start: 0.8460 (ttmm) cc_final: 0.8088 (ttmm) REVERT: A 136 VAL cc_start: 0.7472 (OUTLIER) cc_final: 0.7203 (p) REVERT: A 150 GLU cc_start: 0.7384 (tp30) cc_final: 0.6809 (tp30) REVERT: A 176 LYS cc_start: 0.8566 (ttmt) cc_final: 0.8310 (ttmt) REVERT: A 245 VAL cc_start: 0.8708 (t) cc_final: 0.8369 (p) REVERT: A 246 GLN cc_start: 0.7859 (tp40) cc_final: 0.7503 (tp40) REVERT: A 258 GLN cc_start: 0.8073 (mt0) cc_final: 0.7744 (mt0) REVERT: A 264 SER cc_start: 0.8317 (m) cc_final: 0.7667 (p) REVERT: A 297 THR cc_start: 0.8711 (t) cc_final: 0.8463 (p) REVERT: A 321 ASP cc_start: 0.7342 (t0) cc_final: 0.7127 (t0) REVERT: A 344 LYS cc_start: 0.8183 (ttmm) cc_final: 0.7897 (ttmm) REVERT: A 417 GLN cc_start: 0.7820 (OUTLIER) cc_final: 0.7247 (mt0) REVERT: A 477 ASP cc_start: 0.7432 (m-30) cc_final: 0.7205 (m-30) REVERT: A 482 GLU cc_start: 0.7515 (mm-30) cc_final: 0.6675 (mm-30) REVERT: A 631 TRP cc_start: 0.8095 (t-100) cc_final: 0.7744 (t-100) REVERT: A 635 ILE cc_start: 0.8380 (tp) cc_final: 0.7971 (tt) REVERT: A 647 GLU cc_start: 0.7572 (tm-30) cc_final: 0.7198 (tm-30) REVERT: A 656 ASN cc_start: 0.7862 (t0) cc_final: 0.7525 (t0) REVERT: B 35 TRP cc_start: 0.7796 (m-10) cc_final: 0.7433 (m-10) REVERT: B 44 VAL cc_start: 0.9027 (p) cc_final: 0.8806 (m) REVERT: B 69 TRP cc_start: 0.6892 (m-90) cc_final: 0.6442 (m-90) REVERT: B 93 PHE cc_start: 0.7439 (m-10) cc_final: 0.7110 (m-80) REVERT: B 104 MET cc_start: 0.7785 (ttt) cc_final: 0.7357 (ttm) REVERT: B 106 GLU cc_start: 0.7303 (tp30) cc_final: 0.6927 (tp30) REVERT: B 113 ASP cc_start: 0.7228 (t0) cc_final: 0.6159 (t0) REVERT: B 136 VAL cc_start: 0.7518 (OUTLIER) cc_final: 0.7159 (p) REVERT: B 150 GLU cc_start: 0.7527 (tp30) cc_final: 0.7073 (tp30) REVERT: B 161 THR cc_start: 0.7901 (OUTLIER) cc_final: 0.7679 (m) REVERT: B 205 CYS cc_start: 0.5728 (m) cc_final: 0.5477 (m) REVERT: B 246 GLN cc_start: 0.7782 (tp40) cc_final: 0.7276 (tp40) REVERT: B 268 LYS cc_start: 0.8346 (pptt) cc_final: 0.8027 (pptt) REVERT: B 280 ASN cc_start: 0.8006 (p0) cc_final: 0.7627 (p0) REVERT: B 297 THR cc_start: 0.8755 (t) cc_final: 0.8434 (p) REVERT: B 321 ASP cc_start: 0.7563 (t0) cc_final: 0.7326 (t70) REVERT: B 432 ARG cc_start: 0.6433 (mtt90) cc_final: 0.6127 (mtt90) REVERT: B 490 LYS cc_start: 0.7797 (ttpt) cc_final: 0.7597 (ttpt) REVERT: B 530 MET cc_start: 0.8895 (mmm) cc_final: 0.8640 (tpp) REVERT: B 535 MET cc_start: 0.7039 (tpp) cc_final: 0.6800 (tpp) REVERT: B 656 ASN cc_start: 0.7848 (t0) cc_final: 0.7567 (t0) REVERT: B 657 GLU cc_start: 0.7413 (tp30) cc_final: 0.6947 (tp30) REVERT: C 35 TRP cc_start: 0.7400 (m-10) cc_final: 0.7068 (m-10) REVERT: C 53 PHE cc_start: 0.7124 (p90) cc_final: 0.6808 (p90) REVERT: C 72 HIS cc_start: 0.6743 (OUTLIER) cc_final: 0.6408 (t70) REVERT: C 96 TRP cc_start: 0.7950 (m100) cc_final: 0.6962 (m100) REVERT: C 103 GLN cc_start: 0.7892 (tp-100) cc_final: 0.7268 (tm-30) REVERT: C 106 GLU cc_start: 0.7369 (tp30) cc_final: 0.7082 (tp30) REVERT: C 136 VAL cc_start: 0.7272 (OUTLIER) cc_final: 0.6854 (p) REVERT: C 150 GLU cc_start: 0.7283 (tp30) cc_final: 0.6742 (tp30) REVERT: C 166 LYS cc_start: 0.7962 (mmmt) cc_final: 0.7650 (mmmt) REVERT: C 171 TYR cc_start: 0.7836 (p90) cc_final: 0.7463 (p90) REVERT: C 265 LEU cc_start: 0.8938 (mp) cc_final: 0.8712 (mm) REVERT: C 273 ARG cc_start: 0.8247 (mtt-85) cc_final: 0.7807 (mtt-85) REVERT: C 417 GLN cc_start: 0.7857 (OUTLIER) cc_final: 0.7560 (mt0) REVERT: C 427 TRP cc_start: 0.7690 (m-90) cc_final: 0.7019 (m-10) REVERT: C 439 ILE cc_start: 0.8122 (mp) cc_final: 0.7882 (mm) REVERT: C 482 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7118 (mm-30) REVERT: C 529 THR cc_start: 0.8023 (m) cc_final: 0.7804 (m) REVERT: C 530 MET cc_start: 0.8574 (tpt) cc_final: 0.8108 (mmm) REVERT: C 577 GLN cc_start: 0.7239 (tm-30) cc_final: 0.6909 (tm-30) REVERT: C 626 MET cc_start: 0.7851 (OUTLIER) cc_final: 0.7519 (mtt) REVERT: C 656 ASN cc_start: 0.7871 (t0) cc_final: 0.7577 (t0) REVERT: C 657 GLU cc_start: 0.7587 (tp30) cc_final: 0.7086 (tp30) outliers start: 63 outliers final: 44 residues processed: 479 average time/residue: 0.2748 time to fit residues: 186.1219 Evaluate side-chains 490 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 438 time to evaluate : 1.491 ------------------------------------------------------------------------------- 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 102 ASP Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 202 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 417 GLN Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 642 ILE 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 213 ILE 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 72 HIS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 95 MET 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 182 LEU Chi-restraints excluded: chain C residue 205 CYS 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 576 LEU Chi-restraints excluded: chain C residue 591 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 116 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 165 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.119782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.099378 restraints weight = 21814.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.103277 restraints weight = 12238.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.105933 restraints weight = 8311.415| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.3970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.088 14547 Z= 0.342 Angle : 0.815 12.685 19893 Z= 0.410 Chirality : 0.052 0.288 2418 Planarity : 0.005 0.067 2421 Dihedral : 8.016 57.235 3122 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.80 % Allowed : 22.27 % Favored : 73.93 % 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: -0.45 (0.20), residues: 1656 helix: 1.08 (0.27), residues: 375 sheet: 0.85 (0.27), residues: 369 loop : -1.46 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.003 TRP C 35 HIS 0.010 0.003 HIS B 216 PHE 0.023 0.003 PHE C 376 TYR 0.027 0.003 TYR B 39 ARG 0.007 0.001 ARG A 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00589 ( 45) link_NAG-ASN : angle 2.49425 ( 135) link_BETA1-4 : bond 0.00801 ( 18) link_BETA1-4 : angle 2.62370 ( 54) hydrogen bonds : bond 0.05452 ( 391) hydrogen bonds : angle 4.83308 ( 1092) SS BOND : bond 0.00781 ( 36) SS BOND : angle 3.02643 ( 72) covalent geometry : bond 0.00780 (14448) covalent geometry : angle 0.76054 (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 506 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 449 time to evaluate : 1.455 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: A 69 TRP cc_start: 0.7061 (m-90) cc_final: 0.6806 (m-90) REVERT: A 117 LYS cc_start: 0.8544 (ttmm) cc_final: 0.8153 (ttmm) REVERT: A 136 VAL cc_start: 0.7500 (OUTLIER) cc_final: 0.7213 (p) REVERT: A 150 GLU cc_start: 0.7402 (tp30) cc_final: 0.6823 (tp30) REVERT: A 264 SER cc_start: 0.8353 (m) cc_final: 0.7687 (p) REVERT: A 468 PHE cc_start: 0.8120 (m-80) cc_final: 0.7903 (m-10) REVERT: A 482 GLU cc_start: 0.7454 (mm-30) cc_final: 0.6671 (mm-30) REVERT: A 647 GLU cc_start: 0.7661 (tm-30) cc_final: 0.7230 (tm-30) REVERT: A 656 ASN cc_start: 0.7875 (t0) cc_final: 0.7543 (t0) REVERT: B 35 TRP cc_start: 0.7830 (m-10) cc_final: 0.7531 (m-10) REVERT: B 44 VAL cc_start: 0.9013 (p) cc_final: 0.8810 (m) REVERT: B 69 TRP cc_start: 0.7056 (m-90) cc_final: 0.6582 (m-90) REVERT: B 104 MET cc_start: 0.7861 (ttt) cc_final: 0.7634 (ttt) REVERT: B 106 GLU cc_start: 0.7340 (tp30) cc_final: 0.6931 (tp30) REVERT: B 113 ASP cc_start: 0.7153 (t0) cc_final: 0.6148 (t0) REVERT: B 136 VAL cc_start: 0.7560 (OUTLIER) cc_final: 0.7201 (p) REVERT: B 150 GLU cc_start: 0.7579 (tp30) cc_final: 0.7045 (tp30) REVERT: B 161 THR cc_start: 0.7878 (m) cc_final: 0.7639 (m) REVERT: B 205 CYS cc_start: 0.5963 (m) cc_final: 0.5717 (m) REVERT: B 268 LYS cc_start: 0.8389 (pptt) cc_final: 0.8066 (pptt) REVERT: B 280 ASN cc_start: 0.8117 (p0) cc_final: 0.7751 (p0) REVERT: B 297 THR cc_start: 0.8768 (t) cc_final: 0.8389 (p) REVERT: B 321 ASP cc_start: 0.7554 (t0) cc_final: 0.7331 (t70) REVERT: B 492 GLU cc_start: 0.7422 (mt-10) cc_final: 0.7005 (mt-10) REVERT: B 656 ASN cc_start: 0.7861 (t0) cc_final: 0.7588 (t0) REVERT: B 657 GLU cc_start: 0.7415 (tp30) cc_final: 0.6989 (tp30) REVERT: C 53 PHE cc_start: 0.7193 (p90) cc_final: 0.6947 (p90) REVERT: C 72 HIS cc_start: 0.6735 (OUTLIER) cc_final: 0.6466 (t70) REVERT: C 96 TRP cc_start: 0.8018 (m100) cc_final: 0.6999 (m100) REVERT: C 103 GLN cc_start: 0.7893 (tp-100) cc_final: 0.7320 (tm-30) REVERT: C 106 GLU cc_start: 0.7385 (tp30) cc_final: 0.7148 (tp30) REVERT: C 121 LYS cc_start: 0.8710 (mttt) cc_final: 0.8319 (mttp) REVERT: C 150 GLU cc_start: 0.7344 (tp30) cc_final: 0.6736 (tp30) REVERT: C 166 LYS cc_start: 0.8084 (mmmt) cc_final: 0.7691 (mmmt) REVERT: C 171 TYR cc_start: 0.7895 (p90) cc_final: 0.7530 (p90) REVERT: C 273 ARG cc_start: 0.8254 (mtt-85) cc_final: 0.7780 (mtt-85) REVERT: C 417 GLN cc_start: 0.7969 (OUTLIER) cc_final: 0.7527 (mt0) REVERT: C 427 TRP cc_start: 0.7763 (m-90) cc_final: 0.6970 (m-10) REVERT: C 439 ILE cc_start: 0.8148 (mp) cc_final: 0.7905 (mm) REVERT: C 482 GLU cc_start: 0.7685 (mm-30) cc_final: 0.7194 (mm-30) REVERT: C 529 THR cc_start: 0.8125 (m) cc_final: 0.7876 (m) REVERT: C 577 GLN cc_start: 0.7386 (tm-30) cc_final: 0.6846 (tm-30) REVERT: C 626 MET cc_start: 0.7890 (OUTLIER) cc_final: 0.7619 (mtt) REVERT: C 656 ASN cc_start: 0.7939 (t0) cc_final: 0.7628 (t0) REVERT: C 657 GLU cc_start: 0.7649 (tp30) cc_final: 0.7031 (tp30) outliers start: 57 outliers final: 43 residues processed: 478 average time/residue: 0.2756 time to fit residues: 185.8513 Evaluate side-chains 486 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 438 time to evaluate : 1.477 ------------------------------------------------------------------------------- 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 136 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 202 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 323 ILE 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 616 ASN 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 182 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 95 MET 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 182 LEU Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 215 ILE 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 434 MET Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 576 LEU Chi-restraints excluded: chain C residue 591 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 61 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 118 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 chunk 119 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 155 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 138 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN B 302 ASN B 315 GLN B 577 GLN ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.122401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.102030 restraints weight = 21673.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.106011 restraints weight = 12131.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.108735 restraints weight = 8195.903| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.4110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 14547 Z= 0.161 Angle : 0.711 11.068 19893 Z= 0.356 Chirality : 0.046 0.231 2418 Planarity : 0.005 0.063 2421 Dihedral : 7.659 55.518 3122 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.13 % Allowed : 24.00 % Favored : 72.87 % 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: -0.29 (0.20), residues: 1656 helix: 1.22 (0.27), residues: 378 sheet: 0.89 (0.27), residues: 375 loop : -1.36 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP C 35 HIS 0.004 0.001 HIS C 374 PHE 0.018 0.002 PHE C 53 TYR 0.025 0.002 TYR A 638 ARG 0.013 0.001 ARG A 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00333 ( 45) link_NAG-ASN : angle 2.20835 ( 135) link_BETA1-4 : bond 0.00793 ( 18) link_BETA1-4 : angle 2.53818 ( 54) hydrogen bonds : bond 0.04237 ( 391) hydrogen bonds : angle 4.62677 ( 1092) SS BOND : bond 0.00513 ( 36) SS BOND : angle 2.45725 ( 72) covalent geometry : bond 0.00375 (14448) covalent geometry : angle 0.66210 (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 506 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 459 time to evaluate : 1.433 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 69 TRP cc_start: 0.6927 (m-90) cc_final: 0.6681 (m-90) REVERT: A 117 LYS cc_start: 0.8530 (ttmm) cc_final: 0.8158 (ttmm) REVERT: A 136 VAL cc_start: 0.7485 (OUTLIER) cc_final: 0.7173 (p) REVERT: A 150 GLU cc_start: 0.7377 (tp30) cc_final: 0.6801 (tp30) REVERT: A 245 VAL cc_start: 0.8669 (t) cc_final: 0.8336 (p) REVERT: A 246 GLN cc_start: 0.7690 (tp40) cc_final: 0.7463 (tp40) REVERT: A 264 SER cc_start: 0.8361 (m) cc_final: 0.7743 (p) REVERT: A 297 THR cc_start: 0.8712 (t) cc_final: 0.8483 (p) REVERT: A 308 ARG cc_start: 0.7904 (tpp80) cc_final: 0.7579 (tpp80) REVERT: A 468 PHE cc_start: 0.8073 (m-80) cc_final: 0.7798 (m-10) REVERT: A 482 GLU cc_start: 0.7480 (mm-30) cc_final: 0.6680 (mm-30) REVERT: A 591 GLN cc_start: 0.8127 (tt0) cc_final: 0.7667 (tt0) REVERT: A 631 TRP cc_start: 0.8042 (t-100) cc_final: 0.7767 (t-100) REVERT: A 635 ILE cc_start: 0.8382 (tp) cc_final: 0.7966 (tt) REVERT: A 647 GLU cc_start: 0.7585 (tm-30) cc_final: 0.7202 (tm-30) REVERT: A 656 ASN cc_start: 0.7877 (t0) cc_final: 0.7535 (t0) REVERT: B 69 TRP cc_start: 0.6954 (m-90) cc_final: 0.6465 (m-90) REVERT: B 104 MET cc_start: 0.7780 (ttt) cc_final: 0.7392 (ttt) REVERT: B 106 GLU cc_start: 0.7296 (tp30) cc_final: 0.6848 (tp30) REVERT: B 136 VAL cc_start: 0.7514 (OUTLIER) cc_final: 0.7150 (p) REVERT: B 150 GLU cc_start: 0.7514 (tp30) cc_final: 0.6944 (tp30) REVERT: B 161 THR cc_start: 0.7873 (OUTLIER) cc_final: 0.7646 (m) REVERT: B 205 CYS cc_start: 0.5786 (m) cc_final: 0.5538 (m) REVERT: B 246 GLN cc_start: 0.7802 (tp40) cc_final: 0.7319 (tp40) REVERT: B 268 LYS cc_start: 0.8350 (pptt) cc_final: 0.8018 (pptt) REVERT: B 280 ASN cc_start: 0.8087 (p0) cc_final: 0.7742 (p0) REVERT: B 297 THR cc_start: 0.8750 (t) cc_final: 0.8436 (p) REVERT: B 321 ASP cc_start: 0.7567 (t0) cc_final: 0.7319 (t70) REVERT: B 492 GLU cc_start: 0.7317 (mt-10) cc_final: 0.7030 (mt-10) REVERT: B 656 ASN cc_start: 0.7829 (t0) cc_final: 0.7549 (t0) REVERT: B 657 GLU cc_start: 0.7435 (tp30) cc_final: 0.6994 (tp30) REVERT: C 47 GLU cc_start: 0.7186 (mm-30) cc_final: 0.6831 (mm-30) REVERT: C 53 PHE cc_start: 0.7088 (p90) cc_final: 0.6787 (p90) REVERT: C 96 TRP cc_start: 0.7926 (m100) cc_final: 0.6966 (m100) REVERT: C 106 GLU cc_start: 0.7321 (tp30) cc_final: 0.7044 (tp30) REVERT: C 121 LYS cc_start: 0.8704 (mttt) cc_final: 0.8268 (mttm) REVERT: C 150 GLU cc_start: 0.7290 (tp30) cc_final: 0.6599 (tp30) REVERT: C 166 LYS cc_start: 0.8042 (mmmt) cc_final: 0.7672 (mmmt) REVERT: C 171 TYR cc_start: 0.7810 (p90) cc_final: 0.7414 (p90) REVERT: C 251 ILE cc_start: 0.8450 (mm) cc_final: 0.7925 (tt) REVERT: C 308 ARG cc_start: 0.7757 (mmt90) cc_final: 0.7480 (tpt-90) REVERT: C 322 ILE cc_start: 0.7810 (mt) cc_final: 0.7592 (mt) REVERT: C 350 GLN cc_start: 0.7769 (tt0) cc_final: 0.7499 (tt0) REVERT: C 414 ILE cc_start: 0.8774 (tp) cc_final: 0.8513 (tt) REVERT: C 417 GLN cc_start: 0.7906 (OUTLIER) cc_final: 0.7494 (mt0) REVERT: C 427 TRP cc_start: 0.7726 (m-90) cc_final: 0.6939 (m-10) REVERT: C 439 ILE cc_start: 0.8141 (mp) cc_final: 0.7889 (mm) REVERT: C 482 GLU cc_start: 0.7609 (mm-30) cc_final: 0.7148 (mm-30) REVERT: C 626 MET cc_start: 0.7825 (OUTLIER) cc_final: 0.7536 (mtt) REVERT: C 656 ASN cc_start: 0.7914 (t0) cc_final: 0.7597 (t0) REVERT: C 657 GLU cc_start: 0.7601 (tp30) cc_final: 0.7083 (tp30) outliers start: 47 outliers final: 36 residues processed: 481 average time/residue: 0.2827 time to fit residues: 191.0782 Evaluate side-chains 490 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 449 time to evaluate : 1.503 ------------------------------------------------------------------------------- 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 136 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 202 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 434 MET 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 434 MET Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 119 CYS Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 205 CYS 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 434 MET Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 591 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 113 optimal weight: 0.7980 chunk 158 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 chunk 90 optimal weight: 0.1980 chunk 99 optimal weight: 0.7980 chunk 81 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 302 ASN A 363 GLN B 302 ASN B 363 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.121362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.101009 restraints weight = 22015.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.105043 restraints weight = 12238.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.107767 restraints weight = 8213.724| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.4217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 14547 Z= 0.146 Angle : 0.698 10.555 19893 Z= 0.350 Chirality : 0.046 0.233 2418 Planarity : 0.004 0.053 2421 Dihedral : 7.530 55.521 3122 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.13 % Allowed : 24.07 % Favored : 72.80 % 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: -0.23 (0.20), residues: 1656 helix: 1.31 (0.27), residues: 378 sheet: 1.17 (0.28), residues: 339 loop : -1.36 (0.19), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.003 TRP B 35 HIS 0.004 0.001 HIS C 374 PHE 0.016 0.001 PHE C 53 TYR 0.027 0.002 TYR A 638 ARG 0.013 0.001 ARG A 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00318 ( 45) link_NAG-ASN : angle 2.14025 ( 135) link_BETA1-4 : bond 0.00796 ( 18) link_BETA1-4 : angle 2.49760 ( 54) hydrogen bonds : bond 0.04079 ( 391) hydrogen bonds : angle 4.55069 ( 1092) SS BOND : bond 0.00385 ( 36) SS BOND : angle 2.30696 ( 72) covalent geometry : bond 0.00341 (14448) covalent geometry : angle 0.65182 (19632) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4830.42 seconds wall clock time: 85 minutes 13.04 seconds (5113.04 seconds total)