Starting phenix.real_space_refine on Wed Mar 4 14:25:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eu8_28608/03_2026/8eu8_28608_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eu8_28608/03_2026/8eu8_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 { model { file = "/net/cci-nas-00/data/ceres_data/8eu8_28608/03_2026/8eu8_28608_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eu8_28608/03_2026/8eu8_28608_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8eu8_28608/03_2026/8eu8_28608.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eu8_28608/03_2026/8eu8_28608.map" } resolution = 3.73 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 3.60, per 1000 atoms: 0.25 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: 1.19 Conformation dependent library (CDL) restraints added in 461.0 milliseconds 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: 0.49 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: 2.36 Time building geometry restraints manager: 1.53 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: 0.03 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: 1.580 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 14.220 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.710 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (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 ARG 0.007 0.001 ARG A 585 TYR 0.138 0.023 TYR C 361 PHE 0.082 0.017 PHE B 233 TRP 0.129 0.030 TRP C 610 HIS 0.011 0.003 HIS C 216 Details of bonding type rmsd covalent geometry : bond 0.01396 (14448) covalent geometry : angle 1.80780 (19632) SS BOND : bond 0.01350 ( 36) SS BOND : angle 1.77325 ( 72) hydrogen bonds : bond 0.18548 ( 391) hydrogen bonds : angle 6.92144 ( 1092) link_BETA1-4 : bond 0.02967 ( 18) link_BETA1-4 : angle 5.99643 ( 54) link_NAG-ASN : bond 0.06780 ( 45) link_NAG-ASN : angle 6.12498 ( 135) *********************** 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 : 0.518 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: 0.7760 (p) REVERT: A 46 LYS cc_start: 0.7872 (mmmt) cc_final: 0.7600 (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: 0.7533 (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: 0.7678 (ttm) REVERT: A 106 GLU cc_start: 0.7565 (tp30) cc_final: 0.7286 (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: 0.7488 (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: 0.8040 (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 302 ASN cc_start: 0.8568 (m-40) cc_final: 0.8277 (m110) REVERT: A 321 ASP cc_start: 0.7174 (t0) cc_final: 0.6957 (t0) REVERT: A 327 LYS cc_start: 0.7954 (tptp) cc_final: 0.7725 (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: 0.7324 (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: 0.6542 (m100) REVERT: B 42 VAL cc_start: 0.8350 (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: 0.6877 (tp30) REVERT: B 113 ASP cc_start: 0.7412 (t0) cc_final: 0.6735 (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: 0.8274 (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: 0.7562 (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: 0.7335 (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: 0.7185 (tp30) REVERT: C 35 TRP cc_start: 0.7294 (m100) cc_final: 0.7083 (m100) REVERT: C 42 VAL cc_start: 0.8318 (t) cc_final: 0.7900 (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: 0.7608 (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: 0.6811 (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: 0.8411 (mt0) cc_final: 0.8203 (mt0) REVERT: C 273 ARG cc_start: 0.7803 (mtt90) cc_final: 0.7550 (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: 0.7470 (t0) REVERT: C 327 LYS cc_start: 0.8016 (tptp) cc_final: 0.7813 (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: 0.8130 (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: 0.7159 (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: 0.6904 (tp30) outliers start: 7 outliers final: 2 residues processed: 533 average time/residue: 0.1316 time to fit residues: 98.7606 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 : 0.542 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.2980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.0000 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 3.9990 overall best weight: 0.4584 ------------------------------------------------------------------------------- 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 575 GLN A 630 GLN B 88 ASN B 114 GLN B 315 GLN 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: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.125169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.104273 restraints weight = 21440.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.108436 restraints weight = 11718.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.111287 restraints weight = 7787.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.113263 restraints weight = 5814.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.114525 restraints weight = 4675.320| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 14547 Z= 0.145 Angle : 0.783 9.157 19893 Z= 0.385 Chirality : 0.050 0.312 2418 Planarity : 0.004 0.049 2421 Dihedral : 8.524 59.617 3126 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.11 % Favored : 97.83 % Rotamer: Outliers : 2.60 % Allowed : 9.87 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.19), residues: 1656 helix: 0.69 (0.26), residues: 375 sheet: 1.32 (0.25), residues: 339 loop : -1.05 (0.18), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 432 TYR 0.021 0.002 TYR C 191 PHE 0.022 0.002 PHE C 53 TRP 0.023 0.002 TRP A 628 HIS 0.003 0.001 HIS B 105 Details of bonding type rmsd covalent geometry : bond 0.00317 (14448) covalent geometry : angle 0.70667 (19632) SS BOND : bond 0.00437 ( 36) SS BOND : angle 2.02069 ( 72) hydrogen bonds : bond 0.04820 ( 391) hydrogen bonds : angle 4.69823 ( 1092) link_BETA1-4 : bond 0.00826 ( 18) link_BETA1-4 : angle 3.27042 ( 54) link_NAG-ASN : bond 0.00596 ( 45) link_NAG-ASN : angle 3.34947 ( 135) *********************** 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 492 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 453 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 PHE cc_start: 0.7457 (p90) cc_final: 0.7058 (p90) REVERT: A 69 TRP cc_start: 0.7115 (m-90) cc_final: 0.6175 (m-90) REVERT: A 96 TRP cc_start: 0.8078 (m100) cc_final: 0.7310 (m100) REVERT: A 102 ASP cc_start: 0.7539 (t70) cc_final: 0.7115 (t0) REVERT: A 104 MET cc_start: 0.8075 (ttt) cc_final: 0.7697 (ttt) REVERT: A 106 GLU cc_start: 0.7529 (tp30) cc_final: 0.7208 (tp30) REVERT: A 113 ASP cc_start: 0.7532 (t0) cc_final: 0.7205 (t0) REVERT: A 166 LYS cc_start: 0.7795 (mmmt) cc_final: 0.7548 (mmmt) REVERT: A 198 THR cc_start: 0.8296 (t) cc_final: 0.8042 (t) REVERT: A 264 SER cc_start: 0.8247 (m) cc_final: 0.7672 (p) REVERT: A 420 ILE cc_start: 0.8301 (mt) cc_final: 0.8076 (mm) REVERT: A 468 PHE cc_start: 0.7634 (m-80) cc_final: 0.7376 (m-10) REVERT: A 482 GLU cc_start: 0.7626 (mm-30) cc_final: 0.6843 (mm-30) REVERT: A 535 MET cc_start: 0.6929 (tpp) cc_final: 0.6509 (tpp) REVERT: A 647 GLU cc_start: 0.7490 (tm-30) cc_final: 0.7281 (tm-30) REVERT: A 656 ASN cc_start: 0.7794 (t0) cc_final: 0.7369 (t0) REVERT: B 44 VAL cc_start: 0.8943 (p) cc_final: 0.8600 (m) REVERT: B 47 GLU cc_start: 0.6886 (tt0) cc_final: 0.6673 (tt0) REVERT: B 53 PHE cc_start: 0.7166 (p90) cc_final: 0.6817 (p90) REVERT: B 82 GLN cc_start: 0.7165 (tp40) cc_final: 0.6697 (tp40) REVERT: B 97 LYS cc_start: 0.7947 (tppt) cc_final: 0.7225 (tppt) REVERT: B 104 MET cc_start: 0.7871 (ttt) cc_final: 0.7583 (ttt) REVERT: B 106 GLU cc_start: 0.7341 (tp30) cc_final: 0.6583 (tp30) REVERT: B 113 ASP cc_start: 0.7597 (t0) cc_final: 0.7096 (t70) REVERT: B 195 ASN cc_start: 0.7454 (p0) cc_final: 0.7247 (p0) REVERT: B 202 THR cc_start: 0.8247 (p) cc_final: 0.7954 (p) REVERT: B 234 ASN cc_start: 0.7460 (t0) cc_final: 0.7113 (t0) REVERT: B 245 VAL cc_start: 0.8459 (OUTLIER) cc_final: 0.8246 (p) REVERT: B 268 LYS cc_start: 0.8490 (pptt) cc_final: 0.8237 (pptt) REVERT: B 280 ASN cc_start: 0.7994 (p0) cc_final: 0.7653 (p0) REVERT: B 297 THR cc_start: 0.8655 (t) cc_final: 0.8426 (p) REVERT: B 420 ILE cc_start: 0.8444 (mt) cc_final: 0.8244 (mm) REVERT: B 432 ARG cc_start: 0.6884 (mtt90) cc_final: 0.6502 (mtt90) REVERT: B 447 SER cc_start: 0.8293 (m) cc_final: 0.7959 (p) REVERT: B 535 MET cc_start: 0.6848 (tpp) cc_final: 0.6593 (tpp) REVERT: B 538 THR cc_start: 0.8206 (p) cc_final: 0.7962 (m) REVERT: B 544 LEU cc_start: 0.7871 (OUTLIER) cc_final: 0.7664 (tp) REVERT: B 590 GLN cc_start: 0.8130 (mm-40) cc_final: 0.7897 (mm-40) REVERT: B 656 ASN cc_start: 0.7623 (t0) cc_final: 0.7274 (t0) REVERT: B 657 GLU cc_start: 0.7450 (tp30) cc_final: 0.7226 (tp30) REVERT: C 47 GLU cc_start: 0.6946 (tt0) cc_final: 0.6715 (tt0) REVERT: C 82 GLN cc_start: 0.7157 (tp40) cc_final: 0.6638 (tp40) REVERT: C 92 ASN cc_start: 0.7601 (p0) cc_final: 0.7279 (p0) REVERT: C 106 GLU cc_start: 0.7322 (tp30) cc_final: 0.6952 (tp30) REVERT: C 121 LYS cc_start: 0.8689 (mttt) cc_final: 0.8309 (mttm) REVERT: C 166 LYS cc_start: 0.7910 (mmmt) cc_final: 0.7588 (mmmt) REVERT: C 171 TYR cc_start: 0.7936 (p90) cc_final: 0.7562 (p90) REVERT: C 178 ASP cc_start: 0.7509 (m-30) cc_final: 0.7308 (t70) REVERT: C 223 TYR cc_start: 0.8046 (m-80) cc_final: 0.7821 (m-10) REVERT: C 302 ASN cc_start: 0.8604 (m-40) cc_final: 0.8310 (m110) REVERT: C 327 LYS cc_start: 0.7908 (tptp) cc_final: 0.7707 (tptp) REVERT: C 347 ILE cc_start: 0.8481 (tp) cc_final: 0.8249 (mt) REVERT: C 395 TYR cc_start: 0.7398 (t80) cc_final: 0.7119 (t80) REVERT: C 427 TRP cc_start: 0.7728 (m-90) cc_final: 0.7526 (m-10) REVERT: C 434 MET cc_start: 0.7062 (ttm) cc_final: 0.6757 (ttp) REVERT: C 447 SER cc_start: 0.8403 (m) cc_final: 0.8169 (p) REVERT: C 482 GLU cc_start: 0.7705 (mm-30) cc_final: 0.7262 (mm-30) REVERT: C 656 ASN cc_start: 0.7822 (t0) cc_final: 0.7455 (t0) REVERT: C 657 GLU cc_start: 0.7490 (tp30) cc_final: 0.6772 (tp30) outliers start: 39 outliers final: 20 residues processed: 469 average time/residue: 0.1379 time to fit residues: 91.3747 Evaluate side-chains 433 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 411 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 LEU 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 201 CYS 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 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 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 41 optimal weight: 0.9980 chunk 108 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 165 optimal weight: 0.0020 chunk 24 optimal weight: 0.6980 chunk 160 optimal weight: 0.9980 chunk 94 optimal weight: 4.9990 overall best weight: 1.1390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS A 229 ASN A 302 ASN A 315 GLN A 363 GLN A 374 HIS B 105 HIS B 229 ASN B 302 ASN B 363 GLN C 72 HIS C 105 HIS C 114 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.122706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.102104 restraints weight = 21938.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.106171 restraints weight = 12059.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.108931 restraints weight = 8079.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.110815 restraints weight = 6056.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.112168 restraints weight = 4901.370| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 14547 Z= 0.186 Angle : 0.748 9.643 19893 Z= 0.366 Chirality : 0.050 0.293 2418 Planarity : 0.005 0.057 2421 Dihedral : 8.091 59.091 3122 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.87 % Allowed : 14.40 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.20), residues: 1656 helix: 1.01 (0.27), residues: 369 sheet: 1.37 (0.25), residues: 339 loop : -1.04 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 617 TYR 0.021 0.002 TYR A 638 PHE 0.026 0.002 PHE C 53 TRP 0.029 0.002 TRP A 35 HIS 0.007 0.002 HIS B 216 Details of bonding type rmsd covalent geometry : bond 0.00430 (14448) covalent geometry : angle 0.67832 (19632) SS BOND : bond 0.00447 ( 36) SS BOND : angle 2.41046 ( 72) hydrogen bonds : bond 0.04720 ( 391) hydrogen bonds : angle 4.55280 ( 1092) link_BETA1-4 : bond 0.00923 ( 18) link_BETA1-4 : angle 3.02485 ( 54) link_NAG-ASN : bond 0.00473 ( 45) link_NAG-ASN : angle 2.94909 ( 135) *********************** 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 491 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 433 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ASN cc_start: 0.7456 (t0) cc_final: 0.7212 (t0) REVERT: A 69 TRP cc_start: 0.7136 (m-90) cc_final: 0.6608 (m-90) REVERT: A 96 TRP cc_start: 0.8004 (m100) cc_final: 0.7258 (m100) REVERT: A 106 GLU cc_start: 0.7512 (tp30) cc_final: 0.7248 (tp30) REVERT: A 117 LYS cc_start: 0.8486 (ttmm) cc_final: 0.8056 (ttmm) REVERT: A 150 GLU cc_start: 0.7477 (tp30) cc_final: 0.7120 (tp30) REVERT: A 166 LYS cc_start: 0.7845 (mmmt) cc_final: 0.7540 (mmmt) REVERT: A 178 ASP cc_start: 0.7805 (OUTLIER) cc_final: 0.7444 (t70) REVERT: A 198 THR cc_start: 0.8253 (t) cc_final: 0.8041 (t) REVERT: A 223 TYR cc_start: 0.8294 (m-80) cc_final: 0.7972 (m-80) REVERT: A 246 GLN cc_start: 0.7774 (tp40) cc_final: 0.7462 (tp40) REVERT: A 255 VAL cc_start: 0.8428 (OUTLIER) cc_final: 0.8216 (p) REVERT: A 264 SER cc_start: 0.8263 (m) cc_final: 0.7629 (p) REVERT: A 302 ASN cc_start: 0.8595 (m-40) cc_final: 0.8201 (m110) REVERT: A 321 ASP cc_start: 0.7396 (t0) cc_final: 0.7139 (t70) REVERT: A 344 LYS cc_start: 0.8254 (ttmm) cc_final: 0.8033 (ttmm) REVERT: A 374 HIS cc_start: 0.8354 (OUTLIER) cc_final: 0.8101 (t-170) REVERT: A 420 ILE cc_start: 0.8434 (mt) cc_final: 0.8231 (mm) REVERT: A 447 SER cc_start: 0.8527 (m) cc_final: 0.8023 (p) REVERT: A 468 PHE cc_start: 0.7739 (m-80) cc_final: 0.7465 (m-10) REVERT: A 482 GLU cc_start: 0.7517 (mm-30) cc_final: 0.6727 (mm-30) REVERT: A 535 MET cc_start: 0.6937 (tpp) cc_final: 0.6534 (tpp) REVERT: A 647 GLU cc_start: 0.7519 (tm-30) cc_final: 0.7260 (tm-30) REVERT: A 654 GLU cc_start: 0.7902 (tp30) cc_final: 0.7611 (tp30) REVERT: A 656 ASN cc_start: 0.7876 (t0) cc_final: 0.7483 (t0) REVERT: B 44 VAL cc_start: 0.8969 (p) cc_final: 0.8654 (m) REVERT: B 53 PHE cc_start: 0.7260 (p90) cc_final: 0.7015 (p90) REVERT: B 104 MET cc_start: 0.7824 (ttt) cc_final: 0.7557 (ttt) REVERT: B 106 GLU cc_start: 0.7268 (tp30) cc_final: 0.6870 (tp30) REVERT: B 113 ASP cc_start: 0.7513 (t0) cc_final: 0.6632 (t70) REVERT: B 161 THR cc_start: 0.7604 (m) cc_final: 0.7361 (m) REVERT: B 182 LEU cc_start: 0.7786 (tp) cc_final: 0.7543 (tp) REVERT: B 202 THR cc_start: 0.8349 (p) cc_final: 0.8119 (p) REVERT: B 234 ASN cc_start: 0.7404 (t0) cc_final: 0.7100 (t0) REVERT: B 251 ILE cc_start: 0.8484 (mm) cc_final: 0.8280 (mm) REVERT: B 268 LYS cc_start: 0.8481 (pptt) cc_final: 0.8221 (pptt) REVERT: B 269 GLU cc_start: 0.7958 (tt0) cc_final: 0.7079 (tt0) REVERT: B 280 ASN cc_start: 0.8053 (p0) cc_final: 0.7661 (p0) REVERT: B 297 THR cc_start: 0.8716 (t) cc_final: 0.8317 (p) REVERT: B 432 ARG cc_start: 0.6742 (mtt90) cc_final: 0.6412 (mtt90) REVERT: B 446 ARG cc_start: 0.7598 (mtp85) cc_final: 0.7348 (mtp85) REVERT: B 447 SER cc_start: 0.8220 (m) cc_final: 0.7934 (p) REVERT: B 475 MET cc_start: 0.8085 (tpt) cc_final: 0.7719 (tpp) REVERT: B 482 GLU cc_start: 0.7346 (mm-30) cc_final: 0.7085 (mm-30) REVERT: B 535 MET cc_start: 0.6895 (tpp) cc_final: 0.6593 (tpp) REVERT: B 656 ASN cc_start: 0.7705 (t0) cc_final: 0.7415 (t0) REVERT: B 657 GLU cc_start: 0.7417 (tp30) cc_final: 0.6921 (tp30) REVERT: C 53 PHE cc_start: 0.7325 (p90) cc_final: 0.6974 (p90) REVERT: C 92 ASN cc_start: 0.7592 (p0) cc_final: 0.7323 (p0) REVERT: C 93 PHE cc_start: 0.7754 (m-80) cc_final: 0.7439 (m-10) REVERT: C 96 TRP cc_start: 0.7704 (m-90) cc_final: 0.6974 (m100) REVERT: C 106 GLU cc_start: 0.7303 (tp30) cc_final: 0.6995 (tp30) REVERT: C 116 LEU cc_start: 0.8018 (mt) cc_final: 0.7615 (mp) REVERT: C 121 LYS cc_start: 0.8703 (mttt) cc_final: 0.8277 (mttm) REVERT: C 163 ILE cc_start: 0.7310 (mp) cc_final: 0.7024 (mp) REVERT: C 166 LYS cc_start: 0.7935 (mmmt) cc_final: 0.7603 (mmmt) REVERT: C 171 TYR cc_start: 0.7923 (p90) cc_final: 0.7546 (p90) REVERT: C 195 ASN cc_start: 0.7412 (p0) cc_final: 0.7112 (p0) REVERT: C 417 GLN cc_start: 0.7901 (pt0) cc_final: 0.7446 (mt0) REVERT: C 427 TRP cc_start: 0.7645 (m-90) cc_final: 0.7337 (m-10) REVERT: C 482 GLU cc_start: 0.7630 (mm-30) cc_final: 0.7244 (mm-30) REVERT: C 577 GLN cc_start: 0.7217 (tm-30) cc_final: 0.6889 (tm-30) REVERT: C 617 ARG cc_start: 0.7389 (mtt180) cc_final: 0.6611 (mtt180) REVERT: C 634 GLU cc_start: 0.7462 (mt-10) cc_final: 0.6506 (mt-10) REVERT: C 656 ASN cc_start: 0.7917 (t0) cc_final: 0.7523 (t0) REVERT: C 657 GLU cc_start: 0.7519 (tp30) cc_final: 0.6831 (tp30) outliers start: 58 outliers final: 22 residues processed: 465 average time/residue: 0.1376 time to fit residues: 90.6870 Evaluate side-chains 441 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 416 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain 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 102 ASP 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 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 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 74 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 9 optimal weight: 0.0170 chunk 100 optimal weight: 6.9990 chunk 146 optimal weight: 4.9990 chunk 127 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 13 optimal weight: 0.0030 overall best weight: 1.0034 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 302 ASN B 363 GLN B 625 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 = 0.3545 r_free = 0.3545 target = 0.123103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.102324 restraints weight = 21855.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.106440 restraints weight = 12117.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.109156 restraints weight = 8113.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.111005 restraints weight = 6133.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.112367 restraints weight = 4993.078| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 14547 Z= 0.169 Angle : 0.705 10.555 19893 Z= 0.348 Chirality : 0.049 0.361 2418 Planarity : 0.004 0.055 2421 Dihedral : 7.887 56.360 3122 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.60 % Allowed : 17.00 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.20), residues: 1656 helix: 1.08 (0.27), residues: 372 sheet: 1.22 (0.25), residues: 375 loop : -0.98 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 273 TYR 0.024 0.002 TYR C 638 PHE 0.024 0.002 PHE C 53 TRP 0.034 0.002 TRP B 35 HIS 0.006 0.002 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00391 (14448) covalent geometry : angle 0.63877 (19632) SS BOND : bond 0.00574 ( 36) SS BOND : angle 2.71449 ( 72) hydrogen bonds : bond 0.04312 ( 391) hydrogen bonds : angle 4.50951 ( 1092) link_BETA1-4 : bond 0.00827 ( 18) link_BETA1-4 : angle 2.85379 ( 54) link_NAG-ASN : bond 0.00367 ( 45) link_NAG-ASN : angle 2.60361 ( 135) *********************** 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 487 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 433 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ASN cc_start: 0.7437 (t0) cc_final: 0.7187 (t0) REVERT: A 69 TRP cc_start: 0.7122 (m-90) cc_final: 0.6661 (m-90) REVERT: A 91 GLU cc_start: 0.6686 (mm-30) cc_final: 0.6452 (mm-30) REVERT: A 117 LYS cc_start: 0.8469 (ttmm) cc_final: 0.8035 (ttmm) REVERT: A 150 GLU cc_start: 0.7401 (tp30) cc_final: 0.7030 (tp30) REVERT: A 166 LYS cc_start: 0.7832 (mmmt) cc_final: 0.7529 (mmmt) REVERT: A 198 THR cc_start: 0.8151 (t) cc_final: 0.7939 (t) REVERT: A 202 THR cc_start: 0.8129 (p) cc_final: 0.7841 (p) REVERT: A 246 GLN cc_start: 0.7751 (tp40) cc_final: 0.7335 (tp40) REVERT: A 264 SER cc_start: 0.8250 (m) cc_final: 0.7860 (p) REVERT: A 283 ILE cc_start: 0.8141 (OUTLIER) cc_final: 0.7798 (pt) REVERT: A 302 ASN cc_start: 0.8639 (m-40) cc_final: 0.8261 (m110) REVERT: A 417 GLN cc_start: 0.7809 (pt0) cc_final: 0.7182 (mt0) REVERT: A 447 SER cc_start: 0.8494 (m) cc_final: 0.7947 (p) REVERT: A 468 PHE cc_start: 0.7820 (m-80) cc_final: 0.7505 (m-10) REVERT: A 477 ASP cc_start: 0.7477 (m-30) cc_final: 0.7230 (m-30) REVERT: A 535 MET cc_start: 0.6889 (tpp) cc_final: 0.6592 (tpp) REVERT: A 647 GLU cc_start: 0.7572 (tm-30) cc_final: 0.7238 (tm-30) REVERT: A 654 GLU cc_start: 0.7889 (tp30) cc_final: 0.7614 (tp30) REVERT: A 656 ASN cc_start: 0.7890 (t0) cc_final: 0.7500 (t0) REVERT: B 44 VAL cc_start: 0.9005 (p) cc_final: 0.8694 (m) REVERT: B 53 PHE cc_start: 0.7216 (p90) cc_final: 0.6976 (p90) REVERT: B 97 LYS cc_start: 0.7936 (tppt) cc_final: 0.7152 (tppt) REVERT: B 106 GLU cc_start: 0.7288 (tp30) cc_final: 0.6929 (tp30) REVERT: B 113 ASP cc_start: 0.7515 (t0) cc_final: 0.6707 (t70) REVERT: B 161 THR cc_start: 0.7641 (m) cc_final: 0.7380 (m) REVERT: B 205 CYS cc_start: 0.5640 (m) cc_final: 0.5366 (m) REVERT: B 245 VAL cc_start: 0.8702 (t) cc_final: 0.8468 (p) REVERT: B 268 LYS cc_start: 0.8467 (pptt) cc_final: 0.8220 (pptt) REVERT: B 280 ASN cc_start: 0.8011 (p0) cc_final: 0.7599 (p0) REVERT: B 297 THR cc_start: 0.8699 (t) cc_final: 0.8347 (p) REVERT: B 321 ASP cc_start: 0.7524 (t0) cc_final: 0.7242 (t70) REVERT: B 417 GLN cc_start: 0.7836 (pt0) cc_final: 0.7569 (mt0) REVERT: B 432 ARG cc_start: 0.6676 (mtt90) cc_final: 0.6449 (mtt90) REVERT: B 447 SER cc_start: 0.8208 (m) cc_final: 0.7953 (p) REVERT: B 475 MET cc_start: 0.8053 (tpt) cc_final: 0.7783 (tpp) REVERT: B 535 MET cc_start: 0.6894 (tpp) cc_final: 0.6647 (tpp) REVERT: B 656 ASN cc_start: 0.7734 (t0) cc_final: 0.7442 (t0) REVERT: B 657 GLU cc_start: 0.7394 (tp30) cc_final: 0.6908 (tp30) REVERT: C 53 PHE cc_start: 0.7280 (p90) cc_final: 0.6932 (p90) REVERT: C 72 HIS cc_start: 0.6484 (OUTLIER) cc_final: 0.6271 (t-90) REVERT: C 92 ASN cc_start: 0.7581 (p0) cc_final: 0.7302 (p0) REVERT: C 93 PHE cc_start: 0.7736 (m-80) cc_final: 0.7458 (m-10) REVERT: C 106 GLU cc_start: 0.7356 (tp30) cc_final: 0.7020 (tp30) REVERT: C 121 LYS cc_start: 0.8677 (mttt) cc_final: 0.8256 (mttm) REVERT: C 166 LYS cc_start: 0.7947 (mmmt) cc_final: 0.7606 (mmmt) REVERT: C 171 TYR cc_start: 0.7884 (p90) cc_final: 0.7539 (p90) REVERT: C 178 ASP cc_start: 0.7960 (t0) cc_final: 0.7466 (t70) REVERT: C 417 GLN cc_start: 0.7878 (pt0) cc_final: 0.7375 (mt0) REVERT: C 427 TRP cc_start: 0.7622 (m-90) cc_final: 0.7181 (m-10) REVERT: C 482 GLU cc_start: 0.7632 (mm-30) cc_final: 0.7291 (mm-30) REVERT: C 490 LYS cc_start: 0.7871 (ttpt) cc_final: 0.7642 (ttpp) REVERT: C 577 GLN cc_start: 0.7171 (tm-30) cc_final: 0.6868 (tm-30) REVERT: C 656 ASN cc_start: 0.7887 (t0) cc_final: 0.7531 (t0) REVERT: C 657 GLU cc_start: 0.7469 (tp30) cc_final: 0.6859 (tp30) outliers start: 54 outliers final: 31 residues processed: 461 average time/residue: 0.1357 time to fit residues: 88.4481 Evaluate side-chains 447 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 414 time to evaluate : 0.562 ------------------------------------------------------------------------------- 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 283 ILE Chi-restraints excluded: chain A residue 328 GLN Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 605 CYS Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 344 LYS Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 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 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 629 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 108 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 chunk 141 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 69 optimal weight: 0.5980 chunk 72 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 92 optimal weight: 0.7980 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 363 GLN A 374 HIS 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 = 0.3533 r_free = 0.3533 target = 0.121702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.101170 restraints weight = 22003.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.105184 restraints weight = 12248.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.107934 restraints weight = 8247.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.109779 restraints weight = 6199.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.111112 restraints weight = 5037.669| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.3379 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= 0.154 Angle : 0.679 9.791 19893 Z= 0.336 Chirality : 0.047 0.252 2418 Planarity : 0.005 0.083 2421 Dihedral : 7.735 55.147 3122 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 4.40 % Allowed : 18.07 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.20), residues: 1656 helix: 1.26 (0.27), residues: 375 sheet: 1.06 (0.27), residues: 339 loop : -1.02 (0.19), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 273 TYR 0.024 0.002 TYR C 638 PHE 0.023 0.002 PHE C 53 TRP 0.041 0.002 TRP C 35 HIS 0.004 0.001 HIS C 249 Details of bonding type rmsd covalent geometry : bond 0.00356 (14448) covalent geometry : angle 0.61802 (19632) SS BOND : bond 0.00465 ( 36) SS BOND : angle 2.49923 ( 72) hydrogen bonds : bond 0.04183 ( 391) hydrogen bonds : angle 4.46321 ( 1092) link_BETA1-4 : bond 0.00872 ( 18) link_BETA1-4 : angle 2.76293 ( 54) link_NAG-ASN : bond 0.00367 ( 45) link_NAG-ASN : angle 2.44257 ( 135) *********************** 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 498 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 432 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ASN cc_start: 0.7477 (t0) cc_final: 0.7141 (t0) REVERT: A 69 TRP cc_start: 0.7061 (m-90) cc_final: 0.6749 (m-90) REVERT: A 104 MET cc_start: 0.8239 (ttt) cc_final: 0.7965 (ttt) REVERT: A 117 LYS cc_start: 0.8428 (ttmm) cc_final: 0.8010 (ttmm) REVERT: A 150 GLU cc_start: 0.7375 (tp30) cc_final: 0.6965 (tp30) REVERT: A 166 LYS cc_start: 0.7812 (mmmt) cc_final: 0.7519 (mmmt) REVERT: A 202 THR cc_start: 0.8048 (p) cc_final: 0.7800 (p) REVERT: A 246 GLN cc_start: 0.7769 (tp40) cc_final: 0.7374 (tp40) REVERT: A 255 VAL cc_start: 0.8465 (OUTLIER) cc_final: 0.8253 (p) REVERT: A 264 SER cc_start: 0.8279 (m) cc_final: 0.7692 (p) REVERT: A 283 ILE cc_start: 0.8068 (OUTLIER) cc_final: 0.7823 (pt) REVERT: A 302 ASN cc_start: 0.8645 (m-40) cc_final: 0.8288 (m110) REVERT: A 374 HIS cc_start: 0.7934 (OUTLIER) cc_final: 0.7713 (t-170) REVERT: A 417 GLN cc_start: 0.7765 (pt0) cc_final: 0.7255 (mt0) REVERT: A 468 PHE cc_start: 0.7871 (m-80) cc_final: 0.7533 (m-10) REVERT: A 477 ASP cc_start: 0.7485 (m-30) cc_final: 0.7227 (m-30) REVERT: A 482 GLU cc_start: 0.7492 (mm-30) cc_final: 0.6686 (mm-30) REVERT: A 535 MET cc_start: 0.6892 (tpp) cc_final: 0.6675 (tpp) REVERT: A 647 GLU cc_start: 0.7563 (tm-30) cc_final: 0.7218 (tm-30) REVERT: A 654 GLU cc_start: 0.7882 (tp30) cc_final: 0.7597 (tp30) REVERT: A 656 ASN cc_start: 0.7914 (t0) cc_final: 0.7529 (t0) REVERT: B 44 VAL cc_start: 0.9039 (p) cc_final: 0.8764 (m) REVERT: B 53 PHE cc_start: 0.7145 (p90) cc_final: 0.6941 (p90) REVERT: B 69 TRP cc_start: 0.6959 (m-90) cc_final: 0.6415 (m-90) REVERT: B 100 MET cc_start: 0.8166 (mtm) cc_final: 0.7950 (mtm) REVERT: B 104 MET cc_start: 0.7765 (ttt) cc_final: 0.7526 (ttt) REVERT: B 106 GLU cc_start: 0.7316 (tp30) cc_final: 0.6947 (tp30) REVERT: B 113 ASP cc_start: 0.7491 (t0) cc_final: 0.6711 (t70) REVERT: B 161 THR cc_start: 0.7870 (m) cc_final: 0.7604 (m) REVERT: B 280 ASN cc_start: 0.8004 (p0) cc_final: 0.7624 (p0) REVERT: B 297 THR cc_start: 0.8686 (t) cc_final: 0.8369 (p) REVERT: B 417 GLN cc_start: 0.7840 (OUTLIER) cc_final: 0.7603 (mt0) REVERT: B 432 ARG cc_start: 0.6614 (mtt90) cc_final: 0.6282 (mtt90) REVERT: B 447 SER cc_start: 0.8219 (m) cc_final: 0.7992 (p) REVERT: B 475 MET cc_start: 0.7991 (tpt) cc_final: 0.7692 (tpp) REVERT: B 622 ILE cc_start: 0.8721 (mm) cc_final: 0.8519 (mm) REVERT: B 656 ASN cc_start: 0.7778 (t0) cc_final: 0.7486 (t0) REVERT: B 657 GLU cc_start: 0.7391 (tp30) cc_final: 0.6914 (tp30) REVERT: C 53 PHE cc_start: 0.7218 (p90) cc_final: 0.6909 (p90) REVERT: C 72 HIS cc_start: 0.6605 (OUTLIER) cc_final: 0.6375 (t70) REVERT: C 92 ASN cc_start: 0.7611 (p0) cc_final: 0.7324 (p0) REVERT: C 103 GLN cc_start: 0.7951 (tp40) cc_final: 0.7383 (tm-30) REVERT: C 106 GLU cc_start: 0.7329 (tp30) cc_final: 0.7054 (tp30) REVERT: C 121 LYS cc_start: 0.8686 (mttt) cc_final: 0.8217 (mttm) REVERT: C 166 LYS cc_start: 0.7981 (mmmt) cc_final: 0.7637 (mmmt) REVERT: C 171 TYR cc_start: 0.7881 (p90) cc_final: 0.7480 (p90) REVERT: C 417 GLN cc_start: 0.7878 (OUTLIER) cc_final: 0.7551 (mt0) REVERT: C 427 TRP cc_start: 0.7577 (m-90) cc_final: 0.7173 (m-10) REVERT: C 482 GLU cc_start: 0.7648 (mm-30) cc_final: 0.7236 (mm-30) REVERT: C 529 THR cc_start: 0.7925 (m) cc_final: 0.7607 (m) REVERT: C 617 ARG cc_start: 0.7760 (mtp180) cc_final: 0.6797 (mtm-85) REVERT: C 634 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7374 (mt-10) REVERT: C 656 ASN cc_start: 0.7885 (t0) cc_final: 0.7549 (t0) REVERT: C 657 GLU cc_start: 0.7533 (tp30) cc_final: 0.6941 (tp30) outliers start: 66 outliers final: 42 residues processed: 471 average time/residue: 0.1373 time to fit residues: 91.5609 Evaluate side-chains 465 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 417 time to evaluate : 0.506 ------------------------------------------------------------------------------- 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 205 CYS Chi-restraints excluded: chain A residue 255 VAL 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 374 HIS Chi-restraints excluded: chain A residue 455 THR 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 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 417 GLN 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 90 THR Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 116 LEU 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 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 101 optimal weight: 0.6980 chunk 133 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 162 optimal weight: 1.9990 chunk 157 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 363 GLN A 374 HIS B 302 ASN B 363 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 = 0.3537 r_free = 0.3537 target = 0.121840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.101363 restraints weight = 21991.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.105387 restraints weight = 12280.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.108109 restraints weight = 8274.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.109977 restraints weight = 6247.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.111199 restraints weight = 5066.811| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 14547 Z= 0.151 Angle : 0.677 14.207 19893 Z= 0.332 Chirality : 0.047 0.239 2418 Planarity : 0.004 0.057 2421 Dihedral : 7.658 54.917 3122 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 4.73 % Allowed : 19.67 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.20), residues: 1656 helix: 1.31 (0.27), residues: 375 sheet: 1.04 (0.27), residues: 339 loop : -1.04 (0.19), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 273 TYR 0.023 0.002 TYR C 638 PHE 0.021 0.002 PHE C 53 TRP 0.039 0.002 TRP C 35 HIS 0.007 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00351 (14448) covalent geometry : angle 0.61622 (19632) SS BOND : bond 0.00458 ( 36) SS BOND : angle 2.54934 ( 72) hydrogen bonds : bond 0.04073 ( 391) hydrogen bonds : angle 4.50573 ( 1092) link_BETA1-4 : bond 0.00954 ( 18) link_BETA1-4 : angle 2.69822 ( 54) link_NAG-ASN : bond 0.00347 ( 45) link_NAG-ASN : angle 2.44449 ( 135) *********************** 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 515 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 444 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ASN cc_start: 0.7469 (t0) cc_final: 0.7115 (t0) REVERT: A 69 TRP cc_start: 0.7071 (m-90) cc_final: 0.6785 (m-90) REVERT: A 117 LYS cc_start: 0.8428 (ttmm) cc_final: 0.8009 (ttmm) REVERT: A 136 VAL cc_start: 0.7605 (OUTLIER) cc_final: 0.7329 (p) REVERT: A 150 GLU cc_start: 0.7373 (tp30) cc_final: 0.6956 (tp30) REVERT: A 166 LYS cc_start: 0.7799 (mmmt) cc_final: 0.7528 (mmmt) REVERT: A 246 GLN cc_start: 0.7784 (tp40) cc_final: 0.7438 (tp40) REVERT: A 255 VAL cc_start: 0.8437 (OUTLIER) cc_final: 0.8215 (p) REVERT: A 258 GLN cc_start: 0.7978 (mt0) cc_final: 0.7714 (mt0) REVERT: A 264 SER cc_start: 0.8281 (m) cc_final: 0.7694 (p) REVERT: A 283 ILE cc_start: 0.8082 (OUTLIER) cc_final: 0.7844 (pt) REVERT: A 297 THR cc_start: 0.8693 (t) cc_final: 0.8465 (p) REVERT: A 302 ASN cc_start: 0.8652 (m-40) cc_final: 0.8279 (m110) REVERT: A 417 GLN cc_start: 0.7741 (pt0) cc_final: 0.7246 (mt0) REVERT: A 447 SER cc_start: 0.8601 (m) cc_final: 0.7966 (p) REVERT: A 482 GLU cc_start: 0.7488 (mm-30) cc_final: 0.6675 (mm-30) REVERT: A 535 MET cc_start: 0.6967 (tpp) cc_final: 0.6766 (tpp) REVERT: A 631 TRP cc_start: 0.8089 (t-100) cc_final: 0.7873 (t-100) REVERT: A 647 GLU cc_start: 0.7558 (tm-30) cc_final: 0.7219 (tm-30) REVERT: A 656 ASN cc_start: 0.7903 (t0) cc_final: 0.7514 (t0) REVERT: B 44 VAL cc_start: 0.9040 (p) cc_final: 0.8764 (m) REVERT: B 53 PHE cc_start: 0.7094 (p90) cc_final: 0.6867 (p90) REVERT: B 69 TRP cc_start: 0.6945 (m-90) cc_final: 0.6412 (m-90) REVERT: B 106 GLU cc_start: 0.7305 (tp30) cc_final: 0.6926 (tp30) REVERT: B 113 ASP cc_start: 0.7485 (t0) cc_final: 0.6815 (t0) REVERT: B 136 VAL cc_start: 0.7528 (OUTLIER) cc_final: 0.7255 (p) REVERT: B 150 GLU cc_start: 0.7577 (tp30) cc_final: 0.7113 (tp30) REVERT: B 161 THR cc_start: 0.7852 (m) cc_final: 0.7592 (m) REVERT: B 268 LYS cc_start: 0.8452 (pptt) cc_final: 0.8194 (pptt) REVERT: B 280 ASN cc_start: 0.8021 (p0) cc_final: 0.7611 (p0) REVERT: B 297 THR cc_start: 0.8709 (t) cc_final: 0.8385 (p) REVERT: B 417 GLN cc_start: 0.7833 (OUTLIER) cc_final: 0.7616 (mt0) REVERT: B 432 ARG cc_start: 0.6705 (mtt90) cc_final: 0.6372 (mtt90) REVERT: B 622 ILE cc_start: 0.8744 (mm) cc_final: 0.8538 (mm) REVERT: B 656 ASN cc_start: 0.7777 (t0) cc_final: 0.7498 (t0) REVERT: B 657 GLU cc_start: 0.7395 (tp30) cc_final: 0.6955 (tp30) REVERT: C 53 PHE cc_start: 0.7185 (p90) cc_final: 0.6853 (p90) REVERT: C 72 HIS cc_start: 0.6663 (OUTLIER) cc_final: 0.6357 (t70) REVERT: C 92 ASN cc_start: 0.7712 (p0) cc_final: 0.7436 (p0) REVERT: C 93 PHE cc_start: 0.7369 (m-10) cc_final: 0.7144 (m-10) REVERT: C 96 TRP cc_start: 0.7709 (m-90) cc_final: 0.6638 (m100) REVERT: C 103 GLN cc_start: 0.7947 (tp40) cc_final: 0.7345 (tm-30) REVERT: C 106 GLU cc_start: 0.7329 (tp30) cc_final: 0.7066 (tp30) REVERT: C 136 VAL cc_start: 0.7433 (OUTLIER) cc_final: 0.7108 (p) REVERT: C 166 LYS cc_start: 0.7963 (mmmt) cc_final: 0.7623 (mmmt) REVERT: C 171 TYR cc_start: 0.7876 (p90) cc_final: 0.7450 (p90) REVERT: C 267 GLU cc_start: 0.6997 (tp30) cc_final: 0.6724 (tp30) REVERT: C 283 ILE cc_start: 0.8094 (mt) cc_final: 0.7835 (pt) REVERT: C 417 GLN cc_start: 0.7868 (OUTLIER) cc_final: 0.7595 (mt0) REVERT: C 427 TRP cc_start: 0.7627 (m-90) cc_final: 0.7192 (m-10) REVERT: C 482 GLU cc_start: 0.7651 (mm-30) cc_final: 0.7241 (mm-30) REVERT: C 529 THR cc_start: 0.7989 (m) cc_final: 0.7722 (m) REVERT: C 617 ARG cc_start: 0.7813 (mtp180) cc_final: 0.6785 (mtm-85) REVERT: C 634 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7489 (mt-10) REVERT: C 656 ASN cc_start: 0.7896 (t0) cc_final: 0.7562 (t0) REVERT: C 657 GLU cc_start: 0.7530 (tp30) cc_final: 0.6934 (tp30) outliers start: 71 outliers final: 47 residues processed: 485 average time/residue: 0.1316 time to fit residues: 90.6648 Evaluate side-chains 480 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 425 time to evaluate : 0.535 ------------------------------------------------------------------------------- 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 182 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 255 VAL 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 455 THR 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 102 ASP Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 344 LYS Chi-restraints excluded: chain B residue 417 GLN Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 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 90 THR Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 116 LEU 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 213 ILE Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 417 GLN Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 576 LEU Chi-restraints excluded: chain C residue 626 MET Chi-restraints excluded: chain C residue 629 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 140 optimal weight: 0.0970 chunk 59 optimal weight: 0.0770 chunk 10 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 160 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.5336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 363 GLN B 302 ASN B 363 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.124459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.103812 restraints weight = 21908.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.107886 restraints weight = 12159.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.110666 restraints weight = 8202.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.112553 restraints weight = 6166.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.113829 restraints weight = 5003.713| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.3751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 14547 Z= 0.124 Angle : 0.640 12.519 19893 Z= 0.316 Chirality : 0.045 0.240 2418 Planarity : 0.004 0.057 2421 Dihedral : 7.496 54.814 3122 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 4.27 % Allowed : 20.67 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.20), residues: 1656 helix: 1.44 (0.28), residues: 378 sheet: 1.35 (0.29), residues: 303 loop : -1.11 (0.19), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 419 TYR 0.026 0.001 TYR C 638 PHE 0.019 0.001 PHE C 53 TRP 0.037 0.002 TRP B 35 HIS 0.004 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00286 (14448) covalent geometry : angle 0.58502 (19632) SS BOND : bond 0.00341 ( 36) SS BOND : angle 2.26660 ( 72) hydrogen bonds : bond 0.03782 ( 391) hydrogen bonds : angle 4.45730 ( 1092) link_BETA1-4 : bond 0.00850 ( 18) link_BETA1-4 : angle 2.62709 ( 54) link_NAG-ASN : bond 0.00334 ( 45) link_NAG-ASN : angle 2.24933 ( 135) *********************** 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 510 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 446 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.8237 (ptpt) REVERT: A 67 ASN cc_start: 0.7474 (t0) cc_final: 0.7156 (t0) REVERT: A 69 TRP cc_start: 0.7036 (m-90) cc_final: 0.6825 (m-90) REVERT: A 117 LYS cc_start: 0.8429 (ttmm) cc_final: 0.8031 (ttmm) REVERT: A 136 VAL cc_start: 0.7576 (OUTLIER) cc_final: 0.7292 (p) REVERT: A 150 GLU cc_start: 0.7378 (tp30) cc_final: 0.6927 (tp30) REVERT: A 166 LYS cc_start: 0.7785 (mmmt) cc_final: 0.7506 (mmmt) REVERT: A 245 VAL cc_start: 0.8719 (t) cc_final: 0.8390 (p) REVERT: A 246 GLN cc_start: 0.7793 (tp40) cc_final: 0.7462 (tp40) REVERT: A 264 SER cc_start: 0.8294 (m) cc_final: 0.7691 (p) REVERT: A 297 THR cc_start: 0.8689 (t) cc_final: 0.8439 (p) REVERT: A 302 ASN cc_start: 0.8599 (m-40) cc_final: 0.8239 (m110) REVERT: A 344 LYS cc_start: 0.8165 (ttmm) cc_final: 0.7874 (ttmm) REVERT: A 417 GLN cc_start: 0.7728 (pt0) cc_final: 0.7303 (mt0) REVERT: A 447 SER cc_start: 0.8590 (m) cc_final: 0.7921 (p) REVERT: A 482 GLU cc_start: 0.7498 (mm-30) cc_final: 0.6657 (mm-30) REVERT: A 631 TRP cc_start: 0.8051 (t-100) cc_final: 0.7811 (t-100) REVERT: A 647 GLU cc_start: 0.7551 (tm-30) cc_final: 0.7198 (tm-30) REVERT: A 656 ASN cc_start: 0.7876 (t0) cc_final: 0.7508 (t0) REVERT: B 35 TRP cc_start: 0.7767 (m-10) cc_final: 0.7294 (m-10) REVERT: B 44 VAL cc_start: 0.9023 (p) cc_final: 0.8753 (m) REVERT: B 47 GLU cc_start: 0.7180 (tp30) cc_final: 0.6931 (mm-30) REVERT: B 69 TRP cc_start: 0.6916 (m-90) cc_final: 0.6441 (m-90) REVERT: B 106 GLU cc_start: 0.7311 (tp30) cc_final: 0.6926 (tp30) REVERT: B 113 ASP cc_start: 0.7483 (t0) cc_final: 0.6810 (t0) REVERT: B 136 VAL cc_start: 0.7570 (OUTLIER) cc_final: 0.7258 (p) REVERT: B 150 GLU cc_start: 0.7445 (tp30) cc_final: 0.7056 (tp30) REVERT: B 161 THR cc_start: 0.7839 (m) cc_final: 0.7589 (m) REVERT: B 268 LYS cc_start: 0.8425 (pptt) cc_final: 0.8155 (pptt) REVERT: B 280 ASN cc_start: 0.7952 (p0) cc_final: 0.7549 (p0) REVERT: B 297 THR cc_start: 0.8690 (t) cc_final: 0.8430 (p) REVERT: B 323 ILE cc_start: 0.7909 (OUTLIER) cc_final: 0.7584 (pt) REVERT: B 432 ARG cc_start: 0.6651 (mtt90) cc_final: 0.6279 (mtt90) REVERT: B 622 ILE cc_start: 0.8727 (mm) cc_final: 0.8448 (mt) REVERT: B 656 ASN cc_start: 0.7792 (t0) cc_final: 0.7518 (t0) REVERT: B 657 GLU cc_start: 0.7383 (tp30) cc_final: 0.6937 (tp30) REVERT: C 47 GLU cc_start: 0.7263 (tp30) cc_final: 0.6980 (mm-30) REVERT: C 53 PHE cc_start: 0.7126 (p90) cc_final: 0.6778 (p90) REVERT: C 72 HIS cc_start: 0.6668 (OUTLIER) cc_final: 0.6377 (t70) REVERT: C 92 ASN cc_start: 0.7781 (p0) cc_final: 0.7452 (p0) REVERT: C 96 TRP cc_start: 0.7646 (m-90) cc_final: 0.6557 (m100) REVERT: C 106 GLU cc_start: 0.7337 (tp30) cc_final: 0.7077 (tp30) REVERT: C 121 LYS cc_start: 0.8702 (mttt) cc_final: 0.8220 (mttp) REVERT: C 136 VAL cc_start: 0.7422 (OUTLIER) cc_final: 0.7027 (p) REVERT: C 166 LYS cc_start: 0.7945 (mmmt) cc_final: 0.7616 (mmmt) REVERT: C 171 TYR cc_start: 0.7836 (p90) cc_final: 0.7483 (p90) REVERT: C 258 GLN cc_start: 0.8386 (mt0) cc_final: 0.8172 (mt0) REVERT: C 265 LEU cc_start: 0.8929 (mp) cc_final: 0.8675 (mm) REVERT: C 273 ARG cc_start: 0.8144 (mtt-85) cc_final: 0.7678 (mtt-85) REVERT: C 417 GLN cc_start: 0.7831 (OUTLIER) cc_final: 0.7513 (mt0) REVERT: C 427 TRP cc_start: 0.7648 (m-90) cc_final: 0.7127 (m-10) REVERT: C 434 MET cc_start: 0.7019 (ttm) cc_final: 0.6776 (ttm) REVERT: C 439 ILE cc_start: 0.8090 (mp) cc_final: 0.7868 (mm) REVERT: C 482 GLU cc_start: 0.7613 (mm-30) cc_final: 0.7233 (mm-30) REVERT: C 540 GLN cc_start: 0.7531 (mp10) cc_final: 0.7252 (mp10) REVERT: C 617 ARG cc_start: 0.7775 (mtp180) cc_final: 0.6851 (mtm-85) REVERT: C 634 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7386 (mt-10) REVERT: C 656 ASN cc_start: 0.7888 (t0) cc_final: 0.7560 (t0) REVERT: C 657 GLU cc_start: 0.7549 (tp30) cc_final: 0.6971 (tp30) outliers start: 64 outliers final: 40 residues processed: 480 average time/residue: 0.1267 time to fit residues: 86.8927 Evaluate side-chains 470 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 423 time to evaluate : 0.524 ------------------------------------------------------------------------------- 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 290 THR Chi-restraints excluded: chain A residue 328 GLN 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 120 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 167 GLU 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 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 544 LEU 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 90 THR 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 417 GLN Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 576 LEU Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 626 MET 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 114 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 chunk 83 optimal weight: 7.9990 chunk 137 optimal weight: 0.6980 chunk 123 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 363 GLN B 302 ASN B 315 GLN ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 315 GLN C 350 GLN C 363 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.121070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.100733 restraints weight = 21859.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.104677 restraints weight = 12168.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.107400 restraints weight = 8198.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.109207 restraints weight = 6168.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.110503 restraints weight = 5024.556| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 14547 Z= 0.234 Angle : 0.731 14.075 19893 Z= 0.362 Chirality : 0.048 0.261 2418 Planarity : 0.004 0.063 2421 Dihedral : 7.691 55.604 3122 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.73 % Allowed : 22.27 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.20), residues: 1656 helix: 1.31 (0.27), residues: 378 sheet: 0.97 (0.26), residues: 369 loop : -1.23 (0.19), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 419 TYR 0.024 0.002 TYR A 638 PHE 0.018 0.002 PHE C 376 TRP 0.029 0.002 TRP B 35 HIS 0.006 0.002 HIS B 216 Details of bonding type rmsd covalent geometry : bond 0.00543 (14448) covalent geometry : angle 0.67637 (19632) SS BOND : bond 0.00521 ( 36) SS BOND : angle 2.71948 ( 72) hydrogen bonds : bond 0.04577 ( 391) hydrogen bonds : angle 4.62582 ( 1092) link_BETA1-4 : bond 0.00824 ( 18) link_BETA1-4 : angle 2.61384 ( 54) link_NAG-ASN : bond 0.00426 ( 45) link_NAG-ASN : angle 2.33077 ( 135) *********************** 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 496 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 440 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8092 (ptpt) REVERT: A 67 ASN cc_start: 0.7505 (t0) cc_final: 0.7133 (t0) REVERT: A 117 LYS cc_start: 0.8480 (ttmm) cc_final: 0.8083 (ttmm) REVERT: A 136 VAL cc_start: 0.7544 (OUTLIER) cc_final: 0.7248 (p) REVERT: A 150 GLU cc_start: 0.7432 (tp30) cc_final: 0.6952 (tp30) REVERT: A 166 LYS cc_start: 0.7833 (mmmt) cc_final: 0.7616 (mmmt) REVERT: A 264 SER cc_start: 0.8281 (m) cc_final: 0.7637 (p) REVERT: A 297 THR cc_start: 0.8724 (t) cc_final: 0.8451 (p) REVERT: A 302 ASN cc_start: 0.8611 (m-40) cc_final: 0.8269 (m110) REVERT: A 417 GLN cc_start: 0.7790 (pt0) cc_final: 0.7296 (mt0) REVERT: A 420 ILE cc_start: 0.8534 (mt) cc_final: 0.8231 (mm) REVERT: A 482 GLU cc_start: 0.7503 (mm-30) cc_final: 0.6649 (mm-30) REVERT: A 591 GLN cc_start: 0.8178 (tt0) cc_final: 0.7898 (tt0) REVERT: A 631 TRP cc_start: 0.8133 (t-100) cc_final: 0.7846 (t-100) REVERT: A 635 ILE cc_start: 0.8502 (tp) cc_final: 0.8129 (tt) REVERT: A 647 GLU cc_start: 0.7626 (tm-30) cc_final: 0.7201 (tm-30) REVERT: A 656 ASN cc_start: 0.7901 (t0) cc_final: 0.7537 (t0) REVERT: B 44 VAL cc_start: 0.9031 (p) cc_final: 0.8793 (m) REVERT: B 47 GLU cc_start: 0.7322 (tp30) cc_final: 0.6914 (mm-30) REVERT: B 69 TRP cc_start: 0.6893 (m-90) cc_final: 0.6460 (m-90) REVERT: B 106 GLU cc_start: 0.7330 (tp30) cc_final: 0.6953 (tp30) REVERT: B 113 ASP cc_start: 0.7500 (t0) cc_final: 0.6642 (t0) REVERT: B 136 VAL cc_start: 0.7498 (OUTLIER) cc_final: 0.7164 (p) REVERT: B 150 GLU cc_start: 0.7463 (tp30) cc_final: 0.7065 (tp30) REVERT: B 161 THR cc_start: 0.7878 (OUTLIER) cc_final: 0.7642 (m) REVERT: B 205 CYS cc_start: 0.5763 (m) cc_final: 0.5531 (m) REVERT: B 246 GLN cc_start: 0.7786 (tp40) cc_final: 0.7301 (tp40) REVERT: B 251 ILE cc_start: 0.8312 (mm) cc_final: 0.8071 (mm) REVERT: B 268 LYS cc_start: 0.8420 (pptt) cc_final: 0.8144 (pptt) REVERT: B 280 ASN cc_start: 0.8001 (p0) cc_final: 0.7625 (p0) REVERT: B 432 ARG cc_start: 0.6622 (mtt90) cc_final: 0.6333 (mtt90) REVERT: B 530 MET cc_start: 0.8774 (tpp) cc_final: 0.8268 (tpp) REVERT: B 622 ILE cc_start: 0.8732 (mm) cc_final: 0.8476 (mt) REVERT: B 645 LEU cc_start: 0.8311 (mp) cc_final: 0.8081 (mt) REVERT: B 656 ASN cc_start: 0.7840 (t0) cc_final: 0.7577 (t0) REVERT: B 657 GLU cc_start: 0.7377 (tp30) cc_final: 0.6956 (tp30) REVERT: C 53 PHE cc_start: 0.7157 (p90) cc_final: 0.6803 (p90) REVERT: C 72 HIS cc_start: 0.6635 (OUTLIER) cc_final: 0.6349 (t70) REVERT: C 92 ASN cc_start: 0.7854 (p0) cc_final: 0.7432 (p0) REVERT: C 96 TRP cc_start: 0.7677 (m-90) cc_final: 0.6673 (m100) REVERT: C 106 GLU cc_start: 0.7389 (tp30) cc_final: 0.7089 (tp30) REVERT: C 166 LYS cc_start: 0.8009 (mmmt) cc_final: 0.7642 (mmmt) REVERT: C 171 TYR cc_start: 0.7860 (p90) cc_final: 0.7474 (p90) REVERT: C 258 GLN cc_start: 0.8402 (mt0) cc_final: 0.8027 (mt0) REVERT: C 273 ARG cc_start: 0.8104 (mtt-85) cc_final: 0.7685 (mtt-85) REVERT: C 283 ILE cc_start: 0.8101 (mt) cc_final: 0.7895 (pt) REVERT: C 417 GLN cc_start: 0.7939 (OUTLIER) cc_final: 0.7539 (mt0) REVERT: C 427 TRP cc_start: 0.7710 (m-90) cc_final: 0.7041 (m-10) REVERT: C 439 ILE cc_start: 0.8104 (mp) cc_final: 0.7863 (mm) REVERT: C 482 GLU cc_start: 0.7634 (mm-30) cc_final: 0.7282 (mm-30) REVERT: C 540 GLN cc_start: 0.7513 (mp10) cc_final: 0.7098 (mp10) REVERT: C 617 ARG cc_start: 0.7839 (mtp180) cc_final: 0.6825 (mtm-85) REVERT: C 634 GLU cc_start: 0.7842 (mt-10) cc_final: 0.7523 (mt-10) REVERT: C 656 ASN cc_start: 0.7900 (t0) cc_final: 0.7588 (t0) REVERT: C 657 GLU cc_start: 0.7572 (tp30) cc_final: 0.6993 (tp30) outliers start: 56 outliers final: 38 residues processed: 473 average time/residue: 0.1264 time to fit residues: 85.5428 Evaluate side-chains 476 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 432 time to evaluate : 0.492 ------------------------------------------------------------------------------- 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 119 CYS Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 455 THR 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 102 ASP Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 90 THR 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 290 THR Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 417 GLN Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 576 LEU Chi-restraints excluded: chain C residue 591 GLN Chi-restraints excluded: chain C residue 593 LEU 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 72 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 139 optimal weight: 7.9990 chunk 140 optimal weight: 0.6980 chunk 154 optimal weight: 0.5980 chunk 92 optimal weight: 0.6980 chunk 152 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 82 optimal weight: 0.6980 chunk 155 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 302 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.123460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.103154 restraints weight = 21742.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.107178 restraints weight = 12125.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.109937 restraints weight = 8131.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.111750 restraints weight = 6104.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.112984 restraints weight = 4953.877| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.3972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 14547 Z= 0.137 Angle : 0.669 12.560 19893 Z= 0.331 Chirality : 0.045 0.240 2418 Planarity : 0.004 0.056 2421 Dihedral : 7.466 55.076 3122 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.33 % Allowed : 23.33 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.20), residues: 1656 helix: 1.39 (0.27), residues: 378 sheet: 0.95 (0.26), residues: 375 loop : -1.15 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 273 TYR 0.025 0.001 TYR C 638 PHE 0.018 0.001 PHE C 53 TRP 0.038 0.002 TRP B 35 HIS 0.004 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00317 (14448) covalent geometry : angle 0.61872 (19632) SS BOND : bond 0.00368 ( 36) SS BOND : angle 2.37872 ( 72) hydrogen bonds : bond 0.03864 ( 391) hydrogen bonds : angle 4.54006 ( 1092) link_BETA1-4 : bond 0.00819 ( 18) link_BETA1-4 : angle 2.53763 ( 54) link_NAG-ASN : bond 0.00329 ( 45) link_NAG-ASN : angle 2.16132 ( 135) *********************** 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 485 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 435 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ASN cc_start: 0.7383 (t0) cc_final: 0.7166 (t0) REVERT: A 117 LYS cc_start: 0.8500 (ttmm) cc_final: 0.8101 (ttmm) REVERT: A 136 VAL cc_start: 0.7515 (OUTLIER) cc_final: 0.7226 (p) REVERT: A 150 GLU cc_start: 0.7395 (tp30) cc_final: 0.6901 (tp30) REVERT: A 166 LYS cc_start: 0.7843 (mmmt) cc_final: 0.7642 (mmmt) REVERT: A 178 ASP cc_start: 0.7750 (t0) cc_final: 0.7353 (t70) REVERT: A 245 VAL cc_start: 0.8665 (t) cc_final: 0.8317 (p) REVERT: A 264 SER cc_start: 0.8312 (m) cc_final: 0.7704 (p) REVERT: A 297 THR cc_start: 0.8705 (t) cc_final: 0.8456 (p) REVERT: A 302 ASN cc_start: 0.8611 (m-40) cc_final: 0.8289 (m110) REVERT: A 321 ASP cc_start: 0.7208 (t70) cc_final: 0.6857 (t0) REVERT: A 417 GLN cc_start: 0.7741 (pt0) cc_final: 0.7331 (mt0) REVERT: A 447 SER cc_start: 0.8426 (m) cc_final: 0.7875 (p) REVERT: A 482 GLU cc_start: 0.7468 (mm-30) cc_final: 0.6592 (mm-30) REVERT: A 631 TRP cc_start: 0.8069 (t-100) cc_final: 0.7779 (t-100) REVERT: A 635 ILE cc_start: 0.8415 (tp) cc_final: 0.8062 (tt) REVERT: A 647 GLU cc_start: 0.7556 (tm-30) cc_final: 0.7195 (tm-30) REVERT: A 656 ASN cc_start: 0.7861 (t0) cc_final: 0.7523 (t0) REVERT: B 35 TRP cc_start: 0.7736 (m-10) cc_final: 0.7262 (m-10) REVERT: B 44 VAL cc_start: 0.9015 (p) cc_final: 0.8792 (m) REVERT: B 47 GLU cc_start: 0.7217 (tp30) cc_final: 0.6928 (mm-30) REVERT: B 69 TRP cc_start: 0.6823 (m-90) cc_final: 0.6395 (m-90) REVERT: B 106 GLU cc_start: 0.7264 (tp30) cc_final: 0.6874 (tp30) REVERT: B 113 ASP cc_start: 0.7470 (t0) cc_final: 0.6735 (t0) REVERT: B 136 VAL cc_start: 0.7472 (OUTLIER) cc_final: 0.7121 (p) REVERT: B 150 GLU cc_start: 0.7415 (tp30) cc_final: 0.6948 (tp30) REVERT: B 161 THR cc_start: 0.7884 (OUTLIER) cc_final: 0.7674 (m) REVERT: B 246 GLN cc_start: 0.7781 (tp40) cc_final: 0.7293 (tp40) REVERT: B 269 GLU cc_start: 0.7999 (tt0) cc_final: 0.7662 (tt0) REVERT: B 272 ILE cc_start: 0.8387 (mt) cc_final: 0.7544 (mt) REVERT: B 280 ASN cc_start: 0.7988 (p0) cc_final: 0.7614 (p0) REVERT: B 432 ARG cc_start: 0.6565 (mtt90) cc_final: 0.6289 (mtt90) REVERT: B 530 MET cc_start: 0.8775 (tpp) cc_final: 0.8268 (tpp) REVERT: B 622 ILE cc_start: 0.8740 (mm) cc_final: 0.8504 (mt) REVERT: B 645 LEU cc_start: 0.8251 (mp) cc_final: 0.8018 (mt) REVERT: B 656 ASN cc_start: 0.7835 (t0) cc_final: 0.7550 (t0) REVERT: B 657 GLU cc_start: 0.7378 (tp30) cc_final: 0.6945 (tp30) REVERT: C 47 GLU cc_start: 0.7340 (mm-30) cc_final: 0.6949 (mm-30) REVERT: C 53 PHE cc_start: 0.7114 (p90) cc_final: 0.6777 (p90) REVERT: C 92 ASN cc_start: 0.7741 (p0) cc_final: 0.7352 (p0) REVERT: C 106 GLU cc_start: 0.7330 (tp30) cc_final: 0.7044 (tp30) REVERT: C 121 LYS cc_start: 0.8688 (mttt) cc_final: 0.8217 (mttm) REVERT: C 136 VAL cc_start: 0.7318 (OUTLIER) cc_final: 0.6908 (p) REVERT: C 166 LYS cc_start: 0.7977 (mmmt) cc_final: 0.7658 (mmmt) REVERT: C 171 TYR cc_start: 0.7815 (p90) cc_final: 0.7436 (p90) REVERT: C 258 GLN cc_start: 0.8404 (mt0) cc_final: 0.7946 (mt0) REVERT: C 265 LEU cc_start: 0.8911 (mp) cc_final: 0.8692 (mm) REVERT: C 273 ARG cc_start: 0.8067 (mtt-85) cc_final: 0.7627 (mtt-85) REVERT: C 414 ILE cc_start: 0.8751 (tp) cc_final: 0.8498 (tt) REVERT: C 417 GLN cc_start: 0.7850 (OUTLIER) cc_final: 0.7552 (mt0) REVERT: C 427 TRP cc_start: 0.7704 (m-90) cc_final: 0.7012 (m-10) REVERT: C 439 ILE cc_start: 0.8113 (mp) cc_final: 0.7839 (mt) REVERT: C 482 GLU cc_start: 0.7624 (mm-30) cc_final: 0.7252 (mm-30) REVERT: C 540 GLN cc_start: 0.7532 (mp10) cc_final: 0.7191 (mp10) REVERT: C 610 TRP cc_start: 0.8014 (t-100) cc_final: 0.7685 (t-100) REVERT: C 617 ARG cc_start: 0.7658 (mtp180) cc_final: 0.6798 (mtm-85) REVERT: C 634 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7548 (mt-10) REVERT: C 656 ASN cc_start: 0.7900 (t0) cc_final: 0.7606 (t0) REVERT: C 657 GLU cc_start: 0.7554 (tp30) cc_final: 0.7076 (tp30) outliers start: 50 outliers final: 34 residues processed: 461 average time/residue: 0.1314 time to fit residues: 86.2841 Evaluate side-chains 473 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 434 time to evaluate : 0.623 ------------------------------------------------------------------------------- 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 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 290 THR 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 102 ASP 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 290 THR Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 90 THR 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 417 GLN Chi-restraints excluded: chain C residue 576 LEU Chi-restraints excluded: chain C residue 593 LEU 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 147 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 167 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 128 optimal weight: 0.8980 chunk 125 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 363 GLN B 302 ASN B 363 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.121054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.100907 restraints weight = 21928.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.104851 restraints weight = 12174.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.107588 restraints weight = 8175.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.109356 restraints weight = 6137.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.110654 restraints weight = 4995.127| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.4020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 14547 Z= 0.182 Angle : 0.705 12.671 19893 Z= 0.350 Chirality : 0.047 0.249 2418 Planarity : 0.004 0.056 2421 Dihedral : 7.506 55.264 3122 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.13 % Allowed : 23.93 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.20), residues: 1656 helix: 1.41 (0.27), residues: 378 sheet: 0.91 (0.26), residues: 375 loop : -1.23 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 273 TYR 0.025 0.002 TYR C 638 PHE 0.017 0.002 PHE C 53 TRP 0.038 0.002 TRP B 35 HIS 0.005 0.001 HIS B 216 Details of bonding type rmsd covalent geometry : bond 0.00426 (14448) covalent geometry : angle 0.65626 (19632) SS BOND : bond 0.00415 ( 36) SS BOND : angle 2.46958 ( 72) hydrogen bonds : bond 0.04250 ( 391) hydrogen bonds : angle 4.58500 ( 1092) link_BETA1-4 : bond 0.00799 ( 18) link_BETA1-4 : angle 2.52376 ( 54) link_NAG-ASN : bond 0.00357 ( 45) link_NAG-ASN : angle 2.19822 ( 135) ********************** 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 481 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 434 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LYS cc_start: 0.8502 (ttmm) cc_final: 0.8107 (ttmm) REVERT: A 136 VAL cc_start: 0.7426 (OUTLIER) cc_final: 0.7077 (p) REVERT: A 150 GLU cc_start: 0.7381 (tp30) cc_final: 0.6874 (tp30) REVERT: A 245 VAL cc_start: 0.8714 (t) cc_final: 0.8357 (p) REVERT: A 264 SER cc_start: 0.8265 (m) cc_final: 0.7673 (p) REVERT: A 297 THR cc_start: 0.8714 (t) cc_final: 0.8470 (p) REVERT: A 302 ASN cc_start: 0.8597 (m-40) cc_final: 0.8296 (m110) REVERT: A 321 ASP cc_start: 0.7251 (t70) cc_final: 0.6983 (t0) REVERT: A 417 GLN cc_start: 0.7765 (pt0) cc_final: 0.7355 (mt0) REVERT: A 447 SER cc_start: 0.8462 (m) cc_final: 0.7913 (p) REVERT: A 468 PHE cc_start: 0.8050 (m-80) cc_final: 0.7721 (m-10) REVERT: A 482 GLU cc_start: 0.7447 (mm-30) cc_final: 0.6644 (mm-30) REVERT: A 530 MET cc_start: 0.8805 (tpt) cc_final: 0.8389 (tpt) REVERT: A 631 TRP cc_start: 0.8093 (t-100) cc_final: 0.7761 (t-100) REVERT: A 635 ILE cc_start: 0.8449 (tp) cc_final: 0.8069 (tt) REVERT: A 647 GLU cc_start: 0.7592 (tm-30) cc_final: 0.7212 (tm-30) REVERT: A 656 ASN cc_start: 0.7879 (t0) cc_final: 0.7533 (t0) REVERT: B 35 TRP cc_start: 0.7805 (m-10) cc_final: 0.7318 (m-10) REVERT: B 44 VAL cc_start: 0.9014 (p) cc_final: 0.8811 (m) REVERT: B 47 GLU cc_start: 0.7284 (tp30) cc_final: 0.7028 (mm-30) REVERT: B 69 TRP cc_start: 0.6857 (m-90) cc_final: 0.6441 (m-90) REVERT: B 106 GLU cc_start: 0.7284 (tp30) cc_final: 0.6891 (tp30) REVERT: B 113 ASP cc_start: 0.7462 (t0) cc_final: 0.6633 (t0) REVERT: B 136 VAL cc_start: 0.7459 (OUTLIER) cc_final: 0.7103 (p) REVERT: B 150 GLU cc_start: 0.7413 (tp30) cc_final: 0.6924 (tp30) REVERT: B 161 THR cc_start: 0.7870 (OUTLIER) cc_final: 0.7628 (m) REVERT: B 246 GLN cc_start: 0.7803 (tp40) cc_final: 0.7305 (tp40) REVERT: B 268 LYS cc_start: 0.8351 (pptt) cc_final: 0.8071 (pptt) REVERT: B 280 ASN cc_start: 0.7990 (p0) cc_final: 0.7625 (p0) REVERT: B 432 ARG cc_start: 0.6607 (mtt90) cc_final: 0.6280 (mtt90) REVERT: B 492 GLU cc_start: 0.7337 (mt-10) cc_final: 0.7021 (mt-10) REVERT: B 530 MET cc_start: 0.8841 (tpp) cc_final: 0.8341 (tpp) REVERT: B 622 ILE cc_start: 0.8730 (mm) cc_final: 0.8501 (mt) REVERT: B 645 LEU cc_start: 0.8287 (mp) cc_final: 0.8045 (mt) REVERT: B 656 ASN cc_start: 0.7856 (t0) cc_final: 0.7576 (t0) REVERT: B 657 GLU cc_start: 0.7378 (tp30) cc_final: 0.6946 (tp30) REVERT: C 47 GLU cc_start: 0.7411 (mm-30) cc_final: 0.7016 (mm-30) REVERT: C 53 PHE cc_start: 0.7212 (p90) cc_final: 0.6895 (p90) REVERT: C 92 ASN cc_start: 0.7771 (p0) cc_final: 0.7415 (p0) REVERT: C 96 TRP cc_start: 0.7550 (m-90) cc_final: 0.6588 (m100) REVERT: C 106 GLU cc_start: 0.7364 (tp30) cc_final: 0.7095 (tp30) REVERT: C 166 LYS cc_start: 0.8054 (mmmt) cc_final: 0.7701 (mmmt) REVERT: C 171 TYR cc_start: 0.7822 (p90) cc_final: 0.7442 (p90) REVERT: C 258 GLN cc_start: 0.8479 (mt0) cc_final: 0.8023 (mt0) REVERT: C 265 LEU cc_start: 0.8928 (mp) cc_final: 0.8699 (mm) REVERT: C 273 ARG cc_start: 0.8109 (mtt-85) cc_final: 0.7687 (mtt-85) REVERT: C 414 ILE cc_start: 0.8767 (tp) cc_final: 0.8496 (tt) REVERT: C 417 GLN cc_start: 0.7879 (OUTLIER) cc_final: 0.7561 (mt0) REVERT: C 427 TRP cc_start: 0.7732 (m-90) cc_final: 0.7014 (m-10) REVERT: C 439 ILE cc_start: 0.8114 (mp) cc_final: 0.7855 (mt) REVERT: C 482 GLU cc_start: 0.7621 (mm-30) cc_final: 0.7251 (mm-30) REVERT: C 530 MET cc_start: 0.8823 (tpp) cc_final: 0.8453 (tpp) REVERT: C 540 GLN cc_start: 0.7626 (mp10) cc_final: 0.7228 (mp10) REVERT: C 610 TRP cc_start: 0.8023 (t-100) cc_final: 0.7697 (t-100) REVERT: C 617 ARG cc_start: 0.7623 (mtp180) cc_final: 0.6783 (mtm-85) REVERT: C 634 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7555 (mt-10) REVERT: C 656 ASN cc_start: 0.7943 (t0) cc_final: 0.7629 (t0) REVERT: C 657 GLU cc_start: 0.7576 (tp30) cc_final: 0.7078 (tp30) outliers start: 47 outliers final: 38 residues processed: 455 average time/residue: 0.1302 time to fit residues: 83.9051 Evaluate side-chains 470 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 428 time to evaluate : 0.482 ------------------------------------------------------------------------------- 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 121 LYS 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 290 THR Chi-restraints excluded: chain A residue 292 VAL 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 102 ASP Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 90 THR 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 213 ILE Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 417 GLN 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 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 124 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 134 optimal weight: 0.6980 chunk 128 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 83 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 302 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.121008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.100814 restraints weight = 21901.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.104864 restraints weight = 12143.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.107431 restraints weight = 8115.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.109315 restraints weight = 6147.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.110687 restraints weight = 4966.799| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.4097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 14547 Z= 0.175 Angle : 0.698 12.354 19893 Z= 0.347 Chirality : 0.047 0.245 2418 Planarity : 0.004 0.056 2421 Dihedral : 7.487 55.315 3122 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.00 % Allowed : 24.07 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.20), residues: 1656 helix: 1.39 (0.27), residues: 378 sheet: 0.88 (0.26), residues: 375 loop : -1.24 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 273 TYR 0.026 0.002 TYR C 638 PHE 0.017 0.002 PHE C 53 TRP 0.036 0.002 TRP B 35 HIS 0.004 0.001 HIS B 249 Details of bonding type rmsd covalent geometry : bond 0.00407 (14448) covalent geometry : angle 0.65075 (19632) SS BOND : bond 0.00422 ( 36) SS BOND : angle 2.39326 ( 72) hydrogen bonds : bond 0.04183 ( 391) hydrogen bonds : angle 4.58652 ( 1092) link_BETA1-4 : bond 0.00795 ( 18) link_BETA1-4 : angle 2.50119 ( 54) link_NAG-ASN : bond 0.00343 ( 45) link_NAG-ASN : angle 2.15796 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2522.06 seconds wall clock time: 44 minutes 15.44 seconds (2655.44 seconds total)