Starting phenix.real_space_refine on Sun Nov 17 17:27:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eu8_28608/11_2024/8eu8_28608_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eu8_28608/11_2024/8eu8_28608.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eu8_28608/11_2024/8eu8_28608.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eu8_28608/11_2024/8eu8_28608.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eu8_28608/11_2024/8eu8_28608_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eu8_28608/11_2024/8eu8_28608_neut.cif" } resolution = 3.73 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 105 5.16 5 C 8856 2.51 5 N 2358 2.21 5 O 2862 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 75 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 14181 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 4433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 564, 4433 Classifications: {'peptide': 564} Link IDs: {'PTRANS': 25, 'TRANS': 538} Chain breaks: 5 Chain: "B" Number of atoms: 4433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 564, 4433 Classifications: {'peptide': 564} Link IDs: {'PTRANS': 25, 'TRANS': 538} Chain breaks: 5 Chain: "C" Number of atoms: 4433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 564, 4433 Classifications: {'peptide': 564} Link IDs: {'PTRANS': 25, 'TRANS': 538} Chain breaks: 5 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 9.32, per 1000 atoms: 0.66 Number of scatterers: 14181 At special positions: 0 Unit cell: (130.68, 126.36, 120.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 105 16.00 O 2862 8.00 N 2358 7.00 C 8856 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.05 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 155 " distance=2.02 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.04 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.05 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.01 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.02 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS A 605 " distance=2.04 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.01 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 74 " distance=2.05 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.04 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 155 " distance=2.02 Simple disulfide: pdb=" SG CYS B 201 " - pdb=" SG CYS B 433 " distance=2.04 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.02 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.05 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.01 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.02 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS B 605 " distance=2.04 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.01 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.05 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.04 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 155 " distance=2.02 Simple disulfide: pdb=" SG CYS C 201 " - pdb=" SG CYS C 433 " distance=2.04 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.05 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.01 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.02 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS C 605 " distance=2.04 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.01 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A 801 " - " ASN A 158 " " NAG A 802 " - " ASN A 197 " " NAG A 803 " - " ASN A 234 " " NAG A 804 " - " ASN A 339 " " NAG A 805 " - " ASN A 362 " " NAG A 806 " - " ASN A 386 " " NAG A 807 " - " ASN A 448 " " NAG A 808 " - " ASN A 611 " " NAG A 809 " - " ASN A 618 " " NAG B 801 " - " ASN B 158 " " NAG B 802 " - " ASN B 197 " " NAG B 803 " - " ASN B 234 " " NAG B 804 " - " ASN B 339 " " NAG B 805 " - " ASN B 362 " " NAG B 806 " - " ASN B 386 " " NAG B 807 " - " ASN B 448 " " NAG B 808 " - " ASN B 611 " " NAG B 809 " - " ASN B 618 " " NAG C 801 " - " ASN C 158 " " NAG C 802 " - " ASN C 197 " " NAG C 803 " - " ASN C 234 " " NAG C 804 " - " ASN C 339 " " NAG C 805 " - " ASN C 362 " " NAG C 806 " - " ASN C 386 " " NAG C 807 " - " ASN C 448 " " NAG C 808 " - " ASN C 611 " " NAG C 809 " - " ASN C 618 " " NAG D 1 " - " ASN A 154 " " NAG E 1 " - " ASN A 241 " " NAG F 1 " - " ASN A 262 " " NAG G 1 " - " ASN A 276 " " NAG H 1 " - " ASN A 332 " " NAG I 1 " - " ASN A 392 " " NAG J 1 " - " ASN B 154 " " NAG K 1 " - " ASN B 241 " " NAG L 1 " - " ASN B 262 " " NAG M 1 " - " ASN B 276 " " NAG N 1 " - " ASN B 332 " " NAG O 1 " - " ASN B 392 " " NAG P 1 " - " ASN C 154 " " NAG Q 1 " - " ASN C 241 " " NAG R 1 " - " ASN C 262 " " NAG S 1 " - " ASN C 276 " " NAG T 1 " - " ASN C 332 " " NAG U 1 " - " ASN C 392 " Time building additional restraints: 4.00 Conformation dependent library (CDL) restraints added in 1.9 seconds 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3174 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 21 sheets defined 25.9% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.36 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: 3.94 Time building geometry restraints manager: 4.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4158 1.34 - 1.46: 2182 1.46 - 1.58: 7970 1.58 - 1.70: 0 1.70 - 1.82: 138 Bond restraints: 14448 Sorted by residual: bond pdb=" C4 NAG U 1 " pdb=" O4 NAG U 1 " ideal model delta sigma weight residual 1.409 1.488 -0.079 2.00e-02 2.50e+03 1.57e+01 bond pdb=" C4 NAG I 1 " pdb=" O4 NAG I 1 " ideal model delta sigma weight residual 1.409 1.488 -0.079 2.00e-02 2.50e+03 1.56e+01 bond pdb=" C4 NAG O 1 " pdb=" O4 NAG O 1 " ideal model delta sigma weight residual 1.409 1.487 -0.078 2.00e-02 2.50e+03 1.53e+01 bond pdb=" C4 NAG G 1 " pdb=" O4 NAG G 1 " ideal model delta sigma weight residual 1.409 1.486 -0.077 2.00e-02 2.50e+03 1.50e+01 bond pdb=" C4 NAG S 1 " pdb=" O4 NAG S 1 " ideal model delta sigma weight residual 1.409 1.486 -0.077 2.00e-02 2.50e+03 1.49e+01 ... (remaining 14443 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 10821 1.34 - 2.69: 6052 2.69 - 4.03: 2254 4.03 - 5.37: 401 5.37 - 6.72: 104 Bond angle restraints: 19632 Sorted by residual: angle pdb=" C ASP A 78 " pdb=" CA ASP A 78 " pdb=" CB ASP A 78 " ideal model delta sigma weight residual 111.20 116.25 -5.05 7.10e-01 1.98e+00 5.05e+01 angle pdb=" C ASP C 78 " pdb=" CA ASP C 78 " pdb=" CB ASP C 78 " ideal model delta sigma weight residual 111.20 115.14 -3.94 7.10e-01 1.98e+00 3.08e+01 angle pdb=" CA ASN B 234 " pdb=" CB ASN B 234 " pdb=" CG ASN B 234 " ideal model delta sigma weight residual 112.60 118.14 -5.54 1.00e+00 1.00e+00 3.07e+01 angle pdb=" C ASP B 78 " pdb=" CA ASP B 78 " pdb=" CB ASP B 78 " ideal model delta sigma weight residual 111.20 115.14 -3.94 7.10e-01 1.98e+00 3.07e+01 angle pdb=" CA ASN A 234 " pdb=" CB ASN A 234 " pdb=" CG ASN A 234 " ideal model delta sigma weight residual 112.60 118.14 -5.54 1.00e+00 1.00e+00 3.07e+01 ... (remaining 19627 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 8856 17.68 - 35.36: 523 35.36 - 53.03: 151 53.03 - 70.71: 23 70.71 - 88.39: 14 Dihedral angle restraints: 9567 sinusoidal: 4668 harmonic: 4899 Sorted by residual: dihedral pdb=" CB CYS B 228 " pdb=" SG CYS B 228 " pdb=" SG CYS B 239 " pdb=" CB CYS B 239 " ideal model delta sinusoidal sigma weight residual -86.00 -144.72 58.72 1 1.00e+01 1.00e-02 4.62e+01 dihedral pdb=" CB CYS C 228 " pdb=" SG CYS C 228 " pdb=" SG CYS C 239 " pdb=" CB CYS C 239 " ideal model delta sinusoidal sigma weight residual -86.00 -144.72 58.72 1 1.00e+01 1.00e-02 4.62e+01 dihedral pdb=" CB CYS A 228 " pdb=" SG CYS A 228 " pdb=" SG CYS A 239 " pdb=" CB CYS A 239 " ideal model delta sinusoidal sigma weight residual -86.00 -144.72 58.72 1 1.00e+01 1.00e-02 4.62e+01 ... (remaining 9564 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1147 0.068 - 0.136: 800 0.136 - 0.204: 337 0.204 - 0.272: 116 0.272 - 0.339: 18 Chirality restraints: 2418 Sorted by residual: chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 9.90e+01 chirality pdb=" C1 NAG T 2 " pdb=" O4 NAG T 1 " pdb=" C2 NAG T 2 " pdb=" O5 NAG T 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 9.86e+01 chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 9.80e+01 ... (remaining 2415 not shown) Planarity restraints: 2466 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 618 " 0.192 2.00e-02 2.50e+03 1.81e-01 4.08e+02 pdb=" CG ASN B 618 " -0.075 2.00e-02 2.50e+03 pdb=" OD1 ASN B 618 " -0.091 2.00e-02 2.50e+03 pdb=" ND2 ASN B 618 " -0.250 2.00e-02 2.50e+03 pdb=" C1 NAG B 809 " 0.224 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 618 " 0.192 2.00e-02 2.50e+03 1.81e-01 4.08e+02 pdb=" CG ASN C 618 " -0.075 2.00e-02 2.50e+03 pdb=" OD1 ASN C 618 " -0.091 2.00e-02 2.50e+03 pdb=" ND2 ASN C 618 " -0.250 2.00e-02 2.50e+03 pdb=" C1 NAG C 809 " 0.224 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 618 " 0.192 2.00e-02 2.50e+03 1.81e-01 4.08e+02 pdb=" CG ASN A 618 " -0.075 2.00e-02 2.50e+03 pdb=" OD1 ASN A 618 " -0.091 2.00e-02 2.50e+03 pdb=" ND2 ASN A 618 " -0.250 2.00e-02 2.50e+03 pdb=" C1 NAG A 809 " 0.224 2.00e-02 2.50e+03 ... (remaining 2463 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.38: 12 2.38 - 3.01: 7162 3.01 - 3.64: 19015 3.64 - 4.27: 30204 4.27 - 4.90: 47392 Nonbonded interactions: 103785 Sorted by model distance: nonbonded pdb=" O CYS A 196 " pdb=" CB GLU B 162 " model vdw 1.755 3.440 nonbonded pdb=" CB GLU A 162 " pdb=" O CYS C 196 " model vdw 1.760 3.440 nonbonded pdb=" O CYS B 196 " pdb=" CB GLU C 162 " model vdw 1.762 3.440 nonbonded pdb=" O CYS A 196 " pdb=" CG GLU B 162 " model vdw 2.083 3.440 nonbonded pdb=" CG GLU A 162 " pdb=" O CYS C 196 " model vdw 2.086 3.440 ... (remaining 103780 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 33.950 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.240 ------------------------------------------------------------------------------- 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 0.079 14448 Z= 0.881 Angle : 1.808 6.717 19632 Z= 1.192 Chirality : 0.105 0.339 2418 Planarity : 0.013 0.083 2421 Dihedral : 12.696 88.387 6285 Min Nonbonded Distance : 1.755 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 0.47 % Allowed : 5.67 % Favored : 93.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.18), residues: 1656 helix: -0.84 (0.23), residues: 351 sheet: 1.08 (0.26), residues: 345 loop : -1.18 (0.17), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.129 0.030 TRP C 610 HIS 0.011 0.003 HIS C 216 PHE 0.082 0.017 PHE B 233 TYR 0.138 0.023 TYR C 361 ARG 0.007 0.001 ARG A 585 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 530 time to evaluate : 1.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.7290 (m100) cc_final: 0.6999 (m100) REVERT: A 42 VAL cc_start: 0.8247 (t) cc_final: 0.7761 (p) REVERT: A 46 LYS cc_start: 0.7871 (mmmt) cc_final: 0.7599 (mmmt) REVERT: A 49 LYS cc_start: 0.7763 (OUTLIER) cc_final: 0.7531 (pttm) REVERT: A 53 PHE cc_start: 0.7594 (p90) cc_final: 0.7051 (p90) REVERT: A 69 TRP cc_start: 0.7276 (m-90) cc_final: 0.6158 (m-90) REVERT: A 88 ASN cc_start: 0.7939 (m110) cc_final: 0.7720 (m-40) REVERT: A 98 ASN cc_start: 0.7823 (t0) cc_final: 0.7613 (t0) REVERT: A 99 ASP cc_start: 0.7534 (m-30) cc_final: 0.7216 (m-30) REVERT: A 102 ASP cc_start: 0.7739 (t70) cc_final: 0.7330 (t0) REVERT: A 104 MET cc_start: 0.7962 (ttt) cc_final: 0.7677 (ttm) REVERT: A 106 GLU cc_start: 0.7565 (tp30) cc_final: 0.7285 (tp30) REVERT: A 113 ASP cc_start: 0.7394 (t0) cc_final: 0.6915 (t0) REVERT: A 117 LYS cc_start: 0.8521 (ttmm) cc_final: 0.8109 (ttmm) REVERT: A 150 GLU cc_start: 0.7636 (tp30) cc_final: 0.7335 (tp30) REVERT: A 166 LYS cc_start: 0.7868 (mmmt) cc_final: 0.7456 (mmmt) REVERT: A 199 SER cc_start: 0.7809 (m) cc_final: 0.7487 (t) REVERT: A 223 TYR cc_start: 0.8157 (m-80) cc_final: 0.7881 (m-80) REVERT: A 245 VAL cc_start: 0.8674 (t) cc_final: 0.8407 (p) REVERT: A 258 GLN cc_start: 0.8253 (mt0) cc_final: 0.8039 (mt0) REVERT: A 264 SER cc_start: 0.8165 (m) cc_final: 0.7541 (p) REVERT: A 269 GLU cc_start: 0.8100 (tt0) cc_final: 0.7872 (tt0) REVERT: A 301 ASN cc_start: 0.7705 (t0) cc_final: 0.7502 (t0) REVERT: A 302 ASN cc_start: 0.8568 (m-40) cc_final: 0.8235 (m110) REVERT: A 321 ASP cc_start: 0.7174 (t0) cc_final: 0.6958 (t0) REVERT: A 327 LYS cc_start: 0.7954 (tptp) cc_final: 0.7727 (tptp) REVERT: A 343 GLN cc_start: 0.7618 (tt0) cc_final: 0.7304 (tt0) REVERT: A 414 ILE cc_start: 0.8354 (tp) cc_final: 0.8150 (tp) REVERT: A 420 ILE cc_start: 0.8425 (mt) cc_final: 0.8145 (mm) REVERT: A 421 LYS cc_start: 0.8622 (mtpt) cc_final: 0.8402 (mtpp) REVERT: A 468 PHE cc_start: 0.7650 (m-80) cc_final: 0.7325 (m-10) REVERT: A 482 GLU cc_start: 0.7523 (mm-30) cc_final: 0.6721 (mm-30) REVERT: A 487 LYS cc_start: 0.8294 (tttt) cc_final: 0.7599 (tttt) REVERT: A 500 ARG cc_start: 0.6917 (mtp85) cc_final: 0.6595 (mtp180) REVERT: A 535 MET cc_start: 0.7066 (tpp) cc_final: 0.6564 (tpp) REVERT: A 646 LEU cc_start: 0.8210 (mt) cc_final: 0.7915 (mm) REVERT: A 647 GLU cc_start: 0.7608 (tm-30) cc_final: 0.7189 (tm-30) REVERT: A 656 ASN cc_start: 0.7821 (t0) cc_final: 0.7404 (t0) REVERT: B 35 TRP cc_start: 0.7254 (m100) cc_final: 0.6543 (m100) REVERT: B 42 VAL cc_start: 0.8349 (t) cc_final: 0.7856 (p) REVERT: B 47 GLU cc_start: 0.7200 (tt0) cc_final: 0.6836 (tt0) REVERT: B 50 THR cc_start: 0.8438 (m) cc_final: 0.8200 (p) REVERT: B 93 PHE cc_start: 0.8012 (m-80) cc_final: 0.7795 (m-80) REVERT: B 97 LYS cc_start: 0.8181 (tppt) cc_final: 0.7401 (tppt) REVERT: B 103 GLN cc_start: 0.7882 (tp40) cc_final: 0.7497 (tm-30) REVERT: B 104 MET cc_start: 0.7794 (ttt) cc_final: 0.7385 (ttm) REVERT: B 106 GLU cc_start: 0.7353 (tp30) cc_final: 0.6876 (tp30) REVERT: B 113 ASP cc_start: 0.7412 (t0) cc_final: 0.6736 (t70) REVERT: B 169 LYS cc_start: 0.8007 (tttp) cc_final: 0.7711 (tttp) REVERT: B 205 CYS cc_start: 0.5873 (m) cc_final: 0.5639 (m) REVERT: B 234 ASN cc_start: 0.7538 (t0) cc_final: 0.7208 (t0) REVERT: B 245 VAL cc_start: 0.8574 (t) cc_final: 0.8341 (p) REVERT: B 293 GLU cc_start: 0.7572 (tt0) cc_final: 0.7081 (tt0) REVERT: B 301 ASN cc_start: 0.7762 (t0) cc_final: 0.7483 (t0) REVERT: B 302 ASN cc_start: 0.8556 (m-40) cc_final: 0.8273 (m110) REVERT: B 420 ILE cc_start: 0.8463 (mt) cc_final: 0.8197 (mm) REVERT: B 427 TRP cc_start: 0.7633 (m-90) cc_final: 0.7404 (m-10) REVERT: B 432 ARG cc_start: 0.6973 (mtt90) cc_final: 0.6640 (mtt90) REVERT: B 447 SER cc_start: 0.8286 (m) cc_final: 0.7955 (p) REVERT: B 487 LYS cc_start: 0.8200 (tttt) cc_final: 0.7378 (tttt) REVERT: B 490 LYS cc_start: 0.7892 (ttpt) cc_final: 0.7561 (ttpt) REVERT: B 535 MET cc_start: 0.6940 (tpp) cc_final: 0.6570 (tpp) REVERT: B 536 THR cc_start: 0.8410 (t) cc_final: 0.8152 (p) REVERT: B 591 GLN cc_start: 0.8312 (tt0) cc_final: 0.8018 (tt0) REVERT: B 634 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7945 (mt-10) REVERT: B 640 GLN cc_start: 0.8945 (tp40) cc_final: 0.8340 (tp-100) REVERT: B 650 GLN cc_start: 0.7970 (tp40) cc_final: 0.7342 (tp40) REVERT: B 652 GLN cc_start: 0.7629 (tm-30) cc_final: 0.7336 (tm-30) REVERT: B 656 ASN cc_start: 0.7755 (t0) cc_final: 0.7374 (t0) REVERT: B 657 GLU cc_start: 0.7484 (tp30) cc_final: 0.7184 (tp30) REVERT: C 35 TRP cc_start: 0.7293 (m100) cc_final: 0.7083 (m100) REVERT: C 42 VAL cc_start: 0.8318 (t) cc_final: 0.7899 (p) REVERT: C 47 GLU cc_start: 0.7290 (tt0) cc_final: 0.6905 (tt0) REVERT: C 53 PHE cc_start: 0.7586 (p90) cc_final: 0.7369 (p90) REVERT: C 86 LEU cc_start: 0.8563 (mp) cc_final: 0.8318 (mm) REVERT: C 92 ASN cc_start: 0.7736 (p0) cc_final: 0.7319 (p0) REVERT: C 102 ASP cc_start: 0.7708 (t70) cc_final: 0.7381 (t0) REVERT: C 103 GLN cc_start: 0.8056 (tp40) cc_final: 0.7609 (tm-30) REVERT: C 104 MET cc_start: 0.7848 (ttt) cc_final: 0.7611 (ttp) REVERT: C 113 ASP cc_start: 0.7405 (t0) cc_final: 0.7127 (t70) REVERT: C 164 ARG cc_start: 0.7040 (ttp80) cc_final: 0.6810 (ttp-170) REVERT: C 171 TYR cc_start: 0.7769 (p90) cc_final: 0.7494 (p90) REVERT: C 223 TYR cc_start: 0.7925 (m-80) cc_final: 0.7529 (m-80) REVERT: C 258 GLN cc_start: 0.8412 (mt0) cc_final: 0.8204 (mt0) REVERT: C 273 ARG cc_start: 0.7803 (mtt90) cc_final: 0.7549 (mtt-85) REVERT: C 279 ASN cc_start: 0.8223 (t0) cc_final: 0.7685 (t0) REVERT: C 301 ASN cc_start: 0.7790 (t0) cc_final: 0.7469 (t0) REVERT: C 327 LYS cc_start: 0.8016 (tptp) cc_final: 0.7811 (tptp) REVERT: C 414 ILE cc_start: 0.8473 (tp) cc_final: 0.8252 (tp) REVERT: C 420 ILE cc_start: 0.8516 (mt) cc_final: 0.8249 (mm) REVERT: C 427 TRP cc_start: 0.7676 (m-90) cc_final: 0.7280 (m-10) REVERT: C 443 ILE cc_start: 0.7757 (mt) cc_final: 0.7532 (mm) REVERT: C 447 SER cc_start: 0.8388 (m) cc_final: 0.8131 (p) REVERT: C 484 TYR cc_start: 0.8467 (p90) cc_final: 0.8036 (p90) REVERT: C 487 LYS cc_start: 0.8148 (tttt) cc_final: 0.7158 (tttt) REVERT: C 500 ARG cc_start: 0.6921 (mtp85) cc_final: 0.6640 (mtp180) REVERT: C 575 GLN cc_start: 0.7852 (mm-40) cc_final: 0.7517 (mm-40) REVERT: C 634 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7833 (mt-10) REVERT: C 640 GLN cc_start: 0.9048 (tp40) cc_final: 0.8531 (tp-100) REVERT: C 647 GLU cc_start: 0.7639 (tm-30) cc_final: 0.7421 (tp30) REVERT: C 656 ASN cc_start: 0.7762 (t0) cc_final: 0.7477 (t0) REVERT: C 657 GLU cc_start: 0.7607 (tp30) cc_final: 0.6905 (tp30) outliers start: 7 outliers final: 2 residues processed: 533 average time/residue: 0.2480 time to fit residues: 184.4405 Evaluate side-chains 437 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 434 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LYS Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain C residue 49 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 0.6980 chunk 127 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 43 optimal weight: 0.6980 chunk 85 optimal weight: 0.9980 chunk 68 optimal weight: 0.6980 chunk 131 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 80 optimal weight: 0.5980 chunk 98 optimal weight: 0.9980 chunk 152 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN A 229 ASN A 315 GLN A 350 GLN A 363 GLN A 374 HIS A 575 GLN A 630 GLN B 88 ASN B 114 GLN B 315 GLN B 374 HIS B 575 GLN B 630 GLN B 658 GLN C 229 ASN C 315 GLN C 328 GLN C 350 GLN C 363 GLN C 463 ASN C 478 ASN C 630 GLN C 658 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 14448 Z= 0.220 Angle : 0.713 7.244 19632 Z= 0.369 Chirality : 0.051 0.317 2418 Planarity : 0.004 0.051 2421 Dihedral : 8.563 59.488 3126 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.23 % Favored : 97.71 % Rotamer: Outliers : 2.60 % Allowed : 10.00 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.19), residues: 1656 helix: 0.65 (0.26), residues: 375 sheet: 1.30 (0.25), residues: 339 loop : -1.10 (0.18), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 628 HIS 0.003 0.001 HIS B 216 PHE 0.022 0.002 PHE C 53 TYR 0.022 0.001 TYR C 191 ARG 0.006 0.001 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 454 time to evaluate : 3.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 PHE cc_start: 0.7438 (p90) cc_final: 0.7029 (p90) REVERT: A 69 TRP cc_start: 0.7104 (m-90) cc_final: 0.6048 (m-90) REVERT: A 88 ASN cc_start: 0.8172 (m110) cc_final: 0.7961 (m-40) REVERT: A 96 TRP cc_start: 0.8215 (m100) cc_final: 0.7412 (m100) REVERT: A 102 ASP cc_start: 0.7637 (t70) cc_final: 0.7245 (t0) REVERT: A 104 MET cc_start: 0.8035 (ttt) cc_final: 0.7628 (ttt) REVERT: A 106 GLU cc_start: 0.7533 (tp30) cc_final: 0.7224 (tp30) REVERT: A 113 ASP cc_start: 0.7430 (t0) cc_final: 0.7097 (t0) REVERT: A 165 ASP cc_start: 0.7092 (t0) cc_final: 0.6874 (t0) REVERT: A 166 LYS cc_start: 0.7776 (mmmt) cc_final: 0.7466 (mmmt) REVERT: A 198 THR cc_start: 0.8229 (t) cc_final: 0.7981 (t) REVERT: A 258 GLN cc_start: 0.8273 (mt0) cc_final: 0.8050 (mt0) REVERT: A 264 SER cc_start: 0.8153 (m) cc_final: 0.7586 (p) REVERT: A 269 GLU cc_start: 0.8149 (tt0) cc_final: 0.7804 (tt0) REVERT: A 283 ILE cc_start: 0.8292 (OUTLIER) cc_final: 0.8084 (pt) REVERT: A 344 LYS cc_start: 0.8225 (ttmm) cc_final: 0.7962 (ttmm) REVERT: A 374 HIS cc_start: 0.8238 (OUTLIER) cc_final: 0.7903 (t-170) REVERT: A 420 ILE cc_start: 0.8382 (mt) cc_final: 0.8107 (mm) REVERT: A 468 PHE cc_start: 0.7544 (m-80) cc_final: 0.7292 (m-10) REVERT: A 482 GLU cc_start: 0.7717 (mm-30) cc_final: 0.6879 (mm-30) REVERT: A 535 MET cc_start: 0.7142 (tpp) cc_final: 0.6620 (tpp) REVERT: A 647 GLU cc_start: 0.7668 (tm-30) cc_final: 0.7355 (tm-30) REVERT: A 656 ASN cc_start: 0.7754 (t0) cc_final: 0.7319 (t0) REVERT: B 44 VAL cc_start: 0.8910 (p) cc_final: 0.8567 (m) REVERT: B 47 GLU cc_start: 0.7086 (tt0) cc_final: 0.6841 (tt0) REVERT: B 50 THR cc_start: 0.8471 (m) cc_final: 0.8238 (m) REVERT: B 53 PHE cc_start: 0.7132 (p90) cc_final: 0.6781 (p90) REVERT: B 82 GLN cc_start: 0.7366 (tp40) cc_final: 0.6828 (tp40) REVERT: B 97 LYS cc_start: 0.8045 (tppt) cc_final: 0.7256 (tppt) REVERT: B 104 MET cc_start: 0.7835 (ttt) cc_final: 0.7548 (ttt) REVERT: B 106 GLU cc_start: 0.7371 (tp30) cc_final: 0.6627 (tp30) REVERT: B 113 ASP cc_start: 0.7534 (t0) cc_final: 0.6941 (t70) REVERT: B 202 THR cc_start: 0.8183 (p) cc_final: 0.7902 (p) REVERT: B 234 ASN cc_start: 0.7447 (t0) cc_final: 0.7052 (t0) REVERT: B 245 VAL cc_start: 0.8417 (OUTLIER) cc_final: 0.8190 (p) REVERT: B 268 LYS cc_start: 0.8573 (pptt) cc_final: 0.8262 (pptt) REVERT: B 280 ASN cc_start: 0.8112 (p0) cc_final: 0.7722 (p0) REVERT: B 297 THR cc_start: 0.8618 (t) cc_final: 0.8387 (p) REVERT: B 420 ILE cc_start: 0.8461 (mt) cc_final: 0.8219 (mm) REVERT: B 432 ARG cc_start: 0.7058 (mtt90) cc_final: 0.6572 (mtt90) REVERT: B 447 SER cc_start: 0.8204 (m) cc_final: 0.7858 (p) REVERT: B 456 ARG cc_start: 0.7599 (ttp80) cc_final: 0.7396 (ttp80) REVERT: B 487 LYS cc_start: 0.8100 (tttt) cc_final: 0.7604 (tttt) REVERT: B 490 LYS cc_start: 0.7847 (ttpt) cc_final: 0.7534 (ttpt) REVERT: B 500 ARG cc_start: 0.6615 (mtp180) cc_final: 0.6402 (mtp85) REVERT: B 535 MET cc_start: 0.7076 (tpp) cc_final: 0.6705 (tpp) REVERT: B 590 GLN cc_start: 0.8185 (mm-40) cc_final: 0.7958 (mm-40) REVERT: B 656 ASN cc_start: 0.7612 (t0) cc_final: 0.7251 (t0) REVERT: B 657 GLU cc_start: 0.7545 (tp30) cc_final: 0.7301 (tp30) REVERT: C 47 GLU cc_start: 0.7168 (tt0) cc_final: 0.6874 (tt0) REVERT: C 82 GLN cc_start: 0.7341 (tp40) cc_final: 0.6749 (tp40) REVERT: C 92 ASN cc_start: 0.7662 (p0) cc_final: 0.7311 (p0) REVERT: C 106 GLU cc_start: 0.7321 (tp30) cc_final: 0.6980 (tp30) REVERT: C 121 LYS cc_start: 0.8644 (mttt) cc_final: 0.8247 (mttm) REVERT: C 150 GLU cc_start: 0.7425 (tp30) cc_final: 0.7199 (tp30) REVERT: C 166 LYS cc_start: 0.7831 (mmmt) cc_final: 0.7454 (mmmt) REVERT: C 171 TYR cc_start: 0.7922 (p90) cc_final: 0.7495 (p90) REVERT: C 178 ASP cc_start: 0.7544 (m-30) cc_final: 0.7319 (t70) REVERT: C 223 TYR cc_start: 0.8026 (m-80) cc_final: 0.7824 (m-10) REVERT: C 302 ASN cc_start: 0.8675 (m-40) cc_final: 0.8442 (m110) REVERT: C 321 ASP cc_start: 0.7563 (t0) cc_final: 0.7350 (t70) REVERT: C 347 ILE cc_start: 0.8396 (tp) cc_final: 0.8176 (mt) REVERT: C 395 TYR cc_start: 0.7426 (t80) cc_final: 0.7023 (t80) REVERT: C 414 ILE cc_start: 0.8432 (tp) cc_final: 0.8215 (tp) REVERT: C 420 ILE cc_start: 0.8453 (mt) cc_final: 0.8250 (mm) REVERT: C 427 TRP cc_start: 0.7775 (m-90) cc_final: 0.7427 (m-10) REVERT: C 434 MET cc_start: 0.7173 (ttm) cc_final: 0.6758 (ttp) REVERT: C 447 SER cc_start: 0.8331 (m) cc_final: 0.8101 (p) REVERT: C 482 GLU cc_start: 0.7739 (mm-30) cc_final: 0.7312 (mm-30) REVERT: C 656 ASN cc_start: 0.7800 (t0) cc_final: 0.7417 (t0) REVERT: C 657 GLU cc_start: 0.7632 (tp30) cc_final: 0.6867 (tp30) outliers start: 39 outliers final: 19 residues processed: 472 average time/residue: 0.3002 time to fit residues: 198.9004 Evaluate side-chains 441 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 419 time to evaluate : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 628 TRP Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 576 LEU Chi-restraints excluded: chain C residue 628 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 0.9990 chunk 47 optimal weight: 0.0970 chunk 126 optimal weight: 0.0270 chunk 103 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 152 optimal weight: 1.9990 chunk 165 optimal weight: 0.0000 chunk 136 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 overall best weight: 0.4242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS A 302 ASN A 315 GLN A 363 GLN B 229 ASN B 302 ASN B 363 GLN B 374 HIS C 114 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14448 Z= 0.183 Angle : 0.641 9.208 19632 Z= 0.330 Chirality : 0.048 0.289 2418 Planarity : 0.004 0.049 2421 Dihedral : 7.939 59.857 3122 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.33 % Allowed : 14.07 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.20), residues: 1656 helix: 1.12 (0.27), residues: 369 sheet: 1.19 (0.24), residues: 375 loop : -0.88 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 35 HIS 0.007 0.001 HIS B 374 PHE 0.024 0.002 PHE C 53 TYR 0.017 0.001 TYR A 191 ARG 0.005 0.000 ARG A 273 *********************** 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 487 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 437 time to evaluate : 1.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LYS cc_start: 0.8513 (pttt) cc_final: 0.8294 (pttt) REVERT: A 53 PHE cc_start: 0.7350 (p90) cc_final: 0.6953 (p90) REVERT: A 69 TRP cc_start: 0.7059 (m-90) cc_final: 0.6388 (m-90) REVERT: A 104 MET cc_start: 0.8036 (ttt) cc_final: 0.7784 (ttt) REVERT: A 106 GLU cc_start: 0.7502 (tp30) cc_final: 0.7270 (tp30) REVERT: A 150 GLU cc_start: 0.7625 (tp30) cc_final: 0.7260 (tp30) REVERT: A 165 ASP cc_start: 0.7033 (t0) cc_final: 0.6816 (t0) REVERT: A 166 LYS cc_start: 0.7721 (mmmt) cc_final: 0.7437 (mmmt) REVERT: A 178 ASP cc_start: 0.7799 (OUTLIER) cc_final: 0.7402 (t70) REVERT: A 190 GLU cc_start: 0.7530 (tt0) cc_final: 0.7302 (tt0) REVERT: A 198 THR cc_start: 0.8105 (t) cc_final: 0.7859 (t) REVERT: A 202 THR cc_start: 0.8018 (p) cc_final: 0.7770 (p) REVERT: A 223 TYR cc_start: 0.8133 (m-80) cc_final: 0.7655 (m-80) REVERT: A 264 SER cc_start: 0.8163 (m) cc_final: 0.7951 (p) REVERT: A 269 GLU cc_start: 0.8063 (tt0) cc_final: 0.7832 (tt0) REVERT: A 321 ASP cc_start: 0.7393 (t0) cc_final: 0.7057 (t70) REVERT: A 348 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7543 (mm-30) REVERT: A 420 ILE cc_start: 0.8361 (mt) cc_final: 0.8101 (mm) REVERT: A 447 SER cc_start: 0.8505 (m) cc_final: 0.7953 (p) REVERT: A 468 PHE cc_start: 0.7671 (m-80) cc_final: 0.7387 (m-10) REVERT: A 482 GLU cc_start: 0.7625 (mm-30) cc_final: 0.7415 (mm-30) REVERT: A 535 MET cc_start: 0.7268 (tpp) cc_final: 0.6699 (tpp) REVERT: A 647 GLU cc_start: 0.7681 (tm-30) cc_final: 0.7242 (tm-30) REVERT: A 654 GLU cc_start: 0.7968 (tp30) cc_final: 0.7727 (tp30) REVERT: A 656 ASN cc_start: 0.7794 (t0) cc_final: 0.7370 (t0) REVERT: B 44 VAL cc_start: 0.8948 (p) cc_final: 0.8627 (m) REVERT: B 47 GLU cc_start: 0.7025 (tt0) cc_final: 0.6728 (tt0) REVERT: B 53 PHE cc_start: 0.7169 (p90) cc_final: 0.6865 (p90) REVERT: B 69 TRP cc_start: 0.6830 (m-90) cc_final: 0.6259 (m-90) REVERT: B 104 MET cc_start: 0.7759 (ttt) cc_final: 0.7529 (ttt) REVERT: B 106 GLU cc_start: 0.7275 (tp30) cc_final: 0.6901 (tp30) REVERT: B 113 ASP cc_start: 0.7414 (t0) cc_final: 0.6456 (t70) REVERT: B 202 THR cc_start: 0.8212 (p) cc_final: 0.7989 (p) REVERT: B 234 ASN cc_start: 0.7353 (t0) cc_final: 0.7003 (t0) REVERT: B 280 ASN cc_start: 0.8118 (p0) cc_final: 0.7701 (p0) REVERT: B 297 THR cc_start: 0.8620 (t) cc_final: 0.8218 (p) REVERT: B 321 ASP cc_start: 0.7510 (t0) cc_final: 0.7141 (t70) REVERT: B 420 ILE cc_start: 0.8463 (mt) cc_final: 0.8259 (mm) REVERT: B 432 ARG cc_start: 0.6958 (mtt90) cc_final: 0.6675 (mtt90) REVERT: B 447 SER cc_start: 0.8139 (m) cc_final: 0.7855 (p) REVERT: B 490 LYS cc_start: 0.7912 (ttpt) cc_final: 0.7707 (ttpt) REVERT: B 535 MET cc_start: 0.7170 (tpp) cc_final: 0.6737 (tpp) REVERT: B 625 ASN cc_start: 0.7526 (m110) cc_final: 0.7311 (m-40) REVERT: B 656 ASN cc_start: 0.7621 (t0) cc_final: 0.7260 (t0) REVERT: B 657 GLU cc_start: 0.7508 (tp30) cc_final: 0.6948 (tp30) REVERT: C 47 GLU cc_start: 0.7120 (tt0) cc_final: 0.6878 (tt0) REVERT: C 53 PHE cc_start: 0.7290 (p90) cc_final: 0.7048 (p90) REVERT: C 92 ASN cc_start: 0.7632 (p0) cc_final: 0.7365 (p0) REVERT: C 93 PHE cc_start: 0.7625 (m-80) cc_final: 0.7319 (m-10) REVERT: C 96 TRP cc_start: 0.7685 (m-90) cc_final: 0.6843 (m100) REVERT: C 106 GLU cc_start: 0.7313 (tp30) cc_final: 0.7053 (tp30) REVERT: C 114 GLN cc_start: 0.7338 (tt0) cc_final: 0.7116 (tt0) REVERT: C 116 LEU cc_start: 0.7907 (mt) cc_final: 0.7581 (mp) REVERT: C 150 GLU cc_start: 0.7453 (tp30) cc_final: 0.7196 (tp30) REVERT: C 166 LYS cc_start: 0.7811 (mmmt) cc_final: 0.7485 (mmmt) REVERT: C 171 TYR cc_start: 0.7882 (p90) cc_final: 0.7506 (p90) REVERT: C 302 ASN cc_start: 0.8672 (m-40) cc_final: 0.8468 (m-40) REVERT: C 321 ASP cc_start: 0.7584 (t0) cc_final: 0.7343 (t70) REVERT: C 395 TYR cc_start: 0.7422 (t80) cc_final: 0.7209 (t80) REVERT: C 414 ILE cc_start: 0.8488 (tp) cc_final: 0.8091 (tt) REVERT: C 417 GLN cc_start: 0.7859 (pt0) cc_final: 0.7448 (mt0) REVERT: C 420 ILE cc_start: 0.8455 (mt) cc_final: 0.8242 (mm) REVERT: C 427 TRP cc_start: 0.7686 (m-90) cc_final: 0.7363 (m-10) REVERT: C 482 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7256 (mm-30) REVERT: C 656 ASN cc_start: 0.7861 (t0) cc_final: 0.7454 (t0) REVERT: C 657 GLU cc_start: 0.7631 (tp30) cc_final: 0.6876 (tp30) outliers start: 50 outliers final: 20 residues processed: 465 average time/residue: 0.3194 time to fit residues: 205.7057 Evaluate side-chains 434 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 413 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain C residue 576 LEU Chi-restraints excluded: chain C residue 626 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 0.5980 chunk 114 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 162 optimal weight: 0.0970 chunk 80 optimal weight: 0.9980 chunk 145 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN A 374 HIS B 302 ASN B 363 GLN C 72 HIS C 114 GLN C 374 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 14448 Z= 0.212 Angle : 0.618 8.845 19632 Z= 0.321 Chirality : 0.048 0.471 2418 Planarity : 0.004 0.053 2421 Dihedral : 7.785 56.205 3122 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.60 % Allowed : 15.93 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.20), residues: 1656 helix: 1.19 (0.27), residues: 372 sheet: 1.50 (0.26), residues: 339 loop : -0.95 (0.19), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 35 HIS 0.004 0.001 HIS B 216 PHE 0.026 0.002 PHE C 53 TYR 0.023 0.001 TYR A 638 ARG 0.010 0.001 ARG A 273 *********************** 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 477 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 423 time to evaluate : 1.599 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: A 49 LYS cc_start: 0.8548 (pttt) cc_final: 0.8252 (pttt) REVERT: A 69 TRP cc_start: 0.7047 (m-90) cc_final: 0.6445 (m-90) REVERT: A 91 GLU cc_start: 0.6766 (mm-30) cc_final: 0.6487 (mm-30) REVERT: A 106 GLU cc_start: 0.7540 (tp30) cc_final: 0.7311 (tp30) REVERT: A 165 ASP cc_start: 0.7091 (t0) cc_final: 0.6835 (t0) REVERT: A 166 LYS cc_start: 0.7753 (mmmt) cc_final: 0.7416 (mmmt) REVERT: A 202 THR cc_start: 0.7925 (p) cc_final: 0.7649 (p) REVERT: A 223 TYR cc_start: 0.8185 (m-80) cc_final: 0.7817 (m-80) REVERT: A 264 SER cc_start: 0.8159 (m) cc_final: 0.7613 (p) REVERT: A 269 GLU cc_start: 0.8103 (tt0) cc_final: 0.7768 (tt0) REVERT: A 348 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7499 (mm-30) REVERT: A 420 ILE cc_start: 0.8426 (mt) cc_final: 0.8165 (mm) REVERT: A 447 SER cc_start: 0.8519 (m) cc_final: 0.7966 (p) REVERT: A 468 PHE cc_start: 0.7794 (m-80) cc_final: 0.7439 (m-10) REVERT: A 482 GLU cc_start: 0.7628 (mm-30) cc_final: 0.6770 (mm-30) REVERT: A 535 MET cc_start: 0.7207 (tpp) cc_final: 0.6741 (tpp) REVERT: A 647 GLU cc_start: 0.7715 (tm-30) cc_final: 0.7244 (tm-30) REVERT: A 654 GLU cc_start: 0.8045 (tp30) cc_final: 0.7708 (tp30) REVERT: A 656 ASN cc_start: 0.7831 (t0) cc_final: 0.7426 (t0) REVERT: B 44 VAL cc_start: 0.8965 (p) cc_final: 0.8664 (m) REVERT: B 47 GLU cc_start: 0.7039 (tt0) cc_final: 0.6705 (tt0) REVERT: B 53 PHE cc_start: 0.7183 (p90) cc_final: 0.6906 (p90) REVERT: B 69 TRP cc_start: 0.6795 (m-90) cc_final: 0.6172 (m-90) REVERT: B 106 GLU cc_start: 0.7326 (tp30) cc_final: 0.6957 (tp30) REVERT: B 113 ASP cc_start: 0.7434 (t0) cc_final: 0.6732 (t0) REVERT: B 202 THR cc_start: 0.8380 (p) cc_final: 0.8178 (p) REVERT: B 245 VAL cc_start: 0.8666 (t) cc_final: 0.8420 (p) REVERT: B 273 ARG cc_start: 0.8150 (mtt-85) cc_final: 0.7926 (mtt-85) REVERT: B 280 ASN cc_start: 0.8101 (p0) cc_final: 0.7661 (p0) REVERT: B 297 THR cc_start: 0.8624 (t) cc_final: 0.8267 (p) REVERT: B 321 ASP cc_start: 0.7525 (t0) cc_final: 0.7254 (t70) REVERT: B 420 ILE cc_start: 0.8476 (mt) cc_final: 0.8246 (mm) REVERT: B 432 ARG cc_start: 0.6767 (mtt90) cc_final: 0.6302 (mtt90) REVERT: B 447 SER cc_start: 0.8097 (m) cc_final: 0.7868 (p) REVERT: B 482 GLU cc_start: 0.7630 (mm-30) cc_final: 0.7148 (mm-30) REVERT: B 490 LYS cc_start: 0.7891 (ttpt) cc_final: 0.7673 (ttpt) REVERT: B 535 MET cc_start: 0.7139 (tpp) cc_final: 0.6772 (tpp) REVERT: B 625 ASN cc_start: 0.7532 (m110) cc_final: 0.7324 (m-40) REVERT: B 656 ASN cc_start: 0.7644 (t0) cc_final: 0.7291 (t0) REVERT: B 657 GLU cc_start: 0.7523 (tp30) cc_final: 0.6942 (tp30) REVERT: C 47 GLU cc_start: 0.7124 (tt0) cc_final: 0.6854 (tt0) REVERT: C 53 PHE cc_start: 0.7299 (p90) cc_final: 0.6833 (p90) REVERT: C 92 ASN cc_start: 0.7660 (p0) cc_final: 0.7397 (p0) REVERT: C 93 PHE cc_start: 0.7673 (m-80) cc_final: 0.7368 (m-10) REVERT: C 106 GLU cc_start: 0.7362 (tp30) cc_final: 0.7040 (tp30) REVERT: C 108 ILE cc_start: 0.6935 (mm) cc_final: 0.6641 (tt) REVERT: C 150 GLU cc_start: 0.7450 (tp30) cc_final: 0.7164 (tp30) REVERT: C 153 LYS cc_start: 0.7714 (mmtt) cc_final: 0.7367 (mmtm) REVERT: C 166 LYS cc_start: 0.7832 (mmmt) cc_final: 0.7477 (mmmt) REVERT: C 171 TYR cc_start: 0.7865 (p90) cc_final: 0.7426 (p90) REVERT: C 321 ASP cc_start: 0.7585 (t0) cc_final: 0.7318 (t70) REVERT: C 348 GLU cc_start: 0.7628 (mm-30) cc_final: 0.7368 (mm-30) REVERT: C 414 ILE cc_start: 0.8502 (tp) cc_final: 0.8116 (tt) REVERT: C 417 GLN cc_start: 0.7892 (pt0) cc_final: 0.7364 (mt0) REVERT: C 427 TRP cc_start: 0.7677 (m-90) cc_final: 0.7179 (m-10) REVERT: C 479 TRP cc_start: 0.7844 (m-10) cc_final: 0.7441 (m-10) REVERT: C 482 GLU cc_start: 0.7657 (mm-30) cc_final: 0.7270 (mm-30) REVERT: C 530 MET cc_start: 0.8757 (mmm) cc_final: 0.8530 (tpp) REVERT: C 626 MET cc_start: 0.7933 (OUTLIER) cc_final: 0.7147 (ttm) REVERT: C 656 ASN cc_start: 0.7842 (t0) cc_final: 0.7459 (t0) REVERT: C 657 GLU cc_start: 0.7633 (tp30) cc_final: 0.6913 (tp30) outliers start: 54 outliers final: 28 residues processed: 454 average time/residue: 0.2983 time to fit residues: 189.1307 Evaluate side-chains 440 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 411 time to evaluate : 1.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 328 GLN Chi-restraints excluded: chain A residue 417 GLN Chi-restraints excluded: chain A residue 455 THR 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 138 THR Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 344 LYS Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 119 CYS Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 576 LEU Chi-restraints excluded: chain C residue 626 MET Chi-restraints excluded: chain C residue 629 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 120 optimal weight: 0.4980 chunk 67 optimal weight: 0.5980 chunk 138 optimal weight: 0.5980 chunk 112 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN B 302 ASN B 363 GLN C 105 HIS C 374 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 14448 Z= 0.232 Angle : 0.621 8.999 19632 Z= 0.319 Chirality : 0.048 0.288 2418 Planarity : 0.005 0.092 2421 Dihedral : 7.671 55.540 3122 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 4.20 % Allowed : 17.33 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.20), residues: 1656 helix: 1.27 (0.27), residues: 375 sheet: 1.42 (0.26), residues: 339 loop : -1.07 (0.19), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP C 35 HIS 0.007 0.002 HIS C 374 PHE 0.024 0.002 PHE C 53 TYR 0.026 0.002 TYR A 638 ARG 0.006 0.001 ARG C 617 *********************** 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 502 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 439 time to evaluate : 1.750 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: 0.8582 (pttt) cc_final: 0.8306 (pttt) REVERT: A 69 TRP cc_start: 0.6961 (m-90) cc_final: 0.6598 (m-90) REVERT: A 104 MET cc_start: 0.8172 (ttt) cc_final: 0.7782 (ttt) REVERT: A 136 VAL cc_start: 0.7480 (OUTLIER) cc_final: 0.7166 (p) REVERT: A 150 GLU cc_start: 0.7520 (tp30) cc_final: 0.7116 (tp30) REVERT: A 166 LYS cc_start: 0.7746 (mmmt) cc_final: 0.7427 (mmmt) REVERT: A 202 THR cc_start: 0.7941 (p) cc_final: 0.7712 (p) REVERT: A 223 TYR cc_start: 0.8220 (m-80) cc_final: 0.7918 (m-80) REVERT: A 264 SER cc_start: 0.8203 (m) cc_final: 0.7620 (p) REVERT: A 269 GLU cc_start: 0.8060 (tt0) cc_final: 0.7786 (tt0) REVERT: A 297 THR cc_start: 0.8628 (t) cc_final: 0.8392 (p) REVERT: A 348 GLU cc_start: 0.7782 (mm-30) cc_final: 0.7542 (mm-30) REVERT: A 420 ILE cc_start: 0.8456 (mt) cc_final: 0.8185 (mm) REVERT: A 468 PHE cc_start: 0.7847 (m-80) cc_final: 0.7490 (m-10) REVERT: A 482 GLU cc_start: 0.7623 (mm-30) cc_final: 0.6800 (mm-30) REVERT: A 535 MET cc_start: 0.7134 (tpp) cc_final: 0.6779 (tpp) REVERT: A 647 GLU cc_start: 0.7728 (tm-30) cc_final: 0.7247 (tm-30) REVERT: A 654 GLU cc_start: 0.7980 (tp30) cc_final: 0.7717 (tp30) REVERT: A 656 ASN cc_start: 0.7858 (t0) cc_final: 0.7446 (t0) REVERT: B 44 VAL cc_start: 0.8998 (p) cc_final: 0.8702 (m) REVERT: B 47 GLU cc_start: 0.6989 (tt0) cc_final: 0.6710 (tt0) REVERT: B 53 PHE cc_start: 0.7059 (p90) cc_final: 0.6814 (p90) REVERT: B 69 TRP cc_start: 0.6920 (m-90) cc_final: 0.6317 (m-90) REVERT: B 106 GLU cc_start: 0.7357 (tp30) cc_final: 0.6992 (tp30) REVERT: B 113 ASP cc_start: 0.7394 (t0) cc_final: 0.6707 (t0) REVERT: B 136 VAL cc_start: 0.7486 (OUTLIER) cc_final: 0.7180 (p) REVERT: B 242 VAL cc_start: 0.8708 (t) cc_final: 0.8495 (m) REVERT: B 280 ASN cc_start: 0.8098 (p0) cc_final: 0.7667 (p0) REVERT: B 297 THR cc_start: 0.8634 (t) cc_final: 0.8311 (p) REVERT: B 321 ASP cc_start: 0.7552 (t0) cc_final: 0.7219 (t70) REVERT: B 417 GLN cc_start: 0.7878 (OUTLIER) cc_final: 0.7611 (mt0) REVERT: B 420 ILE cc_start: 0.8525 (mt) cc_final: 0.8311 (mm) REVERT: B 432 ARG cc_start: 0.6771 (mtt90) cc_final: 0.6279 (mtt90) REVERT: B 482 GLU cc_start: 0.7578 (mm-30) cc_final: 0.7316 (mm-30) REVERT: B 490 LYS cc_start: 0.7895 (ttpt) cc_final: 0.7675 (ttpt) REVERT: B 535 MET cc_start: 0.7112 (tpp) cc_final: 0.6786 (tpp) REVERT: B 610 TRP cc_start: 0.7775 (t-100) cc_final: 0.7528 (t60) REVERT: B 622 ILE cc_start: 0.8585 (mm) cc_final: 0.8313 (mm) REVERT: B 656 ASN cc_start: 0.7728 (t0) cc_final: 0.7422 (t0) REVERT: B 657 GLU cc_start: 0.7510 (tp30) cc_final: 0.6966 (tp30) REVERT: C 53 PHE cc_start: 0.7194 (p90) cc_final: 0.6773 (p90) REVERT: C 72 HIS cc_start: 0.6747 (OUTLIER) cc_final: 0.6379 (t70) REVERT: C 92 ASN cc_start: 0.7678 (p0) cc_final: 0.7394 (p0) REVERT: C 93 PHE cc_start: 0.7636 (m-80) cc_final: 0.7383 (m-10) REVERT: C 106 GLU cc_start: 0.7356 (tp30) cc_final: 0.7045 (tp30) REVERT: C 108 ILE cc_start: 0.6924 (mm) cc_final: 0.6595 (tt) REVERT: C 150 GLU cc_start: 0.7451 (tp30) cc_final: 0.7019 (tp30) REVERT: C 153 LYS cc_start: 0.7713 (mmtt) cc_final: 0.7383 (mmtm) REVERT: C 166 LYS cc_start: 0.7820 (mmmt) cc_final: 0.7458 (mmmt) REVERT: C 171 TYR cc_start: 0.7874 (p90) cc_final: 0.7437 (p90) REVERT: C 176 LYS cc_start: 0.8625 (ttmt) cc_final: 0.8415 (ttpt) REVERT: C 414 ILE cc_start: 0.8532 (tp) cc_final: 0.8143 (tt) REVERT: C 417 GLN cc_start: 0.7861 (OUTLIER) cc_final: 0.7474 (mt0) REVERT: C 427 TRP cc_start: 0.7629 (m-90) cc_final: 0.7154 (m-10) REVERT: C 482 GLU cc_start: 0.7678 (mm-30) cc_final: 0.7299 (mm-30) REVERT: C 529 THR cc_start: 0.8017 (m) cc_final: 0.7776 (m) REVERT: C 530 MET cc_start: 0.8842 (mmm) cc_final: 0.8247 (mmm) REVERT: C 544 LEU cc_start: 0.7975 (mt) cc_final: 0.7773 (mt) REVERT: C 617 ARG cc_start: 0.7714 (mtp180) cc_final: 0.7329 (mtm-85) REVERT: C 656 ASN cc_start: 0.7848 (t0) cc_final: 0.7487 (t0) REVERT: C 657 GLU cc_start: 0.7695 (tp30) cc_final: 0.7004 (tp30) outliers start: 63 outliers final: 44 residues processed: 478 average time/residue: 0.3073 time to fit residues: 206.1698 Evaluate side-chains 470 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 421 time to evaluate : 1.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 417 GLN Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 605 CYS Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain 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 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 455 THR Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 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 116 LEU Chi-restraints excluded: chain C residue 119 CYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 374 HIS 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 4.9990 chunk 146 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 95 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN A 363 GLN B 302 ASN B 363 GLN B 374 HIS ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 14448 Z= 0.253 Angle : 0.619 14.025 19632 Z= 0.320 Chirality : 0.047 0.249 2418 Planarity : 0.004 0.059 2421 Dihedral : 7.641 54.859 3122 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 4.60 % Allowed : 18.47 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.20), residues: 1656 helix: 1.30 (0.28), residues: 375 sheet: 1.40 (0.27), residues: 339 loop : -1.12 (0.19), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP C 35 HIS 0.009 0.002 HIS C 374 PHE 0.021 0.002 PHE C 53 TYR 0.025 0.002 TYR C 638 ARG 0.010 0.000 ARG B 273 *********************** 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 501 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 432 time to evaluate : 1.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LYS cc_start: 0.8618 (pttt) cc_final: 0.8278 (pttt) REVERT: A 69 TRP cc_start: 0.6992 (m-90) cc_final: 0.6650 (m-90) REVERT: A 117 LYS cc_start: 0.8424 (ttmm) cc_final: 0.7972 (ttmm) REVERT: A 150 GLU cc_start: 0.7531 (tp30) cc_final: 0.7084 (tp30) REVERT: A 166 LYS cc_start: 0.7729 (mmmt) cc_final: 0.7389 (mmmt) REVERT: A 202 THR cc_start: 0.8119 (p) cc_final: 0.7891 (p) REVERT: A 264 SER cc_start: 0.8189 (m) cc_final: 0.7595 (p) REVERT: A 297 THR cc_start: 0.8633 (t) cc_final: 0.8401 (p) REVERT: A 348 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7465 (mm-30) REVERT: A 447 SER cc_start: 0.8516 (m) cc_final: 0.7847 (p) REVERT: A 482 GLU cc_start: 0.7624 (mm-30) cc_final: 0.6771 (mm-30) REVERT: A 535 MET cc_start: 0.7139 (tpp) cc_final: 0.6801 (tpp) REVERT: A 647 GLU cc_start: 0.7738 (tm-30) cc_final: 0.7248 (tm-30) REVERT: A 654 GLU cc_start: 0.7975 (tp30) cc_final: 0.7719 (tp30) REVERT: A 656 ASN cc_start: 0.7862 (t0) cc_final: 0.7459 (t0) REVERT: B 44 VAL cc_start: 0.9012 (p) cc_final: 0.8751 (m) REVERT: B 47 GLU cc_start: 0.7007 (tt0) cc_final: 0.6734 (tt0) REVERT: B 53 PHE cc_start: 0.7087 (p90) cc_final: 0.6810 (p90) REVERT: B 69 TRP cc_start: 0.6965 (m-90) cc_final: 0.6382 (m-90) REVERT: B 106 GLU cc_start: 0.7358 (tp30) cc_final: 0.6996 (tp30) REVERT: B 113 ASP cc_start: 0.7421 (t0) cc_final: 0.6580 (t0) REVERT: B 242 VAL cc_start: 0.8662 (t) cc_final: 0.8447 (m) REVERT: B 280 ASN cc_start: 0.8110 (p0) cc_final: 0.7712 (p0) REVERT: B 297 THR cc_start: 0.8652 (t) cc_final: 0.8340 (p) REVERT: B 321 ASP cc_start: 0.7544 (t0) cc_final: 0.7222 (t70) REVERT: B 417 GLN cc_start: 0.7878 (OUTLIER) cc_final: 0.7598 (mt0) REVERT: B 420 ILE cc_start: 0.8533 (mt) cc_final: 0.8317 (mm) REVERT: B 432 ARG cc_start: 0.6850 (mtt90) cc_final: 0.6342 (mtt90) REVERT: B 475 MET cc_start: 0.8089 (tpp) cc_final: 0.7802 (tpp) REVERT: B 490 LYS cc_start: 0.7897 (ttpt) cc_final: 0.7677 (ttpt) REVERT: B 530 MET cc_start: 0.8763 (tpt) cc_final: 0.8182 (mmm) REVERT: B 535 MET cc_start: 0.7083 (tpp) cc_final: 0.6829 (tpp) REVERT: B 610 TRP cc_start: 0.7999 (t-100) cc_final: 0.7593 (t-100) REVERT: B 622 ILE cc_start: 0.8589 (mm) cc_final: 0.8282 (mm) REVERT: B 656 ASN cc_start: 0.7725 (t0) cc_final: 0.7424 (t0) REVERT: B 657 GLU cc_start: 0.7529 (tp30) cc_final: 0.7004 (tp30) REVERT: C 53 PHE cc_start: 0.7202 (p90) cc_final: 0.6794 (p90) REVERT: C 72 HIS cc_start: 0.6803 (OUTLIER) cc_final: 0.6361 (t70) REVERT: C 92 ASN cc_start: 0.7663 (p0) cc_final: 0.7407 (p0) REVERT: C 93 PHE cc_start: 0.7655 (m-80) cc_final: 0.7324 (m-10) REVERT: C 96 TRP cc_start: 0.8107 (m100) cc_final: 0.6934 (m100) REVERT: C 103 GLN cc_start: 0.7937 (tp40) cc_final: 0.7352 (tm-30) REVERT: C 106 GLU cc_start: 0.7389 (tp30) cc_final: 0.7132 (tp30) REVERT: C 136 VAL cc_start: 0.7398 (OUTLIER) cc_final: 0.7013 (p) REVERT: C 150 GLU cc_start: 0.7460 (tp30) cc_final: 0.6901 (tp30) REVERT: C 166 LYS cc_start: 0.7830 (mmmt) cc_final: 0.7460 (mmmt) REVERT: C 171 TYR cc_start: 0.7878 (p90) cc_final: 0.7399 (p90) REVERT: C 176 LYS cc_start: 0.8613 (ttmt) cc_final: 0.8337 (ttpt) REVERT: C 267 GLU cc_start: 0.7075 (tp30) cc_final: 0.6834 (tp30) REVERT: C 414 ILE cc_start: 0.8532 (tp) cc_final: 0.8147 (tt) REVERT: C 417 GLN cc_start: 0.7858 (OUTLIER) cc_final: 0.7492 (mt0) REVERT: C 427 TRP cc_start: 0.7701 (m-90) cc_final: 0.7095 (m-10) REVERT: C 482 GLU cc_start: 0.7685 (mm-30) cc_final: 0.7250 (mm-30) REVERT: C 529 THR cc_start: 0.8092 (m) cc_final: 0.7852 (m) REVERT: C 530 MET cc_start: 0.8823 (mmm) cc_final: 0.8555 (tpt) REVERT: C 544 LEU cc_start: 0.7974 (mt) cc_final: 0.7747 (mt) REVERT: C 610 TRP cc_start: 0.7834 (t-100) cc_final: 0.7526 (t-100) REVERT: C 617 ARG cc_start: 0.7695 (mtp180) cc_final: 0.7195 (mtm-85) REVERT: C 656 ASN cc_start: 0.7860 (t0) cc_final: 0.7500 (t0) REVERT: C 657 GLU cc_start: 0.7698 (tp30) cc_final: 0.7003 (tp30) outliers start: 69 outliers final: 48 residues processed: 474 average time/residue: 0.3027 time to fit residues: 199.9015 Evaluate side-chains 477 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 425 time to evaluate : 1.556 ------------------------------------------------------------------------------- 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 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 358 ILE Chi-restraints excluded: chain A residue 417 GLN Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 344 LYS Chi-restraints excluded: chain B residue 417 GLN 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 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 95 MET 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 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 374 HIS 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 628 TRP Chi-restraints excluded: chain C residue 629 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 161 optimal weight: 0.2980 chunk 101 optimal weight: 0.2980 chunk 98 optimal weight: 0.0770 chunk 74 optimal weight: 3.9990 overall best weight: 0.7342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN B 302 ASN B 363 GLN ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.3692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 14448 Z= 0.204 Angle : 0.602 12.848 19632 Z= 0.309 Chirality : 0.046 0.246 2418 Planarity : 0.004 0.060 2421 Dihedral : 7.507 54.758 3122 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 4.67 % Allowed : 19.67 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.20), residues: 1656 helix: 1.37 (0.28), residues: 375 sheet: 1.40 (0.29), residues: 303 loop : -1.07 (0.19), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 631 HIS 0.009 0.001 HIS C 374 PHE 0.020 0.002 PHE C 53 TYR 0.026 0.002 TYR C 638 ARG 0.006 0.000 ARG B 273 *********************** 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 512 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 442 time to evaluate : 1.488 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 47 GLU cc_start: 0.7195 (mm-30) cc_final: 0.6966 (mm-30) REVERT: A 49 LYS cc_start: 0.8640 (pttt) cc_final: 0.8257 (pttt) REVERT: A 69 TRP cc_start: 0.6950 (m-90) cc_final: 0.6726 (m-90) REVERT: A 117 LYS cc_start: 0.8416 (ttmm) cc_final: 0.7957 (ttmm) REVERT: A 136 VAL cc_start: 0.7484 (OUTLIER) cc_final: 0.7156 (p) REVERT: A 150 GLU cc_start: 0.7522 (tp30) cc_final: 0.7032 (tp30) REVERT: A 166 LYS cc_start: 0.7720 (mmmt) cc_final: 0.7388 (mmmt) REVERT: A 245 VAL cc_start: 0.8664 (t) cc_final: 0.8294 (p) REVERT: A 246 GLN cc_start: 0.7802 (tp40) cc_final: 0.7554 (tp40) REVERT: A 264 SER cc_start: 0.8212 (m) cc_final: 0.7613 (p) REVERT: A 297 THR cc_start: 0.8623 (t) cc_final: 0.8397 (p) REVERT: A 417 GLN cc_start: 0.7853 (OUTLIER) cc_final: 0.7238 (mt0) REVERT: A 447 SER cc_start: 0.8549 (m) cc_final: 0.7875 (p) REVERT: A 482 GLU cc_start: 0.7607 (mm-30) cc_final: 0.6750 (mm-30) REVERT: A 535 MET cc_start: 0.7219 (tpp) cc_final: 0.6888 (tpp) REVERT: A 610 TRP cc_start: 0.8111 (t-100) cc_final: 0.7873 (t-100) REVERT: A 631 TRP cc_start: 0.7994 (t-100) cc_final: 0.7260 (t-100) REVERT: A 647 GLU cc_start: 0.7728 (tm-30) cc_final: 0.7269 (tm-30) REVERT: A 654 GLU cc_start: 0.7976 (tp30) cc_final: 0.7703 (tp30) REVERT: A 656 ASN cc_start: 0.7865 (t0) cc_final: 0.7452 (t0) REVERT: B 35 TRP cc_start: 0.7810 (m-10) cc_final: 0.7262 (m-10) REVERT: B 44 VAL cc_start: 0.9012 (p) cc_final: 0.8765 (m) REVERT: B 47 GLU cc_start: 0.7001 (tt0) cc_final: 0.6691 (tt0) REVERT: B 53 PHE cc_start: 0.7045 (p90) cc_final: 0.6796 (p90) REVERT: B 69 TRP cc_start: 0.6924 (m-90) cc_final: 0.6402 (m-90) REVERT: B 106 GLU cc_start: 0.7344 (tp30) cc_final: 0.6980 (tp30) REVERT: B 113 ASP cc_start: 0.7405 (t0) cc_final: 0.6706 (t0) REVERT: B 136 VAL cc_start: 0.7448 (OUTLIER) cc_final: 0.7092 (p) REVERT: B 150 GLU cc_start: 0.7572 (tp30) cc_final: 0.7135 (tp30) REVERT: B 215 ILE cc_start: 0.8151 (mm) cc_final: 0.7693 (tt) REVERT: B 242 VAL cc_start: 0.8636 (t) cc_final: 0.8432 (m) REVERT: B 280 ASN cc_start: 0.8101 (p0) cc_final: 0.7687 (p0) REVERT: B 297 THR cc_start: 0.8633 (t) cc_final: 0.8378 (p) REVERT: B 321 ASP cc_start: 0.7536 (t0) cc_final: 0.7226 (t70) REVERT: B 337 LYS cc_start: 0.8170 (OUTLIER) cc_final: 0.7887 (ttmm) REVERT: B 417 GLN cc_start: 0.7843 (OUTLIER) cc_final: 0.7618 (mt0) REVERT: B 420 ILE cc_start: 0.8535 (mt) cc_final: 0.8316 (mm) REVERT: B 432 ARG cc_start: 0.6902 (mtt90) cc_final: 0.6432 (mtt90) REVERT: B 464 GLU cc_start: 0.7912 (mp0) cc_final: 0.7623 (pm20) REVERT: B 475 MET cc_start: 0.7915 (tpp) cc_final: 0.7658 (tpp) REVERT: B 490 LYS cc_start: 0.7892 (ttpt) cc_final: 0.7663 (ttpt) REVERT: B 535 MET cc_start: 0.7091 (tpp) cc_final: 0.6837 (tpp) REVERT: B 622 ILE cc_start: 0.8586 (mm) cc_final: 0.8322 (mt) REVERT: B 645 LEU cc_start: 0.8126 (mp) cc_final: 0.7910 (mt) REVERT: B 656 ASN cc_start: 0.7736 (t0) cc_final: 0.7437 (t0) REVERT: B 657 GLU cc_start: 0.7525 (tp30) cc_final: 0.6987 (tp30) REVERT: C 53 PHE cc_start: 0.7158 (p90) cc_final: 0.6785 (p90) REVERT: C 72 HIS cc_start: 0.6814 (OUTLIER) cc_final: 0.6385 (t70) REVERT: C 92 ASN cc_start: 0.7685 (p0) cc_final: 0.7419 (p0) REVERT: C 93 PHE cc_start: 0.7577 (m-80) cc_final: 0.7278 (m-10) REVERT: C 103 GLN cc_start: 0.7921 (tp40) cc_final: 0.7308 (tm-30) REVERT: C 106 GLU cc_start: 0.7382 (tp30) cc_final: 0.7116 (tp30) REVERT: C 136 VAL cc_start: 0.7422 (OUTLIER) cc_final: 0.6954 (p) REVERT: C 150 GLU cc_start: 0.7445 (tp30) cc_final: 0.6832 (tp30) REVERT: C 166 LYS cc_start: 0.7806 (mmmt) cc_final: 0.7440 (mmmt) REVERT: C 171 TYR cc_start: 0.7873 (p90) cc_final: 0.7386 (p90) REVERT: C 176 LYS cc_start: 0.8598 (ttmt) cc_final: 0.8290 (ttpt) REVERT: C 265 LEU cc_start: 0.8891 (mp) cc_final: 0.8631 (mm) REVERT: C 414 ILE cc_start: 0.8520 (tp) cc_final: 0.8137 (tt) REVERT: C 417 GLN cc_start: 0.7860 (OUTLIER) cc_final: 0.7529 (mt0) REVERT: C 427 TRP cc_start: 0.7699 (m-90) cc_final: 0.7070 (m-10) REVERT: C 482 GLU cc_start: 0.7634 (mm-30) cc_final: 0.7250 (mm-30) REVERT: C 530 MET cc_start: 0.8857 (mmm) cc_final: 0.8539 (tpp) REVERT: C 610 TRP cc_start: 0.7835 (t-100) cc_final: 0.7593 (t-100) REVERT: C 617 ARG cc_start: 0.7763 (mtp180) cc_final: 0.7261 (mtm-85) REVERT: C 634 GLU cc_start: 0.7964 (tt0) cc_final: 0.7684 (tt0) REVERT: C 656 ASN cc_start: 0.7857 (t0) cc_final: 0.7508 (t0) REVERT: C 657 GLU cc_start: 0.7722 (tp30) cc_final: 0.7028 (tp30) outliers start: 70 outliers final: 49 residues processed: 480 average time/residue: 0.3005 time to fit residues: 201.2705 Evaluate side-chains 475 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 418 time to evaluate : 1.671 ------------------------------------------------------------------------------- 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 90 THR Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 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 358 ILE Chi-restraints excluded: chain A residue 417 GLN Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 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 213 ILE Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain B residue 344 LYS Chi-restraints excluded: chain B residue 417 GLN 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 95 MET Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 119 CYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 215 ILE 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 628 TRP Chi-restraints excluded: chain C residue 629 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 31 optimal weight: 0.0670 chunk 102 optimal weight: 0.0070 chunk 110 optimal weight: 0.8980 chunk 80 optimal weight: 0.4980 chunk 15 optimal weight: 0.9990 chunk 127 optimal weight: 1.9990 chunk 147 optimal weight: 0.7980 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN A 363 GLN B 302 ASN B 363 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.3870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 14448 Z= 0.174 Angle : 0.584 11.551 19632 Z= 0.300 Chirality : 0.045 0.238 2418 Planarity : 0.004 0.058 2421 Dihedral : 7.342 54.710 3122 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.93 % Allowed : 21.07 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.21), residues: 1656 helix: 1.49 (0.28), residues: 375 sheet: 1.06 (0.26), residues: 369 loop : -1.04 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 35 HIS 0.009 0.001 HIS C 374 PHE 0.020 0.001 PHE C 53 TYR 0.025 0.001 TYR C 638 ARG 0.007 0.000 ARG C 419 *********************** 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 513 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 454 time to evaluate : 1.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LYS cc_start: 0.8610 (pttt) cc_final: 0.8225 (pttt) REVERT: A 110 SER cc_start: 0.8113 (t) cc_final: 0.7911 (p) REVERT: A 117 LYS cc_start: 0.8436 (ttmm) cc_final: 0.8002 (ttmm) REVERT: A 136 VAL cc_start: 0.7453 (OUTLIER) cc_final: 0.7128 (p) REVERT: A 150 GLU cc_start: 0.7511 (tp30) cc_final: 0.6998 (tp30) REVERT: A 166 LYS cc_start: 0.7693 (mmmt) cc_final: 0.7371 (mmmt) REVERT: A 245 VAL cc_start: 0.8662 (t) cc_final: 0.8303 (p) REVERT: A 246 GLN cc_start: 0.7847 (tp40) cc_final: 0.7633 (tp40) REVERT: A 264 SER cc_start: 0.8223 (m) cc_final: 0.7611 (p) REVERT: A 297 THR cc_start: 0.8637 (t) cc_final: 0.8414 (p) REVERT: A 417 GLN cc_start: 0.7832 (OUTLIER) cc_final: 0.7265 (mt0) REVERT: A 420 ILE cc_start: 0.8504 (mt) cc_final: 0.8131 (mm) REVERT: A 447 SER cc_start: 0.8514 (m) cc_final: 0.7895 (p) REVERT: A 482 GLU cc_start: 0.7601 (mm-30) cc_final: 0.6737 (mm-30) REVERT: A 490 LYS cc_start: 0.8088 (ttpp) cc_final: 0.7648 (ttpp) REVERT: A 530 MET cc_start: 0.8813 (tpt) cc_final: 0.8384 (tpp) REVERT: A 535 MET cc_start: 0.7200 (tpp) cc_final: 0.6947 (tpp) REVERT: A 610 TRP cc_start: 0.8073 (t-100) cc_final: 0.7853 (t-100) REVERT: A 631 TRP cc_start: 0.7930 (t-100) cc_final: 0.7334 (t-100) REVERT: A 647 GLU cc_start: 0.7711 (tm-30) cc_final: 0.7235 (tm-30) REVERT: A 654 GLU cc_start: 0.7972 (tp30) cc_final: 0.7748 (tp30) REVERT: A 656 ASN cc_start: 0.7856 (t0) cc_final: 0.7455 (t0) REVERT: B 35 TRP cc_start: 0.7792 (m-10) cc_final: 0.7350 (m-10) REVERT: B 44 VAL cc_start: 0.8977 (p) cc_final: 0.8724 (m) REVERT: B 47 GLU cc_start: 0.6972 (tt0) cc_final: 0.6701 (tt0) REVERT: B 53 PHE cc_start: 0.7027 (p90) cc_final: 0.6760 (p90) REVERT: B 69 TRP cc_start: 0.6812 (m-90) cc_final: 0.6245 (m-90) REVERT: B 93 PHE cc_start: 0.7346 (m-10) cc_final: 0.6966 (m-80) REVERT: B 106 GLU cc_start: 0.7326 (tp30) cc_final: 0.6980 (tp30) REVERT: B 113 ASP cc_start: 0.7398 (t0) cc_final: 0.6692 (t0) REVERT: B 136 VAL cc_start: 0.7443 (OUTLIER) cc_final: 0.7059 (p) REVERT: B 242 VAL cc_start: 0.8652 (t) cc_final: 0.8402 (m) REVERT: B 268 LYS cc_start: 0.8456 (pptt) cc_final: 0.8061 (pptt) REVERT: B 272 ILE cc_start: 0.8526 (mt) cc_final: 0.8071 (mm) REVERT: B 280 ASN cc_start: 0.8062 (p0) cc_final: 0.7652 (p0) REVERT: B 420 ILE cc_start: 0.8527 (mt) cc_final: 0.8322 (mm) REVERT: B 432 ARG cc_start: 0.6688 (mtt90) cc_final: 0.6214 (mtt90) REVERT: B 464 GLU cc_start: 0.7936 (mp0) cc_final: 0.7601 (pm20) REVERT: B 475 MET cc_start: 0.7880 (tpp) cc_final: 0.7507 (tpp) REVERT: B 490 LYS cc_start: 0.7893 (ttpt) cc_final: 0.7688 (ttpt) REVERT: B 535 MET cc_start: 0.7128 (tpp) cc_final: 0.6832 (tpp) REVERT: B 622 ILE cc_start: 0.8576 (mm) cc_final: 0.8315 (mt) REVERT: B 645 LEU cc_start: 0.8090 (mp) cc_final: 0.7827 (mt) REVERT: B 656 ASN cc_start: 0.7748 (t0) cc_final: 0.7451 (t0) REVERT: B 657 GLU cc_start: 0.7505 (tp30) cc_final: 0.6964 (tp30) REVERT: C 47 GLU cc_start: 0.7367 (tp30) cc_final: 0.6988 (mm-30) REVERT: C 53 PHE cc_start: 0.7109 (p90) cc_final: 0.6824 (p90) REVERT: C 72 HIS cc_start: 0.6796 (OUTLIER) cc_final: 0.6379 (t70) REVERT: C 92 ASN cc_start: 0.7689 (p0) cc_final: 0.7375 (p0) REVERT: C 93 PHE cc_start: 0.7507 (m-80) cc_final: 0.7263 (m-10) REVERT: C 106 GLU cc_start: 0.7371 (tp30) cc_final: 0.7123 (tp30) REVERT: C 121 LYS cc_start: 0.8613 (mttt) cc_final: 0.8165 (mttm) REVERT: C 136 VAL cc_start: 0.7277 (OUTLIER) cc_final: 0.6796 (p) REVERT: C 150 GLU cc_start: 0.7428 (tp30) cc_final: 0.6938 (tp30) REVERT: C 166 LYS cc_start: 0.7816 (mmmt) cc_final: 0.7510 (mmmt) REVERT: C 171 TYR cc_start: 0.7854 (p90) cc_final: 0.7474 (p90) REVERT: C 258 GLN cc_start: 0.8437 (mt0) cc_final: 0.8221 (mt0) REVERT: C 265 LEU cc_start: 0.8837 (mp) cc_final: 0.8591 (mm) REVERT: C 273 ARG cc_start: 0.8175 (mtt-85) cc_final: 0.7796 (mtt-85) REVERT: C 308 ARG cc_start: 0.7652 (mmt90) cc_final: 0.7363 (tpt-90) REVERT: C 414 ILE cc_start: 0.8591 (tp) cc_final: 0.8215 (tt) REVERT: C 417 GLN cc_start: 0.7887 (OUTLIER) cc_final: 0.7540 (mt0) REVERT: C 427 TRP cc_start: 0.7751 (m-90) cc_final: 0.6935 (m-10) REVERT: C 482 GLU cc_start: 0.7608 (mm-30) cc_final: 0.7257 (mm-30) REVERT: C 490 LYS cc_start: 0.7878 (ttpt) cc_final: 0.7623 (ttpp) REVERT: C 540 GLN cc_start: 0.7511 (mp10) cc_final: 0.7202 (mp10) REVERT: C 610 TRP cc_start: 0.7826 (t-100) cc_final: 0.7574 (t-100) REVERT: C 617 ARG cc_start: 0.7692 (mtp180) cc_final: 0.7142 (mtm-85) REVERT: C 656 ASN cc_start: 0.7857 (t0) cc_final: 0.7504 (t0) REVERT: C 657 GLU cc_start: 0.7698 (tp30) cc_final: 0.7084 (tp30) outliers start: 59 outliers final: 39 residues processed: 485 average time/residue: 0.3033 time to fit residues: 207.8370 Evaluate side-chains 477 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 432 time to evaluate : 1.649 ------------------------------------------------------------------------------- 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 328 GLN Chi-restraints excluded: chain A residue 417 GLN Chi-restraints excluded: chain A residue 434 MET 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 138 THR 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 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 95 MET Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 119 CYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 302 ASN 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 626 MET Chi-restraints excluded: chain C residue 628 TRP Chi-restraints excluded: chain C residue 629 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 2.9990 chunk 141 optimal weight: 0.9990 chunk 150 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 136 optimal weight: 0.8980 chunk 142 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 159 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN A 363 GLN B 105 HIS B 302 ASN B 315 GLN ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 ASN C 315 GLN C 363 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.3877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 14448 Z= 0.388 Angle : 0.695 12.788 19632 Z= 0.357 Chirality : 0.050 0.271 2418 Planarity : 0.005 0.065 2421 Dihedral : 7.666 55.741 3122 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.80 % Allowed : 22.07 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.20), residues: 1656 helix: 1.32 (0.28), residues: 375 sheet: 1.23 (0.27), residues: 333 loop : -1.21 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP A 69 HIS 0.007 0.002 HIS A 216 PHE 0.020 0.002 PHE C 93 TYR 0.026 0.003 TYR C 638 ARG 0.007 0.001 ARG C 419 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 449 time to evaluate : 1.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LYS cc_start: 0.8587 (pttt) cc_final: 0.8206 (pttt) REVERT: A 117 LYS cc_start: 0.8530 (ttmm) cc_final: 0.8085 (ttmm) REVERT: A 136 VAL cc_start: 0.7438 (OUTLIER) cc_final: 0.7084 (p) REVERT: A 150 GLU cc_start: 0.7527 (tp30) cc_final: 0.6986 (tp30) REVERT: A 246 GLN cc_start: 0.7866 (tp40) cc_final: 0.7529 (tp40) REVERT: A 258 GLN cc_start: 0.8180 (mt0) cc_final: 0.7719 (mt0) REVERT: A 264 SER cc_start: 0.8272 (m) cc_final: 0.7643 (p) REVERT: A 297 THR cc_start: 0.8654 (t) cc_final: 0.8406 (p) REVERT: A 348 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7496 (mm-30) REVERT: A 417 GLN cc_start: 0.7915 (OUTLIER) cc_final: 0.7317 (mt0) REVERT: A 482 GLU cc_start: 0.7608 (mm-30) cc_final: 0.6753 (mm-30) REVERT: A 535 MET cc_start: 0.7174 (tpp) cc_final: 0.6956 (tpp) REVERT: A 610 TRP cc_start: 0.8088 (t-100) cc_final: 0.7838 (t-100) REVERT: A 631 TRP cc_start: 0.8034 (t-100) cc_final: 0.7755 (t-100) REVERT: A 635 ILE cc_start: 0.8445 (tp) cc_final: 0.7968 (tt) REVERT: A 647 GLU cc_start: 0.7762 (tm-30) cc_final: 0.7270 (tm-30) REVERT: A 654 GLU cc_start: 0.8021 (tp30) cc_final: 0.7765 (tp30) REVERT: A 656 ASN cc_start: 0.7890 (t0) cc_final: 0.7491 (t0) REVERT: B 35 TRP cc_start: 0.7880 (m-10) cc_final: 0.7400 (m-10) REVERT: B 44 VAL cc_start: 0.9000 (p) cc_final: 0.8769 (m) REVERT: B 47 GLU cc_start: 0.7095 (tt0) cc_final: 0.6796 (tt0) REVERT: B 53 PHE cc_start: 0.6983 (p90) cc_final: 0.6783 (p90) REVERT: B 69 TRP cc_start: 0.6859 (m-90) cc_final: 0.6444 (m-90) REVERT: B 106 GLU cc_start: 0.7339 (tp30) cc_final: 0.6963 (tp30) REVERT: B 113 ASP cc_start: 0.7386 (t0) cc_final: 0.6400 (t0) REVERT: B 136 VAL cc_start: 0.7414 (OUTLIER) cc_final: 0.7032 (p) REVERT: B 150 GLU cc_start: 0.7584 (tp30) cc_final: 0.7098 (tp30) REVERT: B 205 CYS cc_start: 0.5892 (m) cc_final: 0.5627 (m) REVERT: B 268 LYS cc_start: 0.8457 (pptt) cc_final: 0.8047 (pptt) REVERT: B 280 ASN cc_start: 0.8108 (p0) cc_final: 0.7719 (p0) REVERT: B 321 ASP cc_start: 0.7553 (t0) cc_final: 0.7297 (t70) REVERT: B 337 LYS cc_start: 0.8303 (OUTLIER) cc_final: 0.8032 (ttmm) REVERT: B 420 ILE cc_start: 0.8546 (mt) cc_final: 0.8305 (mm) REVERT: B 432 ARG cc_start: 0.6818 (mtt90) cc_final: 0.6276 (mtt90) REVERT: B 464 GLU cc_start: 0.7984 (mp0) cc_final: 0.7633 (pm20) REVERT: B 475 MET cc_start: 0.7928 (tpp) cc_final: 0.7532 (tpp) REVERT: B 490 LYS cc_start: 0.7867 (ttpt) cc_final: 0.7661 (ttpt) REVERT: B 530 MET cc_start: 0.8868 (tpt) cc_final: 0.8603 (mmm) REVERT: B 535 MET cc_start: 0.7098 (tpp) cc_final: 0.6868 (tpp) REVERT: B 622 ILE cc_start: 0.8630 (mm) cc_final: 0.8383 (mt) REVERT: B 656 ASN cc_start: 0.7800 (t0) cc_final: 0.7495 (t0) REVERT: B 657 GLU cc_start: 0.7503 (tp30) cc_final: 0.6997 (tp30) REVERT: C 47 GLU cc_start: 0.7467 (tp30) cc_final: 0.7060 (mm-30) REVERT: C 53 PHE cc_start: 0.7241 (p90) cc_final: 0.6954 (p90) REVERT: C 72 HIS cc_start: 0.6788 (OUTLIER) cc_final: 0.6460 (t70) REVERT: C 92 ASN cc_start: 0.7710 (p0) cc_final: 0.7393 (p0) REVERT: C 93 PHE cc_start: 0.7724 (m-80) cc_final: 0.7480 (m-10) REVERT: C 103 GLN cc_start: 0.7880 (tp-100) cc_final: 0.7255 (tm-30) REVERT: C 106 GLU cc_start: 0.7431 (tp30) cc_final: 0.7163 (tp30) REVERT: C 121 LYS cc_start: 0.8627 (mttt) cc_final: 0.8153 (mttm) REVERT: C 150 GLU cc_start: 0.7435 (tp30) cc_final: 0.6902 (tp30) REVERT: C 166 LYS cc_start: 0.7957 (mmmt) cc_final: 0.7567 (mmmt) REVERT: C 171 TYR cc_start: 0.7899 (p90) cc_final: 0.7382 (p90) REVERT: C 414 ILE cc_start: 0.8544 (tp) cc_final: 0.8150 (tt) REVERT: C 417 GLN cc_start: 0.7927 (OUTLIER) cc_final: 0.7525 (mt0) REVERT: C 427 TRP cc_start: 0.7770 (m-90) cc_final: 0.6944 (m-10) REVERT: C 482 GLU cc_start: 0.7648 (mm-30) cc_final: 0.7273 (mm-30) REVERT: C 530 MET cc_start: 0.8547 (tpt) cc_final: 0.8022 (mmm) REVERT: C 577 GLN cc_start: 0.7359 (tm-30) cc_final: 0.6962 (tm-30) REVERT: C 610 TRP cc_start: 0.7813 (t-100) cc_final: 0.7548 (t-100) REVERT: C 617 ARG cc_start: 0.7696 (mtp180) cc_final: 0.7336 (mtm-85) REVERT: C 656 ASN cc_start: 0.7894 (t0) cc_final: 0.7555 (t0) REVERT: C 657 GLU cc_start: 0.7723 (tp30) cc_final: 0.7125 (tp30) outliers start: 57 outliers final: 39 residues processed: 480 average time/residue: 0.3004 time to fit residues: 202.0096 Evaluate side-chains 485 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 440 time to evaluate : 1.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 417 GLN Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 169 LYS Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 119 CYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 205 CYS 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 626 MET Chi-restraints excluded: chain C residue 628 TRP Chi-restraints excluded: chain C residue 629 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 0.8980 chunk 75 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 167 optimal weight: 4.9990 chunk 154 optimal weight: 0.7980 chunk 133 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 105 optimal weight: 0.0870 chunk 141 optimal weight: 1.9990 overall best weight: 0.9560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 302 ASN ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.4001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 14448 Z= 0.248 Angle : 0.642 11.982 19632 Z= 0.330 Chirality : 0.046 0.240 2418 Planarity : 0.004 0.062 2421 Dihedral : 7.525 55.091 3122 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.07 % Allowed : 23.40 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.20), residues: 1656 helix: 1.37 (0.27), residues: 375 sheet: 1.20 (0.27), residues: 339 loop : -1.19 (0.20), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 614 HIS 0.008 0.001 HIS C 374 PHE 0.018 0.002 PHE C 53 TYR 0.025 0.002 TYR C 638 ARG 0.011 0.001 ARG A 273 ********************** 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 488 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 442 time to evaluate : 1.601 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: 0.8577 (pttt) cc_final: 0.8181 (pttt) REVERT: A 117 LYS cc_start: 0.8528 (ttmm) cc_final: 0.8092 (ttmm) REVERT: A 136 VAL cc_start: 0.7423 (OUTLIER) cc_final: 0.7051 (p) REVERT: A 150 GLU cc_start: 0.7501 (tp30) cc_final: 0.6924 (tp30) REVERT: A 178 ASP cc_start: 0.7791 (t0) cc_final: 0.7338 (t70) REVERT: A 245 VAL cc_start: 0.8680 (t) cc_final: 0.8296 (p) REVERT: A 246 GLN cc_start: 0.7906 (tp40) cc_final: 0.7574 (tp40) REVERT: A 258 GLN cc_start: 0.8121 (mt0) cc_final: 0.7673 (mt0) REVERT: A 264 SER cc_start: 0.8272 (m) cc_final: 0.7653 (p) REVERT: A 297 THR cc_start: 0.8649 (t) cc_final: 0.8423 (p) REVERT: A 308 ARG cc_start: 0.7823 (tpp80) cc_final: 0.7600 (tpt-90) REVERT: A 348 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7491 (mm-30) REVERT: A 417 GLN cc_start: 0.7890 (OUTLIER) cc_final: 0.7283 (mt0) REVERT: A 447 SER cc_start: 0.8414 (m) cc_final: 0.7792 (p) REVERT: A 482 GLU cc_start: 0.7562 (mm-30) cc_final: 0.6690 (mm-30) REVERT: A 530 MET cc_start: 0.8733 (tpt) cc_final: 0.8395 (tpp) REVERT: A 610 TRP cc_start: 0.8047 (t-100) cc_final: 0.7776 (t-100) REVERT: A 631 TRP cc_start: 0.7983 (t-100) cc_final: 0.7712 (t-100) REVERT: A 635 ILE cc_start: 0.8335 (tp) cc_final: 0.7856 (tt) REVERT: A 647 GLU cc_start: 0.7731 (tm-30) cc_final: 0.7263 (tm-30) REVERT: A 654 GLU cc_start: 0.8010 (tp30) cc_final: 0.7772 (tp30) REVERT: A 656 ASN cc_start: 0.7846 (t0) cc_final: 0.7465 (t0) REVERT: B 35 TRP cc_start: 0.7848 (m-10) cc_final: 0.7392 (m-10) REVERT: B 44 VAL cc_start: 0.9003 (p) cc_final: 0.8793 (m) REVERT: B 47 GLU cc_start: 0.7055 (tt0) cc_final: 0.6802 (tt0) REVERT: B 69 TRP cc_start: 0.6831 (m-90) cc_final: 0.6386 (m-90) REVERT: B 82 GLN cc_start: 0.7100 (mp10) cc_final: 0.6757 (mp10) REVERT: B 100 MET cc_start: 0.8014 (mtm) cc_final: 0.7798 (mtm) REVERT: B 106 GLU cc_start: 0.7283 (tp30) cc_final: 0.6874 (tp30) REVERT: B 113 ASP cc_start: 0.7393 (t0) cc_final: 0.6590 (t0) REVERT: B 136 VAL cc_start: 0.7367 (OUTLIER) cc_final: 0.6968 (p) REVERT: B 150 GLU cc_start: 0.7533 (tp30) cc_final: 0.7017 (tp30) REVERT: B 268 LYS cc_start: 0.8377 (pptt) cc_final: 0.7980 (pptt) REVERT: B 280 ASN cc_start: 0.8093 (p0) cc_final: 0.7701 (p0) REVERT: B 321 ASP cc_start: 0.7539 (t0) cc_final: 0.7217 (t70) REVERT: B 337 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7967 (ttmm) REVERT: B 420 ILE cc_start: 0.8570 (mt) cc_final: 0.8328 (mm) REVERT: B 432 ARG cc_start: 0.6802 (mtt90) cc_final: 0.6375 (mtt90) REVERT: B 464 GLU cc_start: 0.7980 (mp0) cc_final: 0.7643 (pm20) REVERT: B 475 MET cc_start: 0.7954 (tpp) cc_final: 0.7537 (tpp) REVERT: B 492 GLU cc_start: 0.7572 (mt-10) cc_final: 0.7119 (mt-10) REVERT: B 530 MET cc_start: 0.8857 (tpt) cc_final: 0.8477 (tpp) REVERT: B 535 MET cc_start: 0.7126 (tpp) cc_final: 0.6874 (tpp) REVERT: B 622 ILE cc_start: 0.8614 (mm) cc_final: 0.8366 (mt) REVERT: B 656 ASN cc_start: 0.7794 (t0) cc_final: 0.7482 (t0) REVERT: B 657 GLU cc_start: 0.7494 (tp30) cc_final: 0.6987 (tp30) REVERT: C 47 GLU cc_start: 0.7418 (tp30) cc_final: 0.6998 (mm-30) REVERT: C 53 PHE cc_start: 0.7213 (p90) cc_final: 0.6945 (p90) REVERT: C 72 HIS cc_start: 0.6766 (OUTLIER) cc_final: 0.6487 (t70) REVERT: C 92 ASN cc_start: 0.7716 (p0) cc_final: 0.7401 (p0) REVERT: C 93 PHE cc_start: 0.7633 (m-80) cc_final: 0.7375 (m-10) REVERT: C 106 GLU cc_start: 0.7405 (tp30) cc_final: 0.7131 (tp30) REVERT: C 108 ILE cc_start: 0.7011 (mt) cc_final: 0.6796 (mm) REVERT: C 121 LYS cc_start: 0.8634 (mttt) cc_final: 0.8143 (mttm) REVERT: C 150 GLU cc_start: 0.7375 (tp30) cc_final: 0.6801 (tp30) REVERT: C 166 LYS cc_start: 0.7917 (mmmt) cc_final: 0.7536 (mmmt) REVERT: C 171 TYR cc_start: 0.7868 (p90) cc_final: 0.7394 (p90) REVERT: C 258 GLN cc_start: 0.8459 (mt0) cc_final: 0.7974 (mt0) REVERT: C 350 GLN cc_start: 0.7932 (tt0) cc_final: 0.7732 (tt0) REVERT: C 414 ILE cc_start: 0.8616 (tp) cc_final: 0.8223 (tt) REVERT: C 417 GLN cc_start: 0.7898 (OUTLIER) cc_final: 0.7525 (mt0) REVERT: C 427 TRP cc_start: 0.7771 (m-90) cc_final: 0.6914 (m-10) REVERT: C 482 GLU cc_start: 0.7621 (mm-30) cc_final: 0.7235 (mm-30) REVERT: C 540 GLN cc_start: 0.7599 (mp10) cc_final: 0.7335 (mp10) REVERT: C 617 ARG cc_start: 0.7529 (mtp180) cc_final: 0.7135 (mtt180) REVERT: C 656 ASN cc_start: 0.7889 (t0) cc_final: 0.7537 (t0) REVERT: C 657 GLU cc_start: 0.7713 (tp30) cc_final: 0.7126 (tp30) outliers start: 46 outliers final: 36 residues processed: 464 average time/residue: 0.3021 time to fit residues: 196.7109 Evaluate side-chains 482 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 440 time to evaluate : 1.634 ------------------------------------------------------------------------------- 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 114 GLN Chi-restraints excluded: chain A residue 121 LYS 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 417 GLN Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 119 CYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 205 CYS 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 626 MET 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 40 optimal weight: 1.9990 chunk 122 optimal weight: 0.5980 chunk 19 optimal weight: 3.9990 chunk 37 optimal weight: 0.0770 chunk 133 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 137 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 117 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN B 302 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.123019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.102458 restraints weight = 21665.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.106493 restraints weight = 12094.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.109229 restraints weight = 8150.551| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.4151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 14448 Z= 0.195 Angle : 0.620 12.266 19632 Z= 0.317 Chirality : 0.045 0.237 2418 Planarity : 0.004 0.059 2421 Dihedral : 7.371 55.187 3122 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.67 % Allowed : 23.87 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.20), residues: 1656 helix: 1.51 (0.28), residues: 375 sheet: 1.22 (0.27), residues: 339 loop : -1.18 (0.20), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 614 HIS 0.008 0.001 HIS C 374 PHE 0.020 0.001 PHE B 53 TYR 0.027 0.001 TYR C 638 ARG 0.020 0.001 ARG C 500 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3757.95 seconds wall clock time: 74 minutes 40.22 seconds (4480.22 seconds total)