Starting phenix.real_space_refine on Fri Feb 16 03:05:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eu8_28608/02_2024/8eu8_28608_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eu8_28608/02_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_28608/02_2024/8eu8_28608.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eu8_28608/02_2024/8eu8_28608.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eu8_28608/02_2024/8eu8_28608_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eu8_28608/02_2024/8eu8_28608_neut.pdb" } 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 Residue "A TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 164": "NH1" <-> "NH2" Residue "A ARG 192": "NH1" <-> "NH2" Residue "A ARG 252": "NH1" <-> "NH2" Residue "A ARG 273": "NH1" <-> "NH2" Residue "A ARG 298": "NH1" <-> "NH2" Residue "A ARG 304": "NH1" <-> "NH2" Residue "A ARG 308": "NH1" <-> "NH2" Residue "A TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 419": "NH1" <-> "NH2" Residue "A ARG 432": "NH1" <-> "NH2" Residue "A ARG 446": "NH1" <-> "NH2" Residue "A ARG 456": "NH1" <-> "NH2" Residue "A ARG 469": "NH1" <-> "NH2" Residue "A ARG 476": "NH1" <-> "NH2" Residue "A ARG 480": "NH1" <-> "NH2" Residue "A ARG 500": "NH1" <-> "NH2" Residue "A ARG 503": "NH1" <-> "NH2" Residue "A ARG 504": "NH1" <-> "NH2" Residue "A ARG 542": "NH1" <-> "NH2" Residue "A ARG 579": "NH1" <-> "NH2" Residue "A ARG 585": "NH1" <-> "NH2" Residue "A ARG 588": "NH1" <-> "NH2" Residue "A ARG 617": "NH1" <-> "NH2" Residue "B TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 164": "NH1" <-> "NH2" Residue "B ARG 192": "NH1" <-> "NH2" Residue "B ARG 252": "NH1" <-> "NH2" Residue "B ARG 273": "NH1" <-> "NH2" Residue "B ARG 298": "NH1" <-> "NH2" Residue "B ARG 304": "NH1" <-> "NH2" Residue "B ARG 308": "NH1" <-> "NH2" Residue "B TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 419": "NH1" <-> "NH2" Residue "B ARG 432": "NH1" <-> "NH2" Residue "B ARG 446": "NH1" <-> "NH2" Residue "B ARG 456": "NH1" <-> "NH2" Residue "B ARG 469": "NH1" <-> "NH2" Residue "B ARG 476": "NH1" <-> "NH2" Residue "B ARG 480": "NH1" <-> "NH2" Residue "B ARG 500": "NH1" <-> "NH2" Residue "B ARG 503": "NH1" <-> "NH2" Residue "B ARG 504": "NH1" <-> "NH2" Residue "B ARG 542": "NH1" <-> "NH2" Residue "B ARG 579": "NH1" <-> "NH2" Residue "B ARG 585": "NH1" <-> "NH2" Residue "B ARG 588": "NH1" <-> "NH2" Residue "B ARG 617": "NH1" <-> "NH2" Residue "C TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 164": "NH1" <-> "NH2" Residue "C ARG 192": "NH1" <-> "NH2" Residue "C ARG 252": "NH1" <-> "NH2" Residue "C ARG 273": "NH1" <-> "NH2" Residue "C ARG 298": "NH1" <-> "NH2" Residue "C ARG 304": "NH1" <-> "NH2" Residue "C ARG 308": "NH1" <-> "NH2" Residue "C TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 419": "NH1" <-> "NH2" Residue "C ARG 432": "NH1" <-> "NH2" Residue "C ARG 446": "NH1" <-> "NH2" Residue "C ARG 456": "NH1" <-> "NH2" Residue "C ARG 469": "NH1" <-> "NH2" Residue "C ARG 476": "NH1" <-> "NH2" Residue "C ARG 480": "NH1" <-> "NH2" Residue "C ARG 500": "NH1" <-> "NH2" Residue "C ARG 503": "NH1" <-> "NH2" Residue "C ARG 504": "NH1" <-> "NH2" Residue "C ARG 542": "NH1" <-> "NH2" Residue "C ARG 579": "NH1" <-> "NH2" Residue "C ARG 585": "NH1" <-> "NH2" Residue "C ARG 588": "NH1" <-> "NH2" Residue "C ARG 617": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 8.00, per 1000 atoms: 0.56 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 - 3.50 Amino acid : False - 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: 6.19 Conformation dependent library (CDL) restraints added in 2.5 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: 1.80 Creating SS restraints... Processing helix chain 'A' and resid 68 through 72 removed outlier: 3.706A pdb=" N THR A 71 " --> pdb=" O VAL A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 115 removed outlier: 4.218A pdb=" N ASP A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 335 through 351 removed outlier: 3.638A pdb=" N GLU A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LYS A 351 " --> pdb=" O ILE A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 475 through 483 removed outlier: 3.775A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 536 through 543 removed outlier: 4.180A pdb=" N GLN A 540 " --> pdb=" O THR A 536 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASN A 543 " --> pdb=" O VAL A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 596 removed outlier: 4.299A pdb=" N GLN A 575 " --> pdb=" O TRP A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 624 Processing helix chain 'A' and resid 627 through 636 Processing helix chain 'A' and resid 638 through 661 removed outlier: 3.703A pdb=" N ILE A 642 " --> pdb=" O TYR A 638 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR A 643 " --> pdb=" O THR A 639 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLY A 644 " --> pdb=" O GLN A 640 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU A 645 " --> pdb=" O ILE A 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 72 Processing helix chain 'B' and resid 98 through 115 removed outlier: 4.218A pdb=" N ASP B 102 " --> pdb=" O ASN B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 126 Processing helix chain 'B' and resid 195 through 198 Processing helix chain 'B' and resid 335 through 351 removed outlier: 3.638A pdb=" N GLU B 348 " --> pdb=" O LYS B 344 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LYS B 351 " --> pdb=" O ILE B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 373 Processing helix chain 'B' and resid 475 through 483 removed outlier: 3.775A pdb=" N TRP B 479 " --> pdb=" O MET B 475 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU B 482 " --> pdb=" O ASN B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 543 removed outlier: 4.180A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 596 removed outlier: 4.435A pdb=" N GLN B 575 " --> pdb=" O TRP B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 638 through 661 removed outlier: 3.702A pdb=" N ILE B 642 " --> pdb=" O TYR B 638 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR B 643 " --> pdb=" O THR B 639 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU B 645 " --> pdb=" O ILE B 641 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 72 Processing helix chain 'C' and resid 98 through 115 removed outlier: 4.218A pdb=" N ASP C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 335 through 351 removed outlier: 3.638A pdb=" N GLU C 348 " --> pdb=" O LYS C 344 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LYS C 351 " --> pdb=" O ILE C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 475 through 483 removed outlier: 3.776A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 534 Processing helix chain 'C' and resid 536 through 543 removed outlier: 4.180A pdb=" N GLN C 540 " --> pdb=" O THR C 536 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASN C 543 " --> pdb=" O VAL C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 596 removed outlier: 4.372A pdb=" N GLN C 575 " --> pdb=" O TRP C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 624 Processing helix chain 'C' and resid 627 through 636 Processing helix chain 'C' and resid 638 through 661 removed outlier: 3.702A pdb=" N ILE C 642 " --> pdb=" O TYR C 638 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TYR C 643 " --> pdb=" O THR C 639 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLY C 644 " --> pdb=" O GLN C 640 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU C 645 " --> pdb=" O ILE C 641 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.458A pdb=" N VAL A 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N VAL A 38 " --> pdb=" O THR A 606 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N THR A 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N TYR A 40 " --> pdb=" O CYS A 604 " (cutoff:3.500A) removed outlier: 8.390A pdb=" N CYS A 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.023A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.537A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 167 through 175 removed outlier: 10.285A pdb=" N GLU A 150 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 11.883A pdb=" N VAL A 136 " --> pdb=" O GLU A 150 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N MET A 152 " --> pdb=" O ALA A 134 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA A 134 " --> pdb=" O MET A 152 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.660A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 284 through 308 removed outlier: 3.939A pdb=" N ASP A 321A" --> pdb=" O THR A 303 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N LYS A 305 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N THR A 320 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N VAL A 307 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N TYR A 318 " --> pdb=" O VAL A 307 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 316 through 322 current: chain 'A' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 381 through 385 current: chain 'A' and resid 465 through 470 Processing sheet with id=AA8, first strand: chain 'B' and resid 494 through 499 removed outlier: 5.457A pdb=" N VAL B 608 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N VAL B 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N THR B 606 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N TYR B 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.390A pdb=" N CYS B 604 " --> pdb=" O TYR B 40 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 45 through 47 removed outlier: 4.022A pdb=" N ILE B 225 " --> pdb=" O VAL B 245 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 75 through 76 Processing sheet with id=AB2, first strand: chain 'B' and resid 91 through 94 removed outlier: 3.536A pdb=" N GLU B 91 " --> pdb=" O CYS B 239 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 167 through 175 removed outlier: 10.285A pdb=" N GLU B 150 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 11.883A pdb=" N VAL B 136 " --> pdb=" O GLU B 150 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N MET B 152 " --> pdb=" O ALA B 134 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA B 134 " --> pdb=" O MET B 152 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 202 through 203 removed outlier: 6.660A pdb=" N THR B 202 " --> pdb=" O TYR B 435 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 259 through 261 current: chain 'B' and resid 284 through 308 removed outlier: 3.939A pdb=" N ASP B 321A" --> pdb=" O THR B 303 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N LYS B 305 " --> pdb=" O THR B 320 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N THR B 320 " --> pdb=" O LYS B 305 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N VAL B 307 " --> pdb=" O TYR B 318 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N TYR B 318 " --> pdb=" O VAL B 307 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 316 through 322 current: chain 'B' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 381 through 385 current: chain 'B' and resid 465 through 470 Processing sheet with id=AB6, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.459A pdb=" N VAL C 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N VAL C 38 " --> pdb=" O THR C 606 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N THR C 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N TYR C 40 " --> pdb=" O CYS C 604 " (cutoff:3.500A) removed outlier: 8.389A pdb=" N CYS C 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.026A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 75 through 76 Processing sheet with id=AB9, first strand: chain 'C' and resid 91 through 94 removed outlier: 3.537A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 167 through 175 removed outlier: 10.285A pdb=" N GLU C 150 " --> pdb=" O VAL C 136 " (cutoff:3.500A) removed outlier: 11.884A pdb=" N VAL C 136 " --> pdb=" O GLU C 150 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N MET C 152 " --> pdb=" O ALA C 134 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA C 134 " --> pdb=" O MET C 152 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 202 through 203 removed outlier: 6.660A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 259 through 261 current: chain 'C' and resid 284 through 308 removed outlier: 3.939A pdb=" N ASP C 321A" --> pdb=" O THR C 303 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N LYS C 305 " --> pdb=" O THR C 320 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N THR C 320 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N VAL C 307 " --> pdb=" O TYR C 318 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N TYR C 318 " --> pdb=" O VAL C 307 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 316 through 322 current: chain 'C' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 381 through 385 current: chain 'C' and resid 465 through 470 391 hydrogen bonds defined for protein. 1092 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.23 Time building geometry restraints manager: 6.68 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: 98.38 - 105.82: 397 105.82 - 113.26: 7498 113.26 - 120.69: 6750 120.69 - 128.13: 4853 128.13 - 135.57: 134 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 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: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.310 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 40.310 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.160 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.890 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 7 poor density : 530 time to evaluate : 1.636 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: 0.2954 time to fit residues: 218.4585 Evaluate side-chains 437 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 434 time to evaluate : 1.598 ------------------------------------------------------------------------------- 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: 0.7980 chunk 127 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 43 optimal weight: 0.0060 chunk 85 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 131 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 80 optimal weight: 0.6980 chunk 98 optimal weight: 0.8980 chunk 152 optimal weight: 0.5980 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN 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 229 ASN B 315 GLN B 374 HIS B 575 GLN B 630 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 Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 14448 Z= 0.210 Angle : 0.704 7.393 19632 Z= 0.364 Chirality : 0.050 0.335 2418 Planarity : 0.004 0.047 2421 Dihedral : 8.711 59.000 3126 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.54 % Favored : 97.34 % Rotamer: Outliers : 2.80 % Allowed : 10.87 % Favored : 86.33 % 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: -0.26 (0.19), residues: 1656 helix: 0.63 (0.26), residues: 375 sheet: 1.38 (0.26), residues: 339 loop : -1.15 (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 0.021 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 500 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 458 time to evaluate : 1.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 PHE cc_start: 0.7442 (p90) cc_final: 0.7030 (p90) REVERT: A 69 TRP cc_start: 0.7172 (m-90) cc_final: 0.6043 (m-90) REVERT: A 88 ASN cc_start: 0.8159 (m110) cc_final: 0.7945 (m-40) REVERT: A 96 TRP cc_start: 0.8221 (m100) cc_final: 0.7412 (m100) REVERT: A 102 ASP cc_start: 0.7615 (t70) cc_final: 0.7203 (t0) REVERT: A 104 MET cc_start: 0.8053 (ttt) cc_final: 0.7662 (ttt) REVERT: A 106 GLU cc_start: 0.7559 (tp30) cc_final: 0.7261 (tp30) REVERT: A 113 ASP cc_start: 0.7428 (t0) cc_final: 0.7091 (t0) REVERT: A 165 ASP cc_start: 0.7090 (t0) cc_final: 0.6890 (t0) REVERT: A 166 LYS cc_start: 0.7785 (mmmt) cc_final: 0.7475 (mmmt) REVERT: A 198 THR cc_start: 0.8203 (t) cc_final: 0.7955 (t) REVERT: A 258 GLN cc_start: 0.8266 (mt0) cc_final: 0.8049 (mt0) REVERT: A 269 GLU cc_start: 0.8116 (tt0) cc_final: 0.7701 (tt0) REVERT: A 283 ILE cc_start: 0.8298 (OUTLIER) cc_final: 0.8092 (pt) REVERT: A 420 ILE cc_start: 0.8377 (mt) cc_final: 0.8098 (mm) REVERT: A 468 PHE cc_start: 0.7603 (m-80) cc_final: 0.7382 (m-10) REVERT: A 482 GLU cc_start: 0.7641 (mm-30) cc_final: 0.7249 (mm-30) REVERT: A 535 MET cc_start: 0.7119 (tpp) cc_final: 0.6593 (tpp) REVERT: A 647 GLU cc_start: 0.7670 (tm-30) cc_final: 0.7358 (tm-30) REVERT: A 656 ASN cc_start: 0.7761 (t0) cc_final: 0.7333 (t0) REVERT: B 44 VAL cc_start: 0.8913 (p) cc_final: 0.8565 (m) REVERT: B 47 GLU cc_start: 0.7102 (tt0) cc_final: 0.6847 (tt0) REVERT: B 50 THR cc_start: 0.8462 (m) cc_final: 0.8228 (m) REVERT: B 53 PHE cc_start: 0.7130 (p90) cc_final: 0.6756 (p90) REVERT: B 82 GLN cc_start: 0.7358 (tp40) cc_final: 0.6921 (tp40) REVERT: B 97 LYS cc_start: 0.8036 (tppt) cc_final: 0.7244 (tppt) REVERT: B 104 MET cc_start: 0.7831 (ttt) cc_final: 0.7558 (ttt) REVERT: B 106 GLU cc_start: 0.7378 (tp30) cc_final: 0.6634 (tp30) REVERT: B 113 ASP cc_start: 0.7497 (t0) cc_final: 0.6845 (t0) REVERT: B 202 THR cc_start: 0.8187 (p) cc_final: 0.7891 (p) REVERT: B 234 ASN cc_start: 0.7442 (t0) cc_final: 0.7027 (t0) REVERT: B 245 VAL cc_start: 0.8443 (OUTLIER) cc_final: 0.8213 (p) REVERT: B 268 LYS cc_start: 0.8574 (pptt) cc_final: 0.8258 (pptt) REVERT: B 280 ASN cc_start: 0.8099 (p0) cc_final: 0.7708 (p0) REVERT: B 293 GLU cc_start: 0.7543 (tt0) cc_final: 0.7139 (tt0) REVERT: B 420 ILE cc_start: 0.8447 (mt) cc_final: 0.8237 (mm) REVERT: B 432 ARG cc_start: 0.6976 (mtt90) cc_final: 0.6371 (mtt90) REVERT: B 447 SER cc_start: 0.8178 (m) cc_final: 0.7842 (p) REVERT: B 456 ARG cc_start: 0.7608 (ttp80) cc_final: 0.7360 (ttp80) REVERT: B 487 LYS cc_start: 0.8118 (tttt) cc_final: 0.7576 (tttt) REVERT: B 490 LYS cc_start: 0.7840 (ttpt) cc_final: 0.7524 (ttpt) REVERT: B 535 MET cc_start: 0.7054 (tpp) cc_final: 0.6702 (tpp) REVERT: B 590 GLN cc_start: 0.8177 (mm-40) cc_final: 0.7948 (mm-40) REVERT: B 656 ASN cc_start: 0.7621 (t0) cc_final: 0.7260 (t0) REVERT: B 657 GLU cc_start: 0.7576 (tp30) cc_final: 0.7317 (tp30) REVERT: C 47 GLU cc_start: 0.7168 (tt0) cc_final: 0.6884 (tt0) REVERT: C 92 ASN cc_start: 0.7669 (p0) cc_final: 0.7322 (p0) REVERT: C 106 GLU cc_start: 0.7358 (tp30) cc_final: 0.7010 (tp30) REVERT: C 121 LYS cc_start: 0.8630 (mttt) cc_final: 0.8212 (mttp) REVERT: C 166 LYS cc_start: 0.7830 (mmmt) cc_final: 0.7449 (mmmt) REVERT: C 171 TYR cc_start: 0.7843 (p90) cc_final: 0.7480 (p90) REVERT: C 178 ASP cc_start: 0.7540 (m-30) cc_final: 0.7311 (t70) REVERT: C 223 TYR cc_start: 0.8022 (m-80) cc_final: 0.7818 (m-10) REVERT: C 300 ASN cc_start: 0.7789 (p0) cc_final: 0.7539 (p0) REVERT: C 302 ASN cc_start: 0.8645 (m-40) cc_final: 0.8441 (m110) REVERT: C 321 ASP cc_start: 0.7572 (t0) cc_final: 0.7357 (t70) REVERT: C 327 LYS cc_start: 0.7975 (tptp) cc_final: 0.7714 (tptp) REVERT: C 347 ILE cc_start: 0.8389 (tp) cc_final: 0.8173 (mt) REVERT: C 395 TYR cc_start: 0.7415 (t80) cc_final: 0.7012 (t80) REVERT: C 414 ILE cc_start: 0.8351 (tp) cc_final: 0.8137 (tp) REVERT: C 427 TRP cc_start: 0.7771 (m-90) cc_final: 0.7396 (m-10) REVERT: C 447 SER cc_start: 0.8333 (m) cc_final: 0.8105 (p) REVERT: C 482 GLU cc_start: 0.7647 (mm-30) cc_final: 0.7233 (mm-30) REVERT: C 575 GLN cc_start: 0.7650 (mm-40) cc_final: 0.7424 (mm110) REVERT: C 577 GLN cc_start: 0.7278 (tm-30) cc_final: 0.6746 (tm-30) REVERT: C 647 GLU cc_start: 0.7671 (tm-30) cc_final: 0.7379 (tm-30) REVERT: C 656 ASN cc_start: 0.7807 (t0) cc_final: 0.7424 (t0) REVERT: C 657 GLU cc_start: 0.7661 (tp30) cc_final: 0.6892 (tp30) outliers start: 42 outliers final: 23 residues processed: 476 average time/residue: 0.2906 time to fit residues: 193.1433 Evaluate side-chains 437 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 412 time to evaluate : 1.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LYS Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 283 ILE 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 78 ASP Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 457 ASP 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: 2.9990 chunk 47 optimal weight: 1.9990 chunk 126 optimal weight: 0.6980 chunk 103 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 152 optimal weight: 0.9980 chunk 165 optimal weight: 0.9980 chunk 136 optimal weight: 2.9990 chunk 151 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS A 302 ASN A 315 GLN A 363 GLN A 374 HIS B 229 ASN B 301 ASN B 302 ASN B 363 GLN B 374 HIS C 114 GLN C 195 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 14448 Z= 0.237 Angle : 0.650 10.221 19632 Z= 0.334 Chirality : 0.049 0.330 2418 Planarity : 0.004 0.050 2421 Dihedral : 8.144 56.837 3126 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 4.27 % Allowed : 15.07 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.02 (0.27), residues: 369 sheet: 1.48 (0.26), residues: 327 loop : -1.06 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 35 HIS 0.006 0.002 HIS B 374 PHE 0.026 0.002 PHE C 53 TYR 0.018 0.002 TYR C 191 ARG 0.006 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 490 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 426 time to evaluate : 1.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 PHE cc_start: 0.7395 (p90) cc_final: 0.6969 (p90) REVERT: A 69 TRP cc_start: 0.7076 (m-90) cc_final: 0.6208 (m-90) REVERT: A 96 TRP cc_start: 0.8119 (m100) cc_final: 0.7420 (m100) REVERT: A 102 ASP cc_start: 0.7732 (t70) cc_final: 0.7438 (t0) REVERT: A 104 MET cc_start: 0.8028 (ttt) cc_final: 0.7806 (ttt) REVERT: A 106 GLU cc_start: 0.7513 (tp30) cc_final: 0.7255 (tp30) REVERT: A 117 LYS cc_start: 0.8498 (ttmm) cc_final: 0.7995 (ttmm) REVERT: A 150 GLU cc_start: 0.7405 (tp30) cc_final: 0.7153 (tp30) REVERT: A 165 ASP cc_start: 0.7046 (t0) cc_final: 0.6826 (t0) REVERT: A 166 LYS cc_start: 0.7763 (mmmt) cc_final: 0.7479 (mmmt) REVERT: A 190 GLU cc_start: 0.7539 (tt0) cc_final: 0.7315 (tt0) REVERT: A 198 THR cc_start: 0.8135 (t) cc_final: 0.7900 (t) REVERT: A 223 TYR cc_start: 0.8188 (m-80) cc_final: 0.7784 (m-80) REVERT: A 269 GLU cc_start: 0.8036 (tt0) cc_final: 0.7680 (tt0) REVERT: A 283 ILE cc_start: 0.8281 (OUTLIER) cc_final: 0.8005 (pt) REVERT: A 348 GLU cc_start: 0.7748 (mm-30) cc_final: 0.7509 (mm-30) REVERT: A 420 ILE cc_start: 0.8393 (mt) cc_final: 0.8126 (mm) REVERT: A 447 SER cc_start: 0.8457 (m) cc_final: 0.7921 (p) REVERT: A 468 PHE cc_start: 0.7762 (m-80) cc_final: 0.7489 (m-10) REVERT: A 482 GLU cc_start: 0.7496 (mm-30) cc_final: 0.7149 (mm-30) REVERT: A 535 MET cc_start: 0.7138 (tpp) cc_final: 0.6646 (tpp) REVERT: A 647 GLU cc_start: 0.7733 (tm-30) cc_final: 0.7276 (tm-30) REVERT: A 654 GLU cc_start: 0.7976 (tp30) cc_final: 0.7717 (tp30) REVERT: A 656 ASN cc_start: 0.7818 (t0) cc_final: 0.7388 (t0) REVERT: B 44 VAL cc_start: 0.8948 (p) cc_final: 0.8639 (m) REVERT: B 47 GLU cc_start: 0.7076 (tt0) cc_final: 0.6838 (tt0) REVERT: B 53 PHE cc_start: 0.7219 (p90) cc_final: 0.6959 (p90) REVERT: B 104 MET cc_start: 0.7795 (ttt) cc_final: 0.7538 (ttt) REVERT: B 106 GLU cc_start: 0.7292 (tp30) cc_final: 0.6905 (tp30) REVERT: B 113 ASP cc_start: 0.7456 (t0) cc_final: 0.6592 (t0) REVERT: B 234 ASN cc_start: 0.7415 (t0) cc_final: 0.7075 (t0) REVERT: B 269 GLU cc_start: 0.8115 (tt0) cc_final: 0.7876 (tt0) REVERT: B 280 ASN cc_start: 0.8146 (p0) cc_final: 0.7721 (p0) REVERT: B 293 GLU cc_start: 0.7451 (tt0) cc_final: 0.7193 (tt0) REVERT: B 432 ARG cc_start: 0.6765 (mtt90) cc_final: 0.6277 (mtt90) REVERT: B 447 SER cc_start: 0.8113 (m) cc_final: 0.7830 (p) REVERT: B 490 LYS cc_start: 0.7895 (ttpt) cc_final: 0.7692 (ttpt) REVERT: B 500 ARG cc_start: 0.6550 (mtp180) cc_final: 0.6259 (mtt-85) REVERT: B 535 MET cc_start: 0.7152 (tpp) cc_final: 0.6712 (tpp) REVERT: B 656 ASN cc_start: 0.7635 (t0) cc_final: 0.7291 (t0) REVERT: B 657 GLU cc_start: 0.7551 (tp30) cc_final: 0.6951 (tp30) REVERT: C 47 GLU cc_start: 0.7144 (tt0) cc_final: 0.6918 (tt0) REVERT: C 53 PHE cc_start: 0.7332 (p90) cc_final: 0.7082 (p90) REVERT: C 92 ASN cc_start: 0.7630 (p0) cc_final: 0.7355 (p0) REVERT: C 93 PHE cc_start: 0.7673 (m-80) cc_final: 0.7313 (m-10) REVERT: C 106 GLU cc_start: 0.7340 (tp30) cc_final: 0.7066 (tp30) REVERT: C 166 LYS cc_start: 0.7833 (mmmt) cc_final: 0.7485 (mmmt) REVERT: C 171 TYR cc_start: 0.7899 (p90) cc_final: 0.7437 (p90) REVERT: C 300 ASN cc_start: 0.7823 (p0) cc_final: 0.7532 (p0) REVERT: C 321 ASP cc_start: 0.7639 (t0) cc_final: 0.7381 (t70) REVERT: C 395 TYR cc_start: 0.7440 (t80) cc_final: 0.7218 (t80) REVERT: C 414 ILE cc_start: 0.8420 (tp) cc_final: 0.8190 (tp) REVERT: C 427 TRP cc_start: 0.7709 (m-90) cc_final: 0.7247 (m-10) REVERT: C 447 SER cc_start: 0.8240 (m) cc_final: 0.8033 (p) REVERT: C 482 GLU cc_start: 0.7502 (mm-30) cc_final: 0.7163 (mm-30) REVERT: C 487 LYS cc_start: 0.8038 (tttt) cc_final: 0.7507 (tttt) REVERT: C 577 GLN cc_start: 0.7252 (tm-30) cc_final: 0.6890 (tm-30) REVERT: C 634 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7366 (tt0) REVERT: C 647 GLU cc_start: 0.7668 (tm-30) cc_final: 0.7453 (tp30) REVERT: C 656 ASN cc_start: 0.7858 (t0) cc_final: 0.7476 (t0) REVERT: C 657 GLU cc_start: 0.7674 (tp30) cc_final: 0.6934 (tp30) outliers start: 64 outliers final: 26 residues processed: 460 average time/residue: 0.2952 time to fit residues: 189.1076 Evaluate side-chains 437 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 410 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LYS Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 616 ASN 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 88 ASN Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 434 MET 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: 0.7980 chunk 114 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 153 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 145 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 105 HIS ** B 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 ASN B 363 GLN B 374 HIS C 72 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 14448 Z= 0.345 Angle : 0.666 9.229 19632 Z= 0.346 Chirality : 0.050 0.294 2418 Planarity : 0.005 0.063 2421 Dihedral : 8.187 56.918 3126 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 4.67 % Allowed : 16.87 % Favored : 78.47 % 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: -0.19 (0.20), residues: 1656 helix: 0.98 (0.27), residues: 372 sheet: 1.59 (0.28), residues: 303 loop : -1.20 (0.18), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 35 HIS 0.009 0.002 HIS B 216 PHE 0.026 0.002 PHE C 53 TYR 0.019 0.002 TYR A 435 ARG 0.009 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 505 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 435 time to evaluate : 1.648 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 69 TRP cc_start: 0.7178 (m-90) cc_final: 0.6575 (m-90) REVERT: A 91 GLU cc_start: 0.6869 (mm-30) cc_final: 0.6584 (mm-30) REVERT: A 104 MET cc_start: 0.8121 (ttt) cc_final: 0.7889 (ttt) REVERT: A 117 LYS cc_start: 0.8527 (ttmm) cc_final: 0.8064 (ttmm) REVERT: A 150 GLU cc_start: 0.7410 (tp30) cc_final: 0.6963 (tp30) REVERT: A 166 LYS cc_start: 0.7802 (mmmt) cc_final: 0.7488 (mmmt) REVERT: A 271 VAL cc_start: 0.8278 (OUTLIER) cc_final: 0.8010 (p) REVERT: A 321 ASP cc_start: 0.7419 (t0) cc_final: 0.7088 (t70) REVERT: A 420 ILE cc_start: 0.8488 (mt) cc_final: 0.8189 (mm) REVERT: A 468 PHE cc_start: 0.7926 (m-80) cc_final: 0.7622 (m-10) REVERT: A 482 GLU cc_start: 0.7479 (mm-30) cc_final: 0.7157 (mm-30) REVERT: A 535 MET cc_start: 0.7106 (tpp) cc_final: 0.6688 (tpp) REVERT: A 635 ILE cc_start: 0.8474 (tp) cc_final: 0.8148 (tt) REVERT: A 647 GLU cc_start: 0.7770 (tm-30) cc_final: 0.7288 (tm-30) REVERT: A 654 GLU cc_start: 0.7976 (tp30) cc_final: 0.7694 (tp30) REVERT: A 656 ASN cc_start: 0.7849 (t0) cc_final: 0.7467 (t0) REVERT: B 35 TRP cc_start: 0.7850 (m-10) cc_final: 0.7622 (m-10) REVERT: B 44 VAL cc_start: 0.9025 (p) cc_final: 0.8734 (m) REVERT: B 47 GLU cc_start: 0.7117 (tt0) cc_final: 0.6785 (tt0) REVERT: B 53 PHE cc_start: 0.7207 (p90) cc_final: 0.6979 (p90) REVERT: B 100 MET cc_start: 0.8056 (mtm) cc_final: 0.7856 (mtm) REVERT: B 106 GLU cc_start: 0.7306 (tp30) cc_final: 0.6929 (tp30) REVERT: B 113 ASP cc_start: 0.7321 (t0) cc_final: 0.6460 (t0) REVERT: B 205 CYS cc_start: 0.5898 (m) cc_final: 0.5624 (m) REVERT: B 234 ASN cc_start: 0.7486 (t0) cc_final: 0.7136 (t0) REVERT: B 245 VAL cc_start: 0.8673 (t) cc_final: 0.8405 (p) REVERT: B 268 LYS cc_start: 0.8563 (pptt) cc_final: 0.8197 (pptt) REVERT: B 280 ASN cc_start: 0.8154 (p0) cc_final: 0.7716 (p0) REVERT: B 321 ASP cc_start: 0.7518 (t0) cc_final: 0.7174 (t70) REVERT: B 432 ARG cc_start: 0.6811 (mtt90) cc_final: 0.6257 (mtt90) REVERT: B 490 LYS cc_start: 0.7862 (ttpt) cc_final: 0.7634 (ttpt) REVERT: B 500 ARG cc_start: 0.6786 (mtp180) cc_final: 0.6505 (mtt-85) REVERT: B 530 MET cc_start: 0.8901 (mmm) cc_final: 0.8190 (tpt) REVERT: B 535 MET cc_start: 0.7106 (tpp) cc_final: 0.6812 (tpp) REVERT: B 622 ILE cc_start: 0.8539 (mm) cc_final: 0.8228 (mm) REVERT: B 656 ASN cc_start: 0.7737 (t0) cc_final: 0.7440 (t0) REVERT: B 657 GLU cc_start: 0.7540 (tp30) cc_final: 0.6964 (tp30) REVERT: C 47 GLU cc_start: 0.7177 (tt0) cc_final: 0.6946 (tt0) REVERT: C 53 PHE cc_start: 0.7257 (p90) cc_final: 0.6892 (p90) REVERT: C 72 HIS cc_start: 0.6555 (OUTLIER) cc_final: 0.6245 (t-90) REVERT: C 92 ASN cc_start: 0.7624 (p0) cc_final: 0.7351 (p0) REVERT: C 93 PHE cc_start: 0.7738 (m-80) cc_final: 0.7538 (m-10) REVERT: C 96 TRP cc_start: 0.8178 (m100) cc_final: 0.7067 (m100) REVERT: C 106 GLU cc_start: 0.7381 (tp30) cc_final: 0.7091 (tp30) REVERT: C 166 LYS cc_start: 0.7892 (mmmt) cc_final: 0.7503 (mmmt) REVERT: C 171 TYR cc_start: 0.7892 (p90) cc_final: 0.7426 (p90) REVERT: C 321 ASP cc_start: 0.7635 (t0) cc_final: 0.7360 (t70) REVERT: C 414 ILE cc_start: 0.8461 (tp) cc_final: 0.8253 (tp) REVERT: C 417 GLN cc_start: 0.7980 (OUTLIER) cc_final: 0.7403 (mt0) REVERT: C 424 ILE cc_start: 0.8026 (pp) cc_final: 0.7820 (pp) REVERT: C 427 TRP cc_start: 0.7685 (m-90) cc_final: 0.7230 (m-10) REVERT: C 447 SER cc_start: 0.8162 (m) cc_final: 0.7856 (p) REVERT: C 475 MET cc_start: 0.7920 (tpp) cc_final: 0.7648 (tpp) REVERT: C 482 GLU cc_start: 0.7525 (mm-30) cc_final: 0.7170 (mm-30) REVERT: C 577 GLN cc_start: 0.7352 (tm-30) cc_final: 0.6996 (tm-30) REVERT: C 634 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7410 (mt-10) REVERT: C 647 GLU cc_start: 0.7689 (tm-30) cc_final: 0.7454 (tp30) REVERT: C 656 ASN cc_start: 0.7891 (t0) cc_final: 0.7548 (t0) REVERT: C 657 GLU cc_start: 0.7664 (tp30) cc_final: 0.6943 (tp30) outliers start: 70 outliers final: 44 residues processed: 473 average time/residue: 0.2904 time to fit residues: 192.0320 Evaluate side-chains 460 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 413 time to evaluate : 1.671 ------------------------------------------------------------------------------- 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 271 VAL Chi-restraints excluded: chain A residue 328 GLN Chi-restraints excluded: chain A residue 417 GLN Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain B residue 78 ASP 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 202 THR Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 344 LYS Chi-restraints excluded: chain B residue 417 GLN Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 78 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 274 SER Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 417 GLN Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 576 LEU Chi-restraints excluded: chain C residue 626 MET Chi-restraints excluded: chain C residue 628 TRP Chi-restraints excluded: chain C residue 629 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 120 optimal weight: 0.0670 chunk 67 optimal weight: 0.9980 chunk 138 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 82 optimal weight: 0.0980 chunk 145 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 overall best weight: 0.8320 ------------------------------------------------------------------------------- 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 A 374 HIS B 302 ASN B 363 GLN B 374 HIS C 72 HIS C 105 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 14448 Z= 0.228 Angle : 0.613 11.427 19632 Z= 0.318 Chirality : 0.047 0.249 2418 Planarity : 0.004 0.058 2421 Dihedral : 7.843 54.902 3122 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 4.60 % Allowed : 18.07 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.20), residues: 1656 helix: 1.17 (0.27), residues: 372 sheet: 1.26 (0.27), residues: 345 loop : -1.14 (0.19), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP C 35 HIS 0.013 0.002 HIS C 72 PHE 0.023 0.002 PHE C 53 TYR 0.022 0.002 TYR C 638 ARG 0.006 0.000 ARG A 273 *********************** 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 508 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 439 time to evaluate : 1.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8241 (pttm) REVERT: A 69 TRP cc_start: 0.7091 (m-90) cc_final: 0.6647 (m-90) REVERT: A 91 GLU cc_start: 0.6813 (mm-30) cc_final: 0.6518 (mm-30) REVERT: A 117 LYS cc_start: 0.8538 (ttmm) cc_final: 0.8057 (ttmm) REVERT: A 150 GLU cc_start: 0.7395 (tp30) cc_final: 0.6986 (tp30) REVERT: A 166 LYS cc_start: 0.7749 (mmmt) cc_final: 0.7411 (mmmt) REVERT: A 202 THR cc_start: 0.7982 (p) cc_final: 0.7723 (p) REVERT: A 321 ASP cc_start: 0.7396 (t0) cc_final: 0.7092 (t70) REVERT: A 420 ILE cc_start: 0.8394 (mt) cc_final: 0.8122 (mm) REVERT: A 468 PHE cc_start: 0.7938 (m-80) cc_final: 0.7638 (m-10) REVERT: A 482 GLU cc_start: 0.7420 (mm-30) cc_final: 0.7083 (mm-30) REVERT: A 535 MET cc_start: 0.7088 (tpp) cc_final: 0.6787 (tpp) REVERT: A 635 ILE cc_start: 0.8402 (tp) cc_final: 0.7983 (tt) REVERT: A 647 GLU cc_start: 0.7740 (tm-30) cc_final: 0.7282 (tm-30) REVERT: A 654 GLU cc_start: 0.7964 (tp30) cc_final: 0.7670 (tp30) REVERT: A 656 ASN cc_start: 0.7851 (t0) cc_final: 0.7462 (t0) REVERT: B 35 TRP cc_start: 0.7771 (m-90) cc_final: 0.7568 (m-10) REVERT: B 44 VAL cc_start: 0.9021 (p) cc_final: 0.8737 (m) REVERT: B 47 GLU cc_start: 0.7038 (tt0) cc_final: 0.6720 (tt0) REVERT: B 53 PHE cc_start: 0.7087 (p90) cc_final: 0.6875 (p90) REVERT: B 106 GLU cc_start: 0.7309 (tp30) cc_final: 0.6937 (tp30) REVERT: B 113 ASP cc_start: 0.7364 (t0) cc_final: 0.6379 (t70) REVERT: B 150 GLU cc_start: 0.7630 (tp30) cc_final: 0.7286 (tp30) REVERT: B 205 CYS cc_start: 0.5858 (m) cc_final: 0.5592 (m) REVERT: B 234 ASN cc_start: 0.7470 (t0) cc_final: 0.7141 (t0) REVERT: B 268 LYS cc_start: 0.8504 (pptt) cc_final: 0.8159 (pptt) REVERT: B 280 ASN cc_start: 0.8138 (p0) cc_final: 0.7689 (p0) REVERT: B 293 GLU cc_start: 0.7832 (mt-10) cc_final: 0.7627 (tt0) REVERT: B 321 ASP cc_start: 0.7492 (t0) cc_final: 0.7157 (t70) REVERT: B 417 GLN cc_start: 0.7868 (pt0) cc_final: 0.7590 (mt0) REVERT: B 432 ARG cc_start: 0.6763 (mtt90) cc_final: 0.6291 (mtt90) REVERT: B 490 LYS cc_start: 0.7890 (ttpt) cc_final: 0.7667 (ttpt) REVERT: B 535 MET cc_start: 0.7074 (tpp) cc_final: 0.6843 (tpp) REVERT: B 622 ILE cc_start: 0.8562 (mm) cc_final: 0.8227 (mm) REVERT: B 656 ASN cc_start: 0.7715 (t0) cc_final: 0.7423 (t0) REVERT: B 657 GLU cc_start: 0.7536 (tp30) cc_final: 0.6955 (tp30) REVERT: C 47 GLU cc_start: 0.7135 (tt0) cc_final: 0.6881 (tt0) REVERT: C 53 PHE cc_start: 0.7106 (p90) cc_final: 0.6789 (p90) REVERT: C 92 ASN cc_start: 0.7653 (p0) cc_final: 0.7430 (p0) REVERT: C 93 PHE cc_start: 0.7649 (m-80) cc_final: 0.7365 (m-10) REVERT: C 106 GLU cc_start: 0.7381 (tp30) cc_final: 0.7107 (tp30) REVERT: C 153 LYS cc_start: 0.7677 (mmtt) cc_final: 0.7387 (mmtm) REVERT: C 166 LYS cc_start: 0.7877 (mmmt) cc_final: 0.7478 (mmmt) REVERT: C 171 TYR cc_start: 0.7866 (p90) cc_final: 0.7407 (p90) REVERT: C 202 THR cc_start: 0.8162 (p) cc_final: 0.7902 (p) REVERT: C 321 ASP cc_start: 0.7639 (t0) cc_final: 0.7330 (t70) REVERT: C 414 ILE cc_start: 0.8477 (tp) cc_final: 0.8078 (tt) REVERT: C 417 GLN cc_start: 0.7896 (OUTLIER) cc_final: 0.7500 (mt0) REVERT: C 427 TRP cc_start: 0.7693 (m-90) cc_final: 0.7142 (m-10) REVERT: C 447 SER cc_start: 0.8143 (m) cc_final: 0.7881 (p) REVERT: C 482 GLU cc_start: 0.7467 (mm-30) cc_final: 0.7102 (mm-30) REVERT: C 529 THR cc_start: 0.7992 (m) cc_final: 0.7748 (m) REVERT: C 530 MET cc_start: 0.8814 (mmm) cc_final: 0.8506 (mmm) REVERT: C 577 GLN cc_start: 0.7306 (tm-30) cc_final: 0.6903 (tm-30) REVERT: C 617 ARG cc_start: 0.7707 (mtt180) cc_final: 0.7344 (mtt180) REVERT: C 647 GLU cc_start: 0.7665 (tm-30) cc_final: 0.7431 (tp30) REVERT: C 656 ASN cc_start: 0.7882 (t0) cc_final: 0.7547 (t0) REVERT: C 657 GLU cc_start: 0.7654 (tp30) cc_final: 0.6945 (tp30) outliers start: 69 outliers final: 47 residues processed: 481 average time/residue: 0.2895 time to fit residues: 194.5543 Evaluate side-chains 479 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 430 time to evaluate : 1.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LYS Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 328 GLN Chi-restraints excluded: chain A residue 417 GLN Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 629 LEU 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 78 ASP 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 202 THR 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 374 HIS Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 119 CYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 417 GLN Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 576 LEU Chi-restraints excluded: chain C residue 626 MET Chi-restraints excluded: chain C residue 628 TRP Chi-restraints excluded: chain C residue 629 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 3.9990 chunk 146 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 162 optimal weight: 0.9980 chunk 134 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 53 optimal weight: 0.5980 chunk 85 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 A 374 HIS B 302 ASN B 363 GLN C 72 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 14448 Z= 0.208 Angle : 0.605 13.776 19632 Z= 0.311 Chirality : 0.046 0.234 2418 Planarity : 0.004 0.075 2421 Dihedral : 7.729 54.644 3122 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 5.27 % Allowed : 18.73 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.20), residues: 1656 helix: 1.30 (0.27), residues: 375 sheet: 1.27 (0.27), residues: 345 loop : -1.20 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP C 35 HIS 0.021 0.002 HIS B 374 PHE 0.021 0.002 PHE C 53 TYR 0.023 0.002 TYR C 638 ARG 0.009 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 514 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 435 time to evaluate : 1.755 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: symmetry clash REVERT: A 49 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.8092 (pttm) REVERT: A 69 TRP cc_start: 0.7021 (m-90) cc_final: 0.6683 (m-90) REVERT: A 91 GLU cc_start: 0.6789 (mm-30) cc_final: 0.6455 (mm-30) REVERT: A 99 ASP cc_start: 0.7911 (m-30) cc_final: 0.7638 (m-30) REVERT: A 104 MET cc_start: 0.8124 (ttt) cc_final: 0.7871 (ttt) REVERT: A 136 VAL cc_start: 0.7498 (OUTLIER) cc_final: 0.7148 (p) REVERT: A 150 GLU cc_start: 0.7390 (tp30) cc_final: 0.6958 (tp30) REVERT: A 166 LYS cc_start: 0.7738 (mmmt) cc_final: 0.7398 (mmmt) REVERT: A 258 GLN cc_start: 0.8029 (mt0) cc_final: 0.7654 (mt0) REVERT: A 321 ASP cc_start: 0.7388 (t0) cc_final: 0.7099 (t70) REVERT: A 344 LYS cc_start: 0.8093 (OUTLIER) cc_final: 0.7877 (ttmm) REVERT: A 420 ILE cc_start: 0.8395 (mt) cc_final: 0.8121 (mm) REVERT: A 482 GLU cc_start: 0.7333 (mm-30) cc_final: 0.6975 (mm-30) REVERT: A 535 MET cc_start: 0.7172 (tpp) cc_final: 0.6908 (tpp) REVERT: A 631 TRP cc_start: 0.8045 (t-100) cc_final: 0.7320 (t-100) REVERT: A 635 ILE cc_start: 0.8336 (tp) cc_final: 0.7910 (tt) REVERT: A 647 GLU cc_start: 0.7733 (tm-30) cc_final: 0.7271 (tm-30) REVERT: A 654 GLU cc_start: 0.7988 (tp30) cc_final: 0.7723 (tp30) REVERT: A 656 ASN cc_start: 0.7856 (t0) cc_final: 0.7467 (t0) REVERT: B 44 VAL cc_start: 0.9014 (p) cc_final: 0.8746 (m) REVERT: B 47 GLU cc_start: 0.7019 (tt0) cc_final: 0.6705 (tt0) REVERT: B 53 PHE cc_start: 0.7051 (p90) cc_final: 0.6832 (p90) REVERT: B 69 TRP cc_start: 0.6974 (m-90) cc_final: 0.6386 (m-90) REVERT: B 82 GLN cc_start: 0.7421 (OUTLIER) cc_final: 0.7030 (mp10) REVERT: B 106 GLU cc_start: 0.7311 (tp30) cc_final: 0.6958 (tp30) REVERT: B 113 ASP cc_start: 0.7369 (t0) cc_final: 0.6432 (t0) REVERT: B 136 VAL cc_start: 0.7463 (OUTLIER) cc_final: 0.7193 (p) REVERT: B 150 GLU cc_start: 0.7616 (tp30) cc_final: 0.7260 (tp30) REVERT: B 205 CYS cc_start: 0.5856 (m) cc_final: 0.5608 (m) REVERT: B 234 ASN cc_start: 0.7479 (t0) cc_final: 0.7164 (t0) REVERT: B 268 LYS cc_start: 0.8493 (pptt) cc_final: 0.8134 (pptt) REVERT: B 280 ASN cc_start: 0.8128 (p0) cc_final: 0.7685 (p0) REVERT: B 321 ASP cc_start: 0.7520 (t0) cc_final: 0.7208 (t70) REVERT: B 417 GLN cc_start: 0.7832 (OUTLIER) cc_final: 0.7570 (mt0) REVERT: B 432 ARG cc_start: 0.6767 (mtt90) cc_final: 0.6222 (mtt90) REVERT: B 490 LYS cc_start: 0.7896 (ttpt) cc_final: 0.7667 (ttpt) REVERT: B 500 ARG cc_start: 0.6528 (OUTLIER) cc_final: 0.5951 (mtp-110) REVERT: B 530 MET cc_start: 0.8910 (mmm) cc_final: 0.8576 (tpp) REVERT: B 535 MET cc_start: 0.7091 (tpp) cc_final: 0.6865 (tpp) REVERT: B 622 ILE cc_start: 0.8533 (mm) cc_final: 0.8264 (mt) REVERT: B 656 ASN cc_start: 0.7729 (t0) cc_final: 0.7440 (t0) REVERT: B 657 GLU cc_start: 0.7521 (tp30) cc_final: 0.6975 (tp30) REVERT: C 47 GLU cc_start: 0.7119 (tt0) cc_final: 0.6896 (tt0) REVERT: C 53 PHE cc_start: 0.7113 (p90) cc_final: 0.6791 (p90) REVERT: C 92 ASN cc_start: 0.7670 (p0) cc_final: 0.7430 (p0) REVERT: C 93 PHE cc_start: 0.7598 (m-80) cc_final: 0.7371 (m-10) REVERT: C 106 GLU cc_start: 0.7384 (tp30) cc_final: 0.7116 (tp30) REVERT: C 166 LYS cc_start: 0.7871 (mmmt) cc_final: 0.7482 (mmmt) REVERT: C 171 TYR cc_start: 0.7859 (p90) cc_final: 0.7382 (p90) REVERT: C 202 THR cc_start: 0.8226 (p) cc_final: 0.8008 (p) REVERT: C 267 GLU cc_start: 0.7119 (tp30) cc_final: 0.6888 (tp30) REVERT: C 321 ASP cc_start: 0.7634 (t0) cc_final: 0.7338 (t70) REVERT: C 414 ILE cc_start: 0.8497 (tp) cc_final: 0.8102 (tt) REVERT: C 417 GLN cc_start: 0.7882 (OUTLIER) cc_final: 0.7529 (mt0) REVERT: C 427 TRP cc_start: 0.7735 (m-90) cc_final: 0.7048 (m-10) REVERT: C 447 SER cc_start: 0.8114 (m) cc_final: 0.7865 (p) REVERT: C 482 GLU cc_start: 0.7451 (mm-30) cc_final: 0.7076 (mm-30) REVERT: C 529 THR cc_start: 0.8125 (m) cc_final: 0.7880 (m) REVERT: C 530 MET cc_start: 0.8817 (mmm) cc_final: 0.8490 (mmm) REVERT: C 617 ARG cc_start: 0.7761 (mtt180) cc_final: 0.7328 (mtt180) REVERT: C 647 GLU cc_start: 0.7646 (tm-30) cc_final: 0.7399 (tp30) REVERT: C 656 ASN cc_start: 0.7872 (t0) cc_final: 0.7538 (t0) REVERT: C 657 GLU cc_start: 0.7701 (tp30) cc_final: 0.7011 (tp30) outliers start: 79 outliers final: 55 residues processed: 480 average time/residue: 0.2851 time to fit residues: 192.1877 Evaluate side-chains 478 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 415 time to evaluate : 1.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LYS Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 136 VAL 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 344 LYS Chi-restraints excluded: chain A residue 417 GLN Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 82 GLN Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 297 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 500 ARG Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 119 CYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 395 TYR Chi-restraints excluded: chain C residue 417 GLN Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 576 LEU Chi-restraints excluded: chain C residue 626 MET Chi-restraints excluded: chain C residue 628 TRP Chi-restraints excluded: chain C residue 629 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 0.0020 chunk 18 optimal weight: 3.9990 chunk 92 optimal weight: 0.5980 chunk 118 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 136 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 161 optimal weight: 0.6980 chunk 101 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.5788 ------------------------------------------------------------------------------- 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 A 374 HIS B 302 ASN B 363 GLN C 72 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 14448 Z= 0.180 Angle : 0.578 12.114 19632 Z= 0.298 Chirality : 0.045 0.226 2418 Planarity : 0.004 0.064 2421 Dihedral : 7.543 54.499 3122 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 5.27 % Allowed : 19.87 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.20), residues: 1656 helix: 1.44 (0.27), residues: 378 sheet: 1.48 (0.27), residues: 339 loop : -1.26 (0.19), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP C 35 HIS 0.006 0.001 HIS B 374 PHE 0.019 0.001 PHE C 53 TYR 0.023 0.001 TYR C 638 ARG 0.007 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 511 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 432 time to evaluate : 1.653 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: symmetry clash REVERT: A 49 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.8208 (pttt) REVERT: A 69 TRP cc_start: 0.6977 (m-90) cc_final: 0.6723 (m-90) REVERT: A 91 GLU cc_start: 0.6785 (mm-30) cc_final: 0.6459 (mm-30) REVERT: A 117 LYS cc_start: 0.8477 (ttmm) cc_final: 0.8034 (ttmm) REVERT: A 136 VAL cc_start: 0.7463 (OUTLIER) cc_final: 0.7129 (p) REVERT: A 150 GLU cc_start: 0.7415 (tp30) cc_final: 0.6932 (tp30) REVERT: A 166 LYS cc_start: 0.7727 (mmmt) cc_final: 0.7401 (mmmt) REVERT: A 242 VAL cc_start: 0.8665 (t) cc_final: 0.8419 (m) REVERT: A 245 VAL cc_start: 0.8666 (t) cc_final: 0.8291 (p) REVERT: A 246 GLN cc_start: 0.7818 (tp40) cc_final: 0.7422 (tp40) REVERT: A 417 GLN cc_start: 0.7863 (OUTLIER) cc_final: 0.7245 (mt0) REVERT: A 420 ILE cc_start: 0.8403 (mt) cc_final: 0.8133 (mm) REVERT: A 482 GLU cc_start: 0.7287 (mm-30) cc_final: 0.6947 (mm-30) REVERT: A 535 MET cc_start: 0.7152 (tpp) cc_final: 0.6935 (tpp) REVERT: A 631 TRP cc_start: 0.8033 (t-100) cc_final: 0.7402 (t-100) REVERT: A 635 ILE cc_start: 0.8289 (tp) cc_final: 0.7846 (tt) REVERT: A 647 GLU cc_start: 0.7724 (tm-30) cc_final: 0.7265 (tm-30) REVERT: A 654 GLU cc_start: 0.7995 (tp30) cc_final: 0.7703 (tp30) REVERT: A 656 ASN cc_start: 0.7868 (t0) cc_final: 0.7487 (t0) REVERT: B 44 VAL cc_start: 0.9010 (p) cc_final: 0.8765 (m) REVERT: B 47 GLU cc_start: 0.7007 (tt0) cc_final: 0.6702 (tt0) REVERT: B 69 TRP cc_start: 0.6948 (m-90) cc_final: 0.6333 (m-90) REVERT: B 82 GLN cc_start: 0.7410 (OUTLIER) cc_final: 0.7010 (mp10) REVERT: B 106 GLU cc_start: 0.7328 (tp30) cc_final: 0.6965 (tp30) REVERT: B 113 ASP cc_start: 0.7339 (t0) cc_final: 0.6414 (t0) REVERT: B 136 VAL cc_start: 0.7479 (OUTLIER) cc_final: 0.7097 (p) REVERT: B 150 GLU cc_start: 0.7599 (tp30) cc_final: 0.7193 (tp30) REVERT: B 234 ASN cc_start: 0.7503 (t0) cc_final: 0.7183 (t0) REVERT: B 268 LYS cc_start: 0.8466 (pptt) cc_final: 0.8105 (pptt) REVERT: B 272 ILE cc_start: 0.8480 (mt) cc_final: 0.8085 (mm) REVERT: B 280 ASN cc_start: 0.8103 (p0) cc_final: 0.7683 (p0) REVERT: B 321 ASP cc_start: 0.7506 (t0) cc_final: 0.7123 (t70) REVERT: B 377 ASN cc_start: 0.8187 (p0) cc_final: 0.7966 (p0) REVERT: B 417 GLN cc_start: 0.7832 (OUTLIER) cc_final: 0.7605 (mt0) REVERT: B 432 ARG cc_start: 0.6689 (mtt90) cc_final: 0.6119 (mtt90) REVERT: B 464 GLU cc_start: 0.7881 (mp0) cc_final: 0.7529 (pm20) REVERT: B 490 LYS cc_start: 0.7905 (ttpt) cc_final: 0.7693 (ttpt) REVERT: B 500 ARG cc_start: 0.6677 (OUTLIER) cc_final: 0.6110 (mtp-110) REVERT: B 530 MET cc_start: 0.8915 (mmm) cc_final: 0.8565 (tpp) REVERT: B 535 MET cc_start: 0.7098 (tpp) cc_final: 0.6895 (tpp) REVERT: B 622 ILE cc_start: 0.8530 (mm) cc_final: 0.8291 (mt) REVERT: B 656 ASN cc_start: 0.7745 (t0) cc_final: 0.7462 (t0) REVERT: B 657 GLU cc_start: 0.7539 (tp30) cc_final: 0.6994 (tp30) REVERT: C 47 GLU cc_start: 0.7112 (tt0) cc_final: 0.6898 (tt0) REVERT: C 53 PHE cc_start: 0.7084 (p90) cc_final: 0.6740 (p90) REVERT: C 72 HIS cc_start: 0.6633 (OUTLIER) cc_final: 0.6371 (t-90) REVERT: C 92 ASN cc_start: 0.7690 (p0) cc_final: 0.7446 (p0) REVERT: C 93 PHE cc_start: 0.7518 (m-80) cc_final: 0.7285 (m-10) REVERT: C 103 GLN cc_start: 0.7786 (tp40) cc_final: 0.7242 (tm-30) REVERT: C 106 GLU cc_start: 0.7391 (tp30) cc_final: 0.7148 (tp30) REVERT: C 121 LYS cc_start: 0.8576 (mttt) cc_final: 0.8184 (mttm) REVERT: C 136 VAL cc_start: 0.7300 (OUTLIER) cc_final: 0.6844 (p) REVERT: C 166 LYS cc_start: 0.7886 (mmmt) cc_final: 0.7505 (mmmt) REVERT: C 171 TYR cc_start: 0.7868 (p90) cc_final: 0.7412 (p90) REVERT: C 202 THR cc_start: 0.8189 (p) cc_final: 0.7974 (p) REVERT: C 251 ILE cc_start: 0.8526 (mt) cc_final: 0.8252 (mm) REVERT: C 308 ARG cc_start: 0.7638 (mmt90) cc_final: 0.7400 (tpt-90) REVERT: C 321 ASP cc_start: 0.7621 (t0) cc_final: 0.7319 (t70) REVERT: C 414 ILE cc_start: 0.8495 (tp) cc_final: 0.8095 (tt) REVERT: C 417 GLN cc_start: 0.7886 (OUTLIER) cc_final: 0.7557 (mt0) REVERT: C 427 TRP cc_start: 0.7765 (m-90) cc_final: 0.6952 (m-10) REVERT: C 447 SER cc_start: 0.8096 (m) cc_final: 0.7883 (p) REVERT: C 482 GLU cc_start: 0.7425 (mm-30) cc_final: 0.6960 (mm-30) REVERT: C 529 THR cc_start: 0.8092 (m) cc_final: 0.7887 (m) REVERT: C 530 MET cc_start: 0.8803 (mmm) cc_final: 0.8506 (mmm) REVERT: C 617 ARG cc_start: 0.7719 (mtt180) cc_final: 0.6871 (mtm-85) REVERT: C 634 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7523 (mt-10) REVERT: C 647 GLU cc_start: 0.7623 (tm-30) cc_final: 0.7402 (tp30) REVERT: C 656 ASN cc_start: 0.7833 (t0) cc_final: 0.7495 (t0) REVERT: C 657 GLU cc_start: 0.7691 (tp30) cc_final: 0.6995 (tp30) outliers start: 79 outliers final: 45 residues processed: 474 average time/residue: 0.2742 time to fit residues: 184.1098 Evaluate side-chains 485 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 430 time to evaluate : 1.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LYS Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 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 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 448 ASN Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain B residue 82 GLN Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 417 GLN Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 500 ARG Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 119 CYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 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 368 ASP Chi-restraints excluded: chain C residue 417 GLN Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 576 LEU Chi-restraints excluded: chain C residue 626 MET Chi-restraints excluded: chain C residue 628 TRP Chi-restraints excluded: chain C residue 629 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 96 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 102 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 127 optimal weight: 4.9990 chunk 147 optimal weight: 2.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- 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 A 374 HIS B 302 ASN B 363 GLN C 72 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.3752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 14448 Z= 0.316 Angle : 0.646 14.101 19632 Z= 0.333 Chirality : 0.048 0.256 2418 Planarity : 0.005 0.067 2421 Dihedral : 7.684 55.188 3122 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 4.40 % Allowed : 20.93 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.20), residues: 1656 helix: 1.37 (0.27), residues: 378 sheet: 1.49 (0.28), residues: 309 loop : -1.37 (0.18), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP C 35 HIS 0.020 0.002 HIS C 72 PHE 0.017 0.002 PHE C 93 TYR 0.023 0.002 TYR C 638 ARG 0.011 0.000 ARG B 273 *********************** 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 511 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 445 time to evaluate : 1.610 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 47 GLU cc_start: 0.7109 (tp30) cc_final: 0.6875 (tp30) REVERT: A 69 TRP cc_start: 0.7012 (m-90) cc_final: 0.6754 (m-90) REVERT: A 91 GLU cc_start: 0.6781 (mm-30) cc_final: 0.6416 (mm-30) REVERT: A 117 LYS cc_start: 0.8525 (ttmm) cc_final: 0.8043 (ttmm) REVERT: A 136 VAL cc_start: 0.7373 (OUTLIER) cc_final: 0.7027 (p) REVERT: A 150 GLU cc_start: 0.7427 (tp30) cc_final: 0.6906 (tp30) REVERT: A 166 LYS cc_start: 0.7780 (mmmt) cc_final: 0.7542 (mmmt) REVERT: A 246 GLN cc_start: 0.7828 (tp40) cc_final: 0.7440 (tp40) REVERT: A 258 GLN cc_start: 0.8070 (mt0) cc_final: 0.7649 (mt0) REVERT: A 482 GLU cc_start: 0.7309 (mm-30) cc_final: 0.6977 (mm-30) REVERT: A 530 MET cc_start: 0.8852 (tpt) cc_final: 0.8479 (tpp) REVERT: A 535 MET cc_start: 0.7142 (tpp) cc_final: 0.6913 (tpp) REVERT: A 631 TRP cc_start: 0.8088 (t-100) cc_final: 0.7694 (t-100) REVERT: A 635 ILE cc_start: 0.8413 (tp) cc_final: 0.7919 (tt) REVERT: A 647 GLU cc_start: 0.7772 (tm-30) cc_final: 0.7273 (tm-30) REVERT: A 654 GLU cc_start: 0.8010 (tp30) cc_final: 0.7664 (tp30) REVERT: A 656 ASN cc_start: 0.7882 (t0) cc_final: 0.7508 (t0) REVERT: B 35 TRP cc_start: 0.7889 (m-10) cc_final: 0.7302 (m-10) REVERT: B 44 VAL cc_start: 0.9039 (p) cc_final: 0.8812 (m) REVERT: B 47 GLU cc_start: 0.7056 (tt0) cc_final: 0.6741 (tt0) REVERT: B 69 TRP cc_start: 0.6917 (m-90) cc_final: 0.6462 (m-90) REVERT: B 106 GLU cc_start: 0.7335 (tp30) cc_final: 0.6962 (tp30) REVERT: B 113 ASP cc_start: 0.7337 (t0) cc_final: 0.6422 (t0) REVERT: B 136 VAL cc_start: 0.7407 (OUTLIER) cc_final: 0.7029 (p) REVERT: B 150 GLU cc_start: 0.7613 (tp30) cc_final: 0.7119 (tp30) REVERT: B 205 CYS cc_start: 0.5951 (m) cc_final: 0.5711 (m) REVERT: B 234 ASN cc_start: 0.7543 (t0) cc_final: 0.7209 (t0) REVERT: B 268 LYS cc_start: 0.8488 (pptt) cc_final: 0.8117 (pptt) REVERT: B 280 ASN cc_start: 0.8130 (p0) cc_final: 0.7798 (p0) REVERT: B 321 ASP cc_start: 0.7493 (t0) cc_final: 0.7085 (t70) REVERT: B 337 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7969 (ttmm) REVERT: B 377 ASN cc_start: 0.8192 (p0) cc_final: 0.7975 (p0) REVERT: B 432 ARG cc_start: 0.6643 (mtt90) cc_final: 0.6103 (mtt90) REVERT: B 464 GLU cc_start: 0.7943 (mp0) cc_final: 0.7555 (pm20) REVERT: B 535 MET cc_start: 0.7103 (tpp) cc_final: 0.6885 (tpp) REVERT: B 622 ILE cc_start: 0.8534 (mm) cc_final: 0.8305 (mt) REVERT: B 656 ASN cc_start: 0.7781 (t0) cc_final: 0.7494 (t0) REVERT: B 657 GLU cc_start: 0.7541 (tp30) cc_final: 0.7015 (tp30) REVERT: C 47 GLU cc_start: 0.7154 (tt0) cc_final: 0.6950 (tt0) REVERT: C 53 PHE cc_start: 0.7145 (p90) cc_final: 0.6872 (p90) REVERT: C 92 ASN cc_start: 0.7696 (p0) cc_final: 0.7417 (p0) REVERT: C 93 PHE cc_start: 0.7651 (m-80) cc_final: 0.7380 (m-10) REVERT: C 103 GLN cc_start: 0.7793 (tp40) cc_final: 0.7257 (tm-30) REVERT: C 106 GLU cc_start: 0.7397 (tp30) cc_final: 0.7164 (tp30) REVERT: C 121 LYS cc_start: 0.8600 (mttt) cc_final: 0.8196 (mttp) REVERT: C 136 VAL cc_start: 0.7264 (OUTLIER) cc_final: 0.6806 (p) REVERT: C 166 LYS cc_start: 0.7911 (mmmt) cc_final: 0.7553 (mmmt) REVERT: C 171 TYR cc_start: 0.7912 (p90) cc_final: 0.7415 (p90) REVERT: C 251 ILE cc_start: 0.8585 (mt) cc_final: 0.8290 (mm) REVERT: C 272 ILE cc_start: 0.8426 (mp) cc_final: 0.8094 (mt) REVERT: C 308 ARG cc_start: 0.7587 (mmt90) cc_final: 0.7364 (tpt-90) REVERT: C 321 ASP cc_start: 0.7613 (t0) cc_final: 0.7316 (t70) REVERT: C 414 ILE cc_start: 0.8539 (tp) cc_final: 0.8137 (tt) REVERT: C 417 GLN cc_start: 0.7918 (OUTLIER) cc_final: 0.7477 (mt0) REVERT: C 427 TRP cc_start: 0.7777 (m-90) cc_final: 0.6941 (m-10) REVERT: C 447 SER cc_start: 0.8088 (m) cc_final: 0.7877 (p) REVERT: C 529 THR cc_start: 0.8133 (m) cc_final: 0.7900 (m) REVERT: C 530 MET cc_start: 0.8795 (mmm) cc_final: 0.8511 (tpp) REVERT: C 544 LEU cc_start: 0.8004 (mt) cc_final: 0.7796 (mt) REVERT: C 577 GLN cc_start: 0.7352 (tm-30) cc_final: 0.6928 (tm-30) REVERT: C 617 ARG cc_start: 0.7665 (mtt180) cc_final: 0.6902 (mtm-85) REVERT: C 634 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7530 (mt-10) REVERT: C 647 GLU cc_start: 0.7650 (tm-30) cc_final: 0.7432 (tp30) REVERT: C 656 ASN cc_start: 0.7855 (t0) cc_final: 0.7520 (t0) REVERT: C 657 GLU cc_start: 0.7697 (tp30) cc_final: 0.7010 (tp30) outliers start: 66 outliers final: 51 residues processed: 483 average time/residue: 0.2816 time to fit residues: 193.2226 Evaluate side-chains 487 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 431 time to evaluate : 1.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 182 LEU 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 374 HIS Chi-restraints excluded: chain A residue 417 GLN Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 616 ASN 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 88 ASN Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 297 THR 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 536 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 119 CYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 267 GLU Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 395 TYR Chi-restraints excluded: chain C residue 417 GLN Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 576 LEU Chi-restraints excluded: chain C residue 626 MET Chi-restraints excluded: chain C residue 628 TRP Chi-restraints excluded: chain C residue 629 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 4.9990 chunk 141 optimal weight: 0.9980 chunk 150 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 118 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 chunk 136 optimal weight: 7.9990 chunk 142 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN A 363 GLN A 374 HIS B 302 ASN B 363 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 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 : 0.004 0.076 14448 Z= 0.269 Angle : 0.635 13.287 19632 Z= 0.327 Chirality : 0.047 0.245 2418 Planarity : 0.004 0.065 2421 Dihedral : 7.640 54.753 3122 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 4.20 % Allowed : 22.33 % Favored : 73.47 % 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: -0.17 (0.20), residues: 1656 helix: 1.37 (0.27), residues: 378 sheet: 1.12 (0.26), residues: 375 loop : -1.39 (0.19), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP C 35 HIS 0.021 0.002 HIS A 374 PHE 0.017 0.002 PHE C 53 TYR 0.023 0.002 TYR C 638 ARG 0.006 0.000 ARG B 273 *********************** 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 500 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 437 time to evaluate : 1.768 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: symmetry clash REVERT: A 69 TRP cc_start: 0.6974 (m-90) cc_final: 0.6698 (m-90) REVERT: A 91 GLU cc_start: 0.6761 (mm-30) cc_final: 0.6440 (mm-30) REVERT: A 117 LYS cc_start: 0.8539 (ttmm) cc_final: 0.8064 (ttmm) REVERT: A 136 VAL cc_start: 0.7376 (OUTLIER) cc_final: 0.6990 (p) REVERT: A 150 GLU cc_start: 0.7414 (tp30) cc_final: 0.6823 (tp30) REVERT: A 166 LYS cc_start: 0.7769 (mmmt) cc_final: 0.7558 (mmmt) REVERT: A 246 GLN cc_start: 0.7834 (tp40) cc_final: 0.7438 (tp40) REVERT: A 258 GLN cc_start: 0.8063 (mt0) cc_final: 0.7672 (mt0) REVERT: A 321 ASP cc_start: 0.7379 (t0) cc_final: 0.7091 (t70) REVERT: A 468 PHE cc_start: 0.8070 (m-80) cc_final: 0.7731 (m-10) REVERT: A 482 GLU cc_start: 0.7298 (mm-30) cc_final: 0.6970 (mm-30) REVERT: A 530 MET cc_start: 0.8807 (tpt) cc_final: 0.8455 (tpp) REVERT: A 535 MET cc_start: 0.7174 (tpp) cc_final: 0.6941 (tpp) REVERT: A 610 TRP cc_start: 0.8068 (t-100) cc_final: 0.7802 (t-100) REVERT: A 631 TRP cc_start: 0.8062 (t-100) cc_final: 0.7689 (t-100) REVERT: A 635 ILE cc_start: 0.8438 (tp) cc_final: 0.7946 (tt) REVERT: A 647 GLU cc_start: 0.7756 (tm-30) cc_final: 0.7293 (tm-30) REVERT: A 654 GLU cc_start: 0.7961 (tp30) cc_final: 0.7671 (tp30) REVERT: A 656 ASN cc_start: 0.7883 (t0) cc_final: 0.7516 (t0) REVERT: B 35 TRP cc_start: 0.7876 (m-10) cc_final: 0.7305 (m-10) REVERT: B 44 VAL cc_start: 0.9026 (p) cc_final: 0.8813 (m) REVERT: B 47 GLU cc_start: 0.7078 (tt0) cc_final: 0.6801 (tt0) REVERT: B 69 TRP cc_start: 0.6911 (m-90) cc_final: 0.6429 (m-90) REVERT: B 100 MET cc_start: 0.8045 (mtm) cc_final: 0.7803 (mtm) REVERT: B 106 GLU cc_start: 0.7326 (tp30) cc_final: 0.6954 (tp30) REVERT: B 113 ASP cc_start: 0.7344 (t0) cc_final: 0.6460 (t0) REVERT: B 136 VAL cc_start: 0.7436 (OUTLIER) cc_final: 0.7054 (p) REVERT: B 150 GLU cc_start: 0.7601 (tp30) cc_final: 0.7081 (tp30) REVERT: B 205 CYS cc_start: 0.5953 (m) cc_final: 0.5713 (m) REVERT: B 234 ASN cc_start: 0.7530 (t0) cc_final: 0.7202 (t0) REVERT: B 268 LYS cc_start: 0.8483 (pptt) cc_final: 0.8130 (pptt) REVERT: B 280 ASN cc_start: 0.8143 (p0) cc_final: 0.7797 (p0) REVERT: B 321 ASP cc_start: 0.7491 (t0) cc_final: 0.7074 (t70) REVERT: B 337 LYS cc_start: 0.8227 (OUTLIER) cc_final: 0.7938 (ttmm) REVERT: B 377 ASN cc_start: 0.8215 (p0) cc_final: 0.7979 (p0) REVERT: B 432 ARG cc_start: 0.6699 (mtt90) cc_final: 0.6154 (mtt90) REVERT: B 464 GLU cc_start: 0.7952 (mp0) cc_final: 0.7557 (pm20) REVERT: B 490 LYS cc_start: 0.7903 (ttpt) cc_final: 0.7677 (ttpt) REVERT: B 492 GLU cc_start: 0.7498 (mt-10) cc_final: 0.7162 (mt-10) REVERT: B 535 MET cc_start: 0.7054 (tpp) cc_final: 0.6852 (tpp) REVERT: B 622 ILE cc_start: 0.8522 (mm) cc_final: 0.8305 (mt) REVERT: B 645 LEU cc_start: 0.8118 (mp) cc_final: 0.7910 (mt) REVERT: B 656 ASN cc_start: 0.7786 (t0) cc_final: 0.7498 (t0) REVERT: B 657 GLU cc_start: 0.7532 (tp30) cc_final: 0.7009 (tp30) REVERT: C 47 GLU cc_start: 0.7158 (tt0) cc_final: 0.6938 (tt0) REVERT: C 53 PHE cc_start: 0.7015 (p90) cc_final: 0.6795 (p90) REVERT: C 92 ASN cc_start: 0.7698 (p0) cc_final: 0.7452 (p0) REVERT: C 93 PHE cc_start: 0.7635 (m-80) cc_final: 0.7408 (m-10) REVERT: C 103 GLN cc_start: 0.7779 (tp40) cc_final: 0.7248 (tm-30) REVERT: C 106 GLU cc_start: 0.7394 (tp30) cc_final: 0.7155 (tp30) REVERT: C 121 LYS cc_start: 0.8620 (mttt) cc_final: 0.8178 (mttp) REVERT: C 136 VAL cc_start: 0.7259 (OUTLIER) cc_final: 0.6832 (p) REVERT: C 166 LYS cc_start: 0.7965 (mmmt) cc_final: 0.7560 (mmmt) REVERT: C 171 TYR cc_start: 0.7878 (p90) cc_final: 0.7378 (p90) REVERT: C 251 ILE cc_start: 0.8532 (mt) cc_final: 0.8310 (mm) REVERT: C 321 ASP cc_start: 0.7614 (t0) cc_final: 0.7313 (t70) REVERT: C 348 GLU cc_start: 0.7450 (mm-30) cc_final: 0.7216 (mm-30) REVERT: C 414 ILE cc_start: 0.8551 (tp) cc_final: 0.8145 (tt) REVERT: C 417 GLN cc_start: 0.7887 (OUTLIER) cc_final: 0.7450 (mt0) REVERT: C 427 TRP cc_start: 0.7772 (m-90) cc_final: 0.6901 (m-10) REVERT: C 529 THR cc_start: 0.8065 (m) cc_final: 0.7833 (m) REVERT: C 530 MET cc_start: 0.8753 (mmm) cc_final: 0.8471 (mmm) REVERT: C 544 LEU cc_start: 0.8010 (mt) cc_final: 0.7802 (mt) REVERT: C 577 GLN cc_start: 0.7349 (tm-30) cc_final: 0.6901 (tm-30) REVERT: C 617 ARG cc_start: 0.7649 (mtt180) cc_final: 0.6905 (mtm-85) REVERT: C 634 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7583 (mt-10) REVERT: C 656 ASN cc_start: 0.7859 (t0) cc_final: 0.7520 (t0) REVERT: C 657 GLU cc_start: 0.7682 (tp30) cc_final: 0.7070 (tp30) outliers start: 63 outliers final: 53 residues processed: 470 average time/residue: 0.2917 time to fit residues: 194.9812 Evaluate side-chains 489 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 431 time to evaluate : 1.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 CYS 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 161 THR 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 373 THR Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 417 GLN Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 325 ASP 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 536 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 119 CYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 395 TYR Chi-restraints excluded: chain C residue 417 GLN Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 576 LEU Chi-restraints excluded: chain C residue 626 MET Chi-restraints excluded: chain C residue 628 TRP Chi-restraints excluded: chain C residue 629 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 167 optimal weight: 4.9990 chunk 154 optimal weight: 0.9980 chunk 133 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 105 optimal weight: 0.0470 chunk 141 optimal weight: 1.9990 overall best weight: 0.7880 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.3970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 14448 Z= 0.211 Angle : 0.609 12.565 19632 Z= 0.314 Chirality : 0.046 0.235 2418 Planarity : 0.004 0.063 2421 Dihedral : 7.531 54.812 3122 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.80 % Allowed : 22.80 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (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: 1.47 (0.27), residues: 378 sheet: 1.12 (0.26), residues: 375 loop : -1.37 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 35 HIS 0.019 0.002 HIS A 374 PHE 0.015 0.002 PHE C 53 TYR 0.023 0.002 TYR C 638 ARG 0.007 0.000 ARG B 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 482 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 425 time to evaluate : 1.657 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: symmetry clash REVERT: A 69 TRP cc_start: 0.6872 (m-90) cc_final: 0.6607 (m-90) REVERT: A 91 GLU cc_start: 0.6752 (mm-30) cc_final: 0.6416 (mm-30) REVERT: A 117 LYS cc_start: 0.8564 (ttmm) cc_final: 0.8093 (ttmm) REVERT: A 136 VAL cc_start: 0.7367 (OUTLIER) cc_final: 0.6971 (p) REVERT: A 150 GLU cc_start: 0.7377 (tp30) cc_final: 0.6812 (tp30) REVERT: A 166 LYS cc_start: 0.7731 (mmmt) cc_final: 0.7507 (mmmt) REVERT: A 245 VAL cc_start: 0.8631 (t) cc_final: 0.8251 (p) REVERT: A 258 GLN cc_start: 0.8042 (mt0) cc_final: 0.7672 (mt0) REVERT: A 417 GLN cc_start: 0.7867 (OUTLIER) cc_final: 0.7245 (mt0) REVERT: A 468 PHE cc_start: 0.8070 (m-80) cc_final: 0.7729 (m-10) REVERT: A 482 GLU cc_start: 0.7274 (mm-30) cc_final: 0.6938 (mm-30) REVERT: A 530 MET cc_start: 0.8745 (tpt) cc_final: 0.8385 (tpp) REVERT: A 535 MET cc_start: 0.7183 (tpp) cc_final: 0.6956 (tpp) REVERT: A 610 TRP cc_start: 0.8011 (t-100) cc_final: 0.7790 (t-100) REVERT: A 631 TRP cc_start: 0.8050 (t-100) cc_final: 0.7677 (t-100) REVERT: A 635 ILE cc_start: 0.8409 (tp) cc_final: 0.7919 (tt) REVERT: A 647 GLU cc_start: 0.7739 (tm-30) cc_final: 0.7271 (tm-30) REVERT: A 654 GLU cc_start: 0.7963 (tp30) cc_final: 0.7669 (tp30) REVERT: A 656 ASN cc_start: 0.7882 (t0) cc_final: 0.7513 (t0) REVERT: B 35 TRP cc_start: 0.7819 (m-10) cc_final: 0.7346 (m-10) REVERT: B 44 VAL cc_start: 0.9020 (p) cc_final: 0.8802 (m) REVERT: B 47 GLU cc_start: 0.7065 (tt0) cc_final: 0.6747 (tt0) REVERT: B 69 TRP cc_start: 0.6887 (m-90) cc_final: 0.6385 (m-90) REVERT: B 106 GLU cc_start: 0.7317 (tp30) cc_final: 0.6948 (tp30) REVERT: B 113 ASP cc_start: 0.7329 (t0) cc_final: 0.6471 (t0) REVERT: B 136 VAL cc_start: 0.7396 (OUTLIER) cc_final: 0.7012 (p) REVERT: B 150 GLU cc_start: 0.7550 (tp30) cc_final: 0.7006 (tp30) REVERT: B 205 CYS cc_start: 0.5876 (m) cc_final: 0.5637 (m) REVERT: B 234 ASN cc_start: 0.7520 (t0) cc_final: 0.7199 (t0) REVERT: B 268 LYS cc_start: 0.8435 (pptt) cc_final: 0.8073 (pptt) REVERT: B 280 ASN cc_start: 0.8140 (p0) cc_final: 0.7735 (p0) REVERT: B 321 ASP cc_start: 0.7474 (t0) cc_final: 0.7063 (t70) REVERT: B 337 LYS cc_start: 0.8207 (OUTLIER) cc_final: 0.7920 (ttmm) REVERT: B 377 ASN cc_start: 0.8179 (p0) cc_final: 0.7930 (p0) REVERT: B 432 ARG cc_start: 0.6696 (mtt90) cc_final: 0.6167 (mtt90) REVERT: B 464 GLU cc_start: 0.7985 (mp0) cc_final: 0.7626 (pm20) REVERT: B 535 MET cc_start: 0.7057 (tpp) cc_final: 0.6851 (tpp) REVERT: B 622 ILE cc_start: 0.8518 (mm) cc_final: 0.8298 (mt) REVERT: B 645 LEU cc_start: 0.8120 (mp) cc_final: 0.7916 (mt) REVERT: B 656 ASN cc_start: 0.7789 (t0) cc_final: 0.7501 (t0) REVERT: B 657 GLU cc_start: 0.7529 (tp30) cc_final: 0.6996 (tp30) REVERT: C 47 GLU cc_start: 0.7159 (tt0) cc_final: 0.6927 (tt0) REVERT: C 53 PHE cc_start: 0.7027 (p90) cc_final: 0.6760 (p90) REVERT: C 92 ASN cc_start: 0.7704 (p0) cc_final: 0.7456 (p0) REVERT: C 103 GLN cc_start: 0.7758 (tp40) cc_final: 0.7225 (tm-30) REVERT: C 106 GLU cc_start: 0.7379 (tp30) cc_final: 0.7162 (tp30) REVERT: C 136 VAL cc_start: 0.7246 (OUTLIER) cc_final: 0.6810 (p) REVERT: C 166 LYS cc_start: 0.7944 (mmmt) cc_final: 0.7541 (mmmt) REVERT: C 171 TYR cc_start: 0.7842 (p90) cc_final: 0.7342 (p90) REVERT: C 321 ASP cc_start: 0.7632 (t0) cc_final: 0.7310 (t70) REVERT: C 414 ILE cc_start: 0.8552 (tp) cc_final: 0.8151 (tt) REVERT: C 417 GLN cc_start: 0.7883 (OUTLIER) cc_final: 0.7513 (mt0) REVERT: C 427 TRP cc_start: 0.7764 (m-90) cc_final: 0.6904 (m-10) REVERT: C 482 GLU cc_start: 0.7327 (mm-30) cc_final: 0.6939 (mm-30) REVERT: C 529 THR cc_start: 0.8075 (m) cc_final: 0.7859 (m) REVERT: C 530 MET cc_start: 0.8749 (mmm) cc_final: 0.8498 (mmm) REVERT: C 544 LEU cc_start: 0.7999 (mt) cc_final: 0.7792 (mt) REVERT: C 577 GLN cc_start: 0.7320 (tm-30) cc_final: 0.6876 (tm-30) REVERT: C 617 ARG cc_start: 0.7659 (mtt180) cc_final: 0.6942 (mtm-85) REVERT: C 634 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7577 (mt-10) REVERT: C 656 ASN cc_start: 0.7868 (t0) cc_final: 0.7523 (t0) REVERT: C 657 GLU cc_start: 0.7706 (tp30) cc_final: 0.7094 (tp30) outliers start: 57 outliers final: 49 residues processed: 456 average time/residue: 0.2989 time to fit residues: 193.4120 Evaluate side-chains 478 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 423 time to evaluate : 1.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 CYS 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 161 THR Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 417 GLN Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 297 THR 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 536 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 119 CYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 395 TYR Chi-restraints excluded: chain C residue 417 GLN Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 576 LEU Chi-restraints excluded: chain C residue 626 MET Chi-restraints excluded: chain C residue 628 TRP Chi-restraints excluded: chain C residue 629 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 19 optimal weight: 0.0770 chunk 37 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 137 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 24 optimal weight: 0.1980 chunk 117 optimal weight: 0.6980 chunk 7 optimal weight: 0.0370 overall best weight: 0.4016 ------------------------------------------------------------------------------- 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 374 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.124332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.104249 restraints weight = 21729.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.108290 restraints weight = 12092.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.110984 restraints weight = 8094.630| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.4149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 14448 Z= 0.158 Angle : 0.571 11.057 19632 Z= 0.294 Chirality : 0.044 0.223 2418 Planarity : 0.004 0.060 2421 Dihedral : 7.273 54.805 3122 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.40 % Allowed : 23.73 % Favored : 72.87 % 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: -0.03 (0.20), residues: 1656 helix: 1.61 (0.27), residues: 378 sheet: 1.11 (0.26), residues: 375 loop : -1.30 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 614 HIS 0.008 0.001 HIS A 374 PHE 0.015 0.001 PHE C 53 TYR 0.023 0.001 TYR C 638 ARG 0.004 0.000 ARG B 273 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3781.92 seconds wall clock time: 68 minutes 55.40 seconds (4135.40 seconds total)