Starting phenix.real_space_refine on Sat Apr 13 04:21:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cn8_30418/04_2024/7cn8_30418_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cn8_30418/04_2024/7cn8_30418.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cn8_30418/04_2024/7cn8_30418.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cn8_30418/04_2024/7cn8_30418.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cn8_30418/04_2024/7cn8_30418_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cn8_30418/04_2024/7cn8_30418_neut_updated.pdb" } resolution = 2.5 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= 0.000 sd= 0.003 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 123 5.16 5 C 17586 2.51 5 N 4491 2.21 5 O 5475 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 86": "OD1" <-> "OD2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "A ARG 111": "NH1" <-> "NH2" Residue "A ARG 156": "NH1" <-> "NH2" Residue "A ARG 188": "NH1" <-> "NH2" Residue "A ARG 216": "NH1" <-> "NH2" Residue "A GLU 307": "OE1" <-> "OE2" Residue "A GLU 404": "OE1" <-> "OE2" Residue "A ARG 455": "NH1" <-> "NH2" Residue "A ARG 464": "NH1" <-> "NH2" Residue "A GLU 514": "OE1" <-> "OE2" Residue "A GLU 625": "OE1" <-> "OE2" Residue "A GLU 652": "OE1" <-> "OE2" Residue "A GLU 659": "OE1" <-> "OE2" Residue "A ARG 679": "NH1" <-> "NH2" Residue "A ARG 684": "NH1" <-> "NH2" Residue "A ARG 841": "NH1" <-> "NH2" Residue "A GLU 984": "OE1" <-> "OE2" Residue "A GLU 1025": "OE1" <-> "OE2" Residue "A ARG 1101": "NH1" <-> "NH2" Residue "B ASP 86": "OD1" <-> "OD2" Residue "B GLU 94": "OE1" <-> "OE2" Residue "B ARG 111": "NH1" <-> "NH2" Residue "B ARG 156": "NH1" <-> "NH2" Residue "B ARG 188": "NH1" <-> "NH2" Residue "B ARG 216": "NH1" <-> "NH2" Residue "B GLU 307": "OE1" <-> "OE2" Residue "B GLU 404": "OE1" <-> "OE2" Residue "B ARG 455": "NH1" <-> "NH2" Residue "B ARG 464": "NH1" <-> "NH2" Residue "B GLU 514": "OE1" <-> "OE2" Residue "B GLU 625": "OE1" <-> "OE2" Residue "B GLU 652": "OE1" <-> "OE2" Residue "B GLU 659": "OE1" <-> "OE2" Residue "B ARG 679": "NH1" <-> "NH2" Residue "B ARG 684": "NH1" <-> "NH2" Residue "B ARG 841": "NH1" <-> "NH2" Residue "B GLU 984": "OE1" <-> "OE2" Residue "B GLU 1025": "OE1" <-> "OE2" Residue "B ARG 1101": "NH1" <-> "NH2" Residue "C ASP 86": "OD1" <-> "OD2" Residue "C GLU 94": "OE1" <-> "OE2" Residue "C ARG 111": "NH1" <-> "NH2" Residue "C GLU 130": "OE1" <-> "OE2" Residue "C ARG 156": "NH1" <-> "NH2" Residue "C ARG 188": "NH1" <-> "NH2" Residue "C ARG 216": "NH1" <-> "NH2" Residue "C GLU 307": "OE1" <-> "OE2" Residue "C GLU 404": "OE1" <-> "OE2" Residue "C ARG 455": "NH1" <-> "NH2" Residue "C ARG 464": "NH1" <-> "NH2" Residue "C GLU 514": "OE1" <-> "OE2" Residue "C GLU 625": "OE1" <-> "OE2" Residue "C GLU 652": "OE1" <-> "OE2" Residue "C GLU 659": "OE1" <-> "OE2" Residue "C ARG 679": "NH1" <-> "NH2" Residue "C ARG 684": "NH1" <-> "NH2" Residue "C ARG 841": "NH1" <-> "NH2" Residue "C GLU 984": "OE1" <-> "OE2" Residue "C GLU 1025": "OE1" <-> "OE2" Residue "C ARG 1101": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 27675 Number of models: 1 Model: "" Number of chains: 39 Chain: "A" Number of atoms: 8771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1125, 8771 Classifications: {'peptide': 1125} Link IDs: {'PTRANS': 54, 'TRANS': 1070} Chain: "B" Number of atoms: 8771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1125, 8771 Classifications: {'peptide': 1125} Link IDs: {'PTRANS': 54, 'TRANS': 1070} Chain: "C" Number of atoms: 8771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1125, 8771 Classifications: {'peptide': 1125} Link IDs: {'PTRANS': 54, 'TRANS': 1070} 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: "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: "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: "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: "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: "V" 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: "W" 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: "X" 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: 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: "b" 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: "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: "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: "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: "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: "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: "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: "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: "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: "Y" 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: "Z" 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: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 146 Unusual residues: {'EIC': 1, 'NAG': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} 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: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 146 Unusual residues: {'EIC': 1, 'NAG': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} 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: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 146 Unusual residues: {'EIC': 1, 'NAG': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 14.14, per 1000 atoms: 0.51 Number of scatterers: 27675 At special positions: 0 Unit cell: (153.715, 141.807, 173.2, 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 123 16.00 O 5475 8.00 N 4491 7.00 C 17586 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 134 " distance=2.03 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 164 " distance=2.03 Simple disulfide: pdb=" SG CYS A 289 " - pdb=" SG CYS A 299 " distance=2.03 Simple disulfide: pdb=" SG CYS A 334 " - pdb=" SG CYS A 359 " distance=2.03 Simple disulfide: pdb=" SG CYS A 377 " - pdb=" SG CYS A 430 " distance=2.03 Simple disulfide: pdb=" SG CYS A 389 " - pdb=" SG CYS A 523 " distance=2.03 Simple disulfide: pdb=" SG CYS A 478 " - pdb=" SG CYS A 486 " distance=2.06 Simple disulfide: pdb=" SG CYS A 536 " - pdb=" SG CYS A 588 " distance=2.02 Simple disulfide: pdb=" SG CYS A 615 " - pdb=" SG CYS A 647 " distance=2.04 Simple disulfide: pdb=" SG CYS A 660 " - pdb=" SG CYS A 669 " distance=2.03 Simple disulfide: pdb=" SG CYS A 732 " - pdb=" SG CYS A 754 " distance=2.04 Simple disulfide: pdb=" SG CYS A 737 " - pdb=" SG CYS A 743 " distance=2.03 Simple disulfide: pdb=" SG CYS A 834 " - pdb=" SG CYS A 845 " distance=2.03 Simple disulfide: pdb=" SG CYS A1026 " - pdb=" SG CYS A1037 " distance=2.03 Simple disulfide: pdb=" SG CYS A1076 " - pdb=" SG CYS A1120 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 134 " distance=2.03 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS B 164 " distance=2.04 Simple disulfide: pdb=" SG CYS B 289 " - pdb=" SG CYS B 299 " distance=2.03 Simple disulfide: pdb=" SG CYS B 334 " - pdb=" SG CYS B 359 " distance=2.03 Simple disulfide: pdb=" SG CYS B 377 " - pdb=" SG CYS B 430 " distance=2.03 Simple disulfide: pdb=" SG CYS B 389 " - pdb=" SG CYS B 523 " distance=2.03 Simple disulfide: pdb=" SG CYS B 478 " - pdb=" SG CYS B 486 " distance=2.07 Simple disulfide: pdb=" SG CYS B 536 " - pdb=" SG CYS B 588 " distance=2.02 Simple disulfide: pdb=" SG CYS B 615 " - pdb=" SG CYS B 647 " distance=2.04 Simple disulfide: pdb=" SG CYS B 660 " - pdb=" SG CYS B 669 " distance=2.03 Simple disulfide: pdb=" SG CYS B 732 " - pdb=" SG CYS B 754 " distance=2.04 Simple disulfide: pdb=" SG CYS B 737 " - pdb=" SG CYS B 743 " distance=2.03 Simple disulfide: pdb=" SG CYS B 834 " - pdb=" SG CYS B 845 " distance=2.03 Simple disulfide: pdb=" SG CYS B1026 " - pdb=" SG CYS B1037 " distance=2.03 Simple disulfide: pdb=" SG CYS B1076 " - pdb=" SG CYS B1120 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 134 " distance=2.03 Simple disulfide: pdb=" SG CYS C 129 " - pdb=" SG CYS C 164 " distance=2.05 Simple disulfide: pdb=" SG CYS C 289 " - pdb=" SG CYS C 299 " distance=2.03 Simple disulfide: pdb=" SG CYS C 334 " - pdb=" SG CYS C 359 " distance=2.03 Simple disulfide: pdb=" SG CYS C 377 " - pdb=" SG CYS C 430 " distance=2.03 Simple disulfide: pdb=" SG CYS C 389 " - pdb=" SG CYS C 523 " distance=2.03 Simple disulfide: pdb=" SG CYS C 478 " - pdb=" SG CYS C 486 " distance=2.03 Simple disulfide: pdb=" SG CYS C 536 " - pdb=" SG CYS C 588 " distance=2.02 Simple disulfide: pdb=" SG CYS C 615 " - pdb=" SG CYS C 647 " distance=2.04 Simple disulfide: pdb=" SG CYS C 660 " - pdb=" SG CYS C 669 " distance=2.03 Simple disulfide: pdb=" SG CYS C 732 " - pdb=" SG CYS C 754 " distance=2.04 Simple disulfide: pdb=" SG CYS C 737 " - pdb=" SG CYS C 743 " distance=2.03 Simple disulfide: pdb=" SG CYS C 834 " - pdb=" SG CYS C 845 " distance=2.03 Simple disulfide: pdb=" SG CYS C1026 " - pdb=" SG CYS C1037 " distance=2.03 Simple disulfide: pdb=" SG CYS C1076 " - pdb=" SG CYS C1120 " distance=2.03 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=2, 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 V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 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 k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " NAG-ASN " NAG A1301 " - " ASN A 280 " " NAG A1302 " - " ASN A 341 " " NAG A1303 " - " ASN A 655 " " NAG A1304 " - " ASN A 703 " " NAG A1305 " - " ASN A 601 " " NAG A1306 " - " ASN A 120 " " NAG A1307 " - " ASN A 61 " " NAG A1308 " - " ASN A 614 " " NAG A1309 " - " ASN A 329 " " NAG B1301 " - " ASN B 280 " " NAG B1302 " - " ASN B 341 " " NAG B1303 " - " ASN B 655 " " NAG B1304 " - " ASN B 703 " " NAG B1305 " - " ASN B 601 " " NAG B1306 " - " ASN B 120 " " NAG B1307 " - " ASN B 61 " " NAG B1308 " - " ASN B 614 " " NAG B1309 " - " ASN B 329 " " NAG C1301 " - " ASN C 280 " " NAG C1302 " - " ASN C 341 " " NAG C1303 " - " ASN C 655 " " NAG C1304 " - " ASN C 703 " " NAG C1305 " - " ASN C 601 " " NAG C1306 " - " ASN C 120 " " NAG C1307 " - " ASN C 61 " " NAG C1308 " - " ASN C 614 " " NAG C1309 " - " ASN C 329 " " NAG D 1 " - " ASN A 17 " " NAG E 1 " - " ASN A 232 " " NAG F 1 " - " ASN A 368 " " NAG G 1 " - " ASN A 711 " " NAG H 1 " - " ASN A 795 " " NAG I 1 " - " ASN A1068 " " NAG J 1 " - " ASN A1092 " " NAG K 1 " - " ASN A 163 " " NAG L 1 " - " ASN A 30 " " NAG M 1 " - " ASN A 147 " " NAG N 1 " - " ASN B 17 " " NAG O 1 " - " ASN B 795 " " NAG P 1 " - " ASN B 232 " " NAG Q 1 " - " ASN B 368 " " NAG R 1 " - " ASN B1092 " " NAG S 1 " - " ASN B1068 " " NAG T 1 " - " ASN B1128 " " NAG U 1 " - " ASN C 17 " " NAG V 1 " - " ASN B 163 " " NAG W 1 " - " ASN B 30 " " NAG X 1 " - " ASN B 147 " " NAG Y 1 " - " ASN C 795 " " NAG Z 1 " - " ASN C1068 " " NAG a 1 " - " ASN C 232 " " NAG b 1 " - " ASN C 368 " " NAG e 1 " - " ASN C1128 " " NAG f 1 " - " ASN C1092 " " NAG g 1 " - " ASN C 163 " " NAG h 1 " - " ASN C 30 " " NAG i 1 " - " ASN C 147 " " NAG k 1 " - " ASN A1128 " " NAG l 1 " - " ASN B 711 " " NAG m 1 " - " ASN C 711 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.91 Conformation dependent library (CDL) restraints added in 4.8 seconds 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6288 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 72 helices and 42 sheets defined 22.8% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.61 Creating SS restraints... Processing helix chain 'A' and resid 293 through 301 Processing helix chain 'A' and resid 336 through 340 Processing helix chain 'A' and resid 366 through 369 No H-bonds generated for 'chain 'A' and resid 366 through 369' Processing helix chain 'A' and resid 382 through 387 removed outlier: 4.108A pdb=" N ASN A 386 " --> pdb=" O THR A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 404 No H-bonds generated for 'chain 'A' and resid 402 through 404' Processing helix chain 'A' and resid 415 through 419 Processing helix chain 'A' and resid 437 through 440 No H-bonds generated for 'chain 'A' and resid 437 through 440' Processing helix chain 'A' and resid 615 through 622 Proline residue: A 619 - end of helix removed outlier: 3.533A pdb=" N ILE A 622 " --> pdb=" O PRO A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 626 No H-bonds generated for 'chain 'A' and resid 624 through 626' Processing helix chain 'A' and resid 629 through 635 removed outlier: 3.559A pdb=" N TYR A 634 " --> pdb=" O ALA A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 737 Processing helix chain 'A' and resid 746 through 776 removed outlier: 3.797A pdb=" N GLN A 749 " --> pdb=" O LEU A 746 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER A 752 " --> pdb=" O GLN A 749 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL A 766 " --> pdb=" O GLY A 763 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE A 776 " --> pdb=" O GLN A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 819 Processing helix chain 'A' and resid 831 through 836 Processing helix chain 'A' and resid 843 through 849 Processing helix chain 'A' and resid 861 through 882 removed outlier: 7.657A pdb=" N TRP A 880 " --> pdb=" O ILE A 876 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N THR A 881 " --> pdb=" O THR A 877 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N PHE A 882 " --> pdb=" O SER A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 892 through 902 Processing helix chain 'A' and resid 907 through 912 Processing helix chain 'A' and resid 914 through 934 Processing helix chain 'A' and resid 940 through 961 removed outlier: 3.579A pdb=" N LEU A 960 " --> pdb=" O LEU A 956 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N SER A 961 " --> pdb=" O VAL A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 977 Processing helix chain 'A' and resid 980 through 1026 removed outlier: 3.795A pdb=" N VAL A 985 " --> pdb=" O PRO A 981 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN A 986 " --> pdb=" O GLU A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 1120 through 1122 No H-bonds generated for 'chain 'A' and resid 1120 through 1122' Processing helix chain 'A' and resid 1134 through 1137 No H-bonds generated for 'chain 'A' and resid 1134 through 1137' Processing helix chain 'B' and resid 293 through 301 Processing helix chain 'B' and resid 336 through 340 Processing helix chain 'B' and resid 366 through 369 No H-bonds generated for 'chain 'B' and resid 366 through 369' Processing helix chain 'B' and resid 382 through 387 removed outlier: 4.109A pdb=" N ASN B 386 " --> pdb=" O THR B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 404 No H-bonds generated for 'chain 'B' and resid 402 through 404' Processing helix chain 'B' and resid 415 through 419 Processing helix chain 'B' and resid 437 through 440 No H-bonds generated for 'chain 'B' and resid 437 through 440' Processing helix chain 'B' and resid 615 through 622 Proline residue: B 619 - end of helix removed outlier: 3.533A pdb=" N ILE B 622 " --> pdb=" O PRO B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 626 No H-bonds generated for 'chain 'B' and resid 624 through 626' Processing helix chain 'B' and resid 629 through 635 removed outlier: 3.559A pdb=" N TYR B 634 " --> pdb=" O ALA B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 737 Processing helix chain 'B' and resid 746 through 776 removed outlier: 3.797A pdb=" N GLN B 749 " --> pdb=" O LEU B 746 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER B 752 " --> pdb=" O GLN B 749 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL B 766 " --> pdb=" O GLY B 763 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE B 776 " --> pdb=" O GLN B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 819 Processing helix chain 'B' and resid 831 through 836 Processing helix chain 'B' and resid 843 through 849 Processing helix chain 'B' and resid 861 through 882 removed outlier: 7.657A pdb=" N TRP B 880 " --> pdb=" O ILE B 876 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N THR B 881 " --> pdb=" O THR B 877 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N PHE B 882 " --> pdb=" O SER B 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 892 through 902 Processing helix chain 'B' and resid 907 through 912 Processing helix chain 'B' and resid 914 through 934 Processing helix chain 'B' and resid 940 through 961 removed outlier: 3.579A pdb=" N LEU B 960 " --> pdb=" O LEU B 956 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N SER B 961 " --> pdb=" O VAL B 957 " (cutoff:3.500A) Processing helix chain 'B' and resid 971 through 977 Processing helix chain 'B' and resid 980 through 1026 removed outlier: 3.795A pdb=" N VAL B 985 " --> pdb=" O PRO B 981 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN B 986 " --> pdb=" O GLU B 982 " (cutoff:3.500A) Processing helix chain 'B' and resid 1120 through 1122 No H-bonds generated for 'chain 'B' and resid 1120 through 1122' Processing helix chain 'B' and resid 1134 through 1137 No H-bonds generated for 'chain 'B' and resid 1134 through 1137' Processing helix chain 'C' and resid 293 through 301 Processing helix chain 'C' and resid 336 through 340 Processing helix chain 'C' and resid 366 through 369 No H-bonds generated for 'chain 'C' and resid 366 through 369' Processing helix chain 'C' and resid 382 through 387 removed outlier: 4.108A pdb=" N ASN C 386 " --> pdb=" O THR C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 404 No H-bonds generated for 'chain 'C' and resid 402 through 404' Processing helix chain 'C' and resid 415 through 419 Processing helix chain 'C' and resid 437 through 440 No H-bonds generated for 'chain 'C' and resid 437 through 440' Processing helix chain 'C' and resid 615 through 622 Proline residue: C 619 - end of helix removed outlier: 3.533A pdb=" N ILE C 622 " --> pdb=" O PRO C 619 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 626 No H-bonds generated for 'chain 'C' and resid 624 through 626' Processing helix chain 'C' and resid 629 through 635 removed outlier: 3.559A pdb=" N TYR C 634 " --> pdb=" O ALA C 630 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 737 Processing helix chain 'C' and resid 746 through 776 removed outlier: 3.797A pdb=" N GLN C 749 " --> pdb=" O LEU C 746 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER C 752 " --> pdb=" O GLN C 749 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL C 766 " --> pdb=" O GLY C 763 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE C 776 " --> pdb=" O GLN C 773 " (cutoff:3.500A) Processing helix chain 'C' and resid 811 through 819 Processing helix chain 'C' and resid 831 through 836 Processing helix chain 'C' and resid 843 through 849 Processing helix chain 'C' and resid 861 through 882 removed outlier: 7.657A pdb=" N TRP C 880 " --> pdb=" O ILE C 876 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N THR C 881 " --> pdb=" O THR C 877 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N PHE C 882 " --> pdb=" O SER C 878 " (cutoff:3.500A) Processing helix chain 'C' and resid 892 through 902 Processing helix chain 'C' and resid 907 through 912 Processing helix chain 'C' and resid 914 through 934 Processing helix chain 'C' and resid 940 through 961 removed outlier: 3.579A pdb=" N LEU C 960 " --> pdb=" O LEU C 956 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N SER C 961 " --> pdb=" O VAL C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 971 through 977 Processing helix chain 'C' and resid 980 through 1026 removed outlier: 3.795A pdb=" N VAL C 985 " --> pdb=" O PRO C 981 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN C 986 " --> pdb=" O GLU C 982 " (cutoff:3.500A) Processing helix chain 'C' and resid 1120 through 1122 No H-bonds generated for 'chain 'C' and resid 1120 through 1122' Processing helix chain 'C' and resid 1134 through 1137 No H-bonds generated for 'chain 'C' and resid 1134 through 1137' Processing sheet with id= A, first strand: chain 'A' and resid 27 through 31 removed outlier: 4.165A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N ASN A 61 " --> pdb=" O TYR A 267 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N TYR A 267 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL A 225 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N SER A 203 " --> pdb=" O PRO A 223 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.948A pdb=" N ASP A 285 " --> pdb=" O SER A 276 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 81 through 83 removed outlier: 3.678A pdb=" N GLY A 101 " --> pdb=" O LEU A 239 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N ARG A 100 " --> pdb=" O ASN A 119 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 138 through 142 removed outlier: 6.515A pdb=" N LEU A 240 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N VAL A 141 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU A 242 " --> pdb=" O VAL A 141 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 322 through 326 removed outlier: 4.813A pdb=" N ILE A 322 " --> pdb=" O CYS A 536 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 352 through 356 removed outlier: 4.337A pdb=" N VAL A 393 " --> pdb=" O ILE A 356 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 359 through 361 Processing sheet with id= H, first strand: chain 'A' and resid 450 through 452 Processing sheet with id= I, first strand: chain 'A' and resid 594 through 597 Processing sheet with id= J, first strand: chain 'A' and resid 685 through 690 removed outlier: 6.512A pdb=" N ALA A 670 " --> pdb=" O PRO A 663 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 705 through 709 removed outlier: 3.699A pdb=" N ALA A1072 " --> pdb=" O PHE A1089 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N PHE A1089 " --> pdb=" O ALA A1072 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 712 through 722 removed outlier: 5.895A pdb=" N TYR A1061 " --> pdb=" O HIS A1042 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N HIS A1042 " --> pdb=" O TYR A1061 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 727 through 730 removed outlier: 4.306A pdb=" N LYS A 727 " --> pdb=" O LEU A 855 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 1082 through 1084 Processing sheet with id= O, first strand: chain 'B' and resid 27 through 31 removed outlier: 4.165A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N ASN B 61 " --> pdb=" O TYR B 267 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N TYR B 267 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL B 225 " --> pdb=" O ILE B 201 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N SER B 203 " --> pdb=" O PRO B 223 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.948A pdb=" N ASP B 285 " --> pdb=" O SER B 276 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 81 through 83 removed outlier: 3.677A pdb=" N GLY B 101 " --> pdb=" O LEU B 239 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N ARG B 100 " --> pdb=" O ASN B 119 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 139 through 142 Processing sheet with id= S, first strand: chain 'B' and resid 322 through 326 removed outlier: 4.813A pdb=" N ILE B 322 " --> pdb=" O CYS B 536 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 352 through 356 removed outlier: 4.337A pdb=" N VAL B 393 " --> pdb=" O ILE B 356 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 359 through 361 Processing sheet with id= V, first strand: chain 'B' and resid 450 through 452 Processing sheet with id= W, first strand: chain 'B' and resid 594 through 597 Processing sheet with id= X, first strand: chain 'B' and resid 685 through 690 removed outlier: 6.512A pdb=" N ALA B 670 " --> pdb=" O PRO B 663 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'B' and resid 705 through 709 removed outlier: 3.699A pdb=" N ALA B1072 " --> pdb=" O PHE B1089 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N PHE B1089 " --> pdb=" O ALA B1072 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'B' and resid 712 through 722 removed outlier: 5.895A pdb=" N TYR B1061 " --> pdb=" O HIS B1042 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N HIS B1042 " --> pdb=" O TYR B1061 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'B' and resid 727 through 730 removed outlier: 4.305A pdb=" N LYS B 727 " --> pdb=" O LEU B 855 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'B' and resid 1082 through 1084 Processing sheet with id= AC, first strand: chain 'C' and resid 27 through 31 removed outlier: 4.166A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N ASN C 61 " --> pdb=" O TYR C 267 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N TYR C 267 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL C 225 " --> pdb=" O ILE C 201 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N SER C 203 " --> pdb=" O PRO C 223 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.948A pdb=" N ASP C 285 " --> pdb=" O SER C 276 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'C' and resid 81 through 83 removed outlier: 3.677A pdb=" N GLY C 101 " --> pdb=" O LEU C 239 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N ARG C 100 " --> pdb=" O ASN C 119 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'C' and resid 138 through 142 removed outlier: 6.510A pdb=" N LEU C 240 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N VAL C 141 " --> pdb=" O LEU C 240 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU C 242 " --> pdb=" O VAL C 141 " (cutoff:3.500A) No H-bonds generated for sheet with id= AF Processing sheet with id= AG, first strand: chain 'C' and resid 322 through 326 removed outlier: 4.812A pdb=" N ILE C 322 " --> pdb=" O CYS C 536 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'C' and resid 352 through 356 removed outlier: 4.337A pdb=" N VAL C 393 " --> pdb=" O ILE C 356 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'C' and resid 359 through 361 Processing sheet with id= AJ, first strand: chain 'C' and resid 450 through 452 Processing sheet with id= AK, first strand: chain 'C' and resid 594 through 597 Processing sheet with id= AL, first strand: chain 'C' and resid 685 through 690 removed outlier: 6.513A pdb=" N ALA C 670 " --> pdb=" O PRO C 663 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'C' and resid 705 through 709 removed outlier: 3.699A pdb=" N ALA C1072 " --> pdb=" O PHE C1089 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N PHE C1089 " --> pdb=" O ALA C1072 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'C' and resid 712 through 722 removed outlier: 5.896A pdb=" N TYR C1061 " --> pdb=" O HIS C1042 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N HIS C1042 " --> pdb=" O TYR C1061 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'C' and resid 727 through 730 removed outlier: 4.306A pdb=" N LYS C 727 " --> pdb=" O LEU C 855 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'C' and resid 1082 through 1084 927 hydrogen bonds defined for protein. 2376 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: 12.68 Time building geometry restraints manager: 13.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5398 1.33 - 1.45: 7102 1.45 - 1.57: 15628 1.57 - 1.69: 0 1.69 - 1.81: 156 Bond restraints: 28284 Sorted by residual: bond pdb=" C12 EIC B1310 " pdb=" C13 EIC B1310 " ideal model delta sigma weight residual 1.332 1.528 -0.196 2.00e-02 2.50e+03 9.58e+01 bond pdb=" C12 EIC A1310 " pdb=" C13 EIC A1310 " ideal model delta sigma weight residual 1.332 1.528 -0.196 2.00e-02 2.50e+03 9.56e+01 bond pdb=" C10 EIC A1310 " pdb=" C9 EIC A1310 " ideal model delta sigma weight residual 1.332 1.527 -0.195 2.00e-02 2.50e+03 9.55e+01 bond pdb=" C12 EIC C1310 " pdb=" C13 EIC C1310 " ideal model delta sigma weight residual 1.332 1.527 -0.195 2.00e-02 2.50e+03 9.54e+01 bond pdb=" C10 EIC C1310 " pdb=" C9 EIC C1310 " ideal model delta sigma weight residual 1.332 1.527 -0.195 2.00e-02 2.50e+03 9.51e+01 ... (remaining 28279 not shown) Histogram of bond angle deviations from ideal: 100.18 - 107.07: 914 107.07 - 113.96: 15900 113.96 - 120.85: 13523 120.85 - 127.74: 8040 127.74 - 134.63: 116 Bond angle restraints: 38493 Sorted by residual: angle pdb=" C THR B 248 " pdb=" CA THR B 248 " pdb=" CB THR B 248 " ideal model delta sigma weight residual 111.20 117.42 -6.22 7.10e-01 1.98e+00 7.67e+01 angle pdb=" C THR A 248 " pdb=" CA THR A 248 " pdb=" CB THR A 248 " ideal model delta sigma weight residual 111.20 117.42 -6.22 7.10e-01 1.98e+00 7.67e+01 angle pdb=" C THR C 248 " pdb=" CA THR C 248 " pdb=" CB THR C 248 " ideal model delta sigma weight residual 111.20 117.40 -6.20 7.10e-01 1.98e+00 7.62e+01 angle pdb=" N PRO C 980 " pdb=" CA PRO C 980 " pdb=" C PRO C 980 " ideal model delta sigma weight residual 110.70 119.56 -8.86 1.22e+00 6.72e-01 5.27e+01 angle pdb=" N PRO B 980 " pdb=" CA PRO B 980 " pdb=" C PRO B 980 " ideal model delta sigma weight residual 110.70 119.53 -8.83 1.22e+00 6.72e-01 5.23e+01 ... (remaining 38488 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.44: 17059 24.44 - 48.88: 805 48.88 - 73.33: 136 73.33 - 97.77: 51 97.77 - 122.21: 3 Dihedral angle restraints: 18054 sinusoidal: 8244 harmonic: 9810 Sorted by residual: dihedral pdb=" C CYS C 164 " pdb=" N CYS C 164 " pdb=" CA CYS C 164 " pdb=" CB CYS C 164 " ideal model delta harmonic sigma weight residual -122.60 -140.88 18.28 0 2.50e+00 1.60e-01 5.35e+01 dihedral pdb=" CB CYS C 478 " pdb=" SG CYS C 478 " pdb=" SG CYS C 486 " pdb=" CB CYS C 486 " ideal model delta sinusoidal sigma weight residual 93.00 152.38 -59.38 1 1.00e+01 1.00e-02 4.71e+01 dihedral pdb=" N CYS C 164 " pdb=" C CYS C 164 " pdb=" CA CYS C 164 " pdb=" CB CYS C 164 " ideal model delta harmonic sigma weight residual 122.80 139.00 -16.20 0 2.50e+00 1.60e-01 4.20e+01 ... (remaining 18051 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.164: 3971 0.164 - 0.329: 636 0.329 - 0.493: 24 0.493 - 0.657: 0 0.657 - 0.822: 4 Chirality restraints: 4635 Sorted by residual: chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-02 2.50e+03 5.33e+02 chirality pdb=" C1 NAG Y 2 " pdb=" O4 NAG Y 1 " pdb=" C2 NAG Y 2 " pdb=" O5 NAG Y 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-02 2.50e+03 1.92e+02 chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-02 2.50e+03 1.15e+02 ... (remaining 4632 not shown) Planarity restraints: 4920 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG O 1 " 0.344 2.00e-02 2.50e+03 2.98e-01 1.11e+03 pdb=" C7 NAG O 1 " -0.082 2.00e-02 2.50e+03 pdb=" C8 NAG O 1 " 0.124 2.00e-02 2.50e+03 pdb=" N2 NAG O 1 " -0.530 2.00e-02 2.50e+03 pdb=" O7 NAG O 1 " 0.144 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 EIC A1310 " 0.420 2.00e-02 2.50e+03 3.16e-01 1.00e+03 pdb=" C11 EIC A1310 " -0.155 2.00e-02 2.50e+03 pdb=" C8 EIC A1310 " 0.155 2.00e-02 2.50e+03 pdb=" C9 EIC A1310 " -0.419 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1301 " -0.323 2.00e-02 2.50e+03 2.81e-01 9.86e+02 pdb=" C7 NAG A1301 " 0.071 2.00e-02 2.50e+03 pdb=" C8 NAG A1301 " -0.125 2.00e-02 2.50e+03 pdb=" N2 NAG A1301 " 0.503 2.00e-02 2.50e+03 pdb=" O7 NAG A1301 " -0.126 2.00e-02 2.50e+03 ... (remaining 4917 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 118 2.63 - 3.20: 23345 3.20 - 3.76: 42381 3.76 - 4.33: 61539 4.33 - 4.90: 97379 Nonbonded interactions: 224762 Sorted by model distance: nonbonded pdb=" O3 NAG Y 2 " pdb=" O7 NAG Y 2 " model vdw 2.059 2.440 nonbonded pdb=" O3 NAG K 2 " pdb=" O7 NAG K 2 " model vdw 2.073 2.440 nonbonded pdb=" OG1 THR B 22 " pdb=" O LYS B 75 " model vdw 2.250 2.440 nonbonded pdb=" OG1 THR C 22 " pdb=" O LYS C 75 " model vdw 2.266 2.440 nonbonded pdb=" CG2 ILE A 838 " pdb=" OD2 ASP C 584 " model vdw 2.282 3.460 ... (remaining 224757 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' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'k' selection = chain 'l' selection = chain 'm' } 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 individual isotropic 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: 1.890 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: 6.570 Check model and map are aligned: 0.390 Set scattering table: 0.240 Process input model: 77.200 Find NCS groups from input model: 1.830 Set up NCS constraints: 0.470 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 101.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 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 : 0.013 0.196 28284 Z= 0.857 Angle : 1.570 15.164 38493 Z= 1.168 Chirality : 0.114 0.822 4635 Planarity : 0.022 0.316 4860 Dihedral : 14.476 122.211 11631 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.53 % Favored : 96.05 % Rotamer: Outliers : 4.88 % Allowed : 9.46 % Favored : 85.66 % Cbeta Deviations : 0.70 % 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: 1.41 (0.14), residues: 3369 helix: 4.20 (0.19), residues: 690 sheet: 1.75 (0.19), residues: 609 loop : -0.52 (0.12), residues: 2070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A 150 HIS 0.005 0.001 HIS A 243 PHE 0.018 0.002 PHE C 131 TYR 0.022 0.002 TYR A 634 ARG 0.015 0.001 ARG C 759 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 272 time to evaluate : 3.099 Fit side-chains revert: symmetry clash REVERT: A 251 ASN cc_start: 0.7728 (t0) cc_final: 0.7473 (t0) REVERT: A 332 ASN cc_start: 0.8028 (p0) cc_final: 0.7696 (p0) REVERT: A 626 GLN cc_start: 0.7624 (pt0) cc_final: 0.7347 (pt0) REVERT: A 817 PHE cc_start: 0.7591 (t80) cc_final: 0.7375 (t80) REVERT: A 1044 MET cc_start: 0.8850 (ptm) cc_final: 0.8561 (ptm) REVERT: A 1132 TYR cc_start: 0.7761 (t80) cc_final: 0.7551 (t80) REVERT: B 916 LEU cc_start: 0.8890 (tp) cc_final: 0.8666 (tp) REVERT: B 1044 MET cc_start: 0.8838 (ptm) cc_final: 0.8612 (ptm) REVERT: B 1132 TYR cc_start: 0.7795 (t80) cc_final: 0.7283 (t80) REVERT: C 626 GLN cc_start: 0.7433 (pt0) cc_final: 0.7082 (pm20) REVERT: C 863 MET cc_start: 0.8986 (mtt) cc_final: 0.8760 (mtm) REVERT: C 1044 MET cc_start: 0.8870 (ptm) cc_final: 0.8491 (ptp) REVERT: C 1132 TYR cc_start: 0.7832 (t80) cc_final: 0.7588 (t80) outliers start: 143 outliers final: 22 residues processed: 397 average time/residue: 1.0925 time to fit residues: 528.3656 Evaluate side-chains 144 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 122 time to evaluate : 3.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 334 CYS Chi-restraints excluded: chain A residue 359 CYS Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 946 VAL Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 359 CYS Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 946 VAL Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 946 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 283 optimal weight: 0.6980 chunk 254 optimal weight: 0.9990 chunk 141 optimal weight: 0.6980 chunk 86 optimal weight: 2.9990 chunk 171 optimal weight: 0.9990 chunk 136 optimal weight: 5.9990 chunk 263 optimal weight: 0.6980 chunk 101 optimal weight: 0.9980 chunk 160 optimal weight: 0.9990 chunk 196 optimal weight: 0.9990 chunk 305 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 GLN A 85 ASN A 113 GLN A 119 ASN A 472 GLN A 496 HIS A 626 GLN A 758 ASN A 895 GLN A1113 ASN B 71 GLN B 85 ASN B 119 ASN B 153 ASN B 496 HIS B 626 GLN B 697 ASN B 758 ASN B 895 GLN C 71 GLN C 85 ASN C 113 GLN C 119 ASN C 472 GLN C 496 HIS C 626 GLN C 697 ASN C 758 ASN C 895 GLN C1113 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28284 Z= 0.189 Angle : 0.648 14.032 38493 Z= 0.327 Chirality : 0.047 0.487 4635 Planarity : 0.004 0.038 4860 Dihedral : 11.506 105.842 5665 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.06 % Favored : 96.91 % Rotamer: Outliers : 2.94 % Allowed : 13.80 % Favored : 83.27 % 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: 0.56 (0.14), residues: 3369 helix: 2.28 (0.19), residues: 735 sheet: 1.22 (0.19), residues: 732 loop : -0.79 (0.13), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 150 HIS 0.003 0.001 HIS B1095 PHE 0.020 0.001 PHE A 390 TYR 0.017 0.001 TYR A1061 ARG 0.008 0.001 ARG C 841 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 150 time to evaluate : 3.089 Fit side-chains revert: symmetry clash REVERT: A 251 ASN cc_start: 0.7763 (t0) cc_final: 0.7507 (t0) REVERT: A 562 GLN cc_start: 0.6947 (OUTLIER) cc_final: 0.5974 (tm130) REVERT: A 626 GLN cc_start: 0.7587 (pt0) cc_final: 0.7352 (pt0) REVERT: A 1044 MET cc_start: 0.8839 (ptm) cc_final: 0.8408 (ptp) REVERT: B 75 LYS cc_start: 0.4974 (OUTLIER) cc_final: 0.4593 (ptmt) REVERT: B 684 ARG cc_start: 0.7855 (mmm-85) cc_final: 0.7551 (mmm-85) REVERT: B 916 LEU cc_start: 0.8884 (tp) cc_final: 0.8664 (tp) REVERT: B 1044 MET cc_start: 0.8737 (ptm) cc_final: 0.8415 (ptp) REVERT: C 562 GLN cc_start: 0.6931 (OUTLIER) cc_final: 0.6659 (tm-30) REVERT: C 626 GLN cc_start: 0.7553 (pt0) cc_final: 0.7166 (pm20) REVERT: C 817 PHE cc_start: 0.7866 (t80) cc_final: 0.7544 (t80) REVERT: C 1044 MET cc_start: 0.8815 (ptm) cc_final: 0.8397 (ptp) REVERT: C 1100 GLN cc_start: 0.8077 (OUTLIER) cc_final: 0.7831 (pt0) REVERT: C 1132 TYR cc_start: 0.7771 (t80) cc_final: 0.7533 (t80) outliers start: 86 outliers final: 26 residues processed: 222 average time/residue: 0.9953 time to fit residues: 275.7283 Evaluate side-chains 142 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 112 time to evaluate : 3.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 279 GLN Chi-restraints excluded: chain A residue 334 CYS Chi-restraints excluded: chain A residue 359 CYS Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 562 GLN Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 1130 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 75 LYS Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 332 ASN Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 1130 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 562 GLN Chi-restraints excluded: chain C residue 746 LEU Chi-restraints excluded: chain C residue 810 SER Chi-restraints excluded: chain C residue 1100 GLN Chi-restraints excluded: chain C residue 1130 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 169 optimal weight: 4.9990 chunk 94 optimal weight: 0.3980 chunk 253 optimal weight: 0.0570 chunk 207 optimal weight: 5.9990 chunk 84 optimal weight: 0.0770 chunk 305 optimal weight: 6.9990 chunk 330 optimal weight: 8.9990 chunk 272 optimal weight: 0.9990 chunk 303 optimal weight: 4.9990 chunk 104 optimal weight: 6.9990 chunk 245 optimal weight: 0.5980 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 HIS B 153 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.070 28284 Z= 0.143 Angle : 0.576 9.068 38493 Z= 0.289 Chirality : 0.046 0.431 4635 Planarity : 0.004 0.042 4860 Dihedral : 10.725 103.252 5649 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.33 % Favored : 95.64 % Rotamer: Outliers : 2.22 % Allowed : 14.75 % Favored : 83.03 % 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: 0.32 (0.14), residues: 3369 helix: 1.91 (0.19), residues: 729 sheet: 1.19 (0.19), residues: 717 loop : -0.89 (0.13), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 256 HIS 0.006 0.001 HIS C 243 PHE 0.025 0.001 PHE A 390 TYR 0.017 0.001 TYR C1061 ARG 0.009 0.000 ARG C 841 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 126 time to evaluate : 3.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 558 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7482 (mt) REVERT: A 626 GLN cc_start: 0.7575 (pt0) cc_final: 0.7349 (pt0) REVERT: A 1044 MET cc_start: 0.8754 (ptm) cc_final: 0.8470 (ptp) REVERT: B 916 LEU cc_start: 0.8849 (tp) cc_final: 0.8624 (tp) REVERT: B 1132 TYR cc_start: 0.7717 (t80) cc_final: 0.7139 (t80) REVERT: C 159 SER cc_start: 0.8797 (OUTLIER) cc_final: 0.8388 (m) REVERT: C 312 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.7791 (mt0) REVERT: C 562 GLN cc_start: 0.6993 (OUTLIER) cc_final: 0.6653 (tm-30) REVERT: C 817 PHE cc_start: 0.7857 (t80) cc_final: 0.7526 (t80) REVERT: C 1044 MET cc_start: 0.8687 (ptm) cc_final: 0.8394 (ptp) REVERT: C 1100 GLN cc_start: 0.8054 (OUTLIER) cc_final: 0.7764 (pt0) REVERT: C 1132 TYR cc_start: 0.7777 (t80) cc_final: 0.7547 (t80) outliers start: 65 outliers final: 26 residues processed: 180 average time/residue: 0.8982 time to fit residues: 207.6231 Evaluate side-chains 133 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 102 time to evaluate : 3.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 279 GLN Chi-restraints excluded: chain A residue 334 CYS Chi-restraints excluded: chain A residue 359 CYS Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 439 GLN Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 708 ILE Chi-restraints excluded: chain B residue 1100 GLN Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 312 GLN Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 562 GLN Chi-restraints excluded: chain C residue 746 LEU Chi-restraints excluded: chain C residue 1100 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 302 optimal weight: 6.9990 chunk 229 optimal weight: 9.9990 chunk 158 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 chunk 205 optimal weight: 6.9990 chunk 306 optimal weight: 3.9990 chunk 324 optimal weight: 5.9990 chunk 160 optimal weight: 0.2980 chunk 290 optimal weight: 0.0570 chunk 87 optimal weight: 3.9990 overall best weight: 1.8704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 830 GLN B 97 ASN B 153 ASN B 830 GLN ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 830 GLN C 895 GLN C 951 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 28284 Z= 0.268 Angle : 0.624 9.558 38493 Z= 0.318 Chirality : 0.048 0.444 4635 Planarity : 0.004 0.045 4860 Dihedral : 10.513 94.884 5647 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.53 % Allowed : 14.89 % Favored : 82.58 % 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: -0.00 (0.14), residues: 3369 helix: 1.55 (0.19), residues: 735 sheet: 0.99 (0.19), residues: 699 loop : -1.04 (0.12), residues: 1935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 64 HIS 0.005 0.001 HIS C1058 PHE 0.025 0.002 PHE A 390 TYR 0.019 0.002 TYR A 493 ARG 0.006 0.001 ARG B 684 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 130 time to evaluate : 2.995 Fit side-chains revert: symmetry clash REVERT: A 251 ASN cc_start: 0.7697 (t0) cc_final: 0.7478 (t0) REVERT: A 620 MET cc_start: 0.8143 (OUTLIER) cc_final: 0.7000 (mpt) REVERT: A 1044 MET cc_start: 0.8866 (ptm) cc_final: 0.8386 (ptm) REVERT: B 52 GLN cc_start: 0.8770 (OUTLIER) cc_final: 0.8565 (tp40) REVERT: B 159 SER cc_start: 0.8893 (OUTLIER) cc_final: 0.8634 (m) REVERT: B 1132 TYR cc_start: 0.7723 (t80) cc_final: 0.7183 (t80) REVERT: C 159 SER cc_start: 0.8857 (OUTLIER) cc_final: 0.8602 (m) REVERT: C 279 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.8039 (tt0) REVERT: C 562 GLN cc_start: 0.7425 (OUTLIER) cc_final: 0.6755 (tm130) REVERT: C 1044 MET cc_start: 0.8868 (ptm) cc_final: 0.8507 (ptp) REVERT: C 1100 GLN cc_start: 0.8220 (OUTLIER) cc_final: 0.7952 (pt0) REVERT: C 1132 TYR cc_start: 0.7830 (t80) cc_final: 0.7588 (t80) outliers start: 74 outliers final: 30 residues processed: 192 average time/residue: 1.1036 time to fit residues: 263.0515 Evaluate side-chains 148 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 111 time to evaluate : 3.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 279 GLN Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 334 CYS Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 620 MET Chi-restraints excluded: chain A residue 774 GLU Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 1130 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 332 ASN Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 620 MET Chi-restraints excluded: chain B residue 708 ILE Chi-restraints excluded: chain B residue 1130 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 279 GLN Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 562 GLN Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 620 MET Chi-restraints excluded: chain C residue 746 LEU Chi-restraints excluded: chain C residue 910 LEU Chi-restraints excluded: chain C residue 1100 GLN Chi-restraints excluded: chain C residue 1130 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 270 optimal weight: 5.9990 chunk 184 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 241 optimal weight: 5.9990 chunk 134 optimal weight: 0.8980 chunk 277 optimal weight: 6.9990 chunk 224 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 165 optimal weight: 6.9990 chunk 291 optimal weight: 3.9990 chunk 81 optimal weight: 9.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN A 626 GLN A 697 ASN A 895 GLN B 153 ASN B 626 GLN B 895 GLN C 270 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.087 28284 Z= 0.499 Angle : 0.734 10.039 38493 Z= 0.379 Chirality : 0.054 0.463 4635 Planarity : 0.005 0.056 4860 Dihedral : 10.443 85.730 5641 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 2.73 % Allowed : 14.45 % Favored : 82.82 % 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: -0.53 (0.13), residues: 3369 helix: 0.81 (0.18), residues: 771 sheet: 0.63 (0.20), residues: 693 loop : -1.27 (0.12), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP B 64 HIS 0.006 0.001 HIS B1058 PHE 0.023 0.002 PHE B 84 TYR 0.031 0.003 TYR A 168 ARG 0.009 0.001 ARG B 212 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 127 time to evaluate : 3.048 Fit side-chains revert: symmetry clash REVERT: A 216 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.8129 (mmm160) REVERT: A 251 ASN cc_start: 0.7744 (t0) cc_final: 0.7533 (t0) REVERT: A 269 GLN cc_start: 0.8938 (OUTLIER) cc_final: 0.8242 (mp10) REVERT: A 675 MET cc_start: 0.5900 (mmp) cc_final: 0.5422 (mmp) REVERT: A 1044 MET cc_start: 0.8951 (ptm) cc_final: 0.8555 (ptp) REVERT: B 52 GLN cc_start: 0.8920 (OUTLIER) cc_final: 0.8625 (tp40) REVERT: B 269 GLN cc_start: 0.8908 (OUTLIER) cc_final: 0.8701 (mm-40) REVERT: B 1132 TYR cc_start: 0.7908 (t80) cc_final: 0.7468 (t80) REVERT: C 269 GLN cc_start: 0.8945 (OUTLIER) cc_final: 0.8342 (mt0) REVERT: C 279 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.8131 (tt0) REVERT: C 562 GLN cc_start: 0.7723 (OUTLIER) cc_final: 0.6832 (tm130) REVERT: C 620 MET cc_start: 0.7886 (OUTLIER) cc_final: 0.7117 (mpt) REVERT: C 1044 MET cc_start: 0.8933 (ptm) cc_final: 0.8550 (ptp) REVERT: C 1100 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.8048 (pt0) outliers start: 80 outliers final: 42 residues processed: 194 average time/residue: 1.1326 time to fit residues: 268.3050 Evaluate side-chains 168 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 117 time to evaluate : 3.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 269 GLN Chi-restraints excluded: chain A residue 279 GLN Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 334 CYS Chi-restraints excluded: chain A residue 478 CYS Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 620 MET Chi-restraints excluded: chain A residue 774 GLU Chi-restraints excluded: chain A residue 1114 THR Chi-restraints excluded: chain A residue 1130 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 75 LYS Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 269 GLN Chi-restraints excluded: chain B residue 332 ASN Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 620 MET Chi-restraints excluded: chain B residue 708 ILE Chi-restraints excluded: chain B residue 1130 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 134 CYS Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 269 GLN Chi-restraints excluded: chain C residue 279 GLN Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 369 SER Chi-restraints excluded: chain C residue 401 LYS Chi-restraints excluded: chain C residue 562 GLN Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 620 MET Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 910 LEU Chi-restraints excluded: chain C residue 1100 GLN Chi-restraints excluded: chain C residue 1114 THR Chi-restraints excluded: chain C residue 1130 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 109 optimal weight: 0.9990 chunk 292 optimal weight: 0.5980 chunk 64 optimal weight: 0.6980 chunk 190 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 325 optimal weight: 3.9990 chunk 269 optimal weight: 5.9990 chunk 150 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 170 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 895 GLN B 895 GLN C 270 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28284 Z= 0.181 Angle : 0.582 9.490 38493 Z= 0.296 Chirality : 0.046 0.427 4635 Planarity : 0.004 0.047 4860 Dihedral : 9.893 84.163 5640 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.60 % Allowed : 14.58 % Favored : 82.82 % 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: -0.37 (0.14), residues: 3369 helix: 1.03 (0.19), residues: 765 sheet: 0.81 (0.19), residues: 717 loop : -1.27 (0.12), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 880 HIS 0.004 0.001 HIS C 243 PHE 0.012 0.001 PHE C 131 TYR 0.015 0.001 TYR C 263 ARG 0.006 0.000 ARG B 684 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 127 time to evaluate : 3.165 Fit side-chains REVERT: A 216 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.8069 (mmm160) REVERT: A 251 ASN cc_start: 0.7623 (t0) cc_final: 0.7419 (t0) REVERT: A 675 MET cc_start: 0.5854 (mmt) cc_final: 0.5569 (mmp) REVERT: A 894 MET cc_start: 0.8440 (OUTLIER) cc_final: 0.8077 (mtt) REVERT: A 1044 MET cc_start: 0.8829 (ptm) cc_final: 0.8468 (ptp) REVERT: B 684 ARG cc_start: 0.7610 (mmm-85) cc_final: 0.7337 (mmm-85) REVERT: B 1132 TYR cc_start: 0.7879 (t80) cc_final: 0.7447 (t80) REVERT: C 269 GLN cc_start: 0.8855 (OUTLIER) cc_final: 0.8299 (mt0) REVERT: C 562 GLN cc_start: 0.7520 (OUTLIER) cc_final: 0.6783 (tm130) REVERT: C 1044 MET cc_start: 0.8879 (ptm) cc_final: 0.8535 (ptp) REVERT: C 1100 GLN cc_start: 0.8171 (OUTLIER) cc_final: 0.7799 (pt0) outliers start: 76 outliers final: 26 residues processed: 190 average time/residue: 1.1202 time to fit residues: 261.0766 Evaluate side-chains 142 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 111 time to evaluate : 3.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 334 CYS Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 673 HIS Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 774 GLU Chi-restraints excluded: chain A residue 894 MET Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 620 MET Chi-restraints excluded: chain B residue 708 ILE Chi-restraints excluded: chain B residue 1114 THR Chi-restraints excluded: chain B residue 1130 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 134 CYS Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 269 GLN Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 369 SER Chi-restraints excluded: chain C residue 562 GLN Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 910 LEU Chi-restraints excluded: chain C residue 1100 GLN Chi-restraints excluded: chain C residue 1130 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 313 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 185 optimal weight: 0.6980 chunk 237 optimal weight: 5.9990 chunk 183 optimal weight: 5.9990 chunk 273 optimal weight: 5.9990 chunk 181 optimal weight: 0.6980 chunk 323 optimal weight: 3.9990 chunk 202 optimal weight: 3.9990 chunk 197 optimal weight: 0.9990 chunk 149 optimal weight: 4.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 626 GLN A 673 HIS B 119 ASN ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 28284 Z= 0.298 Angle : 0.630 11.304 38493 Z= 0.321 Chirality : 0.048 0.437 4635 Planarity : 0.004 0.053 4860 Dihedral : 9.847 80.149 5640 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.46 % Allowed : 14.79 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.48 (0.14), residues: 3369 helix: 0.97 (0.19), residues: 765 sheet: 0.66 (0.19), residues: 735 loop : -1.34 (0.12), residues: 1869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 880 HIS 0.006 0.001 HIS C 144 PHE 0.015 0.001 PHE A 84 TYR 0.019 0.002 TYR B 246 ARG 0.006 0.001 ARG C1085 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 114 time to evaluate : 3.180 Fit side-chains REVERT: A 216 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.8085 (mmm160) REVERT: A 251 ASN cc_start: 0.7699 (t0) cc_final: 0.7499 (t0) REVERT: A 269 GLN cc_start: 0.8961 (OUTLIER) cc_final: 0.8170 (mp10) REVERT: A 620 MET cc_start: 0.8000 (OUTLIER) cc_final: 0.6854 (mpt) REVERT: A 675 MET cc_start: 0.5990 (mmt) cc_final: 0.5602 (mmp) REVERT: A 1044 MET cc_start: 0.8862 (ptm) cc_final: 0.8299 (ptm) REVERT: B 150 TRP cc_start: 0.7417 (m-90) cc_final: 0.7214 (m-90) REVERT: B 242 LEU cc_start: 0.8072 (pp) cc_final: 0.7871 (pp) REVERT: B 1132 TYR cc_start: 0.7879 (t80) cc_final: 0.7441 (t80) REVERT: C 269 GLN cc_start: 0.8885 (OUTLIER) cc_final: 0.8299 (mt0) REVERT: C 562 GLN cc_start: 0.7577 (OUTLIER) cc_final: 0.6807 (tm130) REVERT: C 620 MET cc_start: 0.7888 (OUTLIER) cc_final: 0.6895 (mpt) REVERT: C 1044 MET cc_start: 0.8876 (ptm) cc_final: 0.8510 (ptp) REVERT: C 1108 ILE cc_start: 0.8871 (mt) cc_final: 0.8655 (mm) outliers start: 72 outliers final: 38 residues processed: 176 average time/residue: 1.1223 time to fit residues: 242.1883 Evaluate side-chains 153 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 109 time to evaluate : 3.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASN Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 269 GLN Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 334 CYS Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 620 MET Chi-restraints excluded: chain A residue 673 HIS Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 774 GLU Chi-restraints excluded: chain A residue 1130 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 134 CYS Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 620 MET Chi-restraints excluded: chain B residue 708 ILE Chi-restraints excluded: chain B residue 1114 THR Chi-restraints excluded: chain B residue 1130 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 134 CYS Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 269 GLN Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 369 SER Chi-restraints excluded: chain C residue 562 GLN Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 620 MET Chi-restraints excluded: chain C residue 910 LEU Chi-restraints excluded: chain C residue 1035 ASP Chi-restraints excluded: chain C residue 1130 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 200 optimal weight: 2.9990 chunk 129 optimal weight: 4.9990 chunk 193 optimal weight: 9.9990 chunk 97 optimal weight: 0.9980 chunk 63 optimal weight: 6.9990 chunk 62 optimal weight: 0.1980 chunk 205 optimal weight: 6.9990 chunk 220 optimal weight: 3.9990 chunk 160 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 254 optimal weight: 4.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 673 HIS ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 270 GLN C 66 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 28284 Z= 0.220 Angle : 0.594 9.542 38493 Z= 0.303 Chirality : 0.046 0.414 4635 Planarity : 0.004 0.051 4860 Dihedral : 9.678 76.795 5640 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.02 % Allowed : 15.27 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.50 (0.14), residues: 3369 helix: 0.99 (0.19), residues: 765 sheet: 0.63 (0.19), residues: 732 loop : -1.36 (0.13), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 880 HIS 0.020 0.001 HIS A 673 PHE 0.012 0.001 PHE A 390 TYR 0.018 0.001 TYR A 672 ARG 0.007 0.000 ARG C 212 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 113 time to evaluate : 3.046 Fit side-chains REVERT: A 216 ARG cc_start: 0.8360 (OUTLIER) cc_final: 0.8082 (mmm160) REVERT: A 269 GLN cc_start: 0.8953 (OUTLIER) cc_final: 0.8135 (mp10) REVERT: A 620 MET cc_start: 0.7985 (OUTLIER) cc_final: 0.6849 (mpt) REVERT: A 894 MET cc_start: 0.8436 (OUTLIER) cc_final: 0.8070 (mtt) REVERT: A 1044 MET cc_start: 0.8798 (ptm) cc_final: 0.8438 (ptp) REVERT: B 1132 TYR cc_start: 0.7865 (t80) cc_final: 0.7425 (t80) REVERT: C 269 GLN cc_start: 0.8874 (OUTLIER) cc_final: 0.8284 (mt0) REVERT: C 562 GLN cc_start: 0.7570 (OUTLIER) cc_final: 0.6829 (tm130) REVERT: C 1044 MET cc_start: 0.8858 (ptm) cc_final: 0.8532 (ptp) REVERT: C 1108 ILE cc_start: 0.8849 (mt) cc_final: 0.8647 (mm) outliers start: 59 outliers final: 35 residues processed: 160 average time/residue: 1.1186 time to fit residues: 220.4962 Evaluate side-chains 145 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 104 time to evaluate : 3.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 269 GLN Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 334 CYS Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 620 MET Chi-restraints excluded: chain A residue 673 HIS Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 774 GLU Chi-restraints excluded: chain A residue 894 MET Chi-restraints excluded: chain A residue 1130 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 134 CYS Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 620 MET Chi-restraints excluded: chain B residue 708 ILE Chi-restraints excluded: chain B residue 1114 THR Chi-restraints excluded: chain B residue 1130 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 134 CYS Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 269 GLN Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 369 SER Chi-restraints excluded: chain C residue 401 LYS Chi-restraints excluded: chain C residue 514 GLU Chi-restraints excluded: chain C residue 562 GLN Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 673 HIS Chi-restraints excluded: chain C residue 910 LEU Chi-restraints excluded: chain C residue 1130 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 294 optimal weight: 3.9990 chunk 310 optimal weight: 4.9990 chunk 283 optimal weight: 4.9990 chunk 301 optimal weight: 2.9990 chunk 181 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 236 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 272 optimal weight: 3.9990 chunk 285 optimal weight: 10.0000 chunk 300 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 GLN A 673 HIS A 895 GLN B 97 ASN ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 270 GLN B 929 GLN C 270 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 28284 Z= 0.355 Angle : 0.650 9.677 38493 Z= 0.332 Chirality : 0.049 0.430 4635 Planarity : 0.005 0.051 4860 Dihedral : 9.711 77.023 5640 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.08 % Allowed : 15.33 % Favored : 82.58 % 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: -0.61 (0.14), residues: 3369 helix: 0.89 (0.19), residues: 765 sheet: 0.57 (0.19), residues: 747 loop : -1.44 (0.12), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 150 HIS 0.021 0.001 HIS A 673 PHE 0.017 0.002 PHE A 84 TYR 0.025 0.002 TYR A 672 ARG 0.006 0.001 ARG C 212 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 105 time to evaluate : 3.022 Fit side-chains REVERT: A 216 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.8087 (mmm160) REVERT: A 269 GLN cc_start: 0.8979 (OUTLIER) cc_final: 0.7959 (mp10) REVERT: A 620 MET cc_start: 0.8025 (OUTLIER) cc_final: 0.6863 (mpt) REVERT: A 780 LYS cc_start: 0.8097 (OUTLIER) cc_final: 0.7828 (mmmt) REVERT: A 894 MET cc_start: 0.8531 (OUTLIER) cc_final: 0.8188 (mtt) REVERT: A 1044 MET cc_start: 0.8877 (ptm) cc_final: 0.8319 (ptm) REVERT: B 66 ASN cc_start: 0.8253 (OUTLIER) cc_final: 0.7991 (p0) REVERT: B 1132 TYR cc_start: 0.7886 (t80) cc_final: 0.7411 (t80) REVERT: C 269 GLN cc_start: 0.8911 (OUTLIER) cc_final: 0.8287 (mt0) REVERT: C 332 ASN cc_start: 0.8441 (OUTLIER) cc_final: 0.8024 (p0) REVERT: C 562 GLN cc_start: 0.7642 (OUTLIER) cc_final: 0.6803 (tm130) REVERT: C 620 MET cc_start: 0.7906 (OUTLIER) cc_final: 0.7176 (mpt) REVERT: C 1044 MET cc_start: 0.8895 (ptm) cc_final: 0.8543 (ptp) REVERT: C 1108 ILE cc_start: 0.8850 (mt) cc_final: 0.8650 (mm) outliers start: 61 outliers final: 35 residues processed: 152 average time/residue: 1.1329 time to fit residues: 211.9151 Evaluate side-chains 146 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 101 time to evaluate : 3.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASN Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 269 GLN Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 620 MET Chi-restraints excluded: chain A residue 673 HIS Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 774 GLU Chi-restraints excluded: chain A residue 780 LYS Chi-restraints excluded: chain A residue 894 MET Chi-restraints excluded: chain A residue 1130 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 66 ASN Chi-restraints excluded: chain B residue 134 CYS Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 620 MET Chi-restraints excluded: chain B residue 708 ILE Chi-restraints excluded: chain B residue 1114 THR Chi-restraints excluded: chain B residue 1130 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 134 CYS Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 269 GLN Chi-restraints excluded: chain C residue 332 ASN Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 369 SER Chi-restraints excluded: chain C residue 401 LYS Chi-restraints excluded: chain C residue 514 GLU Chi-restraints excluded: chain C residue 562 GLN Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 620 MET Chi-restraints excluded: chain C residue 910 LEU Chi-restraints excluded: chain C residue 1130 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 198 optimal weight: 0.9990 chunk 319 optimal weight: 5.9990 chunk 194 optimal weight: 0.0870 chunk 151 optimal weight: 0.7980 chunk 221 optimal weight: 2.9990 chunk 334 optimal weight: 2.9990 chunk 308 optimal weight: 1.9990 chunk 266 optimal weight: 0.7980 chunk 27 optimal weight: 7.9990 chunk 205 optimal weight: 5.9990 chunk 163 optimal weight: 7.9990 overall best weight: 0.9362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 895 GLN B 270 GLN B 929 GLN C 270 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 28284 Z= 0.176 Angle : 0.577 9.462 38493 Z= 0.292 Chirality : 0.046 0.410 4635 Planarity : 0.004 0.049 4860 Dihedral : 9.436 72.514 5639 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.64 % Allowed : 15.81 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.51 (0.14), residues: 3369 helix: 1.02 (0.19), residues: 762 sheet: 0.50 (0.19), residues: 756 loop : -1.34 (0.13), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 150 HIS 0.025 0.001 HIS A 673 PHE 0.010 0.001 PHE A 390 TYR 0.028 0.001 TYR A 672 ARG 0.007 0.000 ARG C 212 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 106 time to evaluate : 3.201 Fit side-chains REVERT: A 216 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.8106 (mmm160) REVERT: A 269 GLN cc_start: 0.8943 (OUTLIER) cc_final: 0.7967 (mp10) REVERT: A 620 MET cc_start: 0.7970 (OUTLIER) cc_final: 0.6829 (mpt) REVERT: A 894 MET cc_start: 0.8396 (OUTLIER) cc_final: 0.8034 (mtt) REVERT: A 1044 MET cc_start: 0.8769 (ptm) cc_final: 0.8315 (ptm) REVERT: B 66 ASN cc_start: 0.8302 (OUTLIER) cc_final: 0.8053 (p0) REVERT: B 79 ASN cc_start: 0.7364 (t0) cc_final: 0.7093 (p0) REVERT: B 1132 TYR cc_start: 0.7851 (t80) cc_final: 0.7263 (t80) REVERT: C 269 GLN cc_start: 0.8862 (OUTLIER) cc_final: 0.8271 (mt0) REVERT: C 332 ASN cc_start: 0.8437 (OUTLIER) cc_final: 0.8028 (p0) REVERT: C 1044 MET cc_start: 0.8865 (ptm) cc_final: 0.8536 (ptp) outliers start: 48 outliers final: 28 residues processed: 146 average time/residue: 1.1614 time to fit residues: 207.2734 Evaluate side-chains 139 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 104 time to evaluate : 3.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASN Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 269 GLN Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 620 MET Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 774 GLU Chi-restraints excluded: chain A residue 894 MET Chi-restraints excluded: chain A residue 1130 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 66 ASN Chi-restraints excluded: chain B residue 134 CYS Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 620 MET Chi-restraints excluded: chain B residue 708 ILE Chi-restraints excluded: chain B residue 1114 THR Chi-restraints excluded: chain B residue 1130 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 134 CYS Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 269 GLN Chi-restraints excluded: chain C residue 332 ASN Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 401 LYS Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 910 LEU Chi-restraints excluded: chain C residue 1130 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 211 optimal weight: 0.9990 chunk 283 optimal weight: 4.9990 chunk 81 optimal weight: 9.9990 chunk 245 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 74 optimal weight: 0.5980 chunk 266 optimal weight: 0.0040 chunk 111 optimal weight: 4.9990 chunk 274 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.108353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.078156 restraints weight = 47520.115| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 2.75 r_work: 0.3005 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 28284 Z= 0.147 Angle : 0.551 11.468 38493 Z= 0.275 Chirality : 0.045 0.416 4635 Planarity : 0.004 0.049 4860 Dihedral : 9.040 69.105 5639 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.23 % Allowed : 16.19 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.46 (0.14), residues: 3369 helix: 1.11 (0.19), residues: 762 sheet: 0.44 (0.19), residues: 741 loop : -1.26 (0.13), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 256 HIS 0.003 0.001 HIS B 243 PHE 0.010 0.001 PHE B1115 TYR 0.016 0.001 TYR C 503 ARG 0.007 0.000 ARG C 212 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7199.24 seconds wall clock time: 133 minutes 1.33 seconds (7981.33 seconds total)