Starting phenix.real_space_refine on Mon Mar 18 22:13:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x79_22083/03_2024/6x79_22083.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x79_22083/03_2024/6x79_22083.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x79_22083/03_2024/6x79_22083.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x79_22083/03_2024/6x79_22083.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x79_22083/03_2024/6x79_22083.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x79_22083/03_2024/6x79_22083.pdb" } resolution = 2.9 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= 0.004 sd= 0.106 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 102 5.16 5 C 14187 2.51 5 N 3660 2.21 5 O 4302 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 988": "OE1" <-> "OE2" Residue "A PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 988": "OE1" <-> "OE2" Residue "B PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 988": "OE1" <-> "OE2" Residue "C PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 22251 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 7179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 950, 7179 Classifications: {'peptide': 950} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PTRANS': 45, 'TRANS': 904} Chain breaks: 14 Unresolved non-hydrogen bonds: 260 Unresolved non-hydrogen angles: 334 Unresolved non-hydrogen dihedrals: 214 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 2, 'TYR:plan': 6, 'ASN:plan1': 6, 'ASP:plan': 13, 'PHE:plan': 3, 'GLU:plan': 6, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 186 Chain: "B" Number of atoms: 7179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 950, 7179 Classifications: {'peptide': 950} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PTRANS': 45, 'TRANS': 904} Chain breaks: 14 Unresolved non-hydrogen bonds: 260 Unresolved non-hydrogen angles: 334 Unresolved non-hydrogen dihedrals: 214 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 2, 'TYR:plan': 6, 'ASN:plan1': 6, 'ASP:plan': 13, 'PHE:plan': 3, 'GLU:plan': 6, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 186 Chain: "C" Number of atoms: 7179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 950, 7179 Classifications: {'peptide': 950} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PTRANS': 45, 'TRANS': 904} Chain breaks: 14 Unresolved non-hydrogen bonds: 260 Unresolved non-hydrogen angles: 334 Unresolved non-hydrogen dihedrals: 214 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 2, 'TYR:plan': 6, 'ASN:plan1': 6, 'ASP:plan': 13, 'PHE:plan': 3, 'GLU:plan': 6, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 186 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 12.00, per 1000 atoms: 0.54 Number of scatterers: 22251 At special positions: 0 Unit cell: (128.76, 128.76, 162.4, 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 102 16.00 O 4302 8.00 N 3660 7.00 C 14187 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.06 Simple disulfide: pdb=" SG CYS A 383 " - pdb=" SG CYS B 985 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 985 " - pdb=" SG CYS C 383 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.06 Simple disulfide: pdb=" SG CYS B 383 " - pdb=" SG CYS C 985 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.06 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.02 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG A1301 " - " ASN A 122 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 331 " " NAG A1304 " - " ASN A 343 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A 657 " " NAG A1307 " - " ASN A 709 " " NAG A1308 " - " ASN A1074 " " NAG A1309 " - " ASN A1098 " " NAG A1310 " - " ASN A1134 " " NAG A1311 " - " ASN A 603 " " NAG B1301 " - " ASN B 122 " " NAG B1302 " - " ASN B 282 " " NAG B1303 " - " ASN B 331 " " NAG B1304 " - " ASN B 343 " " NAG B1305 " - " ASN B 616 " " NAG B1306 " - " ASN B 657 " " NAG B1307 " - " ASN B 709 " " NAG B1308 " - " ASN B1074 " " NAG B1309 " - " ASN B1098 " " NAG B1310 " - " ASN B1134 " " NAG B1311 " - " ASN B 603 " " NAG C1301 " - " ASN C 122 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 343 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 657 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C1074 " " NAG C1309 " - " ASN C1098 " " NAG C1310 " - " ASN C1134 " " NAG C1311 " - " ASN C 603 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN B 234 " " NAG H 1 " - " ASN B 717 " " NAG I 1 " - " ASN B 801 " " NAG J 1 " - " ASN C 234 " " NAG K 1 " - " ASN C 717 " " NAG L 1 " - " ASN C 801 " Time building additional restraints: 8.83 Conformation dependent library (CDL) restraints added in 4.1 seconds 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5352 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 45 sheets defined 25.5% alpha, 32.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.18 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 383 through 388 removed outlier: 4.465A pdb=" N ASN A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.371A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 4.112A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.805A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 823 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.512A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.634A pdb=" N SER A 940 " --> pdb=" O ASP A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.947A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.302A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 351 through 353 No H-bonds generated for 'chain 'B' and resid 351 through 353' Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 383 through 388 removed outlier: 4.465A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.371A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 4.112A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.805A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.512A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.635A pdb=" N SER B 940 " --> pdb=" O ASP B 936 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.948A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.454A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 351 through 353 No H-bonds generated for 'chain 'C' and resid 351 through 353' Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 383 through 388 removed outlier: 4.466A pdb=" N ASN C 388 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.371A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 4.113A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.805A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 823 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.512A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.635A pdb=" N SER C 940 " --> pdb=" O ASP C 936 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.948A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.298A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.382A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.486A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.280A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.329A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 348 through 349 removed outlier: 7.172A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.376A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 348 through 349 removed outlier: 7.172A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.376A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.819A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 448 through 453 removed outlier: 5.829A pdb=" N TYR A 449 " --> pdb=" O PHE A 497 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N PHE A 497 " --> pdb=" O TYR A 449 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N TYR A 451 " --> pdb=" O TYR A 495 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.139A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.933A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.461A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.461A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.394A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.854A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.381A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.487A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 83 through 85 Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.280A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.329A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 348 through 349 removed outlier: 7.171A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.376A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 348 through 349 removed outlier: 7.171A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.376A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.820A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 448 through 453 removed outlier: 5.829A pdb=" N TYR B 449 " --> pdb=" O PHE B 497 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N PHE B 497 " --> pdb=" O TYR B 449 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N TYR B 451 " --> pdb=" O TYR B 495 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.139A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.934A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.461A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.461A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.394A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.853A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.382A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 55 removed outlier: 7.486A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 83 through 85 Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.279A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 324 through 328 removed outlier: 4.329A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 348 through 349 removed outlier: 7.172A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 9.377A pdb=" N ARG C 403 " --> pdb=" O ALA C 348 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 348 through 349 removed outlier: 7.172A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 9.377A pdb=" N ARG C 403 " --> pdb=" O ALA C 348 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.820A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 448 through 453 removed outlier: 5.829A pdb=" N TYR C 449 " --> pdb=" O PHE C 497 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N PHE C 497 " --> pdb=" O TYR C 449 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N TYR C 451 " --> pdb=" O TYR C 495 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.140A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.460A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.460A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.394A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.853A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1006 hydrogen bonds defined for protein. 2802 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: 12.24 Time building geometry restraints manager: 9.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 3922 1.32 - 1.45: 6780 1.45 - 1.59: 11860 1.59 - 1.72: 7 1.72 - 1.86: 126 Bond restraints: 22695 Sorted by residual: bond pdb=" NE ARG C 454 " pdb=" CZ ARG C 454 " ideal model delta sigma weight residual 1.326 1.383 -0.057 1.10e-02 8.26e+03 2.66e+01 bond pdb=" NE ARG B 454 " pdb=" CZ ARG B 454 " ideal model delta sigma weight residual 1.326 1.382 -0.056 1.10e-02 8.26e+03 2.62e+01 bond pdb=" NE ARG A 454 " pdb=" CZ ARG A 454 " ideal model delta sigma weight residual 1.326 1.382 -0.056 1.10e-02 8.26e+03 2.60e+01 bond pdb=" C ALA A 989 " pdb=" O ALA A 989 " ideal model delta sigma weight residual 1.236 1.183 0.053 1.15e-02 7.56e+03 2.13e+01 bond pdb=" CA ALA B 989 " pdb=" C ALA B 989 " ideal model delta sigma weight residual 1.524 1.464 0.060 1.32e-02 5.74e+03 2.05e+01 ... (remaining 22690 not shown) Histogram of bond angle deviations from ideal: 99.90 - 106.74: 651 106.74 - 113.58: 12411 113.58 - 120.42: 9017 120.42 - 127.26: 8726 127.26 - 134.10: 98 Bond angle restraints: 30903 Sorted by residual: angle pdb=" C PRO B 862 " pdb=" N PRO B 863 " pdb=" CA PRO B 863 " ideal model delta sigma weight residual 120.03 127.41 -7.38 9.90e-01 1.02e+00 5.56e+01 angle pdb=" C PRO A 862 " pdb=" N PRO A 863 " pdb=" CA PRO A 863 " ideal model delta sigma weight residual 120.03 127.41 -7.38 9.90e-01 1.02e+00 5.56e+01 angle pdb=" C PRO C 862 " pdb=" N PRO C 863 " pdb=" CA PRO C 863 " ideal model delta sigma weight residual 120.03 127.37 -7.34 9.90e-01 1.02e+00 5.50e+01 angle pdb=" C GLN A 498 " pdb=" N PRO A 499 " pdb=" CA PRO A 499 " ideal model delta sigma weight residual 119.56 126.89 -7.33 1.02e+00 9.61e-01 5.16e+01 angle pdb=" C GLN B 498 " pdb=" N PRO B 499 " pdb=" CA PRO B 499 " ideal model delta sigma weight residual 119.56 126.87 -7.31 1.02e+00 9.61e-01 5.13e+01 ... (remaining 30898 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 13550 17.69 - 35.38: 446 35.38 - 53.07: 77 53.07 - 70.76: 66 70.76 - 88.45: 15 Dihedral angle restraints: 14154 sinusoidal: 5892 harmonic: 8262 Sorted by residual: dihedral pdb=" CB CYS B 743 " pdb=" SG CYS B 743 " pdb=" SG CYS B 749 " pdb=" CB CYS B 749 " ideal model delta sinusoidal sigma weight residual -86.00 -160.35 74.35 1 1.00e+01 1.00e-02 7.01e+01 dihedral pdb=" CB CYS A 743 " pdb=" SG CYS A 743 " pdb=" SG CYS A 749 " pdb=" CB CYS A 749 " ideal model delta sinusoidal sigma weight residual -86.00 -160.35 74.35 1 1.00e+01 1.00e-02 7.01e+01 dihedral pdb=" CB CYS C 743 " pdb=" SG CYS C 743 " pdb=" SG CYS C 749 " pdb=" CB CYS C 749 " ideal model delta sinusoidal sigma weight residual -86.00 -160.35 74.35 1 1.00e+01 1.00e-02 7.01e+01 ... (remaining 14151 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 2733 0.084 - 0.168: 759 0.168 - 0.252: 162 0.252 - 0.336: 68 0.336 - 0.420: 46 Chirality restraints: 3768 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.53 0.13 2.00e-02 2.50e+03 4.54e+01 chirality pdb=" C1 NAG L 2 " pdb=" O4 NAG L 1 " pdb=" C2 NAG L 2 " pdb=" O5 NAG L 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.53 0.13 2.00e-02 2.50e+03 4.46e+01 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.53 0.13 2.00e-02 2.50e+03 4.34e+01 ... (remaining 3765 not shown) Planarity restraints: 3948 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 331 " -0.051 2.00e-02 2.50e+03 5.19e-02 3.37e+01 pdb=" CG ASN B 331 " 0.027 2.00e-02 2.50e+03 pdb=" OD1 ASN B 331 " 0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN B 331 " 0.077 2.00e-02 2.50e+03 pdb=" C1 NAG B1303 " -0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " 0.051 2.00e-02 2.50e+03 5.18e-02 3.36e+01 pdb=" CG ASN A 331 " -0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " -0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " -0.077 2.00e-02 2.50e+03 pdb=" C1 NAG A1303 " 0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 331 " 0.051 2.00e-02 2.50e+03 5.16e-02 3.33e+01 pdb=" CG ASN C 331 " -0.027 2.00e-02 2.50e+03 pdb=" OD1 ASN C 331 " -0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN C 331 " -0.077 2.00e-02 2.50e+03 pdb=" C1 NAG C1303 " 0.063 2.00e-02 2.50e+03 ... (remaining 3945 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.89: 7957 2.89 - 3.39: 19584 3.39 - 3.89: 36598 3.89 - 4.40: 41744 4.40 - 4.90: 70192 Nonbonded interactions: 176075 Sorted by model distance: nonbonded pdb=" NZ LYS C 811 " pdb=" OD2 ASP C 820 " model vdw 2.382 2.520 nonbonded pdb=" NZ LYS A 811 " pdb=" OD2 ASP A 820 " model vdw 2.382 2.520 nonbonded pdb=" NZ LYS B 811 " pdb=" OD2 ASP B 820 " model vdw 2.383 2.520 nonbonded pdb=" N PRO C 600 " pdb=" O PRO C 600 " model vdw 2.495 2.496 nonbonded pdb=" N PRO B 600 " pdb=" O PRO B 600 " model vdw 2.495 2.496 ... (remaining 176070 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' } 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: 2.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 9.860 Check model and map are aligned: 0.300 Set scattering table: 0.170 Process input model: 63.470 Find NCS groups from input model: 1.380 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.088 22695 Z= 0.898 Angle : 1.346 8.268 30903 Z= 0.901 Chirality : 0.096 0.420 3768 Planarity : 0.005 0.042 3906 Dihedral : 10.282 88.451 8685 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 0.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.26 % Allowed : 0.39 % Favored : 99.35 % 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: 0.59 (0.14), residues: 2760 helix: 0.27 (0.18), residues: 654 sheet: 1.47 (0.19), residues: 603 loop : 0.09 (0.14), residues: 1503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.006 TRP B 886 HIS 0.003 0.001 HIS C1083 PHE 0.018 0.003 PHE A 58 TYR 0.027 0.004 TYR B 170 ARG 0.004 0.001 ARG C1000 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 484 time to evaluate : 2.549 Fit side-chains revert: symmetry clash REVERT: A 306 PHE cc_start: 0.7828 (m-10) cc_final: 0.7606 (m-80) REVERT: A 787 GLN cc_start: 0.6897 (mt0) cc_final: 0.6659 (mt0) REVERT: A 856 ASN cc_start: 0.7091 (m-40) cc_final: 0.6869 (m-40) REVERT: B 523 THR cc_start: 0.7236 (p) cc_final: 0.6922 (t) REVERT: B 773 GLU cc_start: 0.7178 (tt0) cc_final: 0.6886 (tt0) REVERT: B 786 LYS cc_start: 0.7222 (mtmm) cc_final: 0.7000 (mmtt) REVERT: B 856 ASN cc_start: 0.7135 (m-40) cc_final: 0.6902 (m-40) REVERT: C 731 MET cc_start: 0.8803 (ptm) cc_final: 0.8482 (ptm) REVERT: C 856 ASN cc_start: 0.6953 (m-40) cc_final: 0.6729 (m110) outliers start: 6 outliers final: 4 residues processed: 490 average time/residue: 1.1129 time to fit residues: 633.7913 Evaluate side-chains 254 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 250 time to evaluate : 2.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 985 CYS Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 985 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 240 optimal weight: 0.8980 chunk 216 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 145 optimal weight: 3.9990 chunk 115 optimal weight: 0.6980 chunk 223 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 chunk 135 optimal weight: 5.9990 chunk 166 optimal weight: 0.7980 chunk 258 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 580 GLN A 675 GLN A 935 GLN A1010 GLN A1113 GLN B 207 HIS B 580 GLN B 675 GLN ** B 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 ASN B 935 GLN B 965 GLN B1113 GLN B1119 ASN C 580 GLN C 675 GLN C 762 GLN C 804 GLN C 919 ASN C 935 GLN C 954 GLN C 965 GLN C1010 GLN C1113 GLN C1119 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 22695 Z= 0.242 Angle : 0.606 8.766 30903 Z= 0.328 Chirality : 0.047 0.220 3768 Planarity : 0.004 0.041 3906 Dihedral : 6.050 57.284 4071 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 2.79 % Allowed : 9.41 % Favored : 87.80 % 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: 0.73 (0.15), residues: 2760 helix: 1.23 (0.20), residues: 672 sheet: 1.02 (0.18), residues: 690 loop : -0.09 (0.15), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 886 HIS 0.004 0.001 HIS C1064 PHE 0.025 0.002 PHE B 92 TYR 0.019 0.001 TYR A1067 ARG 0.005 0.001 ARG B 567 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 281 time to evaluate : 2.570 Fit side-chains revert: symmetry clash REVERT: A 195 LYS cc_start: 0.8109 (ptpp) cc_final: 0.7876 (ptpp) REVERT: A 513 LEU cc_start: 0.7298 (mt) cc_final: 0.7007 (mt) REVERT: A 591 SER cc_start: 0.7819 (OUTLIER) cc_final: 0.7602 (m) REVERT: A 645 THR cc_start: 0.7859 (p) cc_final: 0.7504 (t) REVERT: A 787 GLN cc_start: 0.6648 (mt0) cc_final: 0.6414 (mt0) REVERT: A 918 GLU cc_start: 0.7149 (OUTLIER) cc_final: 0.5885 (mp0) REVERT: A 995 ARG cc_start: 0.7635 (OUTLIER) cc_final: 0.7252 (mmm-85) REVERT: B 368 LEU cc_start: 0.7382 (mp) cc_final: 0.7122 (mp) REVERT: B 523 THR cc_start: 0.7658 (p) cc_final: 0.7322 (t) REVERT: B 995 ARG cc_start: 0.7691 (OUTLIER) cc_final: 0.6747 (mpp80) REVERT: C 303 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7652 (mt) REVERT: C 567 ARG cc_start: 0.6603 (mtt90) cc_final: 0.6355 (mpt180) REVERT: C 612 TYR cc_start: 0.8233 (m-80) cc_final: 0.8006 (m-80) REVERT: C 731 MET cc_start: 0.8752 (ptm) cc_final: 0.8396 (ptm) REVERT: C 979 ASP cc_start: 0.7653 (m-30) cc_final: 0.7429 (m-30) outliers start: 64 outliers final: 24 residues processed: 326 average time/residue: 1.0535 time to fit residues: 404.3029 Evaluate side-chains 244 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 215 time to evaluate : 2.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 985 CYS Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 995 ARG Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 776 LYS Chi-restraints excluded: chain C residue 985 CYS Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 1077 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 143 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 215 optimal weight: 9.9990 chunk 176 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 259 optimal weight: 0.8980 chunk 280 optimal weight: 1.9990 chunk 230 optimal weight: 5.9990 chunk 257 optimal weight: 0.0770 chunk 88 optimal weight: 0.9990 chunk 208 optimal weight: 3.9990 overall best weight: 0.7942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 935 GLN A1010 GLN B 613 GLN B 675 GLN B 914 ASN B1010 GLN B1071 GLN C 87 ASN C 544 ASN C 644 GLN C1010 GLN C1119 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 22695 Z= 0.243 Angle : 0.540 6.048 30903 Z= 0.290 Chirality : 0.045 0.192 3768 Planarity : 0.004 0.034 3906 Dihedral : 5.361 48.097 4071 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 3.83 % Allowed : 10.76 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.15), residues: 2760 helix: 1.41 (0.20), residues: 672 sheet: 0.78 (0.18), residues: 687 loop : -0.28 (0.15), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 353 HIS 0.005 0.001 HIS C1064 PHE 0.023 0.002 PHE B 55 TYR 0.019 0.001 TYR A1067 ARG 0.006 0.001 ARG C 319 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 243 time to evaluate : 2.468 Fit side-chains revert: symmetry clash REVERT: A 50 SER cc_start: 0.7795 (t) cc_final: 0.7473 (t) REVERT: A 196 ASN cc_start: 0.8064 (t0) cc_final: 0.7786 (m110) REVERT: A 513 LEU cc_start: 0.7476 (mt) cc_final: 0.7116 (mt) REVERT: A 576 VAL cc_start: 0.8704 (t) cc_final: 0.8497 (p) REVERT: A 731 MET cc_start: 0.8653 (ptt) cc_final: 0.8371 (ptt) REVERT: A 787 GLN cc_start: 0.6751 (mt0) cc_final: 0.6527 (mt0) REVERT: A 918 GLU cc_start: 0.7097 (OUTLIER) cc_final: 0.5870 (mp0) REVERT: A 995 ARG cc_start: 0.7557 (OUTLIER) cc_final: 0.7253 (mtm-85) REVERT: B 584 ILE cc_start: 0.7093 (OUTLIER) cc_final: 0.6432 (mm) REVERT: B 995 ARG cc_start: 0.7660 (OUTLIER) cc_final: 0.6762 (mpp80) REVERT: B 1010 GLN cc_start: 0.7468 (pt0) cc_final: 0.7187 (pt0) REVERT: C 368 LEU cc_start: 0.7373 (mp) cc_final: 0.7036 (mp) REVERT: C 567 ARG cc_start: 0.6787 (mtt90) cc_final: 0.6458 (mpt180) REVERT: C 731 MET cc_start: 0.8796 (ptm) cc_final: 0.8480 (ptm) REVERT: C 979 ASP cc_start: 0.7720 (m-30) cc_final: 0.7495 (m-30) outliers start: 88 outliers final: 40 residues processed: 304 average time/residue: 0.9283 time to fit residues: 337.7100 Evaluate side-chains 263 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 219 time to evaluate : 2.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 383 CYS Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 985 CYS Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 995 ARG Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 985 CYS Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1077 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 256 optimal weight: 4.9990 chunk 194 optimal weight: 4.9990 chunk 134 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 123 optimal weight: 9.9990 chunk 174 optimal weight: 0.7980 chunk 260 optimal weight: 1.9990 chunk 275 optimal weight: 0.4980 chunk 135 optimal weight: 5.9990 chunk 246 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 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 613 GLN A 965 GLN A1010 GLN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B 965 GLN C 613 GLN C 644 GLN C 675 GLN C1010 GLN C1119 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 22695 Z= 0.239 Angle : 0.525 6.365 30903 Z= 0.279 Chirality : 0.045 0.199 3768 Planarity : 0.004 0.037 3906 Dihedral : 5.056 48.670 4071 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 4.01 % Allowed : 11.50 % Favored : 84.49 % 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: 0.48 (0.15), residues: 2760 helix: 1.47 (0.20), residues: 672 sheet: 0.65 (0.18), residues: 696 loop : -0.38 (0.15), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 353 HIS 0.004 0.001 HIS C1064 PHE 0.018 0.002 PHE B 92 TYR 0.019 0.001 TYR A1067 ARG 0.008 0.001 ARG C 319 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 248 time to evaluate : 2.557 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 SER cc_start: 0.7809 (t) cc_final: 0.7528 (t) REVERT: A 196 ASN cc_start: 0.8192 (t0) cc_final: 0.7734 (m110) REVERT: A 368 LEU cc_start: 0.7220 (mp) cc_final: 0.6888 (mp) REVERT: A 513 LEU cc_start: 0.7502 (mt) cc_final: 0.7240 (mt) REVERT: A 645 THR cc_start: 0.7782 (p) cc_final: 0.7473 (t) REVERT: A 731 MET cc_start: 0.8672 (ptt) cc_final: 0.8306 (ptt) REVERT: A 787 GLN cc_start: 0.6879 (mt0) cc_final: 0.6630 (mt0) REVERT: A 918 GLU cc_start: 0.7083 (OUTLIER) cc_final: 0.5864 (mp0) REVERT: A 995 ARG cc_start: 0.7570 (OUTLIER) cc_final: 0.7225 (mmm-85) REVERT: B 584 ILE cc_start: 0.7087 (OUTLIER) cc_final: 0.6376 (mm) REVERT: B 786 LYS cc_start: 0.7495 (mmtt) cc_final: 0.7163 (mmtt) REVERT: B 995 ARG cc_start: 0.7598 (OUTLIER) cc_final: 0.6632 (mpp80) REVERT: C 403 ARG cc_start: 0.6255 (ttp-170) cc_final: 0.5627 (mpt180) REVERT: C 584 ILE cc_start: 0.7381 (OUTLIER) cc_final: 0.6520 (mm) REVERT: C 641 ASN cc_start: 0.6330 (OUTLIER) cc_final: 0.5895 (m110) REVERT: C 731 MET cc_start: 0.8814 (ptm) cc_final: 0.8483 (ptm) outliers start: 92 outliers final: 53 residues processed: 310 average time/residue: 0.9169 time to fit residues: 341.2625 Evaluate side-chains 282 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 223 time to evaluate : 2.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 383 CYS Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 985 CYS Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 995 ARG Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1123 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 229 optimal weight: 0.0970 chunk 156 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 205 optimal weight: 0.9980 chunk 113 optimal weight: 3.9990 chunk 235 optimal weight: 1.9990 chunk 190 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 140 optimal weight: 4.9990 chunk 247 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 overall best weight: 1.0180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 GLN A 965 GLN A1010 GLN A1071 GLN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN B 675 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN C 613 GLN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN C1010 GLN C1071 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 22695 Z= 0.280 Angle : 0.546 6.844 30903 Z= 0.288 Chirality : 0.046 0.161 3768 Planarity : 0.004 0.035 3906 Dihedral : 4.892 46.256 4068 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.97 % Allowed : 12.64 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.15), residues: 2760 helix: 1.42 (0.20), residues: 672 sheet: 0.52 (0.18), residues: 693 loop : -0.54 (0.15), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP B 353 HIS 0.005 0.001 HIS C1064 PHE 0.026 0.002 PHE B 55 TYR 0.020 0.001 TYR A1067 ARG 0.007 0.001 ARG C 319 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 231 time to evaluate : 2.717 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 SER cc_start: 0.7903 (t) cc_final: 0.7601 (t) REVERT: A 196 ASN cc_start: 0.8359 (t0) cc_final: 0.7841 (m110) REVERT: A 585 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8034 (mt) REVERT: A 731 MET cc_start: 0.8677 (ptt) cc_final: 0.8387 (ptt) REVERT: A 787 GLN cc_start: 0.7020 (mt0) cc_final: 0.6767 (mt0) REVERT: A 918 GLU cc_start: 0.7087 (OUTLIER) cc_final: 0.5937 (mp0) REVERT: A 995 ARG cc_start: 0.7594 (OUTLIER) cc_final: 0.7266 (mtm-85) REVERT: B 584 ILE cc_start: 0.7111 (OUTLIER) cc_final: 0.6355 (mm) REVERT: B 995 ARG cc_start: 0.7709 (OUTLIER) cc_final: 0.6700 (mpp80) REVERT: C 403 ARG cc_start: 0.6359 (ttp-170) cc_final: 0.5712 (mpt180) REVERT: C 513 LEU cc_start: 0.6861 (OUTLIER) cc_final: 0.6596 (mp) REVERT: C 584 ILE cc_start: 0.7358 (OUTLIER) cc_final: 0.6568 (mm) REVERT: C 641 ASN cc_start: 0.6508 (OUTLIER) cc_final: 0.6134 (m110) REVERT: C 731 MET cc_start: 0.8776 (ptm) cc_final: 0.8427 (ptm) outliers start: 91 outliers final: 51 residues processed: 299 average time/residue: 0.9664 time to fit residues: 345.9756 Evaluate side-chains 276 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 217 time to evaluate : 1.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 383 CYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 985 CYS Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 995 ARG Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1077 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 92 optimal weight: 0.0570 chunk 248 optimal weight: 0.9990 chunk 54 optimal weight: 0.5980 chunk 161 optimal weight: 0.0000 chunk 68 optimal weight: 0.9980 chunk 275 optimal weight: 0.9980 chunk 228 optimal weight: 7.9990 chunk 127 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 overall best weight: 0.5302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 965 GLN A1010 GLN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 784 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C 644 GLN C 675 GLN C1010 GLN C1119 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22695 Z= 0.179 Angle : 0.490 6.697 30903 Z= 0.259 Chirality : 0.044 0.164 3768 Planarity : 0.004 0.036 3906 Dihedral : 4.682 49.472 4068 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 3.57 % Allowed : 13.46 % Favored : 82.96 % 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: 0.46 (0.15), residues: 2760 helix: 1.64 (0.21), residues: 672 sheet: 0.62 (0.19), residues: 696 loop : -0.50 (0.15), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 353 HIS 0.002 0.001 HIS C1064 PHE 0.023 0.001 PHE B 55 TYR 0.018 0.001 TYR A1067 ARG 0.008 0.000 ARG A 983 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 234 time to evaluate : 2.616 Fit side-chains revert: symmetry clash REVERT: A 50 SER cc_start: 0.7840 (t) cc_final: 0.7533 (t) REVERT: A 196 ASN cc_start: 0.8362 (t0) cc_final: 0.7876 (m110) REVERT: A 201 PHE cc_start: 0.7621 (t80) cc_final: 0.7380 (t80) REVERT: A 513 LEU cc_start: 0.7476 (mt) cc_final: 0.7211 (mt) REVERT: A 585 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8022 (mt) REVERT: A 645 THR cc_start: 0.7691 (p) cc_final: 0.7326 (t) REVERT: A 731 MET cc_start: 0.8647 (ptt) cc_final: 0.8337 (ptt) REVERT: A 787 GLN cc_start: 0.6956 (mt0) cc_final: 0.6712 (mt0) REVERT: A 918 GLU cc_start: 0.7038 (OUTLIER) cc_final: 0.5847 (mp0) REVERT: A 995 ARG cc_start: 0.7563 (OUTLIER) cc_final: 0.7252 (mtm-85) REVERT: B 584 ILE cc_start: 0.7158 (OUTLIER) cc_final: 0.6430 (mm) REVERT: B 886 TRP cc_start: 0.7088 (p90) cc_final: 0.6867 (p90) REVERT: B 995 ARG cc_start: 0.7633 (OUTLIER) cc_final: 0.6790 (mpp80) REVERT: B 1125 ASN cc_start: 0.6617 (OUTLIER) cc_final: 0.6319 (p0) REVERT: C 513 LEU cc_start: 0.6805 (OUTLIER) cc_final: 0.6556 (mp) REVERT: C 584 ILE cc_start: 0.7268 (OUTLIER) cc_final: 0.6461 (mm) REVERT: C 641 ASN cc_start: 0.6422 (OUTLIER) cc_final: 0.6069 (m110) REVERT: C 731 MET cc_start: 0.8771 (ptm) cc_final: 0.8459 (ptm) REVERT: C 1038 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8578 (tppt) outliers start: 82 outliers final: 42 residues processed: 289 average time/residue: 0.8668 time to fit residues: 305.1823 Evaluate side-chains 269 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 217 time to evaluate : 2.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 383 CYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 383 CYS Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 985 CYS Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 995 ARG Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 1038 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 265 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 157 optimal weight: 2.9990 chunk 201 optimal weight: 4.9990 chunk 156 optimal weight: 0.9980 chunk 232 optimal weight: 3.9990 chunk 153 optimal weight: 0.7980 chunk 274 optimal weight: 1.9990 chunk 171 optimal weight: 0.8980 chunk 167 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 965 GLN A1010 GLN A1135 ASN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 784 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN B1135 ASN ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN C 784 GLN C1010 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 22695 Z= 0.346 Angle : 0.580 7.899 30903 Z= 0.302 Chirality : 0.047 0.180 3768 Planarity : 0.004 0.033 3906 Dihedral : 4.997 47.907 4068 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 4.23 % Allowed : 13.55 % Favored : 82.22 % 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: 0.17 (0.15), residues: 2760 helix: 1.29 (0.20), residues: 672 sheet: 0.54 (0.19), residues: 678 loop : -0.66 (0.15), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP A 353 HIS 0.005 0.001 HIS C1064 PHE 0.025 0.002 PHE B 92 TYR 0.020 0.002 TYR A1067 ARG 0.005 0.001 ARG C 319 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 222 time to evaluate : 2.669 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 SER cc_start: 0.7908 (t) cc_final: 0.7626 (t) REVERT: A 584 ILE cc_start: 0.7774 (OUTLIER) cc_final: 0.7337 (mm) REVERT: A 585 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8089 (mt) REVERT: A 731 MET cc_start: 0.8731 (ptt) cc_final: 0.8402 (ptt) REVERT: A 787 GLN cc_start: 0.7114 (mt0) cc_final: 0.6864 (mt0) REVERT: A 918 GLU cc_start: 0.7079 (OUTLIER) cc_final: 0.5919 (mp0) REVERT: B 403 ARG cc_start: 0.6381 (ttp-170) cc_final: 0.5943 (mpt180) REVERT: B 584 ILE cc_start: 0.7196 (OUTLIER) cc_final: 0.6454 (mm) REVERT: B 725 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7699 (tt0) REVERT: B 995 ARG cc_start: 0.7776 (OUTLIER) cc_final: 0.6895 (mpp80) REVERT: B 1125 ASN cc_start: 0.6777 (OUTLIER) cc_final: 0.6299 (p0) REVERT: C 403 ARG cc_start: 0.6340 (ttp-170) cc_final: 0.5754 (mpt180) REVERT: C 513 LEU cc_start: 0.6967 (OUTLIER) cc_final: 0.6624 (mp) REVERT: C 584 ILE cc_start: 0.7520 (OUTLIER) cc_final: 0.6769 (mm) REVERT: C 641 ASN cc_start: 0.6594 (OUTLIER) cc_final: 0.6185 (m110) REVERT: C 731 MET cc_start: 0.8752 (ptm) cc_final: 0.8405 (ptm) outliers start: 97 outliers final: 63 residues processed: 291 average time/residue: 0.8671 time to fit residues: 306.5234 Evaluate side-chains 288 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 215 time to evaluate : 2.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 383 CYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 383 CYS Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 985 CYS Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 995 ARG Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 169 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 chunk 164 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 174 optimal weight: 1.9990 chunk 187 optimal weight: 0.8980 chunk 135 optimal weight: 1.9990 chunk 25 optimal weight: 8.9990 chunk 215 optimal weight: 4.9990 chunk 249 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1010 GLN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 784 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN C 784 GLN C1010 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 22695 Z= 0.257 Angle : 0.535 7.707 30903 Z= 0.279 Chirality : 0.045 0.374 3768 Planarity : 0.004 0.036 3906 Dihedral : 4.962 49.136 4068 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.57 % Allowed : 14.47 % Favored : 81.96 % 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: 0.16 (0.15), residues: 2760 helix: 1.39 (0.21), residues: 672 sheet: 0.43 (0.19), residues: 708 loop : -0.70 (0.15), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 353 HIS 0.004 0.001 HIS C1064 PHE 0.028 0.001 PHE B 92 TYR 0.019 0.001 TYR A1067 ARG 0.009 0.001 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 215 time to evaluate : 2.454 Fit side-chains revert: symmetry clash REVERT: A 50 SER cc_start: 0.7905 (t) cc_final: 0.7605 (t) REVERT: A 513 LEU cc_start: 0.7527 (mt) cc_final: 0.7276 (mt) REVERT: A 585 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8018 (mt) REVERT: A 731 MET cc_start: 0.8730 (ptt) cc_final: 0.8390 (ptt) REVERT: A 787 GLN cc_start: 0.7092 (mt0) cc_final: 0.6847 (mt0) REVERT: A 918 GLU cc_start: 0.7081 (OUTLIER) cc_final: 0.5926 (mp0) REVERT: A 995 ARG cc_start: 0.7614 (OUTLIER) cc_final: 0.7249 (mmm-85) REVERT: B 403 ARG cc_start: 0.6391 (ttp-170) cc_final: 0.5962 (mpt180) REVERT: B 584 ILE cc_start: 0.7118 (OUTLIER) cc_final: 0.6422 (mm) REVERT: B 886 TRP cc_start: 0.7011 (p90) cc_final: 0.6790 (p90) REVERT: B 995 ARG cc_start: 0.7684 (OUTLIER) cc_final: 0.6930 (mpp80) REVERT: B 1125 ASN cc_start: 0.6733 (OUTLIER) cc_final: 0.6266 (p0) REVERT: C 403 ARG cc_start: 0.6479 (ttp-170) cc_final: 0.5738 (mpt180) REVERT: C 513 LEU cc_start: 0.6886 (OUTLIER) cc_final: 0.6575 (mp) REVERT: C 584 ILE cc_start: 0.7493 (OUTLIER) cc_final: 0.6732 (mm) REVERT: C 641 ASN cc_start: 0.6554 (OUTLIER) cc_final: 0.6166 (m110) REVERT: C 731 MET cc_start: 0.8721 (ptm) cc_final: 0.8393 (ptm) REVERT: C 918 GLU cc_start: 0.6886 (OUTLIER) cc_final: 0.6674 (mt-10) REVERT: C 1038 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.8611 (tppt) outliers start: 82 outliers final: 59 residues processed: 276 average time/residue: 0.8873 time to fit residues: 297.0965 Evaluate side-chains 280 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 210 time to evaluate : 2.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 383 CYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 383 CYS Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 985 CYS Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 995 ARG Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 263 optimal weight: 1.9990 chunk 240 optimal weight: 0.7980 chunk 255 optimal weight: 0.9990 chunk 154 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 201 optimal weight: 0.4980 chunk 78 optimal weight: 1.9990 chunk 231 optimal weight: 3.9990 chunk 242 optimal weight: 2.9990 chunk 168 optimal weight: 1.9990 chunk 270 optimal weight: 2.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN B 784 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN C 784 GLN C1010 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.4114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 22695 Z= 0.326 Angle : 0.579 10.668 30903 Z= 0.299 Chirality : 0.046 0.205 3768 Planarity : 0.004 0.035 3906 Dihedral : 5.209 48.063 4068 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.75 % Allowed : 14.60 % Favored : 81.66 % 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: -0.02 (0.15), residues: 2760 helix: 1.25 (0.21), residues: 672 sheet: 0.33 (0.19), residues: 705 loop : -0.81 (0.15), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP B 353 HIS 0.005 0.001 HIS C1064 PHE 0.028 0.002 PHE B 92 TYR 0.020 0.001 TYR A1067 ARG 0.008 0.001 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 218 time to evaluate : 2.277 Fit side-chains revert: symmetry clash REVERT: A 50 SER cc_start: 0.7897 (t) cc_final: 0.7607 (t) REVERT: A 319 ARG cc_start: 0.6578 (mtp-110) cc_final: 0.6170 (tmt-80) REVERT: A 584 ILE cc_start: 0.7748 (OUTLIER) cc_final: 0.7300 (mm) REVERT: A 585 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8000 (mt) REVERT: A 731 MET cc_start: 0.8745 (ptt) cc_final: 0.8379 (ptt) REVERT: A 918 GLU cc_start: 0.7108 (OUTLIER) cc_final: 0.5943 (mp0) REVERT: A 950 ASP cc_start: 0.7703 (m-30) cc_final: 0.7442 (m-30) REVERT: B 403 ARG cc_start: 0.6422 (ttp-170) cc_final: 0.5998 (mpt180) REVERT: B 584 ILE cc_start: 0.7175 (OUTLIER) cc_final: 0.6484 (mm) REVERT: B 886 TRP cc_start: 0.7031 (p90) cc_final: 0.6797 (p90) REVERT: B 995 ARG cc_start: 0.7744 (OUTLIER) cc_final: 0.6973 (mpp80) REVERT: B 1125 ASN cc_start: 0.6875 (OUTLIER) cc_final: 0.6429 (p0) REVERT: C 403 ARG cc_start: 0.6559 (ttp-170) cc_final: 0.5820 (mpt180) REVERT: C 513 LEU cc_start: 0.6986 (OUTLIER) cc_final: 0.6617 (mp) REVERT: C 584 ILE cc_start: 0.7574 (OUTLIER) cc_final: 0.6843 (mm) REVERT: C 641 ASN cc_start: 0.6566 (OUTLIER) cc_final: 0.6157 (m110) REVERT: C 731 MET cc_start: 0.8739 (ptm) cc_final: 0.8416 (ptm) REVERT: C 740 MET cc_start: 0.7306 (ttp) cc_final: 0.7073 (ttt) REVERT: C 918 GLU cc_start: 0.6974 (OUTLIER) cc_final: 0.6757 (mt-10) REVERT: C 1038 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8610 (tppt) outliers start: 86 outliers final: 60 residues processed: 285 average time/residue: 0.8570 time to fit residues: 296.5588 Evaluate side-chains 280 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 209 time to evaluate : 2.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 383 CYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 383 CYS Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 985 CYS Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 995 ARG Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 165 optimal weight: 1.9990 chunk 128 optimal weight: 0.6980 chunk 188 optimal weight: 2.9990 chunk 283 optimal weight: 3.9990 chunk 261 optimal weight: 0.3980 chunk 226 optimal weight: 7.9990 chunk 23 optimal weight: 0.6980 chunk 174 optimal weight: 0.9990 chunk 138 optimal weight: 3.9990 chunk 179 optimal weight: 0.6980 chunk 240 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1010 GLN A1119 ASN B 784 GLN B 914 ASN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN C 784 GLN C1010 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.4162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 22695 Z= 0.209 Angle : 0.520 9.662 30903 Z= 0.270 Chirality : 0.044 0.189 3768 Planarity : 0.004 0.037 3906 Dihedral : 5.046 49.940 4068 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.22 % Allowed : 15.38 % Favored : 81.39 % 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: 0.17 (0.15), residues: 2760 helix: 1.49 (0.21), residues: 672 sheet: 0.40 (0.19), residues: 699 loop : -0.70 (0.15), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP B 353 HIS 0.003 0.001 HIS C1064 PHE 0.024 0.001 PHE B 92 TYR 0.019 0.001 TYR A1067 ARG 0.008 0.000 ARG A 983 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 218 time to evaluate : 2.355 Fit side-chains revert: symmetry clash REVERT: A 50 SER cc_start: 0.7877 (t) cc_final: 0.7559 (t) REVERT: A 513 LEU cc_start: 0.7550 (mt) cc_final: 0.7309 (mt) REVERT: A 731 MET cc_start: 0.8721 (ptt) cc_final: 0.8408 (ptt) REVERT: A 918 GLU cc_start: 0.7054 (OUTLIER) cc_final: 0.5846 (mp0) REVERT: A 950 ASP cc_start: 0.7598 (m-30) cc_final: 0.7338 (m-30) REVERT: A 995 ARG cc_start: 0.7621 (OUTLIER) cc_final: 0.7267 (mtm-85) REVERT: B 403 ARG cc_start: 0.6431 (ttp-170) cc_final: 0.5950 (mpt180) REVERT: B 584 ILE cc_start: 0.7202 (OUTLIER) cc_final: 0.6517 (mm) REVERT: B 995 ARG cc_start: 0.7634 (OUTLIER) cc_final: 0.6856 (mpp80) REVERT: C 403 ARG cc_start: 0.6562 (ttp-170) cc_final: 0.5819 (mpt180) REVERT: C 584 ILE cc_start: 0.7429 (OUTLIER) cc_final: 0.6662 (mm) REVERT: C 641 ASN cc_start: 0.6496 (OUTLIER) cc_final: 0.6105 (m110) REVERT: C 731 MET cc_start: 0.8708 (ptm) cc_final: 0.8384 (ptm) REVERT: C 918 GLU cc_start: 0.6824 (OUTLIER) cc_final: 0.6615 (mp0) REVERT: C 1038 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.8592 (tppt) outliers start: 74 outliers final: 53 residues processed: 276 average time/residue: 0.8572 time to fit residues: 288.3287 Evaluate side-chains 272 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 211 time to evaluate : 2.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 383 CYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 383 CYS Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 985 CYS Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 995 ARG Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1077 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 69 optimal weight: 1.9990 chunk 208 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 62 optimal weight: 0.6980 chunk 226 optimal weight: 8.9990 chunk 94 optimal weight: 0.9980 chunk 232 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 41 optimal weight: 0.0030 chunk 198 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 965 GLN A1010 GLN B 784 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN C 784 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.199629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.154209 restraints weight = 25880.188| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 2.55 r_work: 0.3586 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3446 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.4234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22695 Z= 0.201 Angle : 0.519 9.529 30903 Z= 0.268 Chirality : 0.044 0.180 3768 Planarity : 0.004 0.036 3906 Dihedral : 4.965 51.353 4068 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.92 % Allowed : 15.77 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.16), residues: 2760 helix: 1.64 (0.21), residues: 666 sheet: 0.43 (0.19), residues: 699 loop : -0.70 (0.15), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP B 353 HIS 0.003 0.001 HIS C1064 PHE 0.026 0.001 PHE C 565 TYR 0.019 0.001 TYR A1067 ARG 0.015 0.001 ARG C 357 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6774.80 seconds wall clock time: 120 minutes 59.63 seconds (7259.63 seconds total)