Starting phenix.real_space_refine on Thu Jul 25 04:50:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrv_14922/07_2024/7zrv_14922.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrv_14922/07_2024/7zrv_14922.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrv_14922/07_2024/7zrv_14922.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrv_14922/07_2024/7zrv_14922.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrv_14922/07_2024/7zrv_14922.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrv_14922/07_2024/7zrv_14922.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.023 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 119 5.16 5 C 17846 2.51 5 N 4582 2.21 5 O 5508 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 950": "OD1" <-> "OD2" Residue "A ASP 979": "OD1" <-> "OD2" Residue "B PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 428": "OD1" <-> "OD2" Residue "B TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1127": "OD1" <-> "OD2" Residue "C PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 287": "OD1" <-> "OD2" Residue "C TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 554": "OE1" <-> "OE2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 868": "OE1" <-> "OE2" Residue "C PHE 981": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 990": "OE1" <-> "OE2" Residue "F TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 28055 Number of models: 1 Model: "" Number of chains: 38 Chain: "A" Number of atoms: 8623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1103, 8623 Classifications: {'peptide': 1103} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 56, 'TRANS': 1046} Chain breaks: 4 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 8589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1096, 8589 Classifications: {'peptide': 1096} Link IDs: {'PTRANS': 56, 'TRANS': 1039} Chain breaks: 4 Chain: "C" Number of atoms: 8609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1100, 8609 Classifications: {'peptide': 1100} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 56, 'TRANS': 1043} Chain breaks: 3 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 519 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 5, 'TRANS': 59} Chain: "F" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 519 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 5, 'TRANS': 59} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "b" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 15.49, per 1000 atoms: 0.55 Number of scatterers: 28055 At special positions: 0 Unit cell: (146.87, 151.807, 209.814, 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 119 16.00 O 5508 8.00 N 4582 7.00 C 17846 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 132 " - pdb=" SG CYS A 164 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.02 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 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 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 132 " - pdb=" SG CYS B 164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 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 B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 132 " - pdb=" SG CYS C 164 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 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 C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " 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-ASN " NAG A1301 " - " ASN A 657 " " NAG A1302 " - " ASN A 616 " " NAG A1303 " - " ASN A1074 " " NAG A1304 " - " ASN A 603 " " NAG A1305 " - " ASN A 64 " " NAG B1301 " - " ASN B1074 " " NAG B1302 " - " ASN B 657 " " NAG B1303 " - " ASN B 616 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 234 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 64 " " NAG C1301 " - " ASN C 603 " " NAG C1302 " - " ASN C1074 " " NAG C1303 " - " ASN C 657 " " NAG C1304 " - " ASN C 234 " " NAG D 1 " - " ASN A 331 " " NAG G 1 " - " ASN A 343 " " NAG H 1 " - " ASN A 709 " " NAG I 1 " - " ASN A1098 " " NAG J 1 " - " ASN A 717 " " NAG K 1 " - " ASN A 801 " " NAG L 1 " - " ASN A1134 " " NAG M 1 " - " ASN A 282 " " NAG N 1 " - " ASN A 162 " " NAG O 1 " - " ASN A 123 " " NAG P 1 " - " ASN A 234 " " NAG Q 1 " - " ASN B 801 " " NAG R 1 " - " ASN B 717 " " NAG S 1 " - " ASN B1098 " " NAG T 1 " - " ASN B1134 " " NAG U 1 " - " ASN B 709 " " NAG V 1 " - " ASN B 343 " " NAG W 1 " - " ASN B 282 " " NAG X 1 " - " ASN B 123 " " NAG Y 1 " - " ASN B 162 " " NAG Z 1 " - " ASN C 282 " " NAG a 1 " - " ASN C 801 " " NAG b 1 " - " ASN C 717 " " NAG c 1 " - " ASN C1098 " " NAG d 1 " - " ASN C1134 " " NAG e 1 " - " ASN C 709 " " NAG f 1 " - " ASN C 331 " " NAG g 1 " - " ASN C 343 " " NAG h 1 " - " ASN C 126 " " NAG i 1 " - " ASN C 162 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.08 Conformation dependent library (CDL) restraints added in 5.3 seconds 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6418 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 49 sheets defined 25.7% alpha, 21.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.97 Creating SS restraints... Processing helix chain 'A' and resid 72 through 76 removed outlier: 3.509A pdb=" N ASN A 75 " --> pdb=" O SER A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 158 removed outlier: 4.412A pdb=" N PHE A 155 " --> pdb=" O GLU A 152 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N VAL A 157 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR A 158 " --> pdb=" O PHE A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.961A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 removed outlier: 3.763A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 746 through 756 Processing helix chain 'A' and resid 759 through 783 removed outlier: 4.117A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 827 Processing helix chain 'A' and resid 849 through 855 removed outlier: 3.549A pdb=" N PHE A 855 " --> pdb=" O CYS A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.780A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.314A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 Processing helix chain 'A' and resid 945 through 965 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 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.602A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 365 through 371 removed outlier: 3.556A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 742 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.976A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 783 removed outlier: 3.776A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 827 Processing helix chain 'B' and resid 828 through 830 No H-bonds generated for 'chain 'B' and resid 828 through 830' Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 940 Processing helix chain 'B' and resid 945 through 965 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 984 removed outlier: 3.525A pdb=" N LEU B 984 " --> pdb=" O ILE B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.658A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 76 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.866A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 390 removed outlier: 3.832A pdb=" N LEU C 390 " --> pdb=" O LYS C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 616 through 618 No H-bonds generated for 'chain 'C' and resid 616 through 618' Processing helix chain 'C' and resid 619 through 624 Processing helix chain 'C' and resid 630 through 634 Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 746 through 754 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 759 through 782 removed outlier: 3.528A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 827 Processing helix chain 'C' and resid 849 through 855 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.897A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 940 Processing helix chain 'C' and resid 945 through 965 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 984 removed outlier: 3.552A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU C 984 " --> pdb=" O ILE C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.448A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 25 Processing helix chain 'E' and resid 26 through 49 Processing helix chain 'F' and resid 3 through 25 Processing helix chain 'F' and resid 26 through 49 removed outlier: 3.677A pdb=" N ALA F 30 " --> pdb=" O ASN F 26 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 33 removed outlier: 3.676A pdb=" N VAL A 267 " --> pdb=" O THR A 66 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 39 through 40 removed outlier: 7.055A pdb=" N VAL A 39 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N SER A 203 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N VAL A 227 " --> pdb=" O ILE A 201 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 51 through 58 removed outlier: 3.563A pdb=" N GLN A 271 " --> pdb=" O PHE A 58 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 85 through 86 Processing sheet with id=AA5, first strand: chain 'A' and resid 102 through 103 removed outlier: 3.644A pdb=" N ARG A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 129 through 133 removed outlier: 3.547A pdb=" N PHE A 166 " --> pdb=" O VAL A 131 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N GLU A 133 " --> pdb=" O CYS A 164 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N CYS A 164 " --> pdb=" O GLU A 133 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 316 removed outlier: 3.792A pdb=" N THR A 315 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.549A pdb=" N ARG A 328 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.747A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE A 358 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 660 removed outlier: 5.857A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 8.744A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AB4, first strand: chain 'A' and resid 712 through 713 removed outlier: 3.805A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 717 through 728 removed outlier: 5.734A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.233A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.223A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 31 through 33 Processing sheet with id=AC1, first strand: chain 'B' and resid 45 through 46 Processing sheet with id=AC2, first strand: chain 'B' and resid 50 through 58 removed outlier: 3.600A pdb=" N VAL B 50 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE B 58 " --> pdb=" O GLN B 271 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 69 through 70 removed outlier: 3.507A pdb=" N TYR B 202 " --> pdb=" O VAL B 191 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS B 193 " --> pdb=" O LYS B 200 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL B 227 " --> pdb=" O ILE B 201 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 85 through 86 removed outlier: 3.830A pdb=" N ARG B 237 " --> pdb=" O GLY B 108 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLY B 108 " --> pdb=" O ARG B 237 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 118 through 119 removed outlier: 4.421A pdb=" N PHE B 166 " --> pdb=" O VAL B 131 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 135 through 136 removed outlier: 6.551A pdb=" N GLN B 135 " --> pdb=" O SER B 159 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 313 through 319 removed outlier: 7.169A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 325 through 326 removed outlier: 3.721A pdb=" N GLY B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE B 543 " --> pdb=" O LEU B 546 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.576A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE B 358 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.988A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE B 664 " --> pdb=" O ALA B 672 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 712 through 728 removed outlier: 6.522A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 712 through 728 removed outlier: 6.522A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD6, first strand: chain 'B' and resid 787 through 790 Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.668A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 31 through 33 Processing sheet with id=AD9, first strand: chain 'C' and resid 52 through 58 removed outlier: 3.930A pdb=" N ASP C 56 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 69 through 70 Processing sheet with id=AE2, first strand: chain 'C' and resid 69 through 70 removed outlier: 3.583A pdb=" N TYR C 202 " --> pdb=" O VAL C 191 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS C 193 " --> pdb=" O LYS C 200 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL C 227 " --> pdb=" O ILE C 201 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N SER C 203 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 85 through 86 removed outlier: 3.598A pdb=" N GLY C 108 " --> pdb=" O ARG C 237 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 116 through 117 removed outlier: 7.573A pdb=" N VAL C 131 " --> pdb=" O THR C 165 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR C 165 " --> pdb=" O VAL C 131 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 311 through 313 Processing sheet with id=AE6, first strand: chain 'C' and resid 324 through 325 removed outlier: 6.694A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.875A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE9, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.580A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 712 through 728 removed outlier: 6.511A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 712 through 728 removed outlier: 6.511A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.359A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.316A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 990 hydrogen bonds defined for protein. 2751 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: 11.74 Time building geometry restraints manager: 12.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8813 1.34 - 1.46: 6628 1.46 - 1.58: 13100 1.58 - 1.70: 0 1.70 - 1.82: 151 Bond restraints: 28692 Sorted by residual: bond pdb=" C1 NAG V 2 " pdb=" O5 NAG V 2 " ideal model delta sigma weight residual 1.406 1.484 -0.078 2.00e-02 2.50e+03 1.53e+01 bond pdb=" C1 NAG X 2 " pdb=" O5 NAG X 2 " ideal model delta sigma weight residual 1.406 1.474 -0.068 2.00e-02 2.50e+03 1.17e+01 bond pdb=" C1 NAG i 1 " pdb=" O5 NAG i 1 " ideal model delta sigma weight residual 1.406 1.463 -0.057 2.00e-02 2.50e+03 8.12e+00 bond pdb=" C1 NAG B1301 " pdb=" O5 NAG B1301 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 7.07e+00 bond pdb=" C1 NAG G 1 " pdb=" O5 NAG G 1 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.54e+00 ... (remaining 28687 not shown) Histogram of bond angle deviations from ideal: 99.13 - 106.13: 714 106.13 - 113.13: 15801 113.13 - 120.13: 9515 120.13 - 127.14: 12726 127.14 - 134.14: 259 Bond angle restraints: 39015 Sorted by residual: angle pdb=" N ILE A 101 " pdb=" CA ILE A 101 " pdb=" C ILE A 101 " ideal model delta sigma weight residual 113.71 108.58 5.13 9.50e-01 1.11e+00 2.92e+01 angle pdb=" C LYS B 854 " pdb=" CA LYS B 854 " pdb=" CB LYS B 854 " ideal model delta sigma weight residual 115.79 110.71 5.08 1.19e+00 7.06e-01 1.82e+01 angle pdb=" C GLY C 594 " pdb=" N VAL C 595 " pdb=" CA VAL C 595 " ideal model delta sigma weight residual 121.97 127.65 -5.68 1.80e+00 3.09e-01 9.96e+00 angle pdb=" N GLN B 774 " pdb=" CA GLN B 774 " pdb=" CB GLN B 774 " ideal model delta sigma weight residual 110.28 115.00 -4.72 1.55e+00 4.16e-01 9.29e+00 angle pdb=" C SER B 359 " pdb=" N ASN B 360 " pdb=" CA ASN B 360 " ideal model delta sigma weight residual 121.54 127.31 -5.77 1.91e+00 2.74e-01 9.11e+00 ... (remaining 39010 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.09: 16973 24.09 - 48.18: 906 48.18 - 72.27: 164 72.27 - 96.36: 104 96.36 - 120.45: 113 Dihedral angle restraints: 18260 sinusoidal: 8274 harmonic: 9986 Sorted by residual: dihedral pdb=" CB CYS C 840 " pdb=" SG CYS C 840 " pdb=" SG CYS C 851 " pdb=" CB CYS C 851 " ideal model delta sinusoidal sigma weight residual 93.00 177.95 -84.95 1 1.00e+01 1.00e-02 8.76e+01 dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual -86.00 -159.99 73.99 1 1.00e+01 1.00e-02 6.95e+01 dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual 93.00 166.75 -73.75 1 1.00e+01 1.00e-02 6.91e+01 ... (remaining 18257 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 4419 0.102 - 0.204: 194 0.204 - 0.305: 21 0.305 - 0.407: 2 0.407 - 0.509: 2 Chirality restraints: 4638 Sorted by residual: chirality pdb=" C1 NAG S 1 " pdb=" ND2 ASN B1098 " pdb=" C2 NAG S 1 " pdb=" O5 NAG S 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.89 -0.51 2.00e-01 2.50e+01 6.47e+00 chirality pdb=" C1 NAG h 1 " pdb=" ND2 ASN C 126 " pdb=" C2 NAG h 1 " pdb=" O5 NAG h 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.01e+00 chirality pdb=" C1 NAG i 1 " pdb=" ND2 ASN C 162 " pdb=" C2 NAG i 1 " pdb=" O5 NAG i 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.63e+00 ... (remaining 4635 not shown) Planarity restraints: 4979 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 599 " -0.038 5.00e-02 4.00e+02 5.76e-02 5.30e+00 pdb=" N PRO C 600 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO C 600 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 600 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 67 " -0.014 2.00e-02 2.50e+03 1.42e-02 5.06e+00 pdb=" CG TRP C 67 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP C 67 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP C 67 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 67 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 67 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 67 " -0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 67 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 67 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP C 67 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 67 " -0.012 2.00e-02 2.50e+03 1.39e-02 4.80e+00 pdb=" CG TRP B 67 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP B 67 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP B 67 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 67 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 67 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 67 " -0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 67 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 67 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 67 " 0.000 2.00e-02 2.50e+03 ... (remaining 4976 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 444 2.65 - 3.21: 26633 3.21 - 3.78: 43456 3.78 - 4.34: 58711 4.34 - 4.90: 95760 Nonbonded interactions: 225004 Sorted by model distance: nonbonded pdb=" OH TYR A 756 " pdb=" OD1 ASP A 994 " model vdw 2.089 2.440 nonbonded pdb=" OH TYR B 904 " pdb=" O GLY C1093 " model vdw 2.099 2.440 nonbonded pdb=" OG1 THR B 110 " pdb=" OD1 ASP B 112 " model vdw 2.174 2.440 nonbonded pdb=" OH TYR B 756 " pdb=" OD1 ASP B 994 " model vdw 2.185 2.440 nonbonded pdb=" O PHE B 486 " pdb=" NE2 GLN F 9 " model vdw 2.208 2.520 ... (remaining 224999 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' and (resid 22 through 840 or resid 851 through 1147 or resid 1301 thr \ ough 1304)) selection = (chain 'B' and (resid 22 through 1147 or resid 1301 through 1304)) selection = (chain 'C' and (resid 22 through 840 or resid 851 through 1147 or resid 1301 thr \ ough 1304)) } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'N' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'a' selection = chain 'b' selection = chain 'c' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.950 Check model and map are aligned: 0.200 Set scattering table: 0.230 Process input model: 77.660 Find NCS groups from input model: 5.430 Set up NCS constraints: 0.210 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:10.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 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 : 0.004 0.078 28692 Z= 0.230 Angle : 0.625 7.669 39015 Z= 0.295 Chirality : 0.049 0.509 4638 Planarity : 0.003 0.058 4933 Dihedral : 18.634 120.451 11716 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.74 % Favored : 95.08 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % 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: -0.19 (0.15), residues: 3397 helix: 1.87 (0.19), residues: 809 sheet: -0.03 (0.22), residues: 616 loop : -1.05 (0.13), residues: 1972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP C 67 HIS 0.013 0.001 HIS F 15 PHE 0.029 0.001 PHE C 184 TYR 0.022 0.001 TYR B 904 ARG 0.007 0.000 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 236 time to evaluate : 2.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 VAL cc_start: 0.7955 (t) cc_final: 0.7752 (p) REVERT: A 151 MET cc_start: 0.1815 (tmm) cc_final: 0.0673 (ptp) REVERT: A 396 TYR cc_start: 0.6788 (m-10) cc_final: 0.6587 (m-10) REVERT: B 266 TYR cc_start: 0.8033 (m-80) cc_final: 0.7829 (m-80) REVERT: B 400 PHE cc_start: 0.8274 (p90) cc_final: 0.8053 (p90) REVERT: B 751 ASN cc_start: 0.8896 (m110) cc_final: 0.8674 (m110) REVERT: C 33 ASN cc_start: 0.8454 (t0) cc_final: 0.8182 (t0) REVERT: C 322 PRO cc_start: 0.6728 (Cg_exo) cc_final: 0.6387 (Cg_endo) REVERT: C 357 ARG cc_start: 0.6413 (ttt-90) cc_final: 0.6157 (tmm-80) REVERT: C 740 MET cc_start: 0.7844 (ppp) cc_final: 0.7609 (ppp) REVERT: F 39 GLN cc_start: 0.8951 (tm-30) cc_final: 0.8631 (tm-30) outliers start: 0 outliers final: 2 residues processed: 236 average time/residue: 0.9562 time to fit residues: 283.1472 Evaluate side-chains 152 residues out of total 2981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 150 time to evaluate : 3.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 1092 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 287 optimal weight: 0.8980 chunk 258 optimal weight: 10.0000 chunk 143 optimal weight: 9.9990 chunk 88 optimal weight: 0.9990 chunk 174 optimal weight: 5.9990 chunk 138 optimal weight: 0.8980 chunk 267 optimal weight: 7.9990 chunk 103 optimal weight: 1.9990 chunk 162 optimal weight: 6.9990 chunk 198 optimal weight: 0.8980 chunk 309 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN B 126 ASN ** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 GLN C 965 GLN E 9 GLN E 25 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.0997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 28692 Z= 0.200 Angle : 0.631 11.067 39015 Z= 0.300 Chirality : 0.048 0.385 4638 Planarity : 0.004 0.050 4933 Dihedral : 15.600 107.765 5524 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.21 % Favored : 94.61 % Rotamer: Outliers : 1.01 % Allowed : 7.13 % Favored : 91.86 % 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: -0.19 (0.15), residues: 3397 helix: 2.02 (0.19), residues: 791 sheet: -0.08 (0.21), residues: 623 loop : -1.08 (0.14), residues: 1983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 436 HIS 0.004 0.001 HIS B 519 PHE 0.029 0.001 PHE B 166 TYR 0.033 0.001 TYR C 837 ARG 0.007 0.000 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 175 time to evaluate : 2.799 Fit side-chains revert: symmetry clash REVERT: A 100 ASN cc_start: 0.6527 (OUTLIER) cc_final: 0.6297 (p0) REVERT: A 151 MET cc_start: 0.2370 (tmm) cc_final: 0.1474 (ptp) REVERT: A 396 TYR cc_start: 0.6399 (m-10) cc_final: 0.6187 (m-10) REVERT: A 421 TYR cc_start: 0.7114 (m-10) cc_final: 0.6744 (m-80) REVERT: B 400 PHE cc_start: 0.8351 (p90) cc_final: 0.8079 (p90) REVERT: B 751 ASN cc_start: 0.8945 (m110) cc_final: 0.8701 (m110) REVERT: C 33 ASN cc_start: 0.8363 (t0) cc_final: 0.8053 (t0) REVERT: C 106 ILE cc_start: 0.9082 (pt) cc_final: 0.8820 (pp) REVERT: C 241 LEU cc_start: 0.8151 (mm) cc_final: 0.7319 (tp) REVERT: C 357 ARG cc_start: 0.6588 (ttt-90) cc_final: 0.6227 (tmm-80) REVERT: C 752 LEU cc_start: 0.8979 (pp) cc_final: 0.8696 (mt) REVERT: F 39 GLN cc_start: 0.8936 (tm-30) cc_final: 0.8611 (tm-30) outliers start: 30 outliers final: 13 residues processed: 191 average time/residue: 0.8619 time to fit residues: 210.7698 Evaluate side-chains 162 residues out of total 2981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 148 time to evaluate : 2.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 991 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 172 optimal weight: 2.9990 chunk 96 optimal weight: 0.6980 chunk 257 optimal weight: 9.9990 chunk 210 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 310 optimal weight: 4.9990 chunk 335 optimal weight: 9.9990 chunk 276 optimal weight: 0.5980 chunk 307 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 248 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN B 126 ASN ** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 ASN B 774 GLN ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN E 9 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28692 Z= 0.201 Angle : 0.618 11.091 39015 Z= 0.289 Chirality : 0.048 0.406 4638 Planarity : 0.004 0.053 4933 Dihedral : 12.813 109.757 5519 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.09 % Favored : 94.70 % Rotamer: Outliers : 1.55 % Allowed : 9.69 % Favored : 88.76 % 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 (0.15), residues: 3397 helix: 1.97 (0.19), residues: 796 sheet: -0.19 (0.21), residues: 620 loop : -1.09 (0.14), residues: 1981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 105 HIS 0.004 0.001 HIS B 519 PHE 0.025 0.001 PHE B 166 TYR 0.026 0.001 TYR C 837 ARG 0.004 0.000 ARG B 346 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 169 time to evaluate : 2.932 Fit side-chains revert: symmetry clash REVERT: A 151 MET cc_start: 0.2523 (tmm) cc_final: 0.1709 (ptp) REVERT: A 175 MET cc_start: 0.7466 (mmt) cc_final: 0.7157 (pmm) REVERT: A 396 TYR cc_start: 0.6483 (m-10) cc_final: 0.6246 (m-10) REVERT: A 400 PHE cc_start: 0.8612 (OUTLIER) cc_final: 0.8164 (p90) REVERT: A 421 TYR cc_start: 0.7172 (m-10) cc_final: 0.6811 (m-80) REVERT: A 950 ASP cc_start: 0.7596 (t0) cc_final: 0.7390 (t0) REVERT: B 354 ASN cc_start: 0.9130 (t0) cc_final: 0.8523 (p0) REVERT: B 400 PHE cc_start: 0.8406 (p90) cc_final: 0.8125 (p90) REVERT: B 515 PHE cc_start: 0.7339 (m-10) cc_final: 0.7077 (m-10) REVERT: B 751 ASN cc_start: 0.8941 (m110) cc_final: 0.8685 (m110) REVERT: C 33 ASN cc_start: 0.8403 (t0) cc_final: 0.8060 (t0) REVERT: C 106 ILE cc_start: 0.9083 (pt) cc_final: 0.8828 (pp) REVERT: C 241 LEU cc_start: 0.8133 (mm) cc_final: 0.7266 (tp) REVERT: C 752 LEU cc_start: 0.8995 (pp) cc_final: 0.8742 (mt) REVERT: F 39 GLN cc_start: 0.8934 (tm-30) cc_final: 0.8580 (tm-30) outliers start: 46 outliers final: 21 residues processed: 194 average time/residue: 0.8678 time to fit residues: 213.9328 Evaluate side-chains 168 residues out of total 2981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 146 time to evaluate : 2.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 740 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 306 optimal weight: 3.9990 chunk 233 optimal weight: 7.9990 chunk 161 optimal weight: 1.9990 chunk 34 optimal weight: 10.0000 chunk 148 optimal weight: 0.0470 chunk 208 optimal weight: 2.9990 chunk 311 optimal weight: 5.9990 chunk 329 optimal weight: 7.9990 chunk 162 optimal weight: 7.9990 chunk 295 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 overall best weight: 2.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN A 913 GLN ** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 9 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 28692 Z= 0.278 Angle : 0.627 11.215 39015 Z= 0.299 Chirality : 0.047 0.383 4638 Planarity : 0.004 0.047 4933 Dihedral : 10.642 109.777 5519 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.74 % Favored : 94.08 % Rotamer: Outliers : 1.95 % Allowed : 11.98 % Favored : 86.07 % 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: -0.29 (0.15), residues: 3397 helix: 1.95 (0.19), residues: 794 sheet: -0.21 (0.21), residues: 647 loop : -1.14 (0.14), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 105 HIS 0.005 0.001 HIS A 519 PHE 0.023 0.001 PHE B 93 TYR 0.024 0.001 TYR C 837 ARG 0.011 0.000 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 164 time to evaluate : 2.972 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 151 MET cc_start: 0.2350 (tmm) cc_final: 0.1832 (ptp) REVERT: A 175 MET cc_start: 0.7376 (mmt) cc_final: 0.6942 (pmm) REVERT: A 421 TYR cc_start: 0.7152 (m-10) cc_final: 0.6813 (m-80) REVERT: A 453 TYR cc_start: 0.5912 (p90) cc_final: 0.5529 (p90) REVERT: A 1029 MET cc_start: 0.8534 (OUTLIER) cc_final: 0.8212 (tpp) REVERT: B 362 VAL cc_start: 0.7654 (OUTLIER) cc_final: 0.7356 (m) REVERT: B 400 PHE cc_start: 0.8337 (p90) cc_final: 0.8118 (p90) REVERT: B 751 ASN cc_start: 0.9014 (m110) cc_final: 0.8739 (m110) REVERT: B 855 PHE cc_start: 0.6906 (t80) cc_final: 0.6417 (t80) REVERT: C 33 ASN cc_start: 0.8395 (t0) cc_final: 0.8071 (t0) REVERT: C 740 MET cc_start: 0.8216 (OUTLIER) cc_final: 0.7839 (ppp) REVERT: F 39 GLN cc_start: 0.8923 (tm-30) cc_final: 0.8538 (tm-30) outliers start: 58 outliers final: 27 residues processed: 202 average time/residue: 0.8622 time to fit residues: 222.8050 Evaluate side-chains 173 residues out of total 2981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 143 time to evaluate : 2.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1074 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 274 optimal weight: 10.0000 chunk 187 optimal weight: 5.9990 chunk 4 optimal weight: 0.8980 chunk 245 optimal weight: 0.9980 chunk 135 optimal weight: 7.9990 chunk 281 optimal weight: 7.9990 chunk 227 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 chunk 168 optimal weight: 0.8980 chunk 295 optimal weight: 0.1980 chunk 83 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN A 755 GLN ** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN B1002 GLN C 135 GLN ** C 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 9 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 28692 Z= 0.157 Angle : 0.588 11.083 39015 Z= 0.278 Chirality : 0.046 0.382 4638 Planarity : 0.004 0.080 4933 Dihedral : 9.981 107.790 5519 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.95 % Favored : 94.88 % Rotamer: Outliers : 2.02 % Allowed : 13.73 % Favored : 84.25 % 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 (0.15), residues: 3397 helix: 1.98 (0.19), residues: 809 sheet: -0.27 (0.21), residues: 638 loop : -1.09 (0.14), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 105 HIS 0.004 0.001 HIS B 519 PHE 0.017 0.001 PHE F 33 TYR 0.020 0.001 TYR C 837 ARG 0.006 0.000 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 172 time to evaluate : 3.069 Fit side-chains revert: symmetry clash REVERT: A 84 VAL cc_start: 0.8168 (OUTLIER) cc_final: 0.7940 (p) REVERT: A 175 MET cc_start: 0.7382 (mmt) cc_final: 0.6785 (pmm) REVERT: A 408 ARG cc_start: 0.8216 (tpp-160) cc_final: 0.7980 (tpp-160) REVERT: A 421 TYR cc_start: 0.7254 (m-10) cc_final: 0.6921 (m-10) REVERT: A 453 TYR cc_start: 0.5758 (p90) cc_final: 0.5368 (p90) REVERT: B 354 ASN cc_start: 0.9171 (t0) cc_final: 0.8522 (p0) REVERT: B 400 PHE cc_start: 0.8382 (p90) cc_final: 0.8130 (p90) REVERT: B 751 ASN cc_start: 0.9046 (m110) cc_final: 0.8769 (m110) REVERT: C 33 ASN cc_start: 0.8214 (t0) cc_final: 0.7851 (t0) REVERT: C 135 GLN cc_start: 0.7332 (OUTLIER) cc_final: 0.7098 (pp30) REVERT: C 241 LEU cc_start: 0.8102 (mm) cc_final: 0.7192 (tp) REVERT: C 740 MET cc_start: 0.8113 (OUTLIER) cc_final: 0.7741 (ppp) REVERT: C 752 LEU cc_start: 0.9044 (pp) cc_final: 0.8838 (mt) REVERT: F 39 GLN cc_start: 0.8919 (tm-30) cc_final: 0.8545 (tm-30) outliers start: 60 outliers final: 25 residues processed: 210 average time/residue: 0.8553 time to fit residues: 234.6940 Evaluate side-chains 177 residues out of total 2981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 149 time to evaluate : 2.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 135 GLN Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain F residue 60 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 110 optimal weight: 10.0000 chunk 296 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 193 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 329 optimal weight: 9.9990 chunk 273 optimal weight: 8.9990 chunk 152 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 chunk 109 optimal weight: 0.6980 chunk 173 optimal weight: 0.2980 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 ASN A 613 GLN B 239 GLN ** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN ** C 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 9 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 28692 Z= 0.254 Angle : 0.614 10.733 39015 Z= 0.291 Chirality : 0.047 0.407 4638 Planarity : 0.004 0.050 4933 Dihedral : 9.459 108.041 5519 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.56 % Favored : 94.26 % Rotamer: Outliers : 2.39 % Allowed : 14.27 % Favored : 83.34 % 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: -0.29 (0.15), residues: 3397 helix: 1.92 (0.19), residues: 808 sheet: -0.33 (0.20), residues: 654 loop : -1.10 (0.14), residues: 1935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 105 HIS 0.004 0.001 HIS A 519 PHE 0.032 0.001 PHE B 166 TYR 0.026 0.001 TYR C 837 ARG 0.004 0.000 ARG C1107 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 155 time to evaluate : 2.907 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 VAL cc_start: 0.8257 (OUTLIER) cc_final: 0.7983 (p) REVERT: A 175 MET cc_start: 0.7080 (mmt) cc_final: 0.6509 (pmm) REVERT: A 270 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8452 (mp) REVERT: A 408 ARG cc_start: 0.8249 (tpp-160) cc_final: 0.8012 (tpp-160) REVERT: A 421 TYR cc_start: 0.7399 (m-10) cc_final: 0.7051 (m-10) REVERT: B 362 VAL cc_start: 0.7644 (OUTLIER) cc_final: 0.7367 (m) REVERT: B 400 PHE cc_start: 0.8332 (p90) cc_final: 0.8124 (p90) REVERT: B 402 ILE cc_start: 0.8859 (pt) cc_final: 0.8643 (pt) REVERT: B 751 ASN cc_start: 0.9077 (m110) cc_final: 0.8786 (m110) REVERT: C 33 ASN cc_start: 0.8304 (t0) cc_final: 0.7957 (t0) REVERT: C 740 MET cc_start: 0.8215 (OUTLIER) cc_final: 0.7887 (ppp) REVERT: C 752 LEU cc_start: 0.9107 (pp) cc_final: 0.8864 (mt) REVERT: F 39 GLN cc_start: 0.8942 (tm-30) cc_final: 0.8480 (tm-30) outliers start: 71 outliers final: 34 residues processed: 205 average time/residue: 0.8242 time to fit residues: 220.5830 Evaluate side-chains 186 residues out of total 2981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 148 time to evaluate : 2.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain F residue 60 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 318 optimal weight: 3.9990 chunk 37 optimal weight: 10.0000 chunk 187 optimal weight: 5.9990 chunk 240 optimal weight: 0.9980 chunk 186 optimal weight: 0.9990 chunk 277 optimal weight: 4.9990 chunk 184 optimal weight: 0.4980 chunk 328 optimal weight: 0.3980 chunk 205 optimal weight: 3.9990 chunk 200 optimal weight: 4.9990 chunk 151 optimal weight: 20.0000 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 GLN ** C 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 28692 Z= 0.210 Angle : 0.603 10.961 39015 Z= 0.285 Chirality : 0.046 0.400 4638 Planarity : 0.004 0.048 4933 Dihedral : 8.942 108.863 5519 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.50 % Favored : 94.32 % Rotamer: Outliers : 2.15 % Allowed : 15.01 % Favored : 82.84 % 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: -0.29 (0.15), residues: 3397 helix: 1.98 (0.19), residues: 803 sheet: -0.34 (0.20), residues: 655 loop : -1.11 (0.14), residues: 1939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 105 HIS 0.004 0.001 HIS A 519 PHE 0.018 0.001 PHE B 855 TYR 0.023 0.001 TYR C 837 ARG 0.008 0.000 ARG F 32 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 161 time to evaluate : 3.611 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 VAL cc_start: 0.8251 (OUTLIER) cc_final: 0.7976 (p) REVERT: A 175 MET cc_start: 0.7056 (mmt) cc_final: 0.6523 (pmm) REVERT: A 242 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8068 (mm) REVERT: A 342 PHE cc_start: 0.8550 (OUTLIER) cc_final: 0.7913 (m-80) REVERT: A 421 TYR cc_start: 0.7558 (m-10) cc_final: 0.7230 (m-10) REVERT: A 453 TYR cc_start: 0.6043 (p90) cc_final: 0.5620 (p90) REVERT: B 354 ASN cc_start: 0.9179 (t0) cc_final: 0.8506 (p0) REVERT: B 362 VAL cc_start: 0.7566 (OUTLIER) cc_final: 0.7285 (m) REVERT: B 400 PHE cc_start: 0.8299 (p90) cc_final: 0.8092 (p90) REVERT: B 402 ILE cc_start: 0.8851 (pt) cc_final: 0.8635 (pt) REVERT: B 751 ASN cc_start: 0.9082 (m110) cc_final: 0.8796 (m110) REVERT: C 33 ASN cc_start: 0.8294 (t0) cc_final: 0.7935 (t0) REVERT: C 357 ARG cc_start: 0.6215 (tmm160) cc_final: 0.5967 (tmm-80) REVERT: C 740 MET cc_start: 0.8114 (OUTLIER) cc_final: 0.7841 (ppp) REVERT: C 752 LEU cc_start: 0.9105 (pp) cc_final: 0.8889 (mt) REVERT: F 39 GLN cc_start: 0.8937 (tm-30) cc_final: 0.8482 (tm-30) outliers start: 64 outliers final: 33 residues processed: 205 average time/residue: 0.8314 time to fit residues: 222.3356 Evaluate side-chains 186 residues out of total 2981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 148 time to evaluate : 3.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain F residue 60 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 203 optimal weight: 6.9990 chunk 131 optimal weight: 7.9990 chunk 196 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 208 optimal weight: 3.9990 chunk 223 optimal weight: 10.0000 chunk 162 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 258 optimal weight: 6.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 ASN C 957 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 28692 Z= 0.339 Angle : 0.665 11.224 39015 Z= 0.317 Chirality : 0.048 0.403 4638 Planarity : 0.004 0.045 4933 Dihedral : 8.613 108.582 5519 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.30 % Favored : 93.55 % Rotamer: Outliers : 2.19 % Allowed : 15.58 % Favored : 82.23 % 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: -0.40 (0.15), residues: 3397 helix: 1.83 (0.19), residues: 802 sheet: -0.39 (0.20), residues: 645 loop : -1.15 (0.14), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 105 HIS 0.004 0.001 HIS C 144 PHE 0.038 0.002 PHE B 166 TYR 0.022 0.002 TYR C 904 ARG 0.006 0.001 ARG F 20 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 146 time to evaluate : 2.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 VAL cc_start: 0.8433 (OUTLIER) cc_final: 0.8104 (p) REVERT: A 175 MET cc_start: 0.7133 (mmt) cc_final: 0.6514 (mpp) REVERT: A 242 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8136 (mm) REVERT: A 342 PHE cc_start: 0.8589 (OUTLIER) cc_final: 0.7984 (m-80) REVERT: A 421 TYR cc_start: 0.7464 (m-10) cc_final: 0.7116 (m-80) REVERT: B 751 ASN cc_start: 0.9078 (m110) cc_final: 0.8795 (m110) REVERT: C 33 ASN cc_start: 0.8329 (t0) cc_final: 0.8004 (t0) REVERT: C 740 MET cc_start: 0.8291 (OUTLIER) cc_final: 0.7918 (ppp) REVERT: F 20 ARG cc_start: 0.7303 (mmp80) cc_final: 0.6679 (mmp80) REVERT: F 39 GLN cc_start: 0.8950 (tm-30) cc_final: 0.8478 (tm-30) outliers start: 65 outliers final: 38 residues processed: 191 average time/residue: 0.8673 time to fit residues: 214.4011 Evaluate side-chains 183 residues out of total 2981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 141 time to evaluate : 3.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain F residue 60 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 298 optimal weight: 0.0670 chunk 314 optimal weight: 0.7980 chunk 287 optimal weight: 0.8980 chunk 306 optimal weight: 0.6980 chunk 184 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 240 optimal weight: 7.9990 chunk 93 optimal weight: 2.9990 chunk 276 optimal weight: 0.0170 chunk 289 optimal weight: 0.8980 chunk 305 optimal weight: 0.6980 overall best weight: 0.4556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN C1010 GLN E 9 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 28692 Z= 0.148 Angle : 0.605 12.221 39015 Z= 0.287 Chirality : 0.046 0.390 4638 Planarity : 0.004 0.044 4933 Dihedral : 8.086 108.386 5519 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.18 % Favored : 94.64 % Rotamer: Outliers : 1.55 % Allowed : 16.32 % Favored : 82.13 % 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: -0.29 (0.15), residues: 3397 helix: 2.06 (0.19), residues: 804 sheet: -0.40 (0.20), residues: 652 loop : -1.14 (0.14), residues: 1941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP B 105 HIS 0.003 0.001 HIS A 519 PHE 0.023 0.001 PHE B 93 TYR 0.019 0.001 TYR C1067 ARG 0.007 0.000 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 175 time to evaluate : 3.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 VAL cc_start: 0.8276 (OUTLIER) cc_final: 0.8004 (p) REVERT: A 175 MET cc_start: 0.7038 (mmt) cc_final: 0.6568 (ptp) REVERT: A 242 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8098 (mm) REVERT: A 392 PHE cc_start: 0.6911 (m-10) cc_final: 0.6709 (m-10) REVERT: A 421 TYR cc_start: 0.7579 (m-10) cc_final: 0.7279 (m-10) REVERT: A 453 TYR cc_start: 0.6238 (p90) cc_final: 0.5761 (p90) REVERT: B 354 ASN cc_start: 0.9164 (t0) cc_final: 0.8497 (p0) REVERT: B 362 VAL cc_start: 0.7566 (OUTLIER) cc_final: 0.7301 (m) REVERT: B 751 ASN cc_start: 0.9074 (m110) cc_final: 0.8781 (m110) REVERT: C 33 ASN cc_start: 0.8273 (t0) cc_final: 0.7924 (t0) REVERT: C 106 ILE cc_start: 0.8616 (pp) cc_final: 0.8386 (pp) REVERT: C 193 LYS cc_start: 0.8228 (ttpt) cc_final: 0.7971 (ttpt) REVERT: C 241 LEU cc_start: 0.8034 (mm) cc_final: 0.7198 (tp) REVERT: C 740 MET cc_start: 0.8062 (ppp) cc_final: 0.7775 (ppp) REVERT: C 752 LEU cc_start: 0.9104 (pp) cc_final: 0.8898 (mt) REVERT: F 39 GLN cc_start: 0.8975 (tm-30) cc_final: 0.8579 (tm-30) outliers start: 46 outliers final: 32 residues processed: 207 average time/residue: 0.8837 time to fit residues: 231.6356 Evaluate side-chains 192 residues out of total 2981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 157 time to evaluate : 2.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain F residue 60 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 201 optimal weight: 3.9990 chunk 323 optimal weight: 3.9990 chunk 197 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 chunk 225 optimal weight: 5.9990 chunk 339 optimal weight: 8.9990 chunk 312 optimal weight: 0.7980 chunk 270 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 208 optimal weight: 4.9990 chunk 165 optimal weight: 0.5980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN ** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 28692 Z= 0.247 Angle : 0.629 13.320 39015 Z= 0.299 Chirality : 0.047 0.390 4638 Planarity : 0.004 0.044 4933 Dihedral : 7.936 106.208 5519 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.48 % Favored : 94.35 % Rotamer: Outliers : 1.35 % Allowed : 16.79 % Favored : 81.86 % 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: -0.29 (0.15), residues: 3397 helix: 2.01 (0.19), residues: 804 sheet: -0.35 (0.21), residues: 642 loop : -1.12 (0.14), residues: 1951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP B 105 HIS 0.004 0.001 HIS A 519 PHE 0.038 0.001 PHE B 166 TYR 0.021 0.001 TYR C 904 ARG 0.008 0.000 ARG A 466 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 153 time to evaluate : 3.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 VAL cc_start: 0.8328 (OUTLIER) cc_final: 0.8040 (p) REVERT: A 151 MET cc_start: 0.3082 (tmt) cc_final: 0.2757 (tmm) REVERT: A 175 MET cc_start: 0.7089 (mmt) cc_final: 0.6588 (ptp) REVERT: A 242 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8114 (mm) REVERT: A 342 PHE cc_start: 0.8557 (OUTLIER) cc_final: 0.7925 (m-80) REVERT: A 392 PHE cc_start: 0.6863 (m-10) cc_final: 0.6661 (m-10) REVERT: A 421 TYR cc_start: 0.7567 (m-10) cc_final: 0.7243 (m-80) REVERT: A 453 TYR cc_start: 0.6163 (p90) cc_final: 0.5710 (p90) REVERT: B 362 VAL cc_start: 0.7593 (OUTLIER) cc_final: 0.7294 (m) REVERT: B 751 ASN cc_start: 0.9092 (m110) cc_final: 0.8795 (m110) REVERT: C 33 ASN cc_start: 0.8305 (t0) cc_final: 0.7971 (t0) REVERT: C 193 LYS cc_start: 0.8065 (ttpt) cc_final: 0.7794 (ttpt) REVERT: C 357 ARG cc_start: 0.6624 (ttt180) cc_final: 0.6110 (tmm160) REVERT: C 740 MET cc_start: 0.8195 (ppp) cc_final: 0.7876 (ppp) REVERT: C 752 LEU cc_start: 0.9106 (pp) cc_final: 0.8859 (mt) REVERT: F 39 GLN cc_start: 0.8999 (tm-30) cc_final: 0.8597 (tm-30) outliers start: 40 outliers final: 35 residues processed: 182 average time/residue: 0.8105 time to fit residues: 191.9900 Evaluate side-chains 187 residues out of total 2981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 148 time to evaluate : 2.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain F residue 60 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 214 optimal weight: 2.9990 chunk 288 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 249 optimal weight: 0.2980 chunk 39 optimal weight: 9.9990 chunk 75 optimal weight: 2.9990 chunk 270 optimal weight: 0.9990 chunk 113 optimal weight: 0.6980 chunk 278 optimal weight: 0.0670 chunk 34 optimal weight: 9.9990 chunk 49 optimal weight: 9.9990 overall best weight: 0.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 ASN C 540 ASN C 965 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.135528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.084802 restraints weight = 59504.540| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 3.71 r_work: 0.3210 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 28692 Z= 0.160 Angle : 0.597 11.469 39015 Z= 0.283 Chirality : 0.046 0.386 4638 Planarity : 0.004 0.044 4933 Dihedral : 7.615 103.690 5519 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.42 % Favored : 94.44 % Rotamer: Outliers : 1.45 % Allowed : 16.79 % Favored : 81.76 % 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: -0.28 (0.15), residues: 3397 helix: 2.08 (0.19), residues: 805 sheet: -0.36 (0.20), residues: 638 loop : -1.14 (0.14), residues: 1954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP B 105 HIS 0.003 0.001 HIS A 519 PHE 0.019 0.001 PHE C 565 TYR 0.019 0.001 TYR C1067 ARG 0.010 0.000 ARG F 35 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6678.57 seconds wall clock time: 120 minutes 29.96 seconds (7229.96 seconds total)