Starting phenix.real_space_refine on Fri Feb 16 09:35:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfl_21186/02_2024/6vfl_21186.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfl_21186/02_2024/6vfl_21186.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfl_21186/02_2024/6vfl_21186.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfl_21186/02_2024/6vfl_21186.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfl_21186/02_2024/6vfl_21186.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfl_21186/02_2024/6vfl_21186.pdb" } resolution = 4.14 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.008 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 99 5.16 5 C 9306 2.51 5 N 2466 2.21 5 O 3054 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 140": "OD1" <-> "OD2" Residue "A PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 290": "OE1" <-> "OE2" Residue "A TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 140": "OD1" <-> "OD2" Residue "C PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 290": "OE1" <-> "OE2" Residue "C TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 140": "OD1" <-> "OD2" Residue "E PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 290": "OE1" <-> "OE2" Residue "E TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14925 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 3536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3536 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 20, 'TRANS': 427} Chain breaks: 3 Chain: "B" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 972 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "C" Number of atoms: 3536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3536 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 20, 'TRANS': 427} Chain breaks: 3 Chain: "D" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 972 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "E" Number of atoms: 3536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3536 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 20, 'TRANS': 427} Chain breaks: 3 Chain: "F" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 972 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} 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: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} 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: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} 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: 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: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "E" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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 Time building chain proxies: 8.31, per 1000 atoms: 0.56 Number of scatterers: 14925 At special positions: 0 Unit cell: (129.95, 125.35, 115, 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 99 16.00 O 3054 8.00 N 2466 7.00 C 9306 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 73 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.06 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.05 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.04 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.04 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.11 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 73 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.06 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.05 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.04 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.11 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 73 " distance=2.02 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.06 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.05 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.04 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.04 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.11 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA G 3 " - " MAN G 4 " " BMA Q 3 " - " MAN Q 4 " " BMA a 3 " - " MAN a 4 " ALPHA1-6 " BMA G 3 " - " MAN G 5 " " BMA Q 3 " - " MAN Q 5 " " BMA a 3 " - " MAN a 5 " BETA1-4 " 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 J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " NAG-ASN " NAG A 608 " - " ASN A 160 " " NAG A 609 " - " ASN A 276 " " NAG A 612 " - " ASN A 386 " " NAG A 613 " - " ASN A 363 " " NAG A 618 " - " ASN A 133 " " NAG A 627 " - " ASN A 289 " " NAG A 630 " - " ASN A 339 " " NAG A 631 " - " ASN A 355 " " NAG B 701 " - " ASN B 637 " " NAG B 702 " - " ASN B 618 " " NAG B 703 " - " ASN B 611 " " NAG C 608 " - " ASN C 160 " " NAG C 609 " - " ASN C 276 " " NAG C 612 " - " ASN C 386 " " NAG C 613 " - " ASN C 363 " " NAG C 618 " - " ASN C 133 " " NAG C 627 " - " ASN C 289 " " NAG C 630 " - " ASN C 339 " " NAG C 631 " - " ASN C 355 " " NAG D 701 " - " ASN D 637 " " NAG D 702 " - " ASN D 618 " " NAG D 703 " - " ASN D 611 " " NAG E 608 " - " ASN E 160 " " NAG E 609 " - " ASN E 276 " " NAG E 612 " - " ASN E 386 " " NAG E 613 " - " ASN E 363 " " NAG E 618 " - " ASN E 133 " " NAG E 627 " - " ASN E 289 " " NAG E 630 " - " ASN E 339 " " NAG E 631 " - " ASN E 355 " " NAG F 701 " - " ASN F 637 " " NAG F 702 " - " ASN F 618 " " NAG F 703 " - " ASN F 611 " " NAG G 1 " - " ASN A 262 " " NAG H 1 " - " ASN A 448 " " NAG I 1 " - " ASN A 295 " " NAG J 1 " - " ASN A 234 " " NAG K 1 " - " ASN A 197 " " NAG L 1 " - " ASN A 156 " " NAG M 1 " - " ASN A 301 " " NAG N 1 " - " ASN A 88 " " NAG O 1 " - " ASN A 241 " " NAG P 1 " - " ASN A 332 " " NAG Q 1 " - " ASN C 262 " " NAG R 1 " - " ASN C 448 " " NAG S 1 " - " ASN C 295 " " NAG T 1 " - " ASN C 234 " " NAG U 1 " - " ASN C 197 " " NAG V 1 " - " ASN C 156 " " NAG W 1 " - " ASN C 301 " " NAG X 1 " - " ASN C 88 " " NAG Y 1 " - " ASN C 241 " " NAG Z 1 " - " ASN C 332 " " NAG a 1 " - " ASN E 262 " " NAG b 1 " - " ASN E 448 " " NAG c 1 " - " ASN E 295 " " NAG d 1 " - " ASN E 234 " " NAG e 1 " - " ASN E 197 " " NAG f 1 " - " ASN E 156 " " NAG g 1 " - " ASN E 301 " " NAG h 1 " - " ASN E 88 " " NAG i 1 " - " ASN E 241 " " NAG j 1 " - " ASN E 332 " Time building additional restraints: 6.83 Conformation dependent library (CDL) restraints added in 2.6 seconds 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3198 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 33 sheets defined 29.3% alpha, 51.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.09 Creating SS restraints... Processing helix chain 'A' and resid 61 through 66 Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.228A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 334 through 354 removed outlier: 3.930A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 425 through 429 removed outlier: 4.113A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 484 removed outlier: 4.919A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 542 removed outlier: 3.830A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 544 No H-bonds generated for 'chain 'B' and resid 543 through 544' Processing helix chain 'B' and resid 545 through 549 Processing helix chain 'B' and resid 569 through 596 removed outlier: 3.543A pdb=" N ILE B 573 " --> pdb=" O THR B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 658 Processing helix chain 'C' and resid 61 through 66 Processing helix chain 'C' and resid 98 through 117 removed outlier: 4.228A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 334 through 354 removed outlier: 3.928A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 387 through 391 Processing helix chain 'C' and resid 425 through 429 removed outlier: 4.113A pdb=" N GLN C 428 " --> pdb=" O ASN C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 484 removed outlier: 4.919A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 542 removed outlier: 3.831A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 544 No H-bonds generated for 'chain 'D' and resid 543 through 544' Processing helix chain 'D' and resid 545 through 549 Processing helix chain 'D' and resid 569 through 596 removed outlier: 3.542A pdb=" N ILE D 573 " --> pdb=" O THR D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 625 Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 658 Processing helix chain 'E' and resid 61 through 66 Processing helix chain 'E' and resid 98 through 117 removed outlier: 4.227A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 195 through 198 Processing helix chain 'E' and resid 334 through 354 removed outlier: 3.928A pdb=" N LYS E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 387 through 391 Processing helix chain 'E' and resid 425 through 429 removed outlier: 4.113A pdb=" N GLN E 428 " --> pdb=" O ASN E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 484 removed outlier: 4.919A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 542 removed outlier: 3.830A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 543 through 544 No H-bonds generated for 'chain 'F' and resid 543 through 544' Processing helix chain 'F' and resid 545 through 549 Processing helix chain 'F' and resid 569 through 596 removed outlier: 3.543A pdb=" N ILE F 573 " --> pdb=" O THR F 569 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 625 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 658 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.601A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.706A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.515A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.295A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.814A pdb=" N ILE A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 11.774A pdb=" N LEU A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 10.771A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 10.824A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 274 removed outlier: 4.080A pdb=" N ASN A 301 " --> pdb=" O ILE A 323A" (cutoff:3.500A) removed outlier: 5.449A pdb=" N LYS A 305 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N THR A 320 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ILE A 307 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N TYR A 318 " --> pdb=" O ILE A 307 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 316 through 323A removed outlier: 5.409A pdb=" N TYR A 318 " --> pdb=" O ILE A 307 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ILE A 307 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N THR A 320 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N LYS A 305 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ASN A 301 " --> pdb=" O ILE A 323A" (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 374 through 378 removed outlier: 4.124A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 10.824A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.771A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.774A pdb=" N LEU A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 11.814A pdb=" N ILE A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.295A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 393 through 395 removed outlier: 6.512A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.602A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N TYR C 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N CYS D 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AB6, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AB7, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AB8, first strand: chain 'C' and resid 201 through 203 removed outlier: 6.706A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.516A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N GLY C 441 " --> pdb=" O ASN C 300 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ASN C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLY C 451 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 10.295A pdb=" N GLU C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 11.815A pdb=" N ILE C 453 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 11.774A pdb=" N LEU C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 10.771A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 10.824A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 271 through 274 removed outlier: 4.081A pdb=" N ASN C 301 " --> pdb=" O ILE C 323A" (cutoff:3.500A) removed outlier: 5.448A pdb=" N LYS C 305 " --> pdb=" O THR C 320 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N THR C 320 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ILE C 307 " --> pdb=" O TYR C 318 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N TYR C 318 " --> pdb=" O ILE C 307 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 316 through 323A removed outlier: 5.409A pdb=" N TYR C 318 " --> pdb=" O ILE C 307 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ILE C 307 " --> pdb=" O TYR C 318 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N THR C 320 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N LYS C 305 " --> pdb=" O THR C 320 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ASN C 301 " --> pdb=" O ILE C 323A" (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 374 through 378 removed outlier: 4.124A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 10.824A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 10.771A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.774A pdb=" N LEU C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 11.815A pdb=" N ILE C 453 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 10.295A pdb=" N GLU C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLY C 451 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ASN C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N GLY C 441 " --> pdb=" O ASN C 300 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 393 through 395 removed outlier: 6.512A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.601A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AC7, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AC8, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AC9, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AD1, first strand: chain 'E' and resid 201 through 203 removed outlier: 6.705A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.515A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N GLY E 441 " --> pdb=" O ASN E 300 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ASN E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLY E 451 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.294A pdb=" N GLU E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 11.815A pdb=" N ILE E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 11.774A pdb=" N LEU E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 10.772A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 10.825A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 271 through 274 removed outlier: 4.082A pdb=" N ASN E 301 " --> pdb=" O ILE E 323A" (cutoff:3.500A) removed outlier: 5.449A pdb=" N LYS E 305 " --> pdb=" O THR E 320 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N THR E 320 " --> pdb=" O LYS E 305 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ILE E 307 " --> pdb=" O TYR E 318 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N TYR E 318 " --> pdb=" O ILE E 307 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 316 through 323A removed outlier: 5.408A pdb=" N TYR E 318 " --> pdb=" O ILE E 307 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ILE E 307 " --> pdb=" O TYR E 318 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N THR E 320 " --> pdb=" O LYS E 305 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N LYS E 305 " --> pdb=" O THR E 320 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ASN E 301 " --> pdb=" O ILE E 323A" (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 374 through 378 removed outlier: 4.124A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 10.825A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 10.772A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 11.774A pdb=" N LEU E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 11.815A pdb=" N ILE E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.294A pdb=" N GLU E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLY E 451 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ASN E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N GLY E 441 " --> pdb=" O ASN E 300 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 393 through 395 removed outlier: 6.512A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) 672 hydrogen bonds defined for protein. 1791 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: 5.86 Time building geometry restraints manager: 7.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3408 1.32 - 1.45: 4543 1.45 - 1.58: 7118 1.58 - 1.72: 3 1.72 - 1.85: 129 Bond restraints: 15201 Sorted by residual: bond pdb=" CB HIS A 374 " pdb=" CG HIS A 374 " ideal model delta sigma weight residual 1.497 1.416 0.081 1.40e-02 5.10e+03 3.33e+01 bond pdb=" CB HIS C 374 " pdb=" CG HIS C 374 " ideal model delta sigma weight residual 1.497 1.417 0.080 1.40e-02 5.10e+03 3.29e+01 bond pdb=" CB HIS E 374 " pdb=" CG HIS E 374 " ideal model delta sigma weight residual 1.497 1.417 0.080 1.40e-02 5.10e+03 3.26e+01 bond pdb=" NE1 TRP C 479 " pdb=" CE2 TRP C 479 " ideal model delta sigma weight residual 1.370 1.320 0.050 1.10e-02 8.26e+03 2.05e+01 bond pdb=" NE1 TRP A 479 " pdb=" CE2 TRP A 479 " ideal model delta sigma weight residual 1.370 1.321 0.049 1.10e-02 8.26e+03 2.02e+01 ... (remaining 15196 not shown) Histogram of bond angle deviations from ideal: 100.42 - 107.16: 815 107.16 - 113.89: 8692 113.89 - 120.63: 6100 120.63 - 127.36: 4843 127.36 - 134.10: 187 Bond angle restraints: 20637 Sorted by residual: angle pdb=" C ARG A 298 " pdb=" N PRO A 299 " pdb=" CA PRO A 299 " ideal model delta sigma weight residual 119.56 128.46 -8.90 1.01e+00 9.80e-01 7.77e+01 angle pdb=" C ARG C 298 " pdb=" N PRO C 299 " pdb=" CA PRO C 299 " ideal model delta sigma weight residual 119.56 128.46 -8.90 1.01e+00 9.80e-01 7.76e+01 angle pdb=" C ARG E 298 " pdb=" N PRO E 299 " pdb=" CA PRO E 299 " ideal model delta sigma weight residual 119.56 128.42 -8.86 1.01e+00 9.80e-01 7.70e+01 angle pdb=" N GLN A 258 " pdb=" CA GLN A 258 " pdb=" C GLN A 258 " ideal model delta sigma weight residual 111.36 118.69 -7.33 1.09e+00 8.42e-01 4.52e+01 angle pdb=" N GLN C 258 " pdb=" CA GLN C 258 " pdb=" C GLN C 258 " ideal model delta sigma weight residual 111.36 118.68 -7.32 1.09e+00 8.42e-01 4.51e+01 ... (remaining 20632 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.58: 10030 21.58 - 43.15: 305 43.15 - 64.73: 66 64.73 - 86.30: 33 86.30 - 107.88: 12 Dihedral angle restraints: 10446 sinusoidal: 5508 harmonic: 4938 Sorted by residual: dihedral pdb=" CB CYS E 378 " pdb=" SG CYS E 378 " pdb=" SG CYS E 445 " pdb=" CB CYS E 445 " ideal model delta sinusoidal sigma weight residual -86.00 -134.94 48.94 1 1.00e+01 1.00e-02 3.29e+01 dihedral pdb=" CB CYS A 378 " pdb=" SG CYS A 378 " pdb=" SG CYS A 445 " pdb=" CB CYS A 445 " ideal model delta sinusoidal sigma weight residual -86.00 -134.90 48.90 1 1.00e+01 1.00e-02 3.29e+01 dihedral pdb=" CB CYS C 378 " pdb=" SG CYS C 378 " pdb=" SG CYS C 445 " pdb=" CB CYS C 445 " ideal model delta sinusoidal sigma weight residual -86.00 -134.89 48.89 1 1.00e+01 1.00e-02 3.29e+01 ... (remaining 10443 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 2044 0.119 - 0.239: 545 0.239 - 0.358: 36 0.358 - 0.478: 0 0.478 - 0.597: 3 Chirality restraints: 2628 Sorted by residual: chirality pdb=" C1 BMA G 3 " pdb=" O4 NAG G 2 " pdb=" C2 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 1.01e+02 chirality pdb=" C1 BMA Q 3 " pdb=" O4 NAG Q 2 " pdb=" C2 BMA Q 3 " pdb=" O5 BMA Q 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 1.00e+02 chirality pdb=" C1 BMA a 3 " pdb=" O4 NAG a 2 " pdb=" C2 BMA a 3 " pdb=" O5 BMA a 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 9.79e+01 ... (remaining 2625 not shown) Planarity restraints: 2547 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN F 611 " -0.064 2.00e-02 2.50e+03 6.70e-02 5.62e+01 pdb=" CG ASN F 611 " 0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN F 611 " 0.015 2.00e-02 2.50e+03 pdb=" ND2 ASN F 611 " 0.105 2.00e-02 2.50e+03 pdb=" C1 NAG F 703 " -0.081 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 611 " -0.064 2.00e-02 2.50e+03 6.70e-02 5.60e+01 pdb=" CG ASN B 611 " 0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN B 611 " 0.015 2.00e-02 2.50e+03 pdb=" ND2 ASN B 611 " 0.105 2.00e-02 2.50e+03 pdb=" C1 NAG B 703 " -0.080 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 611 " -0.064 2.00e-02 2.50e+03 6.69e-02 5.59e+01 pdb=" CG ASN D 611 " 0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN D 611 " 0.015 2.00e-02 2.50e+03 pdb=" ND2 ASN D 611 " 0.105 2.00e-02 2.50e+03 pdb=" C1 NAG D 703 " -0.080 2.00e-02 2.50e+03 ... (remaining 2544 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3526 2.78 - 3.31: 13398 3.31 - 3.84: 24752 3.84 - 4.37: 29411 4.37 - 4.90: 46903 Nonbonded interactions: 117990 Sorted by model distance: nonbonded pdb=" OG1 THR A 37 " pdb=" OG1 THR A 499 " model vdw 2.247 2.440 nonbonded pdb=" OG1 THR C 37 " pdb=" OG1 THR C 499 " model vdw 2.247 2.440 nonbonded pdb=" OG1 THR E 37 " pdb=" OG1 THR E 499 " model vdw 2.248 2.440 nonbonded pdb=" N ASN C 355 " pdb=" OD1 ASN C 355 " model vdw 2.391 2.520 nonbonded pdb=" N ASN E 355 " pdb=" OD1 ASN E 355 " model vdw 2.391 2.520 ... (remaining 117985 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'Q' selection = chain 'a' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.200 Check model and map are aligned: 0.230 Set scattering table: 0.150 Process input model: 43.480 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.270 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 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 : 0.020 0.113 15201 Z= 1.299 Angle : 1.694 8.904 20637 Z= 1.071 Chirality : 0.100 0.597 2628 Planarity : 0.009 0.039 2484 Dihedral : 11.834 107.876 7149 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 1.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 0.20 % Allowed : 0.39 % Favored : 99.41 % 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: 0.90 (0.19), residues: 1674 helix: -0.13 (0.24), residues: 420 sheet: 1.34 (0.22), residues: 411 loop : 0.79 (0.20), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.010 TRP E 96 HIS 0.008 0.003 HIS B 585 PHE 0.028 0.006 PHE A 383 TYR 0.068 0.008 TYR B 638 ARG 0.006 0.001 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 1524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 456 time to evaluate : 1.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.8996 (m) cc_final: 0.8660 (p) REVERT: A 180 ASP cc_start: 0.8917 (m-30) cc_final: 0.8615 (m-30) REVERT: A 195 ASN cc_start: 0.9275 (p0) cc_final: 0.9019 (p0) REVERT: A 233 PHE cc_start: 0.9195 (t80) cc_final: 0.8699 (t80) REVERT: A 300 ASN cc_start: 0.8908 (m-40) cc_final: 0.7756 (p0) REVERT: B 530 MET cc_start: 0.8896 (mtp) cc_final: 0.8457 (mtp) REVERT: B 536 THR cc_start: 0.8683 (p) cc_final: 0.8124 (t) REVERT: B 540 GLN cc_start: 0.9170 (mp-120) cc_final: 0.8879 (mp10) REVERT: B 543 ASN cc_start: 0.8475 (m-40) cc_final: 0.7970 (t0) REVERT: B 591 GLN cc_start: 0.9328 (tt0) cc_final: 0.8870 (tt0) REVERT: B 615 SER cc_start: 0.8959 (t) cc_final: 0.8655 (m) REVERT: B 617 ARG cc_start: 0.7662 (ttm-80) cc_final: 0.6978 (mmm-85) REVERT: B 618 ASN cc_start: 0.6401 (m110) cc_final: 0.6179 (m110) REVERT: B 626 MET cc_start: 0.8237 (mmm) cc_final: 0.7674 (tpt) REVERT: C 51 THR cc_start: 0.9008 (m) cc_final: 0.8622 (p) REVERT: C 180 ASP cc_start: 0.8995 (m-30) cc_final: 0.8767 (m-30) REVERT: C 195 ASN cc_start: 0.9257 (p0) cc_final: 0.8998 (p0) REVERT: C 233 PHE cc_start: 0.9200 (t80) cc_final: 0.8900 (t80) REVERT: C 251 ILE cc_start: 0.9153 (mt) cc_final: 0.8795 (mm) REVERT: C 300 ASN cc_start: 0.8930 (m-40) cc_final: 0.7873 (p0) REVERT: C 423 ILE cc_start: 0.9534 (mt) cc_final: 0.9267 (mt) REVERT: D 536 THR cc_start: 0.8298 (p) cc_final: 0.7780 (t) REVERT: D 540 GLN cc_start: 0.9228 (mp-120) cc_final: 0.8889 (mp10) REVERT: D 543 ASN cc_start: 0.8388 (m-40) cc_final: 0.7805 (t0) REVERT: D 614 TRP cc_start: 0.8207 (m-10) cc_final: 0.7737 (m-10) REVERT: D 615 SER cc_start: 0.9012 (t) cc_final: 0.8636 (m) REVERT: D 617 ARG cc_start: 0.7542 (ttm-80) cc_final: 0.7203 (mmm-85) REVERT: E 51 THR cc_start: 0.9040 (m) cc_final: 0.8686 (p) REVERT: E 180 ASP cc_start: 0.9083 (m-30) cc_final: 0.8810 (m-30) REVERT: E 195 ASN cc_start: 0.9224 (p0) cc_final: 0.9006 (p0) REVERT: E 233 PHE cc_start: 0.9110 (t80) cc_final: 0.8641 (t80) REVERT: E 256 SER cc_start: 0.8245 (p) cc_final: 0.7921 (p) REVERT: E 300 ASN cc_start: 0.8959 (m-40) cc_final: 0.8690 (m-40) REVERT: F 530 MET cc_start: 0.8869 (mtp) cc_final: 0.8469 (mtp) REVERT: F 536 THR cc_start: 0.8654 (p) cc_final: 0.8041 (t) REVERT: F 540 GLN cc_start: 0.9253 (mp-120) cc_final: 0.8876 (mp10) REVERT: F 543 ASN cc_start: 0.8447 (m-40) cc_final: 0.8153 (t0) REVERT: F 615 SER cc_start: 0.8697 (t) cc_final: 0.8390 (m) REVERT: F 617 ARG cc_start: 0.7583 (ttm-80) cc_final: 0.7123 (mmm-85) REVERT: F 643 TYR cc_start: 0.8769 (m-10) cc_final: 0.8092 (m-10) outliers start: 3 outliers final: 3 residues processed: 459 average time/residue: 0.2700 time to fit residues: 180.3044 Evaluate side-chains 269 residues out of total 1524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 266 time to evaluate : 1.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 6.9990 chunk 127 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 152 optimal weight: 7.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN A 188 ASN ** B 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 ASN C 188 ASN C 440 GLN D 630 GLN E 185 ASN E 188 ASN E 422 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15201 Z= 0.261 Angle : 0.695 9.363 20637 Z= 0.365 Chirality : 0.047 0.230 2628 Planarity : 0.004 0.049 2484 Dihedral : 9.795 80.821 3933 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.46 % Allowed : 2.30 % Favored : 97.24 % 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: 1.32 (0.19), residues: 1674 helix: 1.29 (0.26), residues: 393 sheet: 1.55 (0.24), residues: 411 loop : 0.45 (0.20), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 479 HIS 0.004 0.001 HIS A 105 PHE 0.015 0.002 PHE C 391 TYR 0.033 0.002 TYR B 643 ARG 0.012 0.001 ARG F 617 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 335 time to evaluate : 1.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.8993 (m) cc_final: 0.8497 (p) REVERT: A 87 GLU cc_start: 0.8490 (tt0) cc_final: 0.8263 (tp30) REVERT: A 180 ASP cc_start: 0.8952 (m-30) cc_final: 0.8642 (m-30) REVERT: A 256 SER cc_start: 0.7987 (p) cc_final: 0.7721 (p) REVERT: A 300 ASN cc_start: 0.8330 (m-40) cc_final: 0.7949 (m-40) REVERT: A 434 MET cc_start: 0.9217 (ttp) cc_final: 0.9016 (ttp) REVERT: B 536 THR cc_start: 0.8334 (p) cc_final: 0.7906 (t) REVERT: B 542 ARG cc_start: 0.8429 (ttm-80) cc_final: 0.7361 (ttm-80) REVERT: B 543 ASN cc_start: 0.8317 (m-40) cc_final: 0.7964 (t0) REVERT: B 615 SER cc_start: 0.8674 (t) cc_final: 0.8386 (m) REVERT: B 656 ASN cc_start: 0.8725 (m-40) cc_final: 0.8467 (m110) REVERT: C 180 ASP cc_start: 0.8985 (m-30) cc_final: 0.8676 (m-30) REVERT: C 233 PHE cc_start: 0.9170 (t80) cc_final: 0.8905 (t80) REVERT: C 251 ILE cc_start: 0.9120 (mt) cc_final: 0.8853 (mm) REVERT: C 256 SER cc_start: 0.8127 (p) cc_final: 0.7871 (p) REVERT: C 300 ASN cc_start: 0.8269 (m-40) cc_final: 0.7910 (m-40) REVERT: C 479 TRP cc_start: 0.8391 (m-10) cc_final: 0.7954 (m-10) REVERT: D 536 THR cc_start: 0.8084 (p) cc_final: 0.7818 (t) REVERT: D 543 ASN cc_start: 0.8314 (m-40) cc_final: 0.7931 (t0) REVERT: D 614 TRP cc_start: 0.8318 (m-10) cc_final: 0.7838 (m-10) REVERT: D 615 SER cc_start: 0.8626 (t) cc_final: 0.8347 (m) REVERT: D 638 TYR cc_start: 0.8336 (m-80) cc_final: 0.8037 (m-10) REVERT: E 51 THR cc_start: 0.9122 (m) cc_final: 0.8714 (p) REVERT: E 175 LEU cc_start: 0.8551 (mt) cc_final: 0.8248 (tp) REVERT: E 180 ASP cc_start: 0.9051 (m-30) cc_final: 0.8817 (m-30) REVERT: E 256 SER cc_start: 0.8115 (p) cc_final: 0.7830 (p) REVERT: E 447 SER cc_start: 0.9309 (m) cc_final: 0.8924 (p) REVERT: F 535 MET cc_start: 0.8572 (mmt) cc_final: 0.8365 (mmt) REVERT: F 536 THR cc_start: 0.8195 (p) cc_final: 0.7911 (t) REVERT: F 543 ASN cc_start: 0.8325 (m-40) cc_final: 0.8100 (t0) REVERT: F 615 SER cc_start: 0.8604 (t) cc_final: 0.8208 (m) REVERT: F 618 ASN cc_start: 0.5789 (m110) cc_final: 0.5523 (m110) REVERT: F 621 GLU cc_start: 0.8320 (tm-30) cc_final: 0.7840 (tm-30) outliers start: 7 outliers final: 0 residues processed: 340 average time/residue: 0.2334 time to fit residues: 120.8118 Evaluate side-chains 247 residues out of total 1524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 247 time to evaluate : 1.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 7.9990 chunk 47 optimal weight: 4.9990 chunk 126 optimal weight: 0.9980 chunk 103 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 chunk 152 optimal weight: 10.0000 chunk 165 optimal weight: 0.7980 chunk 136 optimal weight: 7.9990 chunk 151 optimal weight: 7.9990 chunk 52 optimal weight: 8.9990 chunk 122 optimal weight: 9.9990 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN A 216 HIS A 422 GLN B 658 GLN C 85 HIS C 170 GLN C 216 HIS C 422 GLN E 170 GLN E 216 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 15201 Z= 0.339 Angle : 0.689 11.974 20637 Z= 0.359 Chirality : 0.047 0.297 2628 Planarity : 0.004 0.047 2484 Dihedral : 9.026 76.219 3933 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.39 % Allowed : 2.30 % Favored : 97.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.20), residues: 1674 helix: 1.55 (0.27), residues: 393 sheet: 1.18 (0.24), residues: 417 loop : 0.15 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 479 HIS 0.007 0.001 HIS A 105 PHE 0.013 0.002 PHE C 176 TYR 0.020 0.002 TYR C 217 ARG 0.005 0.001 ARG B 617 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 276 time to evaluate : 1.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.9247 (m) cc_final: 0.8818 (p) REVERT: A 217 TYR cc_start: 0.8672 (m-80) cc_final: 0.8203 (m-80) REVERT: A 256 SER cc_start: 0.8190 (p) cc_final: 0.7971 (p) REVERT: A 342 LEU cc_start: 0.9343 (mm) cc_final: 0.8761 (tp) REVERT: B 536 THR cc_start: 0.8510 (p) cc_final: 0.8220 (t) REVERT: B 543 ASN cc_start: 0.8454 (m-40) cc_final: 0.7897 (t0) REVERT: B 615 SER cc_start: 0.8960 (t) cc_final: 0.8330 (m) REVERT: B 656 ASN cc_start: 0.8672 (m-40) cc_final: 0.8467 (m-40) REVERT: C 251 ILE cc_start: 0.9224 (mt) cc_final: 0.8905 (mm) REVERT: C 256 SER cc_start: 0.8297 (p) cc_final: 0.7988 (p) REVERT: C 300 ASN cc_start: 0.8366 (m-40) cc_final: 0.7593 (p0) REVERT: C 342 LEU cc_start: 0.9342 (mm) cc_final: 0.8780 (tp) REVERT: D 543 ASN cc_start: 0.8364 (m-40) cc_final: 0.7959 (t0) REVERT: D 614 TRP cc_start: 0.8467 (m-10) cc_final: 0.7606 (m-10) REVERT: D 615 SER cc_start: 0.8885 (t) cc_final: 0.8452 (m) REVERT: D 617 ARG cc_start: 0.7654 (mtp180) cc_final: 0.7345 (mtp180) REVERT: D 638 TYR cc_start: 0.8218 (m-80) cc_final: 0.7834 (m-10) REVERT: D 642 ILE cc_start: 0.9560 (mm) cc_final: 0.9278 (mm) REVERT: E 51 THR cc_start: 0.9297 (m) cc_final: 0.8971 (p) REVERT: E 180 ASP cc_start: 0.9037 (m-30) cc_final: 0.8734 (m-30) REVERT: E 256 SER cc_start: 0.8204 (p) cc_final: 0.7934 (p) REVERT: E 342 LEU cc_start: 0.9396 (mm) cc_final: 0.8811 (tp) REVERT: F 536 THR cc_start: 0.8426 (p) cc_final: 0.8213 (t) REVERT: F 543 ASN cc_start: 0.8395 (m-40) cc_final: 0.8088 (t0) REVERT: F 602 LEU cc_start: 0.9128 (mm) cc_final: 0.8863 (mp) REVERT: F 615 SER cc_start: 0.8629 (t) cc_final: 0.8127 (m) REVERT: F 621 GLU cc_start: 0.8643 (tm-30) cc_final: 0.7585 (tp30) outliers start: 6 outliers final: 1 residues processed: 280 average time/residue: 0.2283 time to fit residues: 99.7625 Evaluate side-chains 216 residues out of total 1524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 215 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 8.9990 chunk 114 optimal weight: 5.9990 chunk 79 optimal weight: 8.9990 chunk 16 optimal weight: 0.8980 chunk 72 optimal weight: 0.4980 chunk 102 optimal weight: 10.0000 chunk 153 optimal weight: 3.9990 chunk 162 optimal weight: 0.0770 chunk 80 optimal weight: 5.9990 chunk 145 optimal weight: 0.0980 chunk 43 optimal weight: 2.9990 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.4016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15201 Z= 0.168 Angle : 0.589 11.914 20637 Z= 0.306 Chirality : 0.046 0.312 2628 Planarity : 0.004 0.050 2484 Dihedral : 7.962 70.052 3933 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.20 % Allowed : 1.77 % Favored : 98.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.20), residues: 1674 helix: 1.73 (0.27), residues: 393 sheet: 1.13 (0.23), residues: 447 loop : 0.08 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 479 HIS 0.005 0.001 HIS A 105 PHE 0.010 0.001 PHE A 176 TYR 0.015 0.001 TYR B 638 ARG 0.004 0.000 ARG B 542 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 267 time to evaluate : 1.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.9074 (m) cc_final: 0.8854 (p) REVERT: A 100 MET cc_start: 0.7647 (mtp) cc_final: 0.7305 (mtm) REVERT: A 104 MET cc_start: 0.8995 (tpp) cc_final: 0.8752 (tpp) REVERT: A 180 ASP cc_start: 0.8931 (m-30) cc_final: 0.8644 (m-30) REVERT: A 217 TYR cc_start: 0.8643 (m-80) cc_final: 0.8379 (m-80) REVERT: A 256 SER cc_start: 0.7889 (p) cc_final: 0.7663 (p) REVERT: A 342 LEU cc_start: 0.9186 (mm) cc_final: 0.8623 (tp) REVERT: B 536 THR cc_start: 0.8227 (p) cc_final: 0.8018 (t) REVERT: B 543 ASN cc_start: 0.8322 (m-40) cc_final: 0.7960 (t0) REVERT: B 615 SER cc_start: 0.8847 (t) cc_final: 0.8148 (m) REVERT: B 626 MET cc_start: 0.8641 (mmm) cc_final: 0.8370 (mmm) REVERT: C 51 THR cc_start: 0.9135 (m) cc_final: 0.8872 (p) REVERT: C 114 GLN cc_start: 0.8690 (tp-100) cc_final: 0.8443 (tp40) REVERT: C 251 ILE cc_start: 0.9213 (mt) cc_final: 0.8850 (mm) REVERT: C 256 SER cc_start: 0.8204 (p) cc_final: 0.7927 (p) REVERT: C 284 ILE cc_start: 0.9412 (mt) cc_final: 0.9049 (tt) REVERT: C 300 ASN cc_start: 0.8124 (m-40) cc_final: 0.7256 (p0) REVERT: C 342 LEU cc_start: 0.9235 (mm) cc_final: 0.8630 (tp) REVERT: D 543 ASN cc_start: 0.8296 (m-40) cc_final: 0.8067 (t0) REVERT: D 614 TRP cc_start: 0.8505 (m-10) cc_final: 0.7576 (m-10) REVERT: D 615 SER cc_start: 0.8838 (t) cc_final: 0.8401 (m) REVERT: D 638 TYR cc_start: 0.8061 (m-80) cc_final: 0.7703 (m-10) REVERT: D 642 ILE cc_start: 0.9568 (mm) cc_final: 0.9302 (mm) REVERT: E 51 THR cc_start: 0.9218 (m) cc_final: 0.8972 (p) REVERT: E 256 SER cc_start: 0.8039 (p) cc_final: 0.7750 (p) REVERT: E 342 LEU cc_start: 0.9244 (mm) cc_final: 0.8635 (tp) REVERT: F 543 ASN cc_start: 0.8392 (m-40) cc_final: 0.8154 (t0) REVERT: F 614 TRP cc_start: 0.8273 (m-10) cc_final: 0.7899 (m-10) REVERT: F 615 SER cc_start: 0.8523 (t) cc_final: 0.8000 (m) REVERT: F 621 GLU cc_start: 0.8603 (tm-30) cc_final: 0.8266 (tm-30) outliers start: 3 outliers final: 2 residues processed: 269 average time/residue: 0.2243 time to fit residues: 94.7356 Evaluate side-chains 224 residues out of total 1524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 222 time to evaluate : 1.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 7.9990 chunk 92 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 120 optimal weight: 6.9990 chunk 67 optimal weight: 9.9990 chunk 138 optimal weight: 2.9990 chunk 112 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 82 optimal weight: 0.9990 chunk 145 optimal weight: 0.9990 chunk 40 optimal weight: 20.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 HIS B 656 ASN E 85 HIS E 258 GLN E 374 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.4401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 15201 Z= 0.288 Angle : 0.634 11.724 20637 Z= 0.327 Chirality : 0.047 0.295 2628 Planarity : 0.004 0.045 2484 Dihedral : 7.661 63.373 3933 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % 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: 0.98 (0.20), residues: 1674 helix: 1.67 (0.27), residues: 393 sheet: 1.40 (0.26), residues: 387 loop : -0.12 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 479 HIS 0.005 0.001 HIS F 570 PHE 0.010 0.001 PHE C 176 TYR 0.019 0.002 TYR B 638 ARG 0.004 0.001 ARG C 298 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 248 time to evaluate : 1.850 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.9194 (m) cc_final: 0.8926 (p) REVERT: A 104 MET cc_start: 0.8989 (tpp) cc_final: 0.8746 (tpp) REVERT: A 180 ASP cc_start: 0.8985 (m-30) cc_final: 0.8668 (m-30) REVERT: A 217 TYR cc_start: 0.8568 (m-80) cc_final: 0.8105 (m-80) REVERT: A 256 SER cc_start: 0.8211 (p) cc_final: 0.7958 (p) REVERT: B 543 ASN cc_start: 0.8440 (m-40) cc_final: 0.7920 (t0) REVERT: B 615 SER cc_start: 0.8875 (t) cc_final: 0.8364 (m) REVERT: C 51 THR cc_start: 0.9281 (m) cc_final: 0.9050 (p) REVERT: C 114 GLN cc_start: 0.8806 (tp-100) cc_final: 0.8587 (tp40) REVERT: C 217 TYR cc_start: 0.8871 (m-80) cc_final: 0.8590 (m-80) REVERT: C 256 SER cc_start: 0.8560 (p) cc_final: 0.8317 (p) REVERT: C 284 ILE cc_start: 0.9509 (mt) cc_final: 0.9129 (tt) REVERT: D 614 TRP cc_start: 0.8516 (m-10) cc_final: 0.7625 (m-10) REVERT: D 615 SER cc_start: 0.8734 (t) cc_final: 0.8301 (m) REVERT: D 638 TYR cc_start: 0.8153 (m-80) cc_final: 0.7714 (m-10) REVERT: D 642 ILE cc_start: 0.9577 (mm) cc_final: 0.9316 (mm) REVERT: E 51 THR cc_start: 0.9355 (m) cc_final: 0.8976 (p) REVERT: E 256 SER cc_start: 0.8325 (p) cc_final: 0.8068 (p) REVERT: F 535 MET cc_start: 0.8767 (mmp) cc_final: 0.8502 (mmt) REVERT: F 543 ASN cc_start: 0.8434 (m-40) cc_final: 0.8083 (t0) REVERT: F 615 SER cc_start: 0.8520 (t) cc_final: 0.7707 (m) REVERT: F 617 ARG cc_start: 0.7194 (mmm-85) cc_final: 0.6700 (mtp180) outliers start: 0 outliers final: 0 residues processed: 248 average time/residue: 0.2266 time to fit residues: 87.3916 Evaluate side-chains 200 residues out of total 1524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 1.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 10.0000 chunk 146 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 40 optimal weight: 40.0000 chunk 162 optimal weight: 0.9990 chunk 134 optimal weight: 6.9990 chunk 75 optimal weight: 10.0000 chunk 13 optimal weight: 8.9990 chunk 53 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS C 302 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.4758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 15201 Z= 0.343 Angle : 0.664 11.684 20637 Z= 0.341 Chirality : 0.048 0.250 2628 Planarity : 0.004 0.043 2484 Dihedral : 7.593 56.687 3933 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % 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: 0.55 (0.20), residues: 1674 helix: 0.99 (0.26), residues: 423 sheet: 1.22 (0.25), residues: 411 loop : -0.36 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 479 HIS 0.006 0.001 HIS A 374 PHE 0.012 0.001 PHE D 522 TYR 0.017 0.002 TYR A 217 ARG 0.006 0.001 ARG E 476 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 234 time to evaluate : 1.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.9253 (m) cc_final: 0.8763 (p) REVERT: A 180 ASP cc_start: 0.9045 (m-30) cc_final: 0.8787 (m-30) REVERT: A 256 SER cc_start: 0.8431 (p) cc_final: 0.8173 (p) REVERT: A 284 ILE cc_start: 0.9510 (mm) cc_final: 0.9167 (tt) REVERT: B 530 MET cc_start: 0.9124 (mmm) cc_final: 0.8113 (mmt) REVERT: C 51 THR cc_start: 0.9350 (m) cc_final: 0.9103 (p) REVERT: C 114 GLN cc_start: 0.8846 (tp-100) cc_final: 0.8495 (tp40) REVERT: C 217 TYR cc_start: 0.8905 (m-80) cc_final: 0.8613 (m-80) REVERT: C 256 SER cc_start: 0.8644 (p) cc_final: 0.8382 (p) REVERT: C 284 ILE cc_start: 0.9596 (mt) cc_final: 0.9254 (tt) REVERT: C 475 MET cc_start: 0.8689 (mmm) cc_final: 0.8390 (tpp) REVERT: D 540 GLN cc_start: 0.8952 (mp-120) cc_final: 0.8653 (mp10) REVERT: D 614 TRP cc_start: 0.8666 (m-10) cc_final: 0.7581 (m-10) REVERT: D 615 SER cc_start: 0.8541 (t) cc_final: 0.7764 (m) REVERT: D 638 TYR cc_start: 0.8242 (m-80) cc_final: 0.7801 (m-10) REVERT: D 642 ILE cc_start: 0.9545 (mm) cc_final: 0.9303 (mm) REVERT: E 51 THR cc_start: 0.9375 (m) cc_final: 0.9093 (p) REVERT: E 256 SER cc_start: 0.8366 (p) cc_final: 0.8077 (p) REVERT: E 284 ILE cc_start: 0.9544 (mt) cc_final: 0.9258 (tt) REVERT: F 530 MET cc_start: 0.9166 (mmm) cc_final: 0.8608 (mmt) REVERT: F 535 MET cc_start: 0.8890 (mmp) cc_final: 0.8540 (mmt) REVERT: F 584 GLU cc_start: 0.8775 (tt0) cc_final: 0.8407 (tt0) outliers start: 0 outliers final: 0 residues processed: 234 average time/residue: 0.2573 time to fit residues: 94.2592 Evaluate side-chains 189 residues out of total 1524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 1.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 10.0000 chunk 18 optimal weight: 0.9990 chunk 92 optimal weight: 4.9990 chunk 118 optimal weight: 0.7980 chunk 91 optimal weight: 7.9990 chunk 136 optimal weight: 0.9980 chunk 90 optimal weight: 9.9990 chunk 161 optimal weight: 2.9990 chunk 101 optimal weight: 9.9990 chunk 98 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 114 GLN ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.4903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15201 Z= 0.181 Angle : 0.567 11.388 20637 Z= 0.293 Chirality : 0.045 0.263 2628 Planarity : 0.003 0.045 2484 Dihedral : 6.816 59.287 3933 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % 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: 0.76 (0.21), residues: 1674 helix: 1.51 (0.27), residues: 396 sheet: 1.25 (0.27), residues: 375 loop : -0.25 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP A 479 HIS 0.004 0.000 HIS E 374 PHE 0.010 0.001 PHE A 176 TYR 0.015 0.001 TYR F 638 ARG 0.002 0.000 ARG B 542 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 262 time to evaluate : 1.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.9097 (m) cc_final: 0.8864 (p) REVERT: A 180 ASP cc_start: 0.8982 (m-30) cc_final: 0.8721 (m-30) REVERT: A 256 SER cc_start: 0.8143 (p) cc_final: 0.7853 (p) REVERT: B 530 MET cc_start: 0.9142 (mmm) cc_final: 0.8077 (mmt) REVERT: B 540 GLN cc_start: 0.8879 (mp-120) cc_final: 0.8556 (mp10) REVERT: B 615 SER cc_start: 0.8466 (t) cc_final: 0.7984 (m) REVERT: C 51 THR cc_start: 0.9330 (m) cc_final: 0.9097 (p) REVERT: C 114 GLN cc_start: 0.8836 (tp-100) cc_final: 0.8522 (tp40) REVERT: C 217 TYR cc_start: 0.8795 (m-80) cc_final: 0.8345 (m-80) REVERT: C 256 SER cc_start: 0.8451 (p) cc_final: 0.8153 (p) REVERT: C 284 ILE cc_start: 0.9567 (mt) cc_final: 0.9262 (tt) REVERT: D 614 TRP cc_start: 0.8635 (m-10) cc_final: 0.7624 (m-10) REVERT: D 615 SER cc_start: 0.8380 (t) cc_final: 0.7680 (m) REVERT: D 638 TYR cc_start: 0.8083 (m-80) cc_final: 0.7662 (m-10) REVERT: D 642 ILE cc_start: 0.9457 (mm) cc_final: 0.9249 (mm) REVERT: E 51 THR cc_start: 0.9282 (m) cc_final: 0.8952 (p) REVERT: E 256 SER cc_start: 0.8314 (p) cc_final: 0.8074 (p) REVERT: E 284 ILE cc_start: 0.9526 (mt) cc_final: 0.9274 (tt) REVERT: E 342 LEU cc_start: 0.9102 (mm) cc_final: 0.8587 (tp) REVERT: F 530 MET cc_start: 0.9210 (mmm) cc_final: 0.8420 (mmt) REVERT: F 535 MET cc_start: 0.8834 (mmp) cc_final: 0.8502 (mmt) REVERT: F 540 GLN cc_start: 0.8959 (mp-120) cc_final: 0.8568 (mp10) REVERT: F 584 GLU cc_start: 0.8768 (tt0) cc_final: 0.8353 (tt0) REVERT: F 614 TRP cc_start: 0.8315 (m-10) cc_final: 0.7657 (m-10) REVERT: F 615 SER cc_start: 0.8325 (t) cc_final: 0.7567 (m) outliers start: 0 outliers final: 0 residues processed: 262 average time/residue: 0.2189 time to fit residues: 89.5990 Evaluate side-chains 210 residues out of total 1524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 210 time to evaluate : 1.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 9.9990 chunk 64 optimal weight: 0.8980 chunk 96 optimal weight: 0.0470 chunk 48 optimal weight: 5.9990 chunk 31 optimal weight: 8.9990 chunk 102 optimal weight: 9.9990 chunk 110 optimal weight: 10.0000 chunk 80 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 127 optimal weight: 6.9990 chunk 147 optimal weight: 20.0000 overall best weight: 2.7884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 656 ASN ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.5070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15201 Z= 0.258 Angle : 0.621 11.781 20637 Z= 0.320 Chirality : 0.046 0.280 2628 Planarity : 0.004 0.045 2484 Dihedral : 6.183 55.735 3933 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.20), residues: 1674 helix: 1.45 (0.27), residues: 396 sheet: 1.17 (0.27), residues: 378 loop : -0.29 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A 479 HIS 0.002 0.001 HIS A 374 PHE 0.011 0.001 PHE E 376 TYR 0.018 0.001 TYR F 638 ARG 0.003 0.000 ARG A 476 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 243 time to evaluate : 1.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8639 (tpp) cc_final: 0.8431 (tpp) REVERT: A 161 MET cc_start: 0.9346 (tpp) cc_final: 0.9132 (tpt) REVERT: A 180 ASP cc_start: 0.9014 (m-30) cc_final: 0.8734 (m-30) REVERT: A 247 CYS cc_start: 0.5905 (p) cc_final: 0.5670 (p) REVERT: A 256 SER cc_start: 0.8157 (p) cc_final: 0.7892 (p) REVERT: A 486 TYR cc_start: 0.8800 (m-80) cc_final: 0.8599 (m-10) REVERT: B 530 MET cc_start: 0.9131 (mmm) cc_final: 0.8119 (mmt) REVERT: B 614 TRP cc_start: 0.8302 (m-10) cc_final: 0.7620 (m-10) REVERT: B 642 ILE cc_start: 0.9622 (mm) cc_final: 0.9307 (mm) REVERT: C 114 GLN cc_start: 0.8851 (tp-100) cc_final: 0.8601 (tp40) REVERT: C 247 CYS cc_start: 0.6060 (p) cc_final: 0.5828 (p) REVERT: C 256 SER cc_start: 0.8523 (p) cc_final: 0.8286 (p) REVERT: C 284 ILE cc_start: 0.9602 (mt) cc_final: 0.9311 (tt) REVERT: D 530 MET cc_start: 0.9158 (mmm) cc_final: 0.8911 (mmt) REVERT: D 615 SER cc_start: 0.8401 (t) cc_final: 0.7672 (m) REVERT: D 638 TYR cc_start: 0.8148 (m-80) cc_final: 0.7774 (m-10) REVERT: D 654 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7694 (mt-10) REVERT: E 114 GLN cc_start: 0.8787 (tp40) cc_final: 0.8566 (tp40) REVERT: E 161 MET cc_start: 0.9082 (tpp) cc_final: 0.8821 (tpt) REVERT: E 195 ASN cc_start: 0.8719 (p0) cc_final: 0.8368 (p0) REVERT: E 256 SER cc_start: 0.8445 (p) cc_final: 0.8214 (p) REVERT: E 284 ILE cc_start: 0.9536 (mt) cc_final: 0.9298 (tt) REVERT: F 530 MET cc_start: 0.9094 (mmm) cc_final: 0.8293 (mmt) REVERT: F 535 MET cc_start: 0.8813 (mmp) cc_final: 0.8414 (mmt) REVERT: F 540 GLN cc_start: 0.8943 (mp-120) cc_final: 0.8599 (mp10) REVERT: F 584 GLU cc_start: 0.8659 (tt0) cc_final: 0.8164 (tt0) REVERT: F 614 TRP cc_start: 0.8439 (m-10) cc_final: 0.7819 (m-10) outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.2173 time to fit residues: 83.8806 Evaluate side-chains 206 residues out of total 1524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 1.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 1.9990 chunk 141 optimal weight: 5.9990 chunk 150 optimal weight: 8.9990 chunk 90 optimal weight: 6.9990 chunk 65 optimal weight: 0.4980 chunk 118 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 136 optimal weight: 7.9990 chunk 142 optimal weight: 6.9990 chunk 99 optimal weight: 0.7980 chunk 159 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 656 ASN C 85 HIS ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.5220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15201 Z= 0.172 Angle : 0.578 10.242 20637 Z= 0.300 Chirality : 0.045 0.233 2628 Planarity : 0.004 0.042 2484 Dihedral : 5.763 54.151 3933 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.20), residues: 1674 helix: 1.47 (0.27), residues: 396 sheet: 1.20 (0.27), residues: 375 loop : -0.32 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP A 479 HIS 0.002 0.000 HIS C 249 PHE 0.009 0.001 PHE A 176 TYR 0.016 0.001 TYR F 638 ARG 0.002 0.000 ARG B 542 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 251 time to evaluate : 1.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.9329 (tpp) cc_final: 0.9092 (tpt) REVERT: A 180 ASP cc_start: 0.8978 (m-30) cc_final: 0.8690 (m-30) REVERT: A 217 TYR cc_start: 0.8142 (m-80) cc_final: 0.7817 (m-80) REVERT: A 256 SER cc_start: 0.7841 (p) cc_final: 0.7596 (p) REVERT: B 530 MET cc_start: 0.9097 (mmm) cc_final: 0.8177 (mmt) REVERT: C 114 GLN cc_start: 0.8811 (tp-100) cc_final: 0.8532 (tp40) REVERT: C 256 SER cc_start: 0.8497 (p) cc_final: 0.8257 (p) REVERT: C 284 ILE cc_start: 0.9578 (mt) cc_final: 0.9316 (tt) REVERT: D 530 MET cc_start: 0.9163 (mmm) cc_final: 0.8642 (mmt) REVERT: D 615 SER cc_start: 0.8290 (t) cc_final: 0.7600 (m) REVERT: D 638 TYR cc_start: 0.8074 (m-80) cc_final: 0.7699 (m-10) REVERT: D 654 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7667 (mt-10) REVERT: E 114 GLN cc_start: 0.8743 (tp40) cc_final: 0.8506 (tp40) REVERT: E 195 ASN cc_start: 0.8577 (p0) cc_final: 0.8230 (p0) REVERT: E 256 SER cc_start: 0.8364 (p) cc_final: 0.8143 (p) REVERT: E 284 ILE cc_start: 0.9524 (mt) cc_final: 0.9309 (tt) REVERT: F 530 MET cc_start: 0.9069 (mmm) cc_final: 0.8227 (mmt) REVERT: F 535 MET cc_start: 0.8870 (mmp) cc_final: 0.8459 (mmt) REVERT: F 584 GLU cc_start: 0.8607 (tt0) cc_final: 0.8179 (tt0) REVERT: F 614 TRP cc_start: 0.8340 (m-10) cc_final: 0.7827 (m-10) outliers start: 0 outliers final: 0 residues processed: 251 average time/residue: 0.2153 time to fit residues: 84.9506 Evaluate side-chains 211 residues out of total 1524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 211 time to evaluate : 1.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 9.9990 chunk 75 optimal weight: 6.9990 chunk 110 optimal weight: 5.9990 chunk 167 optimal weight: 9.9990 chunk 154 optimal weight: 1.9990 chunk 133 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 102 optimal weight: 6.9990 chunk 81 optimal weight: 9.9990 chunk 105 optimal weight: 5.9990 chunk 141 optimal weight: 8.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 HIS ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 656 ASN E 85 HIS ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.5362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 15201 Z= 0.451 Angle : 0.742 12.057 20637 Z= 0.380 Chirality : 0.049 0.286 2628 Planarity : 0.005 0.049 2484 Dihedral : 6.666 58.530 3933 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: 0.21 (0.20), residues: 1674 helix: 1.03 (0.26), residues: 405 sheet: 0.77 (0.25), residues: 423 loop : -0.61 (0.21), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.083 0.003 TRP A 479 HIS 0.005 0.001 HIS C 374 PHE 0.017 0.002 PHE E 376 TYR 0.038 0.002 TYR C 217 ARG 0.004 0.001 ARG E 476 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 219 time to evaluate : 1.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.9278 (tpp) cc_final: 0.8964 (tpt) REVERT: A 180 ASP cc_start: 0.9116 (m-30) cc_final: 0.8856 (m-30) REVERT: A 256 SER cc_start: 0.8482 (p) cc_final: 0.8204 (p) REVERT: B 530 MET cc_start: 0.9022 (mmm) cc_final: 0.8126 (mmt) REVERT: C 104 MET cc_start: 0.9181 (tpp) cc_final: 0.8846 (tpp) REVERT: C 114 GLN cc_start: 0.8854 (tp-100) cc_final: 0.8518 (tp40) REVERT: C 217 TYR cc_start: 0.8380 (m-80) cc_final: 0.7916 (m-80) REVERT: C 256 SER cc_start: 0.8763 (p) cc_final: 0.8521 (p) REVERT: C 284 ILE cc_start: 0.9661 (mt) cc_final: 0.9407 (tt) REVERT: D 530 MET cc_start: 0.9130 (mmm) cc_final: 0.8617 (mmt) REVERT: D 538 THR cc_start: 0.9153 (p) cc_final: 0.8748 (t) REVERT: D 615 SER cc_start: 0.8449 (t) cc_final: 0.7680 (m) REVERT: D 638 TYR cc_start: 0.8241 (m-80) cc_final: 0.7873 (m-10) REVERT: D 654 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7658 (mt-10) REVERT: E 195 ASN cc_start: 0.8811 (p0) cc_final: 0.8538 (p0) REVERT: E 256 SER cc_start: 0.8612 (p) cc_final: 0.8370 (p) REVERT: E 284 ILE cc_start: 0.9588 (mt) cc_final: 0.9367 (tt) REVERT: F 530 MET cc_start: 0.8982 (mmm) cc_final: 0.8085 (mmt) REVERT: F 535 MET cc_start: 0.8947 (mmp) cc_final: 0.8468 (mmt) REVERT: F 584 GLU cc_start: 0.8706 (tt0) cc_final: 0.8341 (tt0) REVERT: F 614 TRP cc_start: 0.8476 (m-10) cc_final: 0.7921 (m-10) outliers start: 0 outliers final: 0 residues processed: 219 average time/residue: 0.2159 time to fit residues: 74.7320 Evaluate side-chains 186 residues out of total 1524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 1.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 30.0000 chunk 122 optimal weight: 8.9990 chunk 19 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 133 optimal weight: 3.9990 chunk 55 optimal weight: 10.0000 chunk 137 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 117 optimal weight: 10.0000 chunk 7 optimal weight: 0.7980 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 656 ASN D 656 ASN ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 656 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.103278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.079574 restraints weight = 30251.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.082178 restraints weight = 18737.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.084005 restraints weight = 13890.919| |-----------------------------------------------------------------------------| r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.5478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 15201 Z= 0.300 Angle : 0.654 13.311 20637 Z= 0.337 Chirality : 0.047 0.289 2628 Planarity : 0.004 0.047 2484 Dihedral : 6.518 56.255 3933 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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 (0.20), residues: 1674 helix: 1.21 (0.26), residues: 396 sheet: 0.89 (0.26), residues: 384 loop : -0.64 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.002 TRP A 479 HIS 0.005 0.001 HIS E 374 PHE 0.011 0.001 PHE E 376 TYR 0.022 0.002 TYR C 217 ARG 0.003 0.000 ARG A 476 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2743.29 seconds wall clock time: 51 minutes 24.88 seconds (3084.88 seconds total)