Starting phenix.real_space_refine on Fri Feb 16 22:46:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xrt_22295/02_2024/6xrt_22295_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xrt_22295/02_2024/6xrt_22295.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xrt_22295/02_2024/6xrt_22295.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xrt_22295/02_2024/6xrt_22295.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xrt_22295/02_2024/6xrt_22295_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xrt_22295/02_2024/6xrt_22295_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.014 sd= 0.071 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 115 5.16 5 C 10380 2.51 5 N 2761 2.21 5 O 3391 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G GLU 83": "OE1" <-> "OE2" Residue "G GLU 87": "OE1" <-> "OE2" Residue "G GLU 102": "OE1" <-> "OE2" Residue "G ASP 141": "OD1" <-> "OD2" Residue "G PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 190": "OE1" <-> "OE2" Residue "G PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 321": "OD1" <-> "OD2" Residue "G PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 368": "OD1" <-> "OD2" Residue "G PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 412": "OD1" <-> "OD2" Residue "G ASP 457": "OD1" <-> "OD2" Residue "G GLU 466": "OE1" <-> "OE2" Residue "G PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 621": "OE1" <-> "OE2" Residue "B ASP 624": "OD1" <-> "OD2" Residue "B TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 664": "OD1" <-> "OD2" Residue "E GLU 32": "OE1" <-> "OE2" Residue "E ASP 78": "OD1" <-> "OD2" Residue "E GLU 91": "OE1" <-> "OE2" Residue "E GLU 92": "OE1" <-> "OE2" Residue "E GLU 102": "OE1" <-> "OE2" Residue "E PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 268": "OE1" <-> "OE2" Residue "E GLU 275": "OE1" <-> "OE2" Residue "E PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 492": "OE1" <-> "OE2" Residue "F TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 47": "OD1" <-> "OD2" Residue "F GLU 92": "OE1" <-> "OE2" Residue "F ASP 107": "OD1" <-> "OD2" Residue "F TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 381": "OE1" <-> "OE2" Residue "F PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 632": "OD1" <-> "OD2" Residue "C TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 647": "OE1" <-> "OE2" Residue "A GLU 654": "OE1" <-> "OE2" Residue "H GLU 6": "OE1" <-> "OE2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 54": "NH1" <-> "NH2" Residue "L PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 81": "OE1" <-> "OE2" Residue "L TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 92": "OD1" <-> "OD2" 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: 16647 Number of models: 1 Model: "" Number of chains: 32 Chain: "G" Number of atoms: 3509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3509 Classifications: {'peptide': 446} Link IDs: {'PTRANS': 22, 'TRANS': 423} Chain breaks: 3 Chain: "B" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "E" Number of atoms: 3509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3509 Classifications: {'peptide': 446} Link IDs: {'PTRANS': 22, 'TRANS': 423} Chain breaks: 3 Chain: "F" Number of atoms: 3500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3500 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 22, 'TRANS': 422} Chain breaks: 3 Chain: "C" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1005 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "A" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 976 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 2 Chain: "H" Number of atoms: 1038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1038 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 7, 'TRANS': 125} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TYS:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 795 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 6, 'TRANS': 98} 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: "I" 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: "J" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 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: "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: 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: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 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: "U" 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: "V" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} 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: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: "G" 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: 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: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "F" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 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: 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: 8.91, per 1000 atoms: 0.54 Number of scatterers: 16647 At special positions: 0 Unit cell: (127.33, 132.68, 163.71, 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 115 16.00 O 3391 8.00 N 2761 7.00 C 10380 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.03 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.04 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 201 " - pdb=" SG CYS G 433 " distance=2.04 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.03 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS G 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 433 " 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=2.03 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=2.03 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 C 605 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.03 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.04 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.04 Simple disulfide: pdb=" SG CYS F 201 " - pdb=" SG CYS F 433 " distance=2.03 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.03 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.03 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.03 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.03 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 501 " - pdb=" SG CYS A 605 " distance=2.03 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.03 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN V 4 " - " MAN V 5 " ALPHA1-3 " BMA I 3 " - " MAN I 4 " " BMA J 3 " - " MAN J 6 " " MAN J 4 " - " MAN J 5 " " BMA N 3 " - " MAN N 4 " " BMA T 3 " - " MAN T 4 " " BMA U 3 " - " MAN U 4 " " BMA V 3 " - " MAN V 4 " " MAN V 6 " - " MAN V 7 " ALPHA1-6 " BMA I 3 " - " MAN I 5 " " BMA J 3 " - " MAN J 4 " " BMA N 3 " - " MAN N 5 " " BMA T 3 " - " MAN T 5 " " BMA U 3 " - " MAN U 5 " " BMA V 3 " - " MAN V 6 " " MAN V 6 " - " MAN V 8 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " NAG-ASN " NAG A 701 " - " ASN A 611 " " NAG A 702 " - " ASN A 618 " " NAG A 703 " - " ASN A 637 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 637 " " NAG C 701 " - " ASN C 611 " " NAG C 702 " - " ASN C 618 " " NAG D 1 " - " ASN G 88 " " NAG E 601 " - " ASN E 88 " " NAG E 602 " - " ASN E 133 " " NAG E 608 " - " ASN E 197 " " NAG E 609 " - " ASN E 234 " " NAG E 615 " - " ASN E 276 " " NAG E 616 " - " ASN E 295 " " NAG E 617 " - " ASN E 301 " " NAG E 618 " - " ASN E 332 " " NAG E 619 " - " ASN E 339 " " NAG E 620 " - " ASN E 355 " " NAG E 621 " - " ASN E 363 " " NAG E 622 " - " ASN E 386 " " NAG E 623 " - " ASN E 392 " " NAG E 624 " - " ASN E 448 " " NAG F 601 " - " ASN F 88 " " NAG F 602 " - " ASN F 133 " " NAG F 616 " - " ASN F 197 " " NAG F 617 " - " ASN F 234 " " NAG F 625 " - " ASN F 301 " " NAG F 626 " - " ASN F 332 " " NAG F 627 " - " ASN F 339 " " NAG F 628 " - " ASN F 355 " " NAG F 629 " - " ASN F 363 " " NAG F 630 " - " ASN F 386 " " NAG F 631 " - " ASN F 392 " " NAG G 603 " - " ASN G 133 " " NAG G 624 " - " ASN G 276 " " NAG G 627 " - " ASN G 301 " " NAG G 628 " - " ASN G 332 " " NAG G 629 " - " ASN G 339 " " NAG G 630 " - " ASN G 355 " " NAG G 631 " - " ASN G 363 " " NAG G 634 " - " ASN G 392 " " NAG I 1 " - " ASN G 156 " " NAG J 1 " - " ASN G 160 " " NAG K 1 " - " ASN G 197 " " NAG M 1 " - " ASN G 234 " " NAG N 1 " - " ASN G 262 " " NAG O 1 " - " ASN G 295 " " NAG P 1 " - " ASN G 386 " " NAG Q 1 " - " ASN G 448 " " NAG R 1 " - " ASN E 156 " " NAG S 1 " - " ASN E 160 " " NAG T 1 " - " ASN E 262 " " NAG U 1 " - " ASN F 156 " " NAG V 1 " - " ASN F 160 " " NAG W 1 " - " ASN F 262 " " NAG X 1 " - " ASN F 276 " " NAG Y 1 " - " ASN F 295 " " NAG Z 1 " - " ASN F 448 " Time building additional restraints: 7.70 Conformation dependent library (CDL) restraints added in 2.7 seconds 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3620 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 38 helices and 32 sheets defined 17.5% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.18 Creating SS restraints... Processing helix chain 'G' and resid 100 through 117 removed outlier: 4.497A pdb=" N ILE G 109 " --> pdb=" O HIS G 105 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU G 116 " --> pdb=" O TRP G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 123 through 126 removed outlier: 4.283A pdb=" N CYS G 126 " --> pdb=" O THR G 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 123 through 126' Processing helix chain 'G' and resid 335 through 352 removed outlier: 3.548A pdb=" N VAL G 345 " --> pdb=" O THR G 341 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LYS G 347 " --> pdb=" O GLY G 343 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG G 350 " --> pdb=" O VAL G 346 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LYS G 351 " --> pdb=" O LYS G 347 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N HIS G 352 " --> pdb=" O GLN G 348 " (cutoff:3.500A) Processing helix chain 'G' and resid 369 through 372 No H-bonds generated for 'chain 'G' and resid 369 through 372' Processing helix chain 'G' and resid 475 through 478 removed outlier: 3.687A pdb=" N ASN G 478 " --> pdb=" O MET G 475 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 475 through 478' Processing helix chain 'B' and resid 533 through 535 No H-bonds generated for 'chain 'B' and resid 533 through 535' Processing helix chain 'B' and resid 537 through 542 removed outlier: 3.516A pdb=" N ALA B 541 " --> pdb=" O LEU B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 594 removed outlier: 3.847A pdb=" N LEU B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 615 No H-bonds generated for 'chain 'B' and resid 612 through 615' Processing helix chain 'B' and resid 629 through 634 removed outlier: 4.134A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 629 through 634' Processing helix chain 'B' and resid 639 through 644 Processing helix chain 'B' and resid 646 through 658 removed outlier: 3.974A pdb=" N GLN B 653 " --> pdb=" O SER B 649 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU B 654 " --> pdb=" O GLN B 650 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LYS B 655 " --> pdb=" O ASN B 651 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ASN B 656 " --> pdb=" O GLN B 652 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU B 657 " --> pdb=" O GLN B 653 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 117 removed outlier: 3.538A pdb=" N ASP E 107 " --> pdb=" O GLN E 103 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE E 109 " --> pdb=" O HIS E 105 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TRP E 112 " --> pdb=" O ILE E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 343 Processing helix chain 'E' and resid 346 through 352 removed outlier: 3.618A pdb=" N LYS E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 372 No H-bonds generated for 'chain 'E' and resid 369 through 372' Processing helix chain 'E' and resid 461 through 463 No H-bonds generated for 'chain 'E' and resid 461 through 463' Processing helix chain 'E' and resid 477 through 483 removed outlier: 3.903A pdb=" N SER E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 117 Processing helix chain 'F' and resid 178 through 180 No H-bonds generated for 'chain 'F' and resid 178 through 180' Processing helix chain 'F' and resid 194 through 196 No H-bonds generated for 'chain 'F' and resid 194 through 196' Processing helix chain 'F' and resid 336 through 350 removed outlier: 4.233A pdb=" N GLU F 340 " --> pdb=" O ALA F 336 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N THR F 341 " --> pdb=" O THR F 337 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG F 350 " --> pdb=" O VAL F 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 372 No H-bonds generated for 'chain 'F' and resid 369 through 372' Processing helix chain 'F' and resid 378 through 380 No H-bonds generated for 'chain 'F' and resid 378 through 380' Processing helix chain 'F' and resid 389 through 391 No H-bonds generated for 'chain 'F' and resid 389 through 391' Processing helix chain 'C' and resid 539 through 544 Processing helix chain 'C' and resid 570 through 588 removed outlier: 3.999A pdb=" N LYS C 574 " --> pdb=" O VAL C 570 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN C 575 " --> pdb=" O TRP C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 594 Processing helix chain 'C' and resid 632 through 634 No H-bonds generated for 'chain 'C' and resid 632 through 634' Processing helix chain 'C' and resid 639 through 661 removed outlier: 4.114A pdb=" N TYR C 643 " --> pdb=" O THR C 639 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLY C 644 " --> pdb=" O GLN C 640 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLU C 647 " --> pdb=" O TYR C 643 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLU C 648 " --> pdb=" O GLY C 644 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN C 650 " --> pdb=" O LEU C 646 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU C 661 " --> pdb=" O GLU C 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 533 No H-bonds generated for 'chain 'A' and resid 530 through 533' Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.865A pdb=" N ARG A 542 " --> pdb=" O VAL A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 594 removed outlier: 3.621A pdb=" N ALA A 578 " --> pdb=" O LYS A 574 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL A 583 " --> pdb=" O ARG A 579 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU A 584 " --> pdb=" O VAL A 580 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ASP A 589 " --> pdb=" O ARG A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 615 No H-bonds generated for 'chain 'A' and resid 612 through 615' Processing helix chain 'A' and resid 628 through 634 removed outlier: 3.512A pdb=" N LYS A 633 " --> pdb=" O LEU A 629 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLU A 634 " --> pdb=" O GLN A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 660 removed outlier: 3.614A pdb=" N THR A 639 " --> pdb=" O SER A 636 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N GLN A 640 " --> pdb=" O ASN A 637 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE A 642 " --> pdb=" O THR A 639 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR A 643 " --> pdb=" O GLN A 640 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU A 645 " --> pdb=" O ILE A 642 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU A 647 " --> pdb=" O GLY A 644 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU A 648 " --> pdb=" O LEU A 645 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N SER A 649 " --> pdb=" O LEU A 646 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASN A 651 " --> pdb=" O GLU A 648 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS A 655 " --> pdb=" O GLN A 652 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLU A 657 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LEU A 660 " --> pdb=" O GLU A 657 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 63 No H-bonds generated for 'chain 'H' and resid 61 through 63' Processing helix chain 'H' and resid 84 through 86 No H-bonds generated for 'chain 'H' and resid 84 through 86' Processing sheet with id= A, first strand: chain 'G' and resid 35 through 40 Processing sheet with id= B, first strand: chain 'G' and resid 45 through 47 removed outlier: 3.664A pdb=" N ALA G 224 " --> pdb=" O VAL G 489 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'G' and resid 91 through 94 Processing sheet with id= D, first strand: chain 'G' and resid 130 through 133 removed outlier: 3.633A pdb=" N MET G 161 " --> pdb=" O GLN G 170 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN G 170 " --> pdb=" O MET G 161 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'G' and resid 181 through 183 Processing sheet with id= F, first strand: chain 'G' and resid 271 through 273 removed outlier: 3.615A pdb=" N MET G 271 " --> pdb=" O GLN G 287 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU G 452 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG G 469 " --> pdb=" O THR G 455 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE G 359 " --> pdb=" O TRP G 395 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER G 393 " --> pdb=" O PHE G 361 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'G' and resid 413 through 417 removed outlier: 3.635A pdb=" N HIS G 330 " --> pdb=" O THR G 297 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN G 295 " --> pdb=" O ASN G 332 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N SER G 334 " --> pdb=" O GLN G 293 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N GLN G 293 " --> pdb=" O SER G 334 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL G 292 " --> pdb=" O ILE G 449 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE G 443 " --> pdb=" O ARG G 298 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'G' and resid 304 through 308 Processing sheet with id= I, first strand: chain 'G' and resid 374 through 378 Processing sheet with id= J, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.639A pdb=" N LYS E 487 " --> pdb=" O LEU E 226 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU E 226 " --> pdb=" O LYS E 487 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL E 245 " --> pdb=" O ILE E 225 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 53 through 55 removed outlier: 4.175A pdb=" N PHE E 53 " --> pdb=" O CYS E 218 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N CYS E 218 " --> pdb=" O PHE E 53 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 91 through 94 removed outlier: 3.819A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE E 93 " --> pdb=" O GLY E 237 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLY E 237 " --> pdb=" O PHE E 93 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 181 through 183 removed outlier: 4.102A pdb=" N LYS E 189 " --> pdb=" O CYS E 131 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 271 through 274 removed outlier: 3.630A pdb=" N MET E 271 " --> pdb=" O GLN E 287 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN E 287 " --> pdb=" O MET E 271 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 413 through 417 removed outlier: 3.719A pdb=" N LEU E 416 " --> pdb=" O CYS E 331 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N CYS E 331 " --> pdb=" O LEU E 416 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL E 292 " --> pdb=" O ILE E 449 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 359 through 361 removed outlier: 4.179A pdb=" N ILE E 359 " --> pdb=" O TRP E 395 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 374 through 378 removed outlier: 3.656A pdb=" N PHE E 376 " --> pdb=" O PHE E 383 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU E 381 " --> pdb=" O CYS E 378 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 423 through 425 Processing sheet with id= S, first strand: chain 'E' and resid 304 through 312 removed outlier: 6.736A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 35 through 40 removed outlier: 3.597A pdb=" N THR F 37 " --> pdb=" O ALA F 497 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA F 497 " --> pdb=" O THR F 37 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'F' and resid 83 through 85 removed outlier: 3.749A pdb=" N ILE F 225 " --> pdb=" O VAL F 245 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU F 226 " --> pdb=" O LYS F 487 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS F 487 " --> pdb=" O LEU F 226 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 91 through 93 removed outlier: 3.610A pdb=" N GLU F 91 " --> pdb=" O CYS F 239 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY F 237 " --> pdb=" O PHE F 93 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'F' and resid 169 through 177 removed outlier: 3.522A pdb=" N SER F 158 " --> pdb=" O GLN F 130 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LYS F 189 " --> pdb=" O CYS F 131 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'F' and resid 271 through 273 Processing sheet with id= Y, first strand: chain 'F' and resid 413 through 417 removed outlier: 3.520A pdb=" N CYS F 331 " --> pdb=" O LEU F 416 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N HIS F 330 " --> pdb=" O THR F 297 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N SER F 334 " --> pdb=" O GLN F 293 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N GLN F 293 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL F 292 " --> pdb=" O ILE F 449 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N CYS F 296 " --> pdb=" O CYS F 445 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE F 443 " --> pdb=" O ARG F 298 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU F 260 " --> pdb=" O THR F 450 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'F' and resid 306 through 308 Processing sheet with id= AA, first strand: chain 'F' and resid 393 through 395 removed outlier: 3.887A pdb=" N ILE F 359 " --> pdb=" O TRP F 395 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N GLU F 466 " --> pdb=" O ARG F 360 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N ALA F 362 " --> pdb=" O GLU F 466 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N PHE F 468 " --> pdb=" O ALA F 362 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'F' and resid 374 through 378 removed outlier: 3.970A pdb=" N PHE F 376 " --> pdb=" O PHE F 383 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE F 383 " --> pdb=" O PHE F 376 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'H' and resid 18 through 23 removed outlier: 3.551A pdb=" N LEU H 82 " --> pdb=" O LEU H 18 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE H 78 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'H' and resid 107 through 109 removed outlier: 3.840A pdb=" N TRP H 35A" --> pdb=" O ILE H 51 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TRP H 36 " --> pdb=" O GLY H 49 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N LEU H 45 " --> pdb=" O PRO H 40 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'L' and resid 18 through 23 removed outlier: 3.626A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE L 75 " --> pdb=" O VAL L 19 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N CYS L 23 " --> pdb=" O ALA L 71 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'L' and resid 85 through 89 375 hydrogen bonds defined for protein. 1014 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: 5.31 Time building geometry restraints manager: 8.28 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: 2722 1.32 - 1.45: 4966 1.45 - 1.58: 9125 1.58 - 1.71: 1 1.71 - 1.84: 151 Bond restraints: 16965 Sorted by residual: bond pdb=" N VAL C 608 " pdb=" CA VAL C 608 " ideal model delta sigma weight residual 1.454 1.490 -0.036 7.70e-03 1.69e+04 2.17e+01 bond pdb=" OH TYS H 100D" pdb=" S TYS H 100D" ideal model delta sigma weight residual 1.679 1.595 0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" C3 BMA I 3 " pdb=" O3 BMA I 3 " ideal model delta sigma weight residual 1.406 1.486 -0.080 2.00e-02 2.50e+03 1.61e+01 bond pdb=" C3 BMA J 3 " pdb=" O3 BMA J 3 " ideal model delta sigma weight residual 1.406 1.482 -0.076 2.00e-02 2.50e+03 1.43e+01 bond pdb=" C PRO L 44 " pdb=" O PRO L 44 " ideal model delta sigma weight residual 1.234 1.193 0.040 1.14e-02 7.69e+03 1.24e+01 ... (remaining 16960 not shown) Histogram of bond angle deviations from ideal: 97.97 - 105.25: 297 105.25 - 112.52: 9176 112.52 - 119.80: 5667 119.80 - 127.08: 7674 127.08 - 134.35: 215 Bond angle restraints: 23029 Sorted by residual: angle pdb=" CA PHE L 49 " pdb=" CB PHE L 49 " pdb=" CG PHE L 49 " ideal model delta sigma weight residual 113.80 121.28 -7.48 1.00e+00 1.00e+00 5.59e+01 angle pdb=" N ARG F 166 " pdb=" CA ARG F 166 " pdb=" C ARG F 166 " ideal model delta sigma weight residual 112.93 106.46 6.47 1.12e+00 7.97e-01 3.34e+01 angle pdb=" C ARG G 308 " pdb=" N ILE G 309 " pdb=" CA ILE G 309 " ideal model delta sigma weight residual 120.56 113.85 6.71 1.28e+00 6.10e-01 2.75e+01 angle pdb=" C PHE L 49 " pdb=" CA PHE L 49 " pdb=" CB PHE L 49 " ideal model delta sigma weight residual 110.42 120.66 -10.24 1.99e+00 2.53e-01 2.65e+01 angle pdb=" C LEU L 46 " pdb=" N VAL L 47 " pdb=" CA VAL L 47 " ideal model delta sigma weight residual 123.08 118.12 4.96 1.01e+00 9.80e-01 2.41e+01 ... (remaining 23024 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.09: 10632 24.09 - 48.17: 643 48.17 - 72.26: 108 72.26 - 96.34: 60 96.34 - 120.43: 37 Dihedral angle restraints: 11480 sinusoidal: 5883 harmonic: 5597 Sorted by residual: dihedral pdb=" C PHE L 49 " pdb=" N PHE L 49 " pdb=" CA PHE L 49 " pdb=" CB PHE L 49 " ideal model delta harmonic sigma weight residual -122.60 -141.47 18.87 0 2.50e+00 1.60e-01 5.70e+01 dihedral pdb=" CB CYS E 119 " pdb=" SG CYS E 119 " pdb=" SG CYS E 205 " pdb=" CB CYS E 205 " ideal model delta sinusoidal sigma weight residual -86.00 -147.72 61.72 1 1.00e+01 1.00e-02 5.05e+01 dihedral pdb=" CB CYS F 54 " pdb=" SG CYS F 54 " pdb=" SG CYS F 74 " pdb=" CB CYS F 74 " ideal model delta sinusoidal sigma weight residual -86.00 -25.81 -60.19 1 1.00e+01 1.00e-02 4.83e+01 ... (remaining 11477 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.139: 2794 0.139 - 0.279: 57 0.279 - 0.418: 25 0.418 - 0.557: 3 0.557 - 0.697: 2 Chirality restraints: 2881 Sorted by residual: chirality pdb=" CA PHE L 49 " pdb=" N PHE L 49 " pdb=" C PHE L 49 " pdb=" CB PHE L 49 " both_signs ideal model delta sigma weight residual False 2.51 1.81 0.70 2.00e-01 2.50e+01 1.21e+01 chirality pdb=" CA THR L 42 " pdb=" N THR L 42 " pdb=" C THR L 42 " pdb=" CB THR L 42 " both_signs ideal model delta sigma weight residual False 2.53 1.96 0.57 2.00e-01 2.50e+01 8.03e+00 chirality pdb=" CA TYS H 100D" pdb=" N TYS H 100D" pdb=" C TYS H 100D" pdb=" CB TYS H 100D" both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.25e+00 ... (remaining 2878 not shown) Planarity restraints: 2860 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 624 " 0.343 2.00e-02 2.50e+03 2.97e-01 1.10e+03 pdb=" C7 NAG G 624 " -0.080 2.00e-02 2.50e+03 pdb=" C8 NAG G 624 " 0.070 2.00e-02 2.50e+03 pdb=" N2 NAG G 624 " -0.524 2.00e-02 2.50e+03 pdb=" O7 NAG G 624 " 0.191 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 703 " -0.236 2.00e-02 2.50e+03 2.01e-01 5.05e+02 pdb=" C7 NAG A 703 " 0.053 2.00e-02 2.50e+03 pdb=" C8 NAG A 703 " 0.033 2.00e-02 2.50e+03 pdb=" N2 NAG A 703 " 0.331 2.00e-02 2.50e+03 pdb=" O7 NAG A 703 " -0.181 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 701 " 0.225 2.00e-02 2.50e+03 1.87e-01 4.38e+02 pdb=" C7 NAG A 701 " -0.065 2.00e-02 2.50e+03 pdb=" C8 NAG A 701 " 0.161 2.00e-02 2.50e+03 pdb=" N2 NAG A 701 " -0.307 2.00e-02 2.50e+03 pdb=" O7 NAG A 701 " -0.014 2.00e-02 2.50e+03 ... (remaining 2857 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 4221 2.80 - 3.33: 14393 3.33 - 3.85: 25993 3.85 - 4.38: 28589 4.38 - 4.90: 48959 Nonbonded interactions: 122155 Sorted by model distance: nonbonded pdb=" OG1 THR G 37 " pdb=" O CYS B 604 " model vdw 2.279 2.440 nonbonded pdb=" OG1 THR E 139 " pdb=" OD1 ASP E 141 " model vdw 2.291 2.440 nonbonded pdb=" N ASP L 52 " pdb=" OD1 ASP L 52 " model vdw 2.309 2.520 nonbonded pdb=" O LEU E 369 " pdb=" OG1 THR E 373 " model vdw 2.309 2.440 nonbonded pdb=" OG1 THR F 37 " pdb=" O CYS A 604 " model vdw 2.326 2.440 ... (remaining 122150 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 520 through 664 or resid 701 through 702)) selection = (chain 'B' and (resid 520 through 545 or resid 569 through 624 or resid 626 thro \ ugh 664 or resid 701 through 702)) selection = (chain 'C' and (resid 520 through 545 or resid 569 through 624 or resid 626 thro \ ugh 664 or resid 701 through 702)) } ncs_group { reference = chain 'D' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' } ncs_group { reference = (chain 'E' and (resid 32 through 58 or resid 66 through 185 or resid 189 through \ 398 or resid 412 through 506 or resid 601 through 618)) selection = (chain 'F' and (resid 32 through 185 or resid 189 through 398 or resid 412 throu \ gh 506 or resid 601 through 628)) selection = (chain 'G' and (resid 32 through 58 or resid 66 through 398 or resid 412 through \ 506 or resid 603 through 634)) } ncs_group { reference = chain 'I' selection = chain 'N' selection = chain 'T' selection = chain 'U' } ncs_group { reference = chain 'S' selection = chain 'W' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.790 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 45.250 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 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 : 0.006 0.084 16965 Z= 0.354 Angle : 0.953 12.103 23029 Z= 0.498 Chirality : 0.067 0.697 2881 Planarity : 0.009 0.297 2802 Dihedral : 17.056 120.428 7746 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 0.93 % Allowed : 0.93 % Favored : 98.14 % Cbeta Deviations : 0.22 % 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: -2.77 (0.17), residues: 1902 helix: -3.39 (0.20), residues: 316 sheet: -0.44 (0.28), residues: 370 loop : -1.94 (0.16), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP F 96 HIS 0.003 0.001 HIS G 216 PHE 0.043 0.002 PHE L 49 TYR 0.022 0.002 TYR E 486 ARG 0.013 0.001 ARG F 444 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 249 time to evaluate : 1.821 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: G 195 ASN cc_start: 0.8016 (p0) cc_final: 0.7534 (p0) REVERT: G 482 GLU cc_start: 0.8502 (mm-30) cc_final: 0.7441 (mp0) REVERT: B 542 ARG cc_start: 0.9048 (mtm180) cc_final: 0.8784 (mtm-85) REVERT: B 601 LYS cc_start: 0.9046 (mmmt) cc_final: 0.8800 (tttt) REVERT: B 643 TYR cc_start: 0.8972 (m-10) cc_final: 0.8705 (m-10) REVERT: B 647 GLU cc_start: 0.8824 (pm20) cc_final: 0.8593 (pm20) REVERT: E 46 LYS cc_start: 0.9226 (mtpp) cc_final: 0.8994 (mmmm) REVERT: E 94 ASN cc_start: 0.9036 (t0) cc_final: 0.8700 (t0) REVERT: E 95 MET cc_start: 0.7751 (mmm) cc_final: 0.6934 (ttm) REVERT: E 127 VAL cc_start: 0.8166 (m) cc_final: 0.7361 (p) REVERT: E 309 ILE cc_start: 0.7940 (tt) cc_final: 0.7572 (pt) REVERT: E 338 TRP cc_start: 0.8999 (t-100) cc_final: 0.8722 (t-100) REVERT: E 477 ASP cc_start: 0.8928 (m-30) cc_final: 0.8636 (m-30) REVERT: E 484 TYR cc_start: 0.8790 (p90) cc_final: 0.8495 (p90) REVERT: F 284 ILE cc_start: 0.8644 (mm) cc_final: 0.8141 (mp) REVERT: F 381 GLU cc_start: 0.8203 (tp30) cc_final: 0.6946 (tm-30) REVERT: F 383 PHE cc_start: 0.7697 (m-80) cc_final: 0.7210 (m-80) REVERT: C 588 ARG cc_start: 0.7096 (mmt180) cc_final: 0.6024 (mtt180) REVERT: C 626 MET cc_start: 0.7771 (mmm) cc_final: 0.7074 (tpt) REVERT: C 659 ASP cc_start: 0.9430 (m-30) cc_final: 0.9080 (p0) REVERT: A 592 LEU cc_start: 0.8827 (tp) cc_final: 0.8591 (tp) REVERT: A 593 LEU cc_start: 0.9304 (tp) cc_final: 0.8958 (tp) REVERT: A 596 TRP cc_start: 0.8496 (m-10) cc_final: 0.8151 (m-90) REVERT: A 648 GLU cc_start: 0.8965 (pt0) cc_final: 0.8428 (pp20) REVERT: A 657 GLU cc_start: 0.8597 (mp0) cc_final: 0.8073 (pm20) REVERT: H 5 ARG cc_start: 0.8817 (mmm160) cc_final: 0.8380 (mmm-85) REVERT: H 18 LEU cc_start: 0.8968 (tt) cc_final: 0.8665 (mp) REVERT: H 77 GLN cc_start: 0.8550 (mt0) cc_final: 0.8326 (tp-100) REVERT: H 80 LEU cc_start: 0.8949 (tp) cc_final: 0.8100 (tp) REVERT: H 102 LEU cc_start: 0.8863 (mt) cc_final: 0.8662 (mt) REVERT: L 86 TYR cc_start: 0.8523 (m-80) cc_final: 0.8178 (m-80) REVERT: L 103 ARG cc_start: 0.8721 (tpp-160) cc_final: 0.8349 (mmm160) outliers start: 16 outliers final: 6 residues processed: 263 average time/residue: 0.3164 time to fit residues: 120.4241 Evaluate side-chains 136 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 130 time to evaluate : 1.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain G residue 433 CYS Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain L residue 52 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 161 optimal weight: 7.9990 chunk 144 optimal weight: 10.0000 chunk 80 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 149 optimal weight: 7.9990 chunk 57 optimal weight: 10.0000 chunk 91 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 chunk 173 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 66 HIS G 183 GLN ** G 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 114 GLN F 374 HIS A 640 GLN A 651 ASN H 1 GLN ** H 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN ** L 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 16965 Z= 0.379 Angle : 0.878 15.124 23029 Z= 0.427 Chirality : 0.052 0.310 2881 Planarity : 0.006 0.055 2802 Dihedral : 12.753 92.612 4131 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 2.33 % Allowed : 10.37 % Favored : 87.30 % 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: -2.22 (0.19), residues: 1902 helix: -1.78 (0.25), residues: 329 sheet: -0.77 (0.25), residues: 457 loop : -1.70 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP G 45 HIS 0.010 0.002 HIS G 330 PHE 0.021 0.003 PHE F 383 TYR 0.027 0.003 TYR B 586 ARG 0.006 0.001 ARG H 94 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 119 time to evaluate : 1.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 51 THR cc_start: 0.8987 (OUTLIER) cc_final: 0.8741 (t) REVERT: G 161 MET cc_start: 0.8629 (mmm) cc_final: 0.8354 (mmm) REVERT: B 601 LYS cc_start: 0.9117 (mmmt) cc_final: 0.8742 (tttt) REVERT: E 46 LYS cc_start: 0.9335 (mtpp) cc_final: 0.9042 (mmmm) REVERT: E 95 MET cc_start: 0.7842 (mmm) cc_final: 0.7217 (ttm) REVERT: E 338 TRP cc_start: 0.9328 (t-100) cc_final: 0.9082 (t-100) REVERT: E 426 MET cc_start: 0.6103 (tpp) cc_final: 0.5629 (tpp) REVERT: F 271 MET cc_start: 0.8866 (mtp) cc_final: 0.8348 (mmt) REVERT: C 584 GLU cc_start: 0.8918 (tp30) cc_final: 0.8612 (tp30) REVERT: C 588 ARG cc_start: 0.7432 (mmt180) cc_final: 0.6585 (mtt180) REVERT: C 659 ASP cc_start: 0.9417 (m-30) cc_final: 0.9047 (p0) REVERT: H 5 ARG cc_start: 0.9136 (mmm160) cc_final: 0.8647 (mmm-85) REVERT: H 18 LEU cc_start: 0.9374 (tt) cc_final: 0.8827 (mp) REVERT: H 97 GLU cc_start: 0.8253 (tp30) cc_final: 0.7512 (tp30) REVERT: H 100 ASP cc_start: 0.9627 (t0) cc_final: 0.9275 (p0) REVERT: H 102 LEU cc_start: 0.9168 (mt) cc_final: 0.8937 (mt) REVERT: L 103 ARG cc_start: 0.8856 (tpp-160) cc_final: 0.8409 (mmm160) outliers start: 40 outliers final: 19 residues processed: 147 average time/residue: 0.3169 time to fit residues: 70.5611 Evaluate side-chains 114 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 94 time to evaluate : 1.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain G residue 283 ASN Chi-restraints excluded: chain G residue 479 TRP Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain E residue 271 MET Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 272 ILE Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 52 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 96 optimal weight: 6.9990 chunk 53 optimal weight: 9.9990 chunk 144 optimal weight: 10.0000 chunk 118 optimal weight: 7.9990 chunk 47 optimal weight: 3.9990 chunk 173 optimal weight: 10.0000 chunk 187 optimal weight: 5.9990 chunk 154 optimal weight: 10.0000 chunk 172 optimal weight: 0.0030 chunk 59 optimal weight: 10.0000 chunk 139 optimal weight: 8.9990 overall best weight: 4.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 352 HIS G 432 GLN ** G 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 330 HIS ** C 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 616 ASN ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.5451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 16965 Z= 0.376 Angle : 0.798 10.550 23029 Z= 0.388 Chirality : 0.050 0.350 2881 Planarity : 0.005 0.044 2802 Dihedral : 11.001 89.531 4129 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 2.62 % Allowed : 13.74 % Favored : 83.63 % 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: -2.10 (0.19), residues: 1902 helix: -1.17 (0.27), residues: 345 sheet: -0.92 (0.24), residues: 475 loop : -1.71 (0.18), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP F 96 HIS 0.004 0.001 HIS F 72 PHE 0.038 0.002 PHE H 99 TYR 0.015 0.002 TYR B 638 ARG 0.005 0.001 ARG F 444 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 86 time to evaluate : 1.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 51 THR cc_start: 0.9100 (OUTLIER) cc_final: 0.8852 (t) REVERT: E 195 ASN cc_start: 0.7718 (OUTLIER) cc_final: 0.7236 (t0) REVERT: E 426 MET cc_start: 0.7122 (tpp) cc_final: 0.6641 (tpp) REVERT: F 104 MET cc_start: 0.9180 (OUTLIER) cc_final: 0.8866 (tmm) REVERT: F 150 MET cc_start: 0.8651 (mmm) cc_final: 0.8195 (tpp) REVERT: F 430 ILE cc_start: 0.9123 (OUTLIER) cc_final: 0.8828 (mm) REVERT: C 584 GLU cc_start: 0.9103 (tp30) cc_final: 0.8693 (tp30) REVERT: C 588 ARG cc_start: 0.7607 (mmt180) cc_final: 0.7177 (mmt180) REVERT: C 589 ASP cc_start: 0.9261 (p0) cc_final: 0.8815 (p0) REVERT: H 5 ARG cc_start: 0.9138 (mmm160) cc_final: 0.8624 (mmm-85) REVERT: H 100 ASP cc_start: 0.9655 (t0) cc_final: 0.9362 (p0) REVERT: H 102 LEU cc_start: 0.8864 (mt) cc_final: 0.8600 (mt) REVERT: L 103 ARG cc_start: 0.9110 (tpp-160) cc_final: 0.8691 (tpp80) outliers start: 45 outliers final: 23 residues processed: 122 average time/residue: 0.2845 time to fit residues: 53.9718 Evaluate side-chains 103 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 76 time to evaluate : 1.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain G residue 196 CYS Chi-restraints excluded: chain G residue 283 ASN Chi-restraints excluded: chain G residue 432 GLN Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 195 ASN Chi-restraints excluded: chain E residue 271 MET Chi-restraints excluded: chain E residue 501 CYS Chi-restraints excluded: chain F residue 104 MET Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 272 ILE Chi-restraints excluded: chain F residue 430 ILE Chi-restraints excluded: chain F residue 433 CYS Chi-restraints excluded: chain C residue 604 CYS Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 52 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 171 optimal weight: 2.9990 chunk 130 optimal weight: 9.9990 chunk 90 optimal weight: 8.9990 chunk 19 optimal weight: 9.9990 chunk 82 optimal weight: 3.9990 chunk 116 optimal weight: 0.5980 chunk 174 optimal weight: 0.0670 chunk 184 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 165 optimal weight: 9.9990 chunk 49 optimal weight: 6.9990 overall best weight: 1.9324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 630 GLN C 658 GLN ** L 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.5641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 16965 Z= 0.196 Angle : 0.619 9.422 23029 Z= 0.300 Chirality : 0.046 0.270 2881 Planarity : 0.003 0.041 2802 Dihedral : 9.586 81.441 4126 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 2.04 % Allowed : 15.32 % Favored : 82.64 % 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: -1.86 (0.19), residues: 1902 helix: -0.69 (0.29), residues: 339 sheet: -0.82 (0.25), residues: 465 loop : -1.62 (0.18), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 96 HIS 0.003 0.001 HIS G 216 PHE 0.022 0.001 PHE H 99 TYR 0.018 0.001 TYR B 643 ARG 0.002 0.000 ARG G 429 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 87 time to evaluate : 1.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 150 MET cc_start: 0.9272 (mmp) cc_final: 0.8943 (mmp) REVERT: G 271 MET cc_start: 0.8349 (mmt) cc_final: 0.8121 (mmm) REVERT: B 589 ASP cc_start: 0.9328 (p0) cc_final: 0.9040 (p0) REVERT: E 426 MET cc_start: 0.7059 (tpp) cc_final: 0.6690 (tpp) REVERT: F 104 MET cc_start: 0.9084 (tmm) cc_final: 0.8826 (tmm) REVERT: F 150 MET cc_start: 0.8745 (mmm) cc_final: 0.8377 (tpp) REVERT: F 430 ILE cc_start: 0.9110 (OUTLIER) cc_final: 0.8838 (mm) REVERT: F 475 MET cc_start: 0.8455 (ppp) cc_final: 0.7842 (ppp) REVERT: C 584 GLU cc_start: 0.9096 (tp30) cc_final: 0.8585 (tm-30) REVERT: C 588 ARG cc_start: 0.7703 (mmt180) cc_final: 0.7246 (mmt180) REVERT: C 589 ASP cc_start: 0.9210 (p0) cc_final: 0.8739 (p0) REVERT: A 574 LYS cc_start: 0.9390 (mmmt) cc_final: 0.8766 (tptm) REVERT: H 97 GLU cc_start: 0.8068 (tp30) cc_final: 0.7768 (tp30) REVERT: H 100 ASP cc_start: 0.9593 (t0) cc_final: 0.9297 (p0) REVERT: H 102 LEU cc_start: 0.8842 (mt) cc_final: 0.8561 (mt) REVERT: L 103 ARG cc_start: 0.9121 (tpp-160) cc_final: 0.8589 (mmm160) outliers start: 35 outliers final: 21 residues processed: 116 average time/residue: 0.2997 time to fit residues: 53.2098 Evaluate side-chains 97 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 75 time to evaluate : 1.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain G residue 283 ASN Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 501 CYS Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 272 ILE Chi-restraints excluded: chain F residue 430 ILE Chi-restraints excluded: chain C residue 604 CYS Chi-restraints excluded: chain C residue 641 ILE Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 47 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 153 optimal weight: 2.9990 chunk 104 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 chunk 137 optimal weight: 9.9990 chunk 76 optimal weight: 20.0000 chunk 157 optimal weight: 4.9990 chunk 127 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 94 optimal weight: 10.0000 chunk 165 optimal weight: 8.9990 chunk 46 optimal weight: 0.0970 overall best weight: 4.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 425 ASN ** G 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.6775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 16965 Z= 0.381 Angle : 0.765 12.124 23029 Z= 0.372 Chirality : 0.048 0.279 2881 Planarity : 0.004 0.048 2802 Dihedral : 9.440 73.344 4124 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 18.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 3.79 % Allowed : 16.42 % Favored : 79.79 % 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: -1.94 (0.19), residues: 1902 helix: -0.62 (0.28), residues: 339 sheet: -0.92 (0.24), residues: 475 loop : -1.70 (0.18), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 96 HIS 0.006 0.001 HIS H 50 PHE 0.023 0.002 PHE F 382 TYR 0.018 0.002 TYR L 91 ARG 0.010 0.001 ARG L 100 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 69 time to evaluate : 1.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 150 MET cc_start: 0.9300 (mmp) cc_final: 0.9070 (mmp) REVERT: G 164 GLU cc_start: 0.9084 (OUTLIER) cc_final: 0.8850 (mp0) REVERT: G 271 MET cc_start: 0.8510 (mmt) cc_final: 0.8252 (mmm) REVERT: B 584 GLU cc_start: 0.9402 (tm-30) cc_final: 0.9115 (tm-30) REVERT: B 589 ASP cc_start: 0.9374 (p0) cc_final: 0.9083 (p0) REVERT: E 426 MET cc_start: 0.7136 (tpp) cc_final: 0.6642 (tpp) REVERT: F 114 GLN cc_start: 0.9403 (OUTLIER) cc_final: 0.9188 (tm-30) REVERT: F 430 ILE cc_start: 0.9319 (OUTLIER) cc_final: 0.9116 (mm) REVERT: C 584 GLU cc_start: 0.9150 (tp30) cc_final: 0.8675 (tm-30) REVERT: C 589 ASP cc_start: 0.9434 (p0) cc_final: 0.9022 (p0) REVERT: C 654 GLU cc_start: 0.9318 (tp30) cc_final: 0.9007 (tp30) REVERT: A 574 LYS cc_start: 0.9478 (mmmt) cc_final: 0.9188 (mmmt) REVERT: H 97 GLU cc_start: 0.7828 (tp30) cc_final: 0.7465 (tp30) REVERT: H 100 ASP cc_start: 0.9626 (t0) cc_final: 0.9326 (p0) REVERT: L 60 ASP cc_start: 0.9066 (t0) cc_final: 0.8821 (p0) outliers start: 65 outliers final: 42 residues processed: 129 average time/residue: 0.2749 time to fit residues: 56.2904 Evaluate side-chains 112 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 67 time to evaluate : 1.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain G residue 180 ASP Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 283 ASN Chi-restraints excluded: chain G residue 446 VAL Chi-restraints excluded: chain G residue 501 CYS Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 448 ASN Chi-restraints excluded: chain E residue 475 MET Chi-restraints excluded: chain E residue 501 CYS Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 114 GLN Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 139 THR Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 272 ILE Chi-restraints excluded: chain F residue 430 ILE Chi-restraints excluded: chain F residue 433 CYS Chi-restraints excluded: chain C residue 604 CYS Chi-restraints excluded: chain C residue 633 LYS Chi-restraints excluded: chain C residue 641 ILE Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 47 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 62 optimal weight: 4.9990 chunk 166 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 108 optimal weight: 0.1980 chunk 45 optimal weight: 9.9990 chunk 184 optimal weight: 10.0000 chunk 153 optimal weight: 0.5980 chunk 85 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 97 optimal weight: 9.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 114 GLN ** F 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.6863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16965 Z= 0.200 Angle : 0.625 9.399 23029 Z= 0.302 Chirality : 0.046 0.267 2881 Planarity : 0.004 0.066 2802 Dihedral : 8.669 71.012 4123 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 2.50 % Allowed : 18.00 % Favored : 79.50 % 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: -1.71 (0.19), residues: 1902 helix: -0.31 (0.30), residues: 339 sheet: -0.80 (0.25), residues: 466 loop : -1.58 (0.18), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP E 69 HIS 0.004 0.001 HIS G 216 PHE 0.013 0.001 PHE F 382 TYR 0.016 0.001 TYR E 486 ARG 0.004 0.000 ARG L 100 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 71 time to evaluate : 1.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 104 MET cc_start: 0.9039 (ptm) cc_final: 0.8345 (tmm) REVERT: G 271 MET cc_start: 0.8470 (mmt) cc_final: 0.8226 (mmm) REVERT: B 589 ASP cc_start: 0.9374 (p0) cc_final: 0.9055 (p0) REVERT: E 198 THR cc_start: 0.9570 (OUTLIER) cc_final: 0.9364 (p) REVERT: E 426 MET cc_start: 0.7139 (tpp) cc_final: 0.6859 (tpp) REVERT: F 52 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8528 (mm) REVERT: F 104 MET cc_start: 0.9170 (tmm) cc_final: 0.8893 (tmm) REVERT: F 430 ILE cc_start: 0.9236 (OUTLIER) cc_final: 0.9021 (mm) REVERT: C 584 GLU cc_start: 0.9182 (tp30) cc_final: 0.8792 (tm-30) REVERT: C 589 ASP cc_start: 0.9365 (p0) cc_final: 0.8869 (p0) REVERT: C 654 GLU cc_start: 0.9268 (tp30) cc_final: 0.8978 (tp30) REVERT: A 530 MET cc_start: 0.7155 (pmm) cc_final: 0.6828 (pmm) REVERT: A 574 LYS cc_start: 0.9490 (mmmt) cc_final: 0.9161 (mmmt) REVERT: H 71 MET cc_start: 0.9030 (tmm) cc_final: 0.8814 (tmm) REVERT: H 97 GLU cc_start: 0.7747 (tp30) cc_final: 0.7286 (tp30) REVERT: H 100 GLU cc_start: 0.8983 (OUTLIER) cc_final: 0.8687 (pm20) REVERT: H 100 ASP cc_start: 0.9603 (t0) cc_final: 0.9296 (p0) REVERT: L 60 ASP cc_start: 0.9041 (t0) cc_final: 0.8819 (p0) outliers start: 43 outliers final: 29 residues processed: 110 average time/residue: 0.2742 time to fit residues: 48.3356 Evaluate side-chains 100 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 67 time to evaluate : 1.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 180 ASP Chi-restraints excluded: chain G residue 283 ASN Chi-restraints excluded: chain G residue 446 VAL Chi-restraints excluded: chain G residue 501 CYS Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 475 MET Chi-restraints excluded: chain E residue 501 CYS Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 272 ILE Chi-restraints excluded: chain F residue 326 ILE Chi-restraints excluded: chain F residue 430 ILE Chi-restraints excluded: chain F residue 433 CYS Chi-restraints excluded: chain C residue 573 ILE Chi-restraints excluded: chain C residue 604 CYS Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 52 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 178 optimal weight: 7.9990 chunk 20 optimal weight: 7.9990 chunk 105 optimal weight: 5.9990 chunk 134 optimal weight: 10.0000 chunk 104 optimal weight: 4.9990 chunk 155 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 184 optimal weight: 9.9990 chunk 115 optimal weight: 10.0000 chunk 112 optimal weight: 9.9990 chunk 84 optimal weight: 7.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.7372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 16965 Z= 0.336 Angle : 0.682 9.355 23029 Z= 0.332 Chirality : 0.046 0.281 2881 Planarity : 0.004 0.078 2802 Dihedral : 8.632 69.666 4123 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 2.68 % Allowed : 18.52 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.19), residues: 1902 helix: -0.29 (0.29), residues: 339 sheet: -0.83 (0.25), residues: 471 loop : -1.58 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 69 HIS 0.005 0.001 HIS H 34 PHE 0.019 0.002 PHE F 382 TYR 0.016 0.001 TYR L 91 ARG 0.007 0.000 ARG B 585 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 69 time to evaluate : 1.781 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 104 MET cc_start: 0.9088 (ptm) cc_final: 0.8390 (tmm) REVERT: B 535 MET cc_start: 0.9197 (mpp) cc_final: 0.8905 (mpp) REVERT: B 589 ASP cc_start: 0.9348 (p0) cc_final: 0.9010 (p0) REVERT: E 198 THR cc_start: 0.9551 (OUTLIER) cc_final: 0.9335 (p) REVERT: E 426 MET cc_start: 0.7111 (tpp) cc_final: 0.6685 (tpp) REVERT: F 52 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8676 (mm) REVERT: C 584 GLU cc_start: 0.9175 (tp30) cc_final: 0.8825 (tm-30) REVERT: C 589 ASP cc_start: 0.9435 (p0) cc_final: 0.8955 (p0) REVERT: A 574 LYS cc_start: 0.9516 (mmmt) cc_final: 0.9208 (tppp) REVERT: A 626 MET cc_start: 0.9159 (ppp) cc_final: 0.8762 (ppp) REVERT: H 97 GLU cc_start: 0.7701 (tp30) cc_final: 0.7257 (tp30) REVERT: H 100 GLU cc_start: 0.8978 (OUTLIER) cc_final: 0.8758 (pm20) REVERT: H 100 ASP cc_start: 0.9592 (t0) cc_final: 0.9301 (p0) REVERT: L 60 ASP cc_start: 0.9070 (t0) cc_final: 0.8850 (p0) outliers start: 46 outliers final: 35 residues processed: 111 average time/residue: 0.2764 time to fit residues: 49.4662 Evaluate side-chains 103 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 65 time to evaluate : 2.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain G residue 180 ASP Chi-restraints excluded: chain G residue 283 ASN Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain G residue 446 VAL Chi-restraints excluded: chain G residue 501 CYS Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 475 MET Chi-restraints excluded: chain E residue 501 CYS Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 272 ILE Chi-restraints excluded: chain F residue 326 ILE Chi-restraints excluded: chain F residue 433 CYS Chi-restraints excluded: chain C residue 573 ILE Chi-restraints excluded: chain C residue 604 CYS Chi-restraints excluded: chain C residue 633 LYS Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 52 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 113 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 109 optimal weight: 8.9990 chunk 55 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 117 optimal weight: 0.9980 chunk 125 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 144 optimal weight: 9.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 114 GLN ** F 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.7475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 16965 Z= 0.207 Angle : 0.614 9.334 23029 Z= 0.296 Chirality : 0.046 0.268 2881 Planarity : 0.004 0.073 2802 Dihedral : 8.156 68.211 4123 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 2.97 % Allowed : 18.81 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.19), residues: 1902 helix: -0.09 (0.30), residues: 336 sheet: -0.77 (0.25), residues: 474 loop : -1.52 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 69 HIS 0.004 0.001 HIS G 216 PHE 0.011 0.001 PHE H 99 TYR 0.014 0.001 TYR E 486 ARG 0.004 0.000 ARG L 100 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 71 time to evaluate : 1.908 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 104 MET cc_start: 0.9053 (ptm) cc_final: 0.8488 (tmm) REVERT: B 535 MET cc_start: 0.9162 (mpp) cc_final: 0.8875 (mpp) REVERT: B 589 ASP cc_start: 0.9339 (p0) cc_final: 0.9013 (p0) REVERT: E 150 MET cc_start: 0.7848 (mpp) cc_final: 0.7629 (mpp) REVERT: E 198 THR cc_start: 0.9534 (OUTLIER) cc_final: 0.9318 (p) REVERT: E 426 MET cc_start: 0.6968 (tpp) cc_final: 0.6662 (tpp) REVERT: F 104 MET cc_start: 0.9171 (tmm) cc_final: 0.8906 (tmm) REVERT: F 434 MET cc_start: 0.8120 (mmm) cc_final: 0.7919 (tpp) REVERT: C 584 GLU cc_start: 0.9131 (tp30) cc_final: 0.8813 (tm-30) REVERT: C 589 ASP cc_start: 0.9388 (p0) cc_final: 0.8854 (p0) REVERT: A 530 MET cc_start: 0.7182 (pmm) cc_final: 0.6894 (pmm) REVERT: A 574 LYS cc_start: 0.9496 (mmmt) cc_final: 0.9163 (tppp) REVERT: H 97 GLU cc_start: 0.7768 (tp30) cc_final: 0.7287 (tp30) REVERT: H 100 GLU cc_start: 0.9003 (OUTLIER) cc_final: 0.8794 (pm20) REVERT: H 100 ASP cc_start: 0.9571 (t0) cc_final: 0.9332 (p0) REVERT: L 60 ASP cc_start: 0.9034 (t0) cc_final: 0.8820 (p0) outliers start: 51 outliers final: 36 residues processed: 118 average time/residue: 0.2588 time to fit residues: 48.7829 Evaluate side-chains 106 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 68 time to evaluate : 1.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain G residue 180 ASP Chi-restraints excluded: chain G residue 283 ASN Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain G residue 446 VAL Chi-restraints excluded: chain G residue 501 CYS Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 475 MET Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain E residue 501 CYS Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 272 ILE Chi-restraints excluded: chain F residue 433 CYS Chi-restraints excluded: chain C residue 573 ILE Chi-restraints excluded: chain C residue 604 CYS Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 52 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 167 optimal weight: 2.9990 chunk 176 optimal weight: 10.0000 chunk 160 optimal weight: 0.6980 chunk 171 optimal weight: 0.9990 chunk 103 optimal weight: 0.0970 chunk 74 optimal weight: 10.0000 chunk 134 optimal weight: 10.0000 chunk 52 optimal weight: 7.9990 chunk 155 optimal weight: 2.9990 chunk 162 optimal weight: 6.9990 chunk 170 optimal weight: 20.0000 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 130 GLN ** F 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.7527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16965 Z= 0.173 Angle : 0.603 9.439 23029 Z= 0.290 Chirality : 0.046 0.280 2881 Planarity : 0.003 0.058 2802 Dihedral : 7.814 66.288 4123 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 2.39 % Allowed : 19.57 % Favored : 78.04 % 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: -1.48 (0.20), residues: 1902 helix: 0.04 (0.31), residues: 329 sheet: -0.69 (0.25), residues: 477 loop : -1.45 (0.19), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP E 112 HIS 0.003 0.001 HIS H 34 PHE 0.010 0.001 PHE H 99 TYR 0.014 0.001 TYR E 486 ARG 0.003 0.000 ARG L 100 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 71 time to evaluate : 1.828 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 104 MET cc_start: 0.9032 (ptm) cc_final: 0.8430 (tmm) REVERT: G 150 MET cc_start: 0.9252 (mmt) cc_final: 0.9048 (mmm) REVERT: B 535 MET cc_start: 0.9179 (mpp) cc_final: 0.8884 (mpp) REVERT: B 589 ASP cc_start: 0.9344 (p0) cc_final: 0.9026 (p0) REVERT: E 198 THR cc_start: 0.9525 (OUTLIER) cc_final: 0.9308 (p) REVERT: E 426 MET cc_start: 0.6981 (tpp) cc_final: 0.6684 (tpp) REVERT: F 104 MET cc_start: 0.9149 (tmm) cc_final: 0.8897 (tmm) REVERT: F 271 MET cc_start: 0.9079 (mtp) cc_final: 0.8286 (mmt) REVERT: C 584 GLU cc_start: 0.9129 (tp30) cc_final: 0.8832 (tm-30) REVERT: C 589 ASP cc_start: 0.9386 (p0) cc_final: 0.8842 (p0) REVERT: C 654 GLU cc_start: 0.9270 (tp30) cc_final: 0.9003 (tp30) REVERT: C 657 GLU cc_start: 0.9105 (tm-30) cc_final: 0.8802 (tm-30) REVERT: A 530 MET cc_start: 0.7277 (pmm) cc_final: 0.6937 (pmm) REVERT: A 574 LYS cc_start: 0.9480 (mmmt) cc_final: 0.9086 (mmmt) REVERT: H 97 GLU cc_start: 0.7749 (tp30) cc_final: 0.7258 (tp30) REVERT: H 100 GLU cc_start: 0.8960 (OUTLIER) cc_final: 0.8618 (pm20) REVERT: H 100 ASP cc_start: 0.9560 (t0) cc_final: 0.9320 (p0) outliers start: 41 outliers final: 35 residues processed: 109 average time/residue: 0.2646 time to fit residues: 46.5268 Evaluate side-chains 107 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 70 time to evaluate : 1.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain G residue 180 ASP Chi-restraints excluded: chain G residue 283 ASN Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain G residue 446 VAL Chi-restraints excluded: chain G residue 501 CYS Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 475 MET Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain E residue 501 CYS Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 272 ILE Chi-restraints excluded: chain F residue 326 ILE Chi-restraints excluded: chain F residue 433 CYS Chi-restraints excluded: chain C residue 573 ILE Chi-restraints excluded: chain C residue 604 CYS Chi-restraints excluded: chain C residue 633 LYS Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 50 GLU Chi-restraints excluded: chain L residue 52 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 112 optimal weight: 8.9990 chunk 181 optimal weight: 5.9990 chunk 110 optimal weight: 0.0770 chunk 86 optimal weight: 8.9990 chunk 126 optimal weight: 10.0000 chunk 190 optimal weight: 6.9990 chunk 175 optimal weight: 10.0000 chunk 151 optimal weight: 7.9990 chunk 15 optimal weight: 8.9990 chunk 117 optimal weight: 6.9990 chunk 92 optimal weight: 0.9990 overall best weight: 4.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.7914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 16965 Z= 0.307 Angle : 0.674 9.398 23029 Z= 0.326 Chirality : 0.046 0.279 2881 Planarity : 0.004 0.069 2802 Dihedral : 8.103 66.178 4123 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 2.45 % Allowed : 19.51 % Favored : 78.04 % 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: -1.57 (0.19), residues: 1902 helix: -0.07 (0.30), residues: 334 sheet: -0.80 (0.25), residues: 485 loop : -1.48 (0.18), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 69 HIS 0.006 0.001 HIS H 34 PHE 0.016 0.002 PHE F 382 TYR 0.016 0.001 TYR L 91 ARG 0.005 0.000 ARG L 100 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 68 time to evaluate : 1.832 Fit side-chains revert: symmetry clash REVERT: G 104 MET cc_start: 0.9129 (ptm) cc_final: 0.8556 (tmm) REVERT: B 535 MET cc_start: 0.9140 (mpp) cc_final: 0.8879 (mpp) REVERT: B 589 ASP cc_start: 0.9363 (p0) cc_final: 0.9037 (p0) REVERT: E 198 THR cc_start: 0.9512 (OUTLIER) cc_final: 0.9296 (p) REVERT: E 426 MET cc_start: 0.7058 (tpp) cc_final: 0.6718 (tpp) REVERT: F 104 MET cc_start: 0.9182 (tmm) cc_final: 0.8820 (ppp) REVERT: C 530 MET cc_start: 0.8904 (OUTLIER) cc_final: 0.8306 (mtm) REVERT: C 539 VAL cc_start: 0.8985 (OUTLIER) cc_final: 0.8754 (p) REVERT: C 584 GLU cc_start: 0.9128 (tp30) cc_final: 0.8832 (tm-30) REVERT: C 589 ASP cc_start: 0.9456 (p0) cc_final: 0.8986 (p0) REVERT: C 654 GLU cc_start: 0.9315 (tp30) cc_final: 0.9031 (tp30) REVERT: C 657 GLU cc_start: 0.9119 (tm-30) cc_final: 0.8822 (tm-30) REVERT: A 574 LYS cc_start: 0.9485 (mmmt) cc_final: 0.9093 (mmmt) REVERT: H 5 ARG cc_start: 0.9120 (mmm160) cc_final: 0.8819 (mmp80) REVERT: H 100 ASP cc_start: 0.9560 (t0) cc_final: 0.9332 (p0) outliers start: 42 outliers final: 34 residues processed: 106 average time/residue: 0.2669 time to fit residues: 45.7442 Evaluate side-chains 103 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 66 time to evaluate : 1.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain G residue 180 ASP Chi-restraints excluded: chain G residue 283 ASN Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain G residue 446 VAL Chi-restraints excluded: chain G residue 501 CYS Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 475 MET Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain E residue 501 CYS Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 272 ILE Chi-restraints excluded: chain F residue 433 CYS Chi-restraints excluded: chain C residue 530 MET Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 573 ILE Chi-restraints excluded: chain C residue 604 CYS Chi-restraints excluded: chain C residue 633 LYS Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 52 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 120 optimal weight: 3.9990 chunk 161 optimal weight: 9.9990 chunk 46 optimal weight: 5.9990 chunk 139 optimal weight: 8.9990 chunk 22 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 chunk 151 optimal weight: 0.0370 chunk 63 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 overall best weight: 2.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.035193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.029173 restraints weight = 151108.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.029947 restraints weight = 89344.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.030534 restraints weight = 62908.705| |-----------------------------------------------------------------------------| r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.8019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16965 Z= 0.222 Angle : 0.624 9.310 23029 Z= 0.300 Chirality : 0.045 0.275 2881 Planarity : 0.004 0.061 2802 Dihedral : 7.856 65.910 4123 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 2.10 % Allowed : 19.86 % Favored : 78.04 % 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: -1.44 (0.19), residues: 1902 helix: 0.26 (0.31), residues: 315 sheet: -0.75 (0.25), residues: 492 loop : -1.43 (0.19), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 69 HIS 0.005 0.001 HIS H 34 PHE 0.010 0.001 PHE F 382 TYR 0.013 0.001 TYR E 486 ARG 0.004 0.000 ARG L 100 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2574.00 seconds wall clock time: 49 minutes 22.20 seconds (2962.20 seconds total)