Starting phenix.real_space_refine on Sun Mar 17 06:30:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fl1_29264/03_2024/8fl1_29264_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fl1_29264/03_2024/8fl1_29264.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fl1_29264/03_2024/8fl1_29264.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fl1_29264/03_2024/8fl1_29264.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fl1_29264/03_2024/8fl1_29264_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fl1_29264/03_2024/8fl1_29264_updated.pdb" } resolution = 3.75 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.048 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 117 5.16 5 C 10538 2.51 5 N 2808 2.21 5 O 3488 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 657": "OE1" <-> "OE2" Residue "C PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 83": "OE1" <-> "OE2" Residue "C GLU 92": "OE1" <-> "OE2" Residue "C ASP 140": "OD1" <-> "OD2" Residue "C TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 275": "OE1" <-> "OE2" Residue "C TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 466": "OE1" <-> "OE2" Residue "G GLU 92": "OE1" <-> "OE2" Residue "G GLU 153": "OE1" <-> "OE2" Residue "G PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 164": "OE1" <-> "OE2" Residue "G TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 140": "OD1" <-> "OD2" Residue "I GLU 211": "OE1" <-> "OE2" Residue "I GLU 267": "OE1" <-> "OE2" Residue "I ASP 457": "OD1" <-> "OD2" Residue "I PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 482": "OE1" <-> "OE2" Residue "I GLU 492": "OE1" <-> "OE2" Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 16951 Number of models: 1 Model: "" Number of chains: 37 Chain: "A" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 997 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 1, 'TRANS': 123} Chain breaks: 1 Chain: "B" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 990 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "C" Number of atoms: 3535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3535 Classifications: {'peptide': 450} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 427} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "F" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1001 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "G" Number of atoms: 3543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3543 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 428} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "I" Number of atoms: 3544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3544 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 428} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "H" Number of atoms: 1094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1094 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 3, 'TRANS': 132} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TYS:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "L" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 801 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 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: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 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: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 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: "e" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "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 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 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: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" 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: "I" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 9.20, per 1000 atoms: 0.54 Number of scatterers: 16951 At special positions: 0 Unit cell: (132.126, 129.96, 168.948, 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 117 16.00 O 3488 8.00 N 2808 7.00 C 10538 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS A 605 " - pdb=" SG CYS C 501 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS B 605 " - pdb=" SG CYS G 501 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 201 " - pdb=" SG CYS C 433 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 605 " - pdb=" SG CYS I 501 " distance=2.03 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.04 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 I 54 " - pdb=" SG CYS I 74 " distance=2.03 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.03 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.03 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.03 Simple disulfide: pdb=" SG CYS I 201 " - pdb=" SG CYS I 433 " distance=2.03 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.04 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.03 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.03 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.03 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.04 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 J 4 " - " MAN J 5 " " MAN Q 4 " - " MAN Q 5 " " MAN X 4 " - " MAN X 5 " ALPHA1-3 " BMA J 3 " - " MAN J 4 " " BMA Q 3 " - " MAN Q 4 " " BMA V 3 " - " MAN V 4 " " BMA X 3 " - " MAN X 4 " " BMA d 3 " - " MAN d 4 " " BMA e 3 " - " MAN e 7 " " MAN e 4 " - " MAN e 5 " ALPHA1-6 " BMA J 3 " - " MAN J 6 " " BMA V 3 " - " MAN V 5 " " BMA X 3 " - " MAN X 6 " " BMA d 3 " - " MAN d 5 " " BMA e 3 " - " MAN e 4 " " MAN e 4 " - " MAN e 6 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " 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 O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " NAG-ASN " NAG A 701 " - " ASN A 611 " " NAG A 702 " - " ASN A 637 " " NAG A 703 " - " ASN A 618 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 637 " " NAG C 601 " - " ASN C 88 " " NAG C 602 " - " ASN C 133 " " NAG C 603 " - " ASN C 156 " " NAG C 604 " - " ASN C 234 " " NAG C 605 " - " ASN C 301 " " NAG C 606 " - " ASN C 332 " " NAG C 607 " - " ASN C 339 " " NAG C 608 " - " ASN C 355 " " NAG C 609 " - " ASN C 392 " " NAG C 610 " - " ASN C 448 " " NAG C 611 " - " ASN C 137 " " NAG D 1 " - " ASN C 160 " " NAG E 1 " - " ASN C 197 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 637 " " NAG F 703 " - " ASN F 618 " " NAG G 601 " - " ASN G 88 " " NAG G 602 " - " ASN G 133 " " NAG G 603 " - " ASN G 156 " " NAG G 604 " - " ASN G 234 " " NAG G 605 " - " ASN G 301 " " NAG G 606 " - " ASN G 332 " " NAG G 607 " - " ASN G 339 " " NAG G 608 " - " ASN G 355 " " NAG G 609 " - " ASN G 392 " " NAG G 610 " - " ASN G 137 " " NAG G 611 " - " ASN G 276 " " NAG I 601 " - " ASN I 88 " " NAG I 602 " - " ASN I 133 " " NAG I 603 " - " ASN I 234 " " NAG I 604 " - " ASN I 301 " " NAG I 605 " - " ASN I 332 " " NAG I 606 " - " ASN I 339 " " NAG I 607 " - " ASN I 355 " " NAG I 608 " - " ASN I 392 " " NAG I 609 " - " ASN I 137 " " NAG I 610 " - " ASN I 462 " " NAG J 1 " - " ASN C 262 " " NAG K 1 " - " ASN C 276 " " NAG M 1 " - " ASN C 295 " " NAG N 1 " - " ASN C 363 " " NAG O 1 " - " ASN C 386 " " NAG P 1 " - " ASN G 197 " " NAG Q 1 " - " ASN G 262 " " NAG R 1 " - " ASN G 295 " " NAG S 1 " - " ASN G 363 " " NAG T 1 " - " ASN G 386 " " NAG U 1 " - " ASN G 448 " " NAG V 1 " - " ASN G 160 " " NAG W 1 " - " ASN I 197 " " NAG X 1 " - " ASN I 262 " " NAG Y 1 " - " ASN I 276 " " NAG Z 1 " - " ASN I 295 " " NAG a 1 " - " ASN I 363 " " NAG b 1 " - " ASN I 386 " " NAG c 1 " - " ASN I 448 " " NAG d 1 " - " ASN I 156 " " NAG e 1 " - " ASN I 160 " Time building additional restraints: 7.82 Conformation dependent library (CDL) restraints added in 2.7 seconds 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3668 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 41 helices and 32 sheets defined 20.7% alpha, 22.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.34 Creating SS restraints... Processing helix chain 'A' and resid 530 through 543 removed outlier: 3.963A pdb=" N MET A 535 " --> pdb=" O GLY A 531 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N THR A 536 " --> pdb=" O ALA A 532 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU A 537 " --> pdb=" O ALA A 533 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N THR A 538 " --> pdb=" O SER A 534 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N VAL A 539 " --> pdb=" O MET A 535 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N GLN A 540 " --> pdb=" O THR A 536 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA A 541 " --> pdb=" O LEU A 537 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG A 542 " --> pdb=" O THR A 538 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ASN A 543 " --> pdb=" O VAL A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 595 removed outlier: 3.626A pdb=" N ALA A 578 " --> pdb=" O LYS A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 628 through 635 removed outlier: 3.647A pdb=" N LYS A 633 " --> pdb=" O LEU A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 663 removed outlier: 3.508A pdb=" N LEU A 645 " --> pdb=" O ILE A 641 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU A 646 " --> pdb=" O ILE A 642 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU A 647 " --> pdb=" O TYR A 643 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU A 648 " --> pdb=" O GLY A 644 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASN A 651 " --> pdb=" O GLU A 647 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP A 659 " --> pdb=" O LYS A 655 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 660 " --> pdb=" O ASN A 656 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU A 661 " --> pdb=" O GLU A 657 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA A 662 " --> pdb=" O GLN A 658 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LEU A 663 " --> pdb=" O ASP A 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 530 through 535 removed outlier: 4.498A pdb=" N MET B 535 " --> pdb=" O GLY B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 544 removed outlier: 3.779A pdb=" N ARG B 542 " --> pdb=" O THR B 538 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LEU B 544 " --> pdb=" O GLN B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 596 removed outlier: 3.556A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TRP B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 634 removed outlier: 3.810A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 663 removed outlier: 3.805A pdb=" N GLN B 640 " --> pdb=" O ASN B 637 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU B 646 " --> pdb=" O TYR B 643 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU B 648 " --> pdb=" O LEU B 645 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLN B 650 " --> pdb=" O GLU B 647 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN B 651 " --> pdb=" O GLU B 648 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU B 660 " --> pdb=" O GLU B 657 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU B 661 " --> pdb=" O GLN B 658 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA B 662 " --> pdb=" O ASP B 659 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU B 663 " --> pdb=" O LEU B 660 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 63 removed outlier: 3.580A pdb=" N THR C 63 " --> pdb=" O LYS C 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 59 through 63' Processing helix chain 'C' and resid 100 through 114 Processing helix chain 'C' and resid 123 through 125 No H-bonds generated for 'chain 'C' and resid 123 through 125' Processing helix chain 'C' and resid 140 through 150 No H-bonds generated for 'chain 'C' and resid 140 through 150' Processing helix chain 'C' and resid 178 through 180 No H-bonds generated for 'chain 'C' and resid 178 through 180' Processing helix chain 'C' and resid 335 through 351 removed outlier: 3.736A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 372 No H-bonds generated for 'chain 'C' and resid 369 through 372' Processing helix chain 'C' and resid 479 through 481 No H-bonds generated for 'chain 'C' and resid 479 through 481' Processing helix chain 'F' and resid 530 through 544 removed outlier: 3.941A pdb=" N MET F 535 " --> pdb=" O GLY F 531 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N THR F 536 " --> pdb=" O ALA F 532 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU F 537 " --> pdb=" O ALA F 533 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N THR F 538 " --> pdb=" O SER F 534 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL F 539 " --> pdb=" O MET F 535 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA F 541 " --> pdb=" O LEU F 537 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG F 542 " --> pdb=" O THR F 538 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU F 544 " --> pdb=" O GLN F 540 " (cutoff:3.500A) Processing helix chain 'F' and resid 573 through 596 removed outlier: 3.987A pdb=" N ALA F 578 " --> pdb=" O LYS F 574 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG F 579 " --> pdb=" O GLN F 575 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU F 593 " --> pdb=" O ASP F 589 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N TRP F 596 " --> pdb=" O LEU F 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 619 through 624 Processing helix chain 'F' and resid 628 through 634 removed outlier: 3.562A pdb=" N ASP F 632 " --> pdb=" O TRP F 628 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LYS F 633 " --> pdb=" O LEU F 629 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU F 634 " --> pdb=" O GLN F 630 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 628 through 634' Processing helix chain 'F' and resid 639 through 663 removed outlier: 3.594A pdb=" N GLY F 644 " --> pdb=" O GLN F 640 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N LEU F 663 " --> pdb=" O ASP F 659 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 62 Processing helix chain 'G' and resid 99 through 116 removed outlier: 3.586A pdb=" N LEU G 116 " --> pdb=" O TRP G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 123 through 125 No H-bonds generated for 'chain 'G' and resid 123 through 125' Processing helix chain 'G' and resid 178 through 180 No H-bonds generated for 'chain 'G' and resid 178 through 180' Processing helix chain 'G' and resid 194 through 196 No H-bonds generated for 'chain 'G' and resid 194 through 196' Processing helix chain 'G' and resid 335 through 352 removed outlier: 3.541A pdb=" N LYS G 347 " --> pdb=" O GLY G 343 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS G 351 " --> pdb=" O LYS G 347 " (cutoff:3.500A) removed outlier: 4.631A 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 480 removed outlier: 3.568A pdb=" N TRP G 479 " --> pdb=" O MET G 475 " (cutoff:3.500A) Processing helix chain 'I' and resid 60 through 63 No H-bonds generated for 'chain 'I' and resid 60 through 63' Processing helix chain 'I' and resid 99 through 114 removed outlier: 3.634A pdb=" N ILE I 109 " --> pdb=" O HIS I 105 " (cutoff:3.500A) Processing helix chain 'I' and resid 178 through 180 No H-bonds generated for 'chain 'I' and resid 178 through 180' Processing helix chain 'I' and resid 194 through 197 removed outlier: 3.915A pdb=" N ASN I 197 " --> pdb=" O ILE I 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 194 through 197' Processing helix chain 'I' and resid 335 through 352 removed outlier: 3.837A pdb=" N LYS I 351 " --> pdb=" O LYS I 347 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N HIS I 352 " --> pdb=" O GLN I 348 " (cutoff:3.500A) Processing helix chain 'I' and resid 369 through 372 No H-bonds generated for 'chain 'I' and resid 369 through 372' Processing helix chain 'I' and resid 476 through 480 Processing helix chain 'H' and resid 84 through 86 No H-bonds generated for 'chain 'H' and resid 84 through 86' Processing helix chain 'L' and resid 27 through 27C No H-bonds generated for 'chain 'L' and resid 27 through 27C' Processing helix chain 'L' and resid 80 through 82 No H-bonds generated for 'chain 'L' and resid 80 through 82' Processing sheet with id= A, first strand: chain 'C' and resid 35 through 40 Processing sheet with id= B, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.650A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 53 through 55 Processing sheet with id= D, first strand: chain 'C' and resid 91 through 94 removed outlier: 3.932A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE C 93 " --> pdb=" O GLY C 237 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY C 237 " --> pdb=" O PHE C 93 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 169 through 177 Processing sheet with id= F, first strand: chain 'C' and resid 271 through 273 removed outlier: 3.556A pdb=" N MET C 271 " --> pdb=" O GLN C 287 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 8.705A pdb=" N ALA C 362 " --> pdb=" O PRO C 470 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER C 393 " --> pdb=" O PHE C 361 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 414 through 417 removed outlier: 3.572A pdb=" N VAL C 292 " --> pdb=" O ILE C 449 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 304 through 308 Processing sheet with id= I, first strand: chain 'C' and resid 374 through 378 Processing sheet with id= J, first strand: chain 'G' and resid 35 through 40 removed outlier: 3.638A pdb=" N TRP G 35 " --> pdb=" O THR G 499 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'G' and resid 45 through 47 removed outlier: 4.316A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N VAL G 242 " --> pdb=" O LEU G 86 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'G' and resid 91 through 94 removed outlier: 4.081A pdb=" N GLU G 91 " --> pdb=" O CYS G 239 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE G 93 " --> pdb=" O GLY G 237 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY G 237 " --> pdb=" O PHE G 93 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 169 through 177 removed outlier: 3.505A pdb=" N LYS G 189 " --> pdb=" O CYS G 131 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 271 through 274 removed outlier: 3.635A pdb=" N MET G 271 " --> pdb=" O GLN G 287 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASP G 457 " --> pdb=" O THR G 467 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N THR G 467 " --> pdb=" O ASP G 457 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ILE G 358 " --> pdb=" O GLU G 466 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N PHE G 468 " --> pdb=" O ILE G 358 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ARG G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) removed outlier: 8.558A pdb=" N ALA G 362 " --> pdb=" O PRO G 470 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE G 359 " --> pdb=" O TRP G 395 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER G 393 " --> pdb=" O PHE G 361 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 443 through 449 removed outlier: 3.864A pdb=" N ILE G 443 " --> pdb=" O ARG G 298 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL G 292 " --> pdb=" O ILE G 449 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N GLN G 293 " --> pdb=" O SER G 334 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N SER G 334 " --> pdb=" O GLN G 293 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N HIS G 330 " --> pdb=" O THR G 297 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'G' and resid 374 through 378 Processing sheet with id= Q, first strand: chain 'G' and resid 304 through 312 removed outlier: 6.862A pdb=" N GLN G 315 " --> pdb=" O ILE G 309 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'I' and resid 35 through 40 Processing sheet with id= S, first strand: chain 'I' and resid 45 through 47 removed outlier: 3.577A pdb=" N LYS I 46 " --> pdb=" O LYS I 490 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N VAL I 242 " --> pdb=" O LEU I 86 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'I' and resid 53 through 55 Processing sheet with id= U, first strand: chain 'I' and resid 91 through 94 removed outlier: 4.369A pdb=" N GLU I 91 " --> pdb=" O CYS I 239 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE I 93 " --> pdb=" O GLY I 237 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY I 237 " --> pdb=" O PHE I 93 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'I' and resid 130 through 133 Processing sheet with id= W, first strand: chain 'I' and resid 181 through 183 Processing sheet with id= X, first strand: chain 'I' and resid 271 through 274 removed outlier: 3.600A pdb=" N MET I 271 " --> pdb=" O GLN I 287 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER I 393 " --> pdb=" O PHE I 361 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'I' and resid 414 through 417 removed outlier: 3.685A pdb=" N HIS I 330 " --> pdb=" O THR I 297 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL I 292 " --> pdb=" O ILE I 449 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ILE I 443 " --> pdb=" O ARG I 298 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N LEU I 260 " --> pdb=" O THR I 450 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'I' and resid 374 through 378 removed outlier: 3.853A pdb=" N GLU I 381 " --> pdb=" O CYS I 378 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N PHE I 382 " --> pdb=" O LYS I 421 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS I 421 " --> pdb=" O PHE I 382 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR I 384 " --> pdb=" O ARG I 419 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ARG I 419 " --> pdb=" O TYR I 384 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'I' and resid 302 through 308 removed outlier: 3.845A pdb=" N ASP I 321A" --> pdb=" O THR I 303 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N LYS I 305 " --> pdb=" O THR I 320 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N THR I 320 " --> pdb=" O LYS I 305 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE I 307 " --> pdb=" O TYR I 318 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N TYR I 318 " --> pdb=" O ILE I 307 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.752A pdb=" N ARG H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER H 25 " --> pdb=" O ARG H 3 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL H 5 " --> pdb=" O ALA H 23 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU H 18 " --> pdb=" O MET H 82 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N MET H 82 " --> pdb=" O LEU H 18 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER H 70 " --> pdb=" O TYR H 79 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'H' and resid 89 through 94 removed outlier: 3.871A pdb=" N VAL H 93 " --> pdb=" O HIS H 35 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.083A pdb=" N LYS L 103 " --> pdb=" O VAL L 11 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N GLY L 13 " --> pdb=" O LYS L 103 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N THR L 105 " --> pdb=" O GLY L 13 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR L 86 " --> pdb=" O THR L 102 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU L 104 " --> pdb=" O GLY L 84 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N GLY L 84 " --> pdb=" O LEU L 104 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'L' and resid 19 through 22 removed outlier: 3.526A pdb=" N ILE L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE L 75 " --> pdb=" O ILE L 19 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'L' and resid 89 through 91 removed outlier: 3.687A pdb=" N SER L 90 " --> pdb=" O VAL L 97 " (cutoff:3.500A) 447 hydrogen bonds defined for protein. 1209 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: 4.79 Time building geometry restraints manager: 8.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5004 1.34 - 1.46: 4416 1.46 - 1.59: 7694 1.59 - 1.71: 1 1.71 - 1.83: 154 Bond restraints: 17269 Sorted by residual: bond pdb=" O3 TYS H 100H" pdb=" S TYS H 100H" ideal model delta sigma weight residual 1.458 1.635 -0.177 2.00e-02 2.50e+03 7.86e+01 bond pdb=" OH TYS H 100H" pdb=" S TYS H 100H" ideal model delta sigma weight residual 1.679 1.535 0.144 2.00e-02 2.50e+03 5.18e+01 bond pdb=" OH TYS H 100G" pdb=" S TYS H 100G" ideal model delta sigma weight residual 1.679 1.546 0.133 2.00e-02 2.50e+03 4.41e+01 bond pdb=" C3 MAN e 4 " pdb=" O3 MAN e 4 " ideal model delta sigma weight residual 1.408 1.474 -0.066 2.00e-02 2.50e+03 1.08e+01 bond pdb=" CZ TYS H 100G" pdb=" OH TYS H 100G" ideal model delta sigma weight residual 1.371 1.425 -0.054 2.00e-02 2.50e+03 7.28e+00 ... (remaining 17264 not shown) Histogram of bond angle deviations from ideal: 100.22 - 106.98: 542 106.98 - 113.74: 10262 113.74 - 120.50: 5776 120.50 - 127.26: 6649 127.26 - 134.02: 208 Bond angle restraints: 23437 Sorted by residual: angle pdb=" CA TYS H 100G" pdb=" C TYS H 100G" pdb=" O TYS H 100G" ideal model delta sigma weight residual 120.80 113.83 6.97 1.70e+00 3.46e-01 1.68e+01 angle pdb=" C CYS I 218 " pdb=" N ALA I 219 " pdb=" CA ALA I 219 " ideal model delta sigma weight residual 120.97 131.74 -10.77 2.84e+00 1.24e-01 1.44e+01 angle pdb=" C2 MAN e 4 " pdb=" C3 MAN e 4 " pdb=" O3 MAN e 4 " ideal model delta sigma weight residual 107.58 118.58 -11.00 3.00e+00 1.11e-01 1.34e+01 angle pdb=" OH TYS H 100H" pdb=" S TYS H 100H" pdb=" O3 TYS H 100H" ideal model delta sigma weight residual 100.21 109.42 -9.21 3.00e+00 1.11e-01 9.43e+00 angle pdb=" CA GLY G 354 " pdb=" C GLY G 354 " pdb=" O GLY G 354 " ideal model delta sigma weight residual 122.24 119.79 2.45 8.70e-01 1.32e+00 7.91e+00 ... (remaining 23432 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.65: 10917 23.65 - 47.30: 663 47.30 - 70.95: 112 70.95 - 94.59: 55 94.59 - 118.24: 27 Dihedral angle restraints: 11774 sinusoidal: 6094 harmonic: 5680 Sorted by residual: dihedral pdb=" CB CYS A 605 " pdb=" SG CYS A 605 " pdb=" SG CYS C 501 " pdb=" CB CYS C 501 " ideal model delta sinusoidal sigma weight residual -86.00 -150.38 64.38 1 1.00e+01 1.00e-02 5.45e+01 dihedral pdb=" CB CYS G 119 " pdb=" SG CYS G 119 " pdb=" SG CYS G 205 " pdb=" CB CYS G 205 " ideal model delta sinusoidal sigma weight residual -86.00 -150.22 64.22 1 1.00e+01 1.00e-02 5.43e+01 dihedral pdb=" CB CYS I 378 " pdb=" SG CYS I 378 " pdb=" SG CYS I 445 " pdb=" CB CYS I 445 " ideal model delta sinusoidal sigma weight residual -86.00 -146.05 60.05 1 1.00e+01 1.00e-02 4.81e+01 ... (remaining 11771 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 2480 0.061 - 0.123: 420 0.123 - 0.184: 32 0.184 - 0.246: 0 0.246 - 0.307: 9 Chirality restraints: 2941 Sorted by residual: chirality pdb=" C1 NAG G 608 " pdb=" ND2 ASN G 355 " pdb=" C2 NAG G 608 " pdb=" O5 NAG G 608 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" C3 MAN e 4 " pdb=" C2 MAN e 4 " pdb=" C4 MAN e 4 " pdb=" O3 MAN e 4 " both_signs ideal model delta sigma weight residual False 2.47 2.17 0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" C5 BMA X 3 " pdb=" C4 BMA X 3 " pdb=" C6 BMA X 3 " pdb=" O5 BMA X 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.28 2.00e-01 2.50e+01 2.03e+00 ... (remaining 2938 not shown) Planarity restraints: 2909 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG H 3 " -0.109 9.50e-02 1.11e+02 4.88e-02 1.47e+00 pdb=" NE ARG H 3 " 0.007 2.00e-02 2.50e+03 pdb=" CZ ARG H 3 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG H 3 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG H 3 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 448 " 0.011 2.00e-02 2.50e+03 9.82e-03 1.21e+00 pdb=" CG ASN C 448 " -0.012 2.00e-02 2.50e+03 pdb=" OD1 ASN C 448 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN C 448 " -0.011 2.00e-02 2.50e+03 pdb=" C1 NAG C 610 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL I 75 " 0.018 5.00e-02 4.00e+02 2.73e-02 1.19e+00 pdb=" N PRO I 76 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO I 76 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO I 76 " 0.015 5.00e-02 4.00e+02 ... (remaining 2906 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3521 2.79 - 3.32: 15349 3.32 - 3.84: 25744 3.84 - 4.37: 30061 4.37 - 4.90: 52027 Nonbonded interactions: 126702 Sorted by model distance: nonbonded pdb=" OD1 ASN C 137 " pdb=" N2 NAG C 611 " model vdw 2.259 2.520 nonbonded pdb=" NH1 ARG G 298 " pdb=" OD1 ASN G 302 " model vdw 2.273 2.520 nonbonded pdb=" OG1 THR G 163 " pdb=" OE1 GLU G 164 " model vdw 2.274 2.440 nonbonded pdb=" OG SER L 14 " pdb=" OE1 GLN L 17 " model vdw 2.278 2.440 nonbonded pdb=" O LEU L 4 " pdb=" OG1 THR L 100 " model vdw 2.280 2.440 ... (remaining 126697 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 519 through 664 or resid 701 through 702)) selection = chain 'B' selection = (chain 'F' and (resid 519 through 546 or resid 569 through 664 or resid 701 thro \ ugh 702)) } ncs_group { reference = (chain 'C' and (resid 33 through 505 or resid 601 through 610)) selection = (chain 'G' and (resid 33 through 185 or resid 189 through 505 or resid 601 throu \ gh 610)) selection = (chain 'I' and (resid 33 through 505 or resid 601 through 610)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' } ncs_group { reference = (chain 'J' and (resid 1 or resid 4 through 6)) selection = (chain 'X' and (resid 1 or resid 4 through 6)) selection = (chain 'e' and (resid 2 or resid 5 through 7)) } ncs_group { reference = chain 'Q' selection = chain 'V' selection = chain 'd' } 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: 2.590 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: 9.100 Check model and map are aligned: 0.240 Set scattering table: 0.150 Process input model: 45.290 Find NCS groups from input model: 1.000 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 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 : 0.005 0.177 17269 Z= 0.310 Angle : 0.677 10.997 23437 Z= 0.290 Chirality : 0.048 0.307 2941 Planarity : 0.003 0.049 2846 Dihedral : 16.101 118.243 7992 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.19), residues: 1934 helix: 0.41 (0.28), residues: 362 sheet: 1.01 (0.24), residues: 490 loop : -0.31 (0.18), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 103 HIS 0.003 0.000 HIS I 374 PHE 0.010 0.001 PHE C 223 TYR 0.008 0.001 TYR L 49 ARG 0.008 0.000 ARG A 588 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 1736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 408 time to evaluate : 1.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 655 LYS cc_start: 0.8127 (mmmt) cc_final: 0.7469 (ptmm) REVERT: B 579 ARG cc_start: 0.8932 (ttm-80) cc_final: 0.8674 (ttm170) REVERT: B 612 SER cc_start: 0.8931 (m) cc_final: 0.8405 (p) REVERT: B 615 SER cc_start: 0.8688 (t) cc_final: 0.8361 (m) REVERT: C 128 THR cc_start: 0.8773 (m) cc_final: 0.8484 (p) REVERT: G 97 LYS cc_start: 0.7919 (mttp) cc_final: 0.7624 (mttp) REVERT: G 246 GLN cc_start: 0.6151 (mp10) cc_final: 0.5516 (mp10) REVERT: G 277 ILE cc_start: 0.8144 (mm) cc_final: 0.7880 (mm) REVERT: I 121 LYS cc_start: 0.8141 (mttp) cc_final: 0.7899 (tttm) REVERT: I 474 ASP cc_start: 0.6285 (t0) cc_final: 0.6079 (t0) REVERT: H 34 MET cc_start: 0.6912 (mmt) cc_final: 0.6343 (mmt) REVERT: H 52 LYS cc_start: 0.7686 (mtpt) cc_final: 0.6705 (mtpp) REVERT: H 70 SER cc_start: 0.8258 (t) cc_final: 0.7944 (p) REVERT: H 100 ASP cc_start: 0.8659 (t0) cc_final: 0.8450 (t70) REVERT: H 100 MET cc_start: 0.8044 (mtt) cc_final: 0.7686 (mtp) outliers start: 0 outliers final: 0 residues processed: 408 average time/residue: 0.3049 time to fit residues: 181.6367 Evaluate side-chains 231 residues out of total 1736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 1.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 163 optimal weight: 0.9980 chunk 147 optimal weight: 0.5980 chunk 81 optimal weight: 0.6980 chunk 50 optimal weight: 0.3980 chunk 99 optimal weight: 0.9980 chunk 78 optimal weight: 0.5980 chunk 152 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 176 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 653 GLN C 67 ASN ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 HIS ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 591 GLN F 656 ASN G 188 ASN ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17269 Z= 0.200 Angle : 0.612 9.915 23437 Z= 0.300 Chirality : 0.047 0.410 2941 Planarity : 0.004 0.037 2846 Dihedral : 12.342 104.904 4331 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.42 % Allowed : 9.46 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.19), residues: 1934 helix: 0.42 (0.28), residues: 358 sheet: 0.68 (0.23), residues: 529 loop : -0.31 (0.19), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP L 35 HIS 0.005 0.001 HIS G 105 PHE 0.028 0.002 PHE C 382 TYR 0.023 0.001 TYR F 638 ARG 0.005 0.000 ARG G 503 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 255 time to evaluate : 2.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 626 MET cc_start: 0.9207 (ttm) cc_final: 0.8594 (ttt) REVERT: B 607 ASN cc_start: 0.7664 (p0) cc_final: 0.7205 (p0) REVERT: B 612 SER cc_start: 0.8589 (m) cc_final: 0.8367 (p) REVERT: B 615 SER cc_start: 0.8726 (t) cc_final: 0.8430 (m) REVERT: B 655 LYS cc_start: 0.8514 (ptpt) cc_final: 0.8081 (pptt) REVERT: C 102 GLU cc_start: 0.7798 (tm-30) cc_final: 0.7535 (tm-30) REVERT: C 217 TYR cc_start: 0.8452 (m-80) cc_final: 0.8019 (m-80) REVERT: C 434 MET cc_start: 0.7400 (tmm) cc_final: 0.6963 (tmm) REVERT: G 97 LYS cc_start: 0.8115 (mttp) cc_final: 0.7808 (mttp) REVERT: G 188 ASN cc_start: 0.6570 (OUTLIER) cc_final: 0.6241 (m-40) REVERT: G 475 MET cc_start: 0.7395 (mmm) cc_final: 0.7182 (mmm) REVERT: I 39 TYR cc_start: 0.8794 (m-80) cc_final: 0.8593 (m-80) REVERT: I 121 LYS cc_start: 0.8275 (mttp) cc_final: 0.7997 (tttm) REVERT: H 32 GLN cc_start: 0.7043 (mt0) cc_final: 0.6838 (mt0) outliers start: 42 outliers final: 34 residues processed: 278 average time/residue: 0.2966 time to fit residues: 121.7265 Evaluate side-chains 241 residues out of total 1736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 206 time to evaluate : 1.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 653 GLN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 321 ASP Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 591 GLN Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 188 ASN Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 464 THR Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 141 ASP Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 272 ILE Chi-restraints excluded: chain I residue 303 THR Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain L residue 89 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 97 optimal weight: 0.1980 chunk 54 optimal weight: 0.9990 chunk 146 optimal weight: 1.9990 chunk 119 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 176 optimal weight: 6.9990 chunk 190 optimal weight: 20.0000 chunk 157 optimal weight: 0.7980 chunk 175 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 141 optimal weight: 0.0170 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 653 GLN C 85 HIS ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 591 GLN F 625 ASN G 188 ASN ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 258 GLN L 37 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 17269 Z= 0.183 Angle : 0.586 16.776 23437 Z= 0.286 Chirality : 0.047 0.543 2941 Planarity : 0.003 0.040 2846 Dihedral : 11.218 100.206 4331 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.54 % Allowed : 12.06 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.19), residues: 1934 helix: 0.72 (0.29), residues: 349 sheet: 0.74 (0.24), residues: 510 loop : -0.32 (0.18), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP L 35 HIS 0.005 0.001 HIS G 105 PHE 0.017 0.001 PHE C 382 TYR 0.019 0.001 TYR A 638 ARG 0.009 0.000 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 218 time to evaluate : 1.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 655 LYS cc_start: 0.7813 (tptp) cc_final: 0.7594 (ptmt) REVERT: B 615 SER cc_start: 0.8822 (t) cc_final: 0.8539 (m) REVERT: B 655 LYS cc_start: 0.8445 (ptpt) cc_final: 0.8041 (pptt) REVERT: C 102 GLU cc_start: 0.7747 (tm-30) cc_final: 0.7503 (tm-30) REVERT: C 337 THR cc_start: 0.8537 (OUTLIER) cc_final: 0.8248 (m) REVERT: F 542 ARG cc_start: 0.7799 (mtp85) cc_final: 0.7475 (mtm-85) REVERT: F 590 GLN cc_start: 0.9030 (tp40) cc_final: 0.8688 (tp40) REVERT: G 97 LYS cc_start: 0.8173 (mttp) cc_final: 0.7812 (mttp) REVERT: G 274 SER cc_start: 0.8277 (t) cc_final: 0.7939 (p) REVERT: I 104 MET cc_start: 0.8348 (ttt) cc_final: 0.8053 (ttt) REVERT: I 121 LYS cc_start: 0.8313 (mttp) cc_final: 0.8020 (tttm) REVERT: H 32 GLN cc_start: 0.7104 (mt0) cc_final: 0.6894 (mt0) REVERT: H 56 GLU cc_start: 0.8530 (pm20) cc_final: 0.7655 (pp20) REVERT: H 83 ARG cc_start: 0.7111 (mmt-90) cc_final: 0.6474 (mmt-90) REVERT: H 100 TYR cc_start: 0.8466 (m-80) cc_final: 0.8115 (m-80) outliers start: 44 outliers final: 36 residues processed: 243 average time/residue: 0.2875 time to fit residues: 104.7373 Evaluate side-chains 241 residues out of total 1736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 204 time to evaluate : 1.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 321 ASP Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 575 GLN Chi-restraints excluded: chain F residue 591 GLN Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 464 THR Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 141 ASP Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 272 ILE Chi-restraints excluded: chain I residue 373 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain L residue 89 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 174 optimal weight: 0.9980 chunk 132 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 118 optimal weight: 3.9990 chunk 177 optimal weight: 8.9990 chunk 187 optimal weight: 4.9990 chunk 92 optimal weight: 0.6980 chunk 167 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 653 GLN ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 188 ASN ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 17269 Z= 0.374 Angle : 0.704 11.479 23437 Z= 0.340 Chirality : 0.050 0.473 2941 Planarity : 0.004 0.040 2846 Dihedral : 10.405 97.539 4331 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.64 % Allowed : 14.31 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.19), residues: 1934 helix: 0.44 (0.28), residues: 354 sheet: 0.50 (0.24), residues: 498 loop : -0.44 (0.18), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP I 479 HIS 0.007 0.001 HIS I 330 PHE 0.020 0.002 PHE C 382 TYR 0.017 0.002 TYR C 191 ARG 0.013 0.001 ARG I 308 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 207 time to evaluate : 1.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 626 MET cc_start: 0.9045 (ttm) cc_final: 0.8390 (ttt) REVERT: A 655 LYS cc_start: 0.7799 (tptp) cc_final: 0.7433 (ptmm) REVERT: B 607 ASN cc_start: 0.8067 (p0) cc_final: 0.7703 (p0) REVERT: B 615 SER cc_start: 0.8808 (t) cc_final: 0.8543 (m) REVERT: B 648 GLU cc_start: 0.7597 (pp20) cc_final: 0.7187 (pm20) REVERT: B 655 LYS cc_start: 0.8449 (ptpt) cc_final: 0.8075 (pptt) REVERT: C 337 THR cc_start: 0.8852 (OUTLIER) cc_final: 0.8620 (m) REVERT: G 97 LYS cc_start: 0.8257 (mttp) cc_final: 0.7848 (mttp) REVERT: G 161 MET cc_start: 0.8110 (tpt) cc_final: 0.7681 (tpt) REVERT: I 104 MET cc_start: 0.8501 (ttt) cc_final: 0.8287 (ttt) REVERT: I 121 LYS cc_start: 0.8338 (mttp) cc_final: 0.8008 (tttm) REVERT: H 56 GLU cc_start: 0.8695 (pm20) cc_final: 0.7859 (pp20) REVERT: H 77 THR cc_start: 0.6660 (p) cc_final: 0.6374 (p) outliers start: 63 outliers final: 48 residues processed: 251 average time/residue: 0.2890 time to fit residues: 109.4081 Evaluate side-chains 234 residues out of total 1736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 185 time to evaluate : 1.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 653 GLN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 321 ASP Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain F residue 537 LEU Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 217 TYR Chi-restraints excluded: chain G residue 278 THR Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 464 THR Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 272 ILE Chi-restraints excluded: chain I residue 297 THR Chi-restraints excluded: chain I residue 322 ILE Chi-restraints excluded: chain I residue 373 THR Chi-restraints excluded: chain I residue 419 ARG Chi-restraints excluded: chain I residue 481 SER Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain L residue 89 LYS Chi-restraints excluded: chain L residue 92 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 156 optimal weight: 0.8980 chunk 106 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 139 optimal weight: 0.5980 chunk 77 optimal weight: 0.9980 chunk 160 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 chunk 168 optimal weight: 0.6980 chunk 47 optimal weight: 0.1980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 653 GLN ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 625 ASN G 67 ASN G 249 HIS ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 17269 Z= 0.181 Angle : 0.592 11.947 23437 Z= 0.285 Chirality : 0.047 0.498 2941 Planarity : 0.003 0.039 2846 Dihedral : 9.418 99.528 4331 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.17 % Allowed : 15.98 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.19), residues: 1934 helix: 0.68 (0.29), residues: 352 sheet: 0.58 (0.24), residues: 475 loop : -0.45 (0.18), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 64 HIS 0.004 0.001 HIS G 105 PHE 0.022 0.001 PHE C 382 TYR 0.018 0.001 TYR F 638 ARG 0.005 0.000 ARG I 166 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 203 time to evaluate : 1.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 626 MET cc_start: 0.8961 (ttm) cc_final: 0.8279 (ttt) REVERT: B 615 SER cc_start: 0.8807 (t) cc_final: 0.8532 (m) REVERT: B 648 GLU cc_start: 0.7579 (pp20) cc_final: 0.7342 (pm20) REVERT: B 655 LYS cc_start: 0.8484 (ptpt) cc_final: 0.8079 (pptt) REVERT: F 621 GLU cc_start: 0.6999 (tm-30) cc_final: 0.6071 (tm-30) REVERT: G 69 TRP cc_start: 0.7197 (m-90) cc_final: 0.6895 (m-90) REVERT: G 97 LYS cc_start: 0.8228 (mttp) cc_final: 0.7838 (mttp) REVERT: G 102 GLU cc_start: 0.6797 (OUTLIER) cc_final: 0.6112 (mp0) REVERT: G 161 MET cc_start: 0.8183 (tpt) cc_final: 0.7751 (tpt) REVERT: I 121 LYS cc_start: 0.8314 (mttp) cc_final: 0.8010 (tttm) REVERT: L 31 GLU cc_start: 0.8501 (tm-30) cc_final: 0.8298 (tm-30) outliers start: 55 outliers final: 40 residues processed: 242 average time/residue: 0.2652 time to fit residues: 98.6587 Evaluate side-chains 230 residues out of total 1736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 189 time to evaluate : 1.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 321 ASP Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain F residue 575 GLN Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain G residue 67 ASN Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 464 THR Chi-restraints excluded: chain G residue 501 CYS Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 141 ASP Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 272 ILE Chi-restraints excluded: chain I residue 292 VAL Chi-restraints excluded: chain I residue 419 ARG Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain L residue 92 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 63 optimal weight: 0.7980 chunk 168 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 187 optimal weight: 7.9990 chunk 155 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 62 optimal weight: 0.6980 chunk 98 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 653 GLN ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 17269 Z= 0.217 Angle : 0.599 12.783 23437 Z= 0.288 Chirality : 0.047 0.493 2941 Planarity : 0.003 0.039 2846 Dihedral : 8.893 103.502 4331 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.12 % Allowed : 16.45 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.19), residues: 1934 helix: 0.71 (0.29), residues: 352 sheet: 0.49 (0.24), residues: 485 loop : -0.49 (0.18), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 64 HIS 0.004 0.001 HIS G 105 PHE 0.018 0.001 PHE C 382 TYR 0.026 0.001 TYR A 638 ARG 0.006 0.000 ARG G 503 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 194 time to evaluate : 1.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 626 MET cc_start: 0.8932 (ttm) cc_final: 0.8242 (ttt) REVERT: B 615 SER cc_start: 0.8829 (t) cc_final: 0.8509 (m) REVERT: B 655 LYS cc_start: 0.8506 (ptpt) cc_final: 0.8111 (pptt) REVERT: F 621 GLU cc_start: 0.7075 (tm-30) cc_final: 0.6178 (tm-30) REVERT: G 69 TRP cc_start: 0.7049 (m-90) cc_final: 0.6837 (m-90) REVERT: G 97 LYS cc_start: 0.8342 (mttp) cc_final: 0.7932 (mttp) REVERT: G 102 GLU cc_start: 0.6809 (OUTLIER) cc_final: 0.6186 (mp0) REVERT: G 161 MET cc_start: 0.8196 (tpt) cc_final: 0.7756 (tpt) REVERT: I 121 LYS cc_start: 0.8323 (mttp) cc_final: 0.8008 (tttm) REVERT: L 89 LYS cc_start: 0.6868 (tmtt) cc_final: 0.6622 (tmtt) outliers start: 54 outliers final: 46 residues processed: 229 average time/residue: 0.2891 time to fit residues: 100.3595 Evaluate side-chains 231 residues out of total 1736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 184 time to evaluate : 1.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 653 GLN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 203 GLN Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 321 ASP Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain F residue 575 GLN Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 464 THR Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 141 ASP Chi-restraints excluded: chain I residue 180 ASP Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 272 ILE Chi-restraints excluded: chain I residue 292 VAL Chi-restraints excluded: chain I residue 320 THR Chi-restraints excluded: chain I residue 322 ILE Chi-restraints excluded: chain I residue 373 THR Chi-restraints excluded: chain I residue 419 ARG Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain L residue 85 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 180 optimal weight: 6.9990 chunk 21 optimal weight: 0.9990 chunk 106 optimal weight: 0.7980 chunk 137 optimal weight: 0.0670 chunk 158 optimal weight: 4.9990 chunk 104 optimal weight: 0.0670 chunk 186 optimal weight: 20.0000 chunk 117 optimal weight: 2.9990 chunk 113 optimal weight: 0.3980 chunk 86 optimal weight: 3.9990 chunk 115 optimal weight: 0.9980 overall best weight: 0.4656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 543 ASN ** A 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 653 GLN ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.3565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 17269 Z= 0.160 Angle : 0.569 11.345 23437 Z= 0.275 Chirality : 0.046 0.495 2941 Planarity : 0.003 0.039 2846 Dihedral : 8.282 106.113 4331 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.23 % Allowed : 16.62 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.19), residues: 1934 helix: 0.83 (0.29), residues: 352 sheet: 0.50 (0.24), residues: 486 loop : -0.47 (0.18), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 64 HIS 0.003 0.001 HIS G 105 PHE 0.017 0.001 PHE C 382 TYR 0.025 0.001 TYR A 638 ARG 0.005 0.000 ARG G 503 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 196 time to evaluate : 2.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 615 SER cc_start: 0.8883 (t) cc_final: 0.8582 (m) REVERT: B 655 LYS cc_start: 0.8439 (ptpt) cc_final: 0.8086 (pptt) REVERT: F 621 GLU cc_start: 0.7116 (tm-30) cc_final: 0.6909 (tm-30) REVERT: G 69 TRP cc_start: 0.7202 (m-90) cc_final: 0.6939 (m-90) REVERT: G 97 LYS cc_start: 0.8345 (mttp) cc_final: 0.7926 (mttp) REVERT: G 102 GLU cc_start: 0.6758 (OUTLIER) cc_final: 0.6104 (mp0) REVERT: G 161 MET cc_start: 0.8224 (tpt) cc_final: 0.7778 (tpt) REVERT: I 121 LYS cc_start: 0.8300 (mttp) cc_final: 0.8011 (tttm) REVERT: H 46 GLU cc_start: 0.8582 (mm-30) cc_final: 0.8340 (mm-30) REVERT: L 89 LYS cc_start: 0.6848 (tmtt) cc_final: 0.6639 (tmtt) outliers start: 56 outliers final: 43 residues processed: 234 average time/residue: 0.2728 time to fit residues: 97.6741 Evaluate side-chains 229 residues out of total 1736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 185 time to evaluate : 1.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 321 ASP Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain F residue 537 LEU Chi-restraints excluded: chain F residue 575 GLN Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 464 THR Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 141 ASP Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 272 ILE Chi-restraints excluded: chain I residue 292 VAL Chi-restraints excluded: chain I residue 320 THR Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain L residue 92 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 74 optimal weight: 0.2980 chunk 111 optimal weight: 0.6980 chunk 56 optimal weight: 0.0970 chunk 36 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 146 optimal weight: 0.9980 chunk 170 optimal weight: 0.9980 chunk 179 optimal weight: 10.0000 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 653 GLN ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 17269 Z= 0.185 Angle : 0.584 13.613 23437 Z= 0.283 Chirality : 0.046 0.484 2941 Planarity : 0.003 0.039 2846 Dihedral : 8.044 108.534 4331 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.00 % Allowed : 17.31 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.19), residues: 1934 helix: 0.88 (0.29), residues: 352 sheet: 0.44 (0.24), residues: 490 loop : -0.47 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 631 HIS 0.003 0.001 HIS G 105 PHE 0.016 0.001 PHE C 382 TYR 0.017 0.001 TYR F 638 ARG 0.005 0.000 ARG I 166 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 189 time to evaluate : 1.834 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 615 SER cc_start: 0.8869 (t) cc_final: 0.8567 (m) REVERT: B 655 LYS cc_start: 0.8448 (ptpt) cc_final: 0.8109 (pptt) REVERT: C 484 TYR cc_start: 0.8951 (p90) cc_final: 0.8672 (p90) REVERT: G 97 LYS cc_start: 0.8321 (mttp) cc_final: 0.7932 (mttp) REVERT: G 102 GLU cc_start: 0.6817 (OUTLIER) cc_final: 0.6174 (mp0) REVERT: G 161 MET cc_start: 0.8231 (tpt) cc_final: 0.7767 (tpt) REVERT: G 215 ILE cc_start: 0.8449 (tp) cc_final: 0.8058 (tp) REVERT: I 121 LYS cc_start: 0.8306 (mttp) cc_final: 0.8005 (tttm) REVERT: H 46 GLU cc_start: 0.8599 (mm-30) cc_final: 0.8367 (mm-30) REVERT: L 89 LYS cc_start: 0.6870 (tmtt) cc_final: 0.6599 (tmtt) outliers start: 52 outliers final: 45 residues processed: 220 average time/residue: 0.2719 time to fit residues: 92.3002 Evaluate side-chains 225 residues out of total 1736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 179 time to evaluate : 1.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain B residue 653 GLN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 321 ASP Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain F residue 537 LEU Chi-restraints excluded: chain F residue 575 GLN Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 464 THR Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 141 ASP Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 272 ILE Chi-restraints excluded: chain I residue 292 VAL Chi-restraints excluded: chain I residue 297 THR Chi-restraints excluded: chain I residue 320 THR Chi-restraints excluded: chain I residue 322 ILE Chi-restraints excluded: chain I residue 373 THR Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain L residue 85 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 163 optimal weight: 0.7980 chunk 174 optimal weight: 2.9990 chunk 179 optimal weight: 8.9990 chunk 104 optimal weight: 2.9990 chunk 75 optimal weight: 0.0270 chunk 136 optimal weight: 2.9990 chunk 53 optimal weight: 0.0470 chunk 157 optimal weight: 2.9990 chunk 164 optimal weight: 0.7980 chunk 173 optimal weight: 0.3980 chunk 114 optimal weight: 0.5980 overall best weight: 0.3736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 653 GLN ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.3747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 17269 Z= 0.156 Angle : 0.575 13.312 23437 Z= 0.278 Chirality : 0.046 0.480 2941 Planarity : 0.003 0.038 2846 Dihedral : 7.787 109.298 4331 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.71 % Allowed : 17.77 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.19), residues: 1934 helix: 0.96 (0.30), residues: 353 sheet: 0.37 (0.24), residues: 502 loop : -0.39 (0.19), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 35 HIS 0.003 0.001 HIS G 105 PHE 0.017 0.001 PHE C 382 TYR 0.016 0.001 TYR F 638 ARG 0.005 0.000 ARG I 166 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 188 time to evaluate : 1.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 615 SER cc_start: 0.8864 (t) cc_final: 0.8561 (m) REVERT: B 655 LYS cc_start: 0.8361 (ptpt) cc_final: 0.8028 (pptt) REVERT: C 484 TYR cc_start: 0.8941 (p90) cc_final: 0.8646 (p90) REVERT: G 97 LYS cc_start: 0.8311 (mttp) cc_final: 0.7928 (mttp) REVERT: G 102 GLU cc_start: 0.6774 (OUTLIER) cc_final: 0.6102 (mp0) REVERT: G 161 MET cc_start: 0.8241 (tpt) cc_final: 0.7815 (tpt) REVERT: G 215 ILE cc_start: 0.8381 (tp) cc_final: 0.7997 (tp) REVERT: I 39 TYR cc_start: 0.8891 (m-80) cc_final: 0.8622 (m-10) REVERT: I 121 LYS cc_start: 0.8279 (mttp) cc_final: 0.8009 (tttm) REVERT: H 46 GLU cc_start: 0.8597 (mm-30) cc_final: 0.8365 (mm-30) outliers start: 47 outliers final: 42 residues processed: 219 average time/residue: 0.2743 time to fit residues: 92.4033 Evaluate side-chains 225 residues out of total 1736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 182 time to evaluate : 1.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain F residue 537 LEU Chi-restraints excluded: chain F residue 575 GLN Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 464 THR Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 141 ASP Chi-restraints excluded: chain I residue 180 ASP Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 272 ILE Chi-restraints excluded: chain I residue 292 VAL Chi-restraints excluded: chain I residue 320 THR Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain L residue 85 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 184 optimal weight: 0.4980 chunk 112 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 128 optimal weight: 0.6980 chunk 193 optimal weight: 7.9990 chunk 177 optimal weight: 10.0000 chunk 153 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 122 optimal weight: 0.5980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 653 GLN ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.3943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 17269 Z= 0.236 Angle : 0.615 13.186 23437 Z= 0.298 Chirality : 0.046 0.460 2941 Planarity : 0.003 0.039 2846 Dihedral : 7.818 111.471 4331 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.83 % Allowed : 17.83 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.19), residues: 1934 helix: 0.88 (0.29), residues: 353 sheet: 0.29 (0.24), residues: 498 loop : -0.48 (0.18), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP H 64 HIS 0.003 0.001 HIS G 105 PHE 0.019 0.001 PHE C 382 TYR 0.017 0.001 TYR F 638 ARG 0.006 0.000 ARG I 166 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 186 time to evaluate : 1.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 659 ASP cc_start: 0.8612 (p0) cc_final: 0.8235 (p0) REVERT: B 615 SER cc_start: 0.8859 (t) cc_final: 0.8552 (m) REVERT: B 655 LYS cc_start: 0.8501 (ptpt) cc_final: 0.8133 (pptt) REVERT: C 484 TYR cc_start: 0.8978 (p90) cc_final: 0.8709 (p90) REVERT: G 97 LYS cc_start: 0.8406 (mttp) cc_final: 0.7979 (mttp) REVERT: G 102 GLU cc_start: 0.6959 (OUTLIER) cc_final: 0.6446 (mp0) REVERT: G 161 MET cc_start: 0.8222 (tpt) cc_final: 0.7748 (tpt) REVERT: G 215 ILE cc_start: 0.8357 (tp) cc_final: 0.7931 (tp) REVERT: I 39 TYR cc_start: 0.8939 (m-80) cc_final: 0.8676 (m-80) REVERT: I 121 LYS cc_start: 0.8340 (mttp) cc_final: 0.8009 (tttm) REVERT: H 46 GLU cc_start: 0.8618 (mm-30) cc_final: 0.8396 (mm-30) REVERT: L 89 LYS cc_start: 0.6710 (OUTLIER) cc_final: 0.6465 (ptmm) outliers start: 49 outliers final: 43 residues processed: 220 average time/residue: 0.2739 time to fit residues: 91.7752 Evaluate side-chains 221 residues out of total 1736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 176 time to evaluate : 1.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain B residue 653 GLN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain F residue 575 GLN Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 464 THR Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 141 ASP Chi-restraints excluded: chain I residue 180 ASP Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 272 ILE Chi-restraints excluded: chain I residue 292 VAL Chi-restraints excluded: chain I residue 320 THR Chi-restraints excluded: chain I residue 373 THR Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain L residue 89 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 163 optimal weight: 0.9990 chunk 47 optimal weight: 0.0980 chunk 141 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 154 optimal weight: 0.9980 chunk 64 optimal weight: 0.3980 chunk 158 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 28 optimal weight: 0.0270 chunk 135 optimal weight: 2.9990 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 653 GLN ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.161325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.131492 restraints weight = 25906.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.133078 restraints weight = 22965.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.134890 restraints weight = 18956.205| |-----------------------------------------------------------------------------| r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.3971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 17269 Z= 0.167 Angle : 0.594 13.137 23437 Z= 0.288 Chirality : 0.046 0.465 2941 Planarity : 0.003 0.039 2846 Dihedral : 7.632 111.472 4331 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.65 % Allowed : 18.41 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.19), residues: 1934 helix: 0.99 (0.30), residues: 352 sheet: 0.30 (0.24), residues: 500 loop : -0.44 (0.19), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP H 64 HIS 0.003 0.001 HIS G 105 PHE 0.025 0.001 PHE H 91 TYR 0.019 0.001 TYR F 638 ARG 0.005 0.000 ARG I 166 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3271.58 seconds wall clock time: 60 minutes 19.31 seconds (3619.31 seconds total)