Starting phenix.real_space_refine on Thu Mar 21 06:22:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t9t_25767/03_2024/7t9t_25767_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t9t_25767/03_2024/7t9t_25767.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t9t_25767/03_2024/7t9t_25767.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t9t_25767/03_2024/7t9t_25767.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t9t_25767/03_2024/7t9t_25767_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t9t_25767/03_2024/7t9t_25767_neut.pdb" } resolution = 3.7 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= 0.003 sd= 0.129 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5430 atoms to isotropic. 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 140 5.16 5 C 15078 2.51 5 N 4074 2.21 5 O 4773 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 24065 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 3454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3454 Classifications: {'peptide': 439} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 418} Chain breaks: 4 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 969 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "C" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1677 Classifications: {'peptide': 220} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 206} Chain breaks: 1 Chain: "D" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1635 Classifications: {'peptide': 211} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 201} Chain: "E" Number of atoms: 3453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3453 Classifications: {'peptide': 439} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 417} Chain breaks: 4 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "F" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 969 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "G" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1677 Classifications: {'peptide': 220} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 206} Chain breaks: 1 Chain: "H" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1635 Classifications: {'peptide': 211} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 201} Chain: "I" Number of atoms: 3454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3454 Classifications: {'peptide': 439} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 418} Chain breaks: 4 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "J" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 969 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "K" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1677 Classifications: {'peptide': 220} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 206} Chain breaks: 1 Chain: "L" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1635 Classifications: {'peptide': 211} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 201} Chain: "a" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 53 Unusual residues: {'BMA': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 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: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 53 Unusual residues: {'BMA': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 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: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 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: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 53 Unusual residues: {'BMA': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: "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: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 12.15, per 1000 atoms: 0.50 Number of scatterers: 24065 At special positions: 0 Unit cell: (168.48, 184.68, 123.12, 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 140 16.00 O 4773 8.00 N 4074 7.00 C 15078 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.04 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 499 " - pdb=" SG CYS B 605 " distance=2.02 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.04 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 499 " - pdb=" SG CYS F 605 " distance=2.02 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.04 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 74 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.03 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.03 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 I 499 " - pdb=" SG CYS J 605 " distance=2.02 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.02 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 ALPHA1-3 " BMA R 3 " - " MAN R 6 " " BMA X 3 " - " MAN X 6 " " BMA d 3 " - " MAN d 6 " ALPHA1-6 " BMA R 3 " - " MAN R 4 " " MAN R 4 " - " MAN R 5 " " BMA X 3 " - " MAN X 4 " " MAN X 4 " - " MAN X 5 " " BMA d 3 " - " MAN d 4 " " MAN d 4 " - " MAN d 5 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " BMA O 3 " - " NAG O 4 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " BMA U 3 " - " NAG U 4 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " BMA a 3 " - " NAG a 4 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " NAG-ASN " NAG A 601 " - " ASN A 230 " " NAG A 602 " - " ASN A 241 " " NAG E 601 " - " ASN E 230 " " NAG E 602 " - " ASN E 241 " " NAG I 601 " - " ASN I 230 " " NAG I 602 " - " ASN I 241 " " NAG M 1 " - " ASN A 386 " " NAG N 1 " - " ASN A 339 " " NAG O 1 " - " ASN A 262 " " NAG P 1 " - " ASN A 160 " " NAG Q 1 " - " ASN A 392 " " NAG R 1 " - " ASN A 197 " " NAG S 1 " - " ASN E 386 " " NAG T 1 " - " ASN E 339 " " NAG U 1 " - " ASN E 262 " " NAG V 1 " - " ASN E 160 " " NAG W 1 " - " ASN E 392 " " NAG X 1 " - " ASN E 197 " " NAG Y 1 " - " ASN I 386 " " NAG Z 1 " - " ASN I 339 " " NAG a 1 " - " ASN I 262 " " NAG b 1 " - " ASN I 160 " " NAG c 1 " - " ASN I 392 " " NAG d 1 " - " ASN I 197 " Time building additional restraints: 9.31 Conformation dependent library (CDL) restraints added in 3.7 seconds 5832 Ramachandran restraints generated. 2916 Oldfield, 0 Emsley, 2916 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5550 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 46 sheets defined 16.7% alpha, 22.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.26 Creating SS restraints... Processing helix chain 'A' and resid 99 through 117 Processing helix chain 'A' and resid 122 through 127 removed outlier: 3.982A pdb=" N VAL A 127 " --> pdb=" O PRO A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 473 through 479 removed outlier: 3.965A pdb=" N TRP A 477 " --> pdb=" O MET A 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 542 removed outlier: 3.859A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 596 removed outlier: 3.617A pdb=" N VAL B 580 " --> pdb=" O LEU B 576 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N TRP B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 623 removed outlier: 3.807A pdb=" N ILE B 622 " --> pdb=" O ASN B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 638 through 662 removed outlier: 3.881A pdb=" N TYR B 643 " --> pdb=" O THR B 639 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU B 645 " --> pdb=" O ILE B 641 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 removed outlier: 4.007A pdb=" N TYR C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 64 removed outlier: 3.945A pdb=" N ARG C 64 " --> pdb=" O GLY C 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 61 through 64' Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'C' and resid 156 through 158 No H-bonds generated for 'chain 'C' and resid 156 through 158' Processing helix chain 'C' and resid 187 through 191 Processing helix chain 'D' and resid 121 through 127 Processing helix chain 'D' and resid 182 through 187 Processing helix chain 'E' and resid 99 through 117 Processing helix chain 'E' and resid 122 through 127 removed outlier: 3.996A pdb=" N VAL E 127 " --> pdb=" O PRO E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 350 Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 387 through 392 removed outlier: 3.570A pdb=" N PHE E 391 " --> pdb=" O THR E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 473 through 478 removed outlier: 3.929A pdb=" N TRP E 477 " --> pdb=" O MET E 473 " (cutoff:3.500A) Processing helix chain 'F' and resid 521 through 526 removed outlier: 3.933A pdb=" N ALA F 525 " --> pdb=" O PHE F 522 " (cutoff:3.500A) Processing helix chain 'F' and resid 531 through 535 Processing helix chain 'F' and resid 536 through 542 Processing helix chain 'F' and resid 576 through 596 removed outlier: 3.627A pdb=" N VAL F 580 " --> pdb=" O LEU F 576 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N TRP F 596 " --> pdb=" O LEU F 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 623 removed outlier: 3.630A pdb=" N ILE F 622 " --> pdb=" O ASN F 618 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 636 removed outlier: 3.754A pdb=" N TRP F 631 " --> pdb=" O THR F 627 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 662 removed outlier: 3.834A pdb=" N TYR F 643 " --> pdb=" O THR F 639 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N GLY F 644 " --> pdb=" O GLN F 640 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU F 645 " --> pdb=" O ILE F 641 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 32 removed outlier: 4.077A pdb=" N TYR G 32 " --> pdb=" O PHE G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 64 removed outlier: 3.856A pdb=" N ARG G 64 " --> pdb=" O GLY G 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 61 through 64' Processing helix chain 'G' and resid 83 through 87 removed outlier: 3.553A pdb=" N THR G 87 " --> pdb=" O TYR G 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 156 through 158 No H-bonds generated for 'chain 'G' and resid 156 through 158' Processing helix chain 'G' and resid 187 through 191 Processing helix chain 'H' and resid 121 through 127 Processing helix chain 'H' and resid 182 through 187 Processing helix chain 'I' and resid 99 through 117 Processing helix chain 'I' and resid 122 through 127 removed outlier: 3.895A pdb=" N VAL I 127 " --> pdb=" O PRO I 124 " (cutoff:3.500A) Processing helix chain 'I' and resid 335 through 350 Processing helix chain 'I' and resid 368 through 373 Processing helix chain 'I' and resid 387 through 392 removed outlier: 3.611A pdb=" N PHE I 391 " --> pdb=" O THR I 387 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN I 392 " --> pdb=" O SER I 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 387 through 392' Processing helix chain 'I' and resid 473 through 479 removed outlier: 4.023A pdb=" N TRP I 477 " --> pdb=" O MET I 473 " (cutoff:3.500A) Processing helix chain 'J' and resid 531 through 535 Processing helix chain 'J' and resid 536 through 542 removed outlier: 3.598A pdb=" N GLN J 540 " --> pdb=" O THR J 536 " (cutoff:3.500A) Processing helix chain 'J' and resid 575 through 596 removed outlier: 3.593A pdb=" N ARG J 579 " --> pdb=" O GLN J 575 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA J 582 " --> pdb=" O ALA J 578 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL J 583 " --> pdb=" O ARG J 579 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N TRP J 596 " --> pdb=" O LEU J 592 " (cutoff:3.500A) Processing helix chain 'J' and resid 627 through 636 removed outlier: 3.577A pdb=" N GLU J 634 " --> pdb=" O GLN J 630 " (cutoff:3.500A) Processing helix chain 'J' and resid 638 through 662 removed outlier: 4.518A pdb=" N GLY J 644 " --> pdb=" O GLN J 640 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU J 645 " --> pdb=" O ILE J 641 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 32 removed outlier: 4.046A pdb=" N TYR K 32 " --> pdb=" O PHE K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 61 through 64 removed outlier: 3.802A pdb=" N ARG K 64 " --> pdb=" O GLY K 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 61 through 64' Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'K' and resid 156 through 158 No H-bonds generated for 'chain 'K' and resid 156 through 158' Processing helix chain 'K' and resid 187 through 191 Processing helix chain 'L' and resid 121 through 127 Processing helix chain 'L' and resid 182 through 187 Processing sheet with id=AA1, first strand: chain 'A' and resid 493 through 497 removed outlier: 5.456A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.972A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR A 244 " --> pdb=" O MET A 84 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET A 84 " --> pdb=" O THR A 244 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 129 through 130 Processing sheet with id=AA5, first strand: chain 'A' and resid 143 through 144 Processing sheet with id=AA6, first strand: chain 'A' and resid 158 through 162 Processing sheet with id=AA7, first strand: chain 'A' and resid 200 through 203 removed outlier: 3.675A pdb=" N ALA A 433 " --> pdb=" O VAL A 200 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 284 through 298 removed outlier: 7.269A pdb=" N LYS A 293 " --> pdb=" O ASN A 334 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ASN A 334 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR A 330 " --> pdb=" O THR A 297 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 330 through 334 current: chain 'A' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 381 through 385 current: chain 'A' and resid 464 through 468 Processing sheet with id=AA9, first strand: chain 'A' and resid 301 through 308 removed outlier: 6.024A pdb=" N THR A 305 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N THR A 320 " --> pdb=" O THR A 305 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ILE A 307 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N TYR A 318 " --> pdb=" O ILE A 307 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.508A pdb=" N SER C 25 " --> pdb=" O ARG C 3 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA C 5 " --> pdb=" O VAL C 23 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR C 7 " --> pdb=" O SER C 21 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER C 21 " --> pdb=" O TYR C 7 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N MET C 80 " --> pdb=" O LEU C 20 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR C 70 " --> pdb=" O TYR C 79 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 10 through 12 current: chain 'C' and resid 46 through 51 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 57 through 59 current: chain 'C' and resid 100B through 100D Processing sheet with id=AB3, first strand: chain 'C' and resid 120 through 124 removed outlier: 3.948A pdb=" N GLY C 139 " --> pdb=" O LEU C 124 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 135 through 145 current: chain 'C' and resid 176 through 185 Processing sheet with id=AB4, first strand: chain 'C' and resid 151 through 154 Processing sheet with id=AB5, first strand: chain 'D' and resid 5 through 7 removed outlier: 3.537A pdb=" N GLU D 70 " --> pdb=" O SER D 67 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 10 through 13 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 10 through 13 current: chain 'D' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 53 through 54 current: chain 'D' and resid 97 through 98 Processing sheet with id=AB7, first strand: chain 'D' and resid 114 through 118 removed outlier: 3.539A pdb=" N VAL D 133 " --> pdb=" O PHE D 118 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N TYR D 173 " --> pdb=" O ASN D 138 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 153 through 155 removed outlier: 4.264A pdb=" N TRP D 148 " --> pdb=" O GLN D 155 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 493 through 497 removed outlier: 5.466A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.721A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR E 244 " --> pdb=" O MET E 84 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N MET E 84 " --> pdb=" O THR E 244 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AC3, first strand: chain 'E' and resid 129 through 130 Processing sheet with id=AC4, first strand: chain 'E' and resid 158 through 162 Processing sheet with id=AC5, first strand: chain 'E' and resid 201 through 203 removed outlier: 6.556A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 259 through 261 current: chain 'E' and resid 284 through 308 removed outlier: 6.040A pdb=" N THR E 305 " --> pdb=" O THR E 320 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N THR E 320 " --> pdb=" O THR E 305 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ILE E 307 " --> pdb=" O TYR E 318 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N TYR E 318 " --> pdb=" O ILE E 307 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 316 through 323 current: chain 'E' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 381 through 385 current: chain 'E' and resid 464 through 468 Processing sheet with id=AC7, first strand: chain 'G' and resid 5 through 7 removed outlier: 3.565A pdb=" N TYR G 7 " --> pdb=" O SER G 21 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER G 21 " --> pdb=" O TYR G 7 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N MET G 80 " --> pdb=" O LEU G 20 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR G 70 " --> pdb=" O TYR G 79 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 10 through 12 current: chain 'G' and resid 46 through 51 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 57 through 59 current: chain 'G' and resid 100E through 103 Processing sheet with id=AC9, first strand: chain 'G' and resid 120 through 124 removed outlier: 3.947A pdb=" N GLY G 139 " --> pdb=" O LEU G 124 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 135 through 145 current: chain 'G' and resid 176 through 185 Processing sheet with id=AD1, first strand: chain 'G' and resid 150 through 154 Processing sheet with id=AD2, first strand: chain 'H' and resid 5 through 7 removed outlier: 3.555A pdb=" N ARG H 24 " --> pdb=" O THR H 5 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR H 22 " --> pdb=" O SER H 7 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU H 70 " --> pdb=" O SER H 67 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 10 through 13 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 10 through 13 current: chain 'H' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 53 through 54 current: chain 'H' and resid 97 through 98 Processing sheet with id=AD4, first strand: chain 'H' and resid 114 through 118 removed outlier: 3.622A pdb=" N VAL H 133 " --> pdb=" O PHE H 118 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N TYR H 173 " --> pdb=" O ASN H 138 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 153 through 155 removed outlier: 4.277A pdb=" N TRP H 148 " --> pdb=" O GLN H 155 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 493 through 497 removed outlier: 5.560A pdb=" N VAL J 608 " --> pdb=" O VAL I 36 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N VAL I 38 " --> pdb=" O THR J 606 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N THR J 606 " --> pdb=" O VAL I 38 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 45 through 47 removed outlier: 3.812A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N VAL I 242 " --> pdb=" O LEU I 86 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR I 244 " --> pdb=" O MET I 84 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 129 through 130 Processing sheet with id=AD9, first strand: chain 'I' and resid 158 through 162 Processing sheet with id=AE1, first strand: chain 'I' and resid 201 through 203 removed outlier: 6.519A pdb=" N THR I 202 " --> pdb=" O TYR I 435 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 259 through 261 current: chain 'I' and resid 284 through 307 removed outlier: 5.717A pdb=" N THR I 305 " --> pdb=" O THR I 320 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N THR I 320 " --> pdb=" O THR I 305 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ILE I 307 " --> pdb=" O TYR I 318 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N TYR I 318 " --> pdb=" O ILE I 307 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 317 through 323 current: chain 'I' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 381 through 385 current: chain 'I' and resid 463 through 468 Processing sheet with id=AE3, first strand: chain 'K' and resid 5 through 7 removed outlier: 3.575A pdb=" N TYR K 7 " --> pdb=" O SER K 21 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER K 21 " --> pdb=" O TYR K 7 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N MET K 80 " --> pdb=" O LEU K 20 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N TYR K 70 " --> pdb=" O TYR K 79 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 10 through 12 current: chain 'K' and resid 46 through 51 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 57 through 59 current: chain 'K' and resid 100E through 103 Processing sheet with id=AE5, first strand: chain 'K' and resid 120 through 124 removed outlier: 3.951A pdb=" N GLY K 139 " --> pdb=" O LEU K 124 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 135 through 145 current: chain 'K' and resid 176 through 185 Processing sheet with id=AE6, first strand: chain 'K' and resid 151 through 154 Processing sheet with id=AE7, first strand: chain 'L' and resid 5 through 7 removed outlier: 3.567A pdb=" N ARG L 24 " --> pdb=" O THR L 5 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR L 22 " --> pdb=" O SER L 7 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'L' and resid 10 through 13 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 10 through 13 current: chain 'L' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 45 through 48 current: chain 'L' and resid 97 through 98 No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'L' and resid 114 through 118 removed outlier: 3.530A pdb=" N VAL L 133 " --> pdb=" O PHE L 118 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 153 through 155 removed outlier: 4.181A pdb=" N TRP L 148 " --> pdb=" O GLN L 155 " (cutoff:3.500A) 578 hydrogen bonds defined for protein. 1500 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: 6.86 Time building geometry restraints manager: 10.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 7646 1.35 - 1.47: 6103 1.47 - 1.59: 10613 1.59 - 1.71: 0 1.71 - 1.83: 187 Bond restraints: 24549 Sorted by residual: bond pdb=" C6 BMA R 3 " pdb=" O6 BMA R 3 " ideal model delta sigma weight residual 1.411 1.468 -0.057 2.00e-02 2.50e+03 8.21e+00 bond pdb=" C6 BMA d 3 " pdb=" O6 BMA d 3 " ideal model delta sigma weight residual 1.411 1.466 -0.055 2.00e-02 2.50e+03 7.65e+00 bond pdb=" C6 BMA X 3 " pdb=" O6 BMA X 3 " ideal model delta sigma weight residual 1.411 1.464 -0.053 2.00e-02 2.50e+03 7.15e+00 bond pdb=" C3 BMA R 3 " pdb=" O3 BMA R 3 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.73e+00 bond pdb=" C3 BMA d 3 " pdb=" O3 BMA d 3 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.63e+00 ... (remaining 24544 not shown) Histogram of bond angle deviations from ideal: 99.31 - 106.28: 647 106.28 - 113.25: 13757 113.25 - 120.21: 8117 120.21 - 127.18: 10492 127.18 - 134.15: 309 Bond angle restraints: 33322 Sorted by residual: angle pdb=" N HIS G 100D" pdb=" CA HIS G 100D" pdb=" C HIS G 100D" ideal model delta sigma weight residual 110.35 116.06 -5.71 1.40e+00 5.10e-01 1.66e+01 angle pdb=" N ASN A 133 " pdb=" CA ASN A 133 " pdb=" C ASN A 133 " ideal model delta sigma weight residual 110.91 115.65 -4.74 1.17e+00 7.31e-01 1.64e+01 angle pdb=" N SER B 615 " pdb=" CA SER B 615 " pdb=" CB SER B 615 " ideal model delta sigma weight residual 114.17 109.97 4.20 1.14e+00 7.69e-01 1.36e+01 angle pdb=" C LEU G 100C" pdb=" N HIS G 100D" pdb=" CA HIS G 100D" ideal model delta sigma weight residual 121.31 126.26 -4.95 1.49e+00 4.50e-01 1.10e+01 angle pdb=" N ASN I 133 " pdb=" CA ASN I 133 " pdb=" C ASN I 133 " ideal model delta sigma weight residual 110.91 114.72 -3.81 1.17e+00 7.31e-01 1.06e+01 ... (remaining 33317 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.83: 14578 21.83 - 43.67: 766 43.67 - 65.50: 108 65.50 - 87.33: 106 87.33 - 109.17: 54 Dihedral angle restraints: 15612 sinusoidal: 6993 harmonic: 8619 Sorted by residual: dihedral pdb=" CB CYS I 54 " pdb=" SG CYS I 54 " pdb=" SG CYS I 74 " pdb=" CB CYS I 74 " ideal model delta sinusoidal sigma weight residual -86.00 -171.20 85.20 1 1.00e+01 1.00e-02 8.80e+01 dihedral pdb=" CB CYS E 126 " pdb=" SG CYS E 126 " pdb=" SG CYS E 196 " pdb=" CB CYS E 196 " ideal model delta sinusoidal sigma weight residual -86.00 -131.23 45.23 1 1.00e+01 1.00e-02 2.84e+01 dihedral pdb=" CB CYS E 119 " pdb=" SG CYS E 119 " pdb=" SG CYS E 205 " pdb=" CB CYS E 205 " ideal model delta sinusoidal sigma weight residual -86.00 -131.08 45.08 1 1.00e+01 1.00e-02 2.82e+01 ... (remaining 15609 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.146: 3921 0.146 - 0.292: 28 0.292 - 0.437: 2 0.437 - 0.583: 0 0.583 - 0.729: 3 Chirality restraints: 3954 Sorted by residual: chirality pdb=" C1 NAG a 1 " pdb=" ND2 ASN I 262 " pdb=" C2 NAG a 1 " pdb=" O5 NAG a 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.67 -0.73 2.00e-01 2.50e+01 1.33e+01 chirality pdb=" C1 NAG O 1 " pdb=" ND2 ASN A 262 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.71 -0.69 2.00e-01 2.50e+01 1.18e+01 chirality pdb=" C1 NAG U 1 " pdb=" ND2 ASN E 262 " pdb=" C2 NAG U 1 " pdb=" O5 NAG U 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.74 -0.66 2.00e-01 2.50e+01 1.08e+01 ... (remaining 3951 not shown) Planarity restraints: 4182 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN L 93 " 0.010 2.00e-02 2.50e+03 2.05e-02 4.20e+00 pdb=" C ASN L 93 " -0.035 2.00e-02 2.50e+03 pdb=" O ASN L 93 " 0.013 2.00e-02 2.50e+03 pdb=" N TRP L 94 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER L 203 " 0.031 5.00e-02 4.00e+02 4.61e-02 3.40e+00 pdb=" N PRO L 204 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO L 204 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO L 204 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA K 125 " 0.030 5.00e-02 4.00e+02 4.52e-02 3.27e+00 pdb=" N PRO K 126 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO K 126 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO K 126 " 0.025 5.00e-02 4.00e+02 ... (remaining 4179 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 271 2.61 - 3.18: 21530 3.18 - 3.75: 35538 3.75 - 4.33: 49818 4.33 - 4.90: 83335 Nonbonded interactions: 190492 Sorted by model distance: nonbonded pdb=" O ASN B 625 " pdb=" OG1 THR B 627 " model vdw 2.036 2.440 nonbonded pdb=" OG1 THR I 37 " pdb=" O CYS J 604 " model vdw 2.157 2.440 nonbonded pdb=" OH TYR G 84 " pdb=" O GLN G 171 " model vdw 2.191 2.440 nonbonded pdb=" O MET A 145 " pdb=" N CYS A 157 " model vdw 2.200 2.520 nonbonded pdb=" OH TYR C 84 " pdb=" O GLN C 171 " model vdw 2.201 2.440 ... (remaining 190487 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 32 through 144 or resid 157 through 503 or resid 601 throu \ gh 602)) selection = (chain 'E' and (resid 32 through 309 or resid 314 through 503 or resid 601 throu \ gh 602)) selection = (chain 'I' and (resid 32 through 144 or resid 157 through 503 or resid 601 throu \ gh 602)) } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'Q' selection = chain 'S' selection = chain 'W' selection = chain 'Y' selection = chain 'c' } ncs_group { reference = chain 'N' selection = chain 'P' selection = chain 'T' selection = chain 'V' selection = chain 'Z' selection = chain 'b' } ncs_group { reference = chain 'O' selection = chain 'U' selection = chain 'a' } ncs_group { reference = chain 'R' selection = chain 'X' 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: 2.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.190 Construct map_model_manager: 0.020 Extract box with map and model: 8.350 Check model and map are aligned: 0.340 Set scattering table: 0.210 Process input model: 57.610 Find NCS groups from input model: 1.480 Set up NCS constraints: 0.310 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 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 0.057 24549 Z= 0.300 Angle : 0.827 8.309 33322 Z= 0.424 Chirality : 0.053 0.729 3954 Planarity : 0.004 0.046 4158 Dihedral : 16.296 109.168 9954 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.25 % Favored : 94.68 % Rotamer: Outliers : 0.12 % Allowed : 0.08 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.15), residues: 2916 helix: 1.21 (0.28), residues: 378 sheet: -1.21 (0.16), residues: 957 loop : -1.00 (0.16), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP E 427 HIS 0.011 0.001 HIS K 100D PHE 0.022 0.002 PHE A 210 TYR 0.019 0.001 TYR D 91 ARG 0.005 0.001 ARG C 66 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5832 Ramachandran restraints generated. 2916 Oldfield, 0 Emsley, 2916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5832 Ramachandran restraints generated. 2916 Oldfield, 0 Emsley, 2916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 2595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 69 time to evaluate : 2.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 626 MET cc_start: 0.7474 (mtt) cc_final: 0.7147 (mmp) REVERT: I 84 MET cc_start: 0.7647 (mpp) cc_final: 0.7404 (mpp) REVERT: K 89 MET cc_start: 0.7659 (ppp) cc_final: 0.7314 (ppp) outliers start: 3 outliers final: 3 residues processed: 72 average time/residue: 0.3819 time to fit residues: 45.8902 Evaluate side-chains 54 residues out of total 2595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 51 time to evaluate : 2.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain I residue 197 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 248 optimal weight: 9.9990 chunk 222 optimal weight: 10.0000 chunk 123 optimal weight: 20.0000 chunk 76 optimal weight: 9.9990 chunk 150 optimal weight: 7.9990 chunk 119 optimal weight: 10.0000 chunk 230 optimal weight: 30.0000 chunk 89 optimal weight: 40.0000 chunk 140 optimal weight: 6.9990 chunk 171 optimal weight: 10.0000 chunk 266 optimal weight: 9.9990 overall best weight: 8.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 HIS A 321AGLN A 422 GLN ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 GLN D 38 HIS D 137 ASN ** E 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 216 HIS E 246 GLN E 321AGLN E 422 GLN ** F 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 651 ASN G 6 GLN G 164 HIS ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 ASN ** I 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 216 HIS ** I 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 321AGLN I 357 ASN I 422 GLN ** J 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 6 GLN L 32 ASN L 92 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.120 24549 Z= 0.599 Angle : 0.948 13.890 33322 Z= 0.476 Chirality : 0.055 0.529 3954 Planarity : 0.007 0.052 4158 Dihedral : 12.442 83.078 4557 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.85 % Favored : 92.08 % Rotamer: Outliers : 0.85 % Allowed : 6.52 % Favored : 92.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.15), residues: 2916 helix: 0.94 (0.27), residues: 378 sheet: -1.37 (0.16), residues: 990 loop : -1.51 (0.15), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP I 427 HIS 0.021 0.003 HIS G 100D PHE 0.033 0.003 PHE F 519 TYR 0.035 0.003 TYR H 49 ARG 0.008 0.001 ARG G 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5832 Ramachandran restraints generated. 2916 Oldfield, 0 Emsley, 2916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5832 Ramachandran restraints generated. 2916 Oldfield, 0 Emsley, 2916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 2595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 52 time to evaluate : 2.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 626 MET cc_start: 0.7397 (mtt) cc_final: 0.7111 (mmt) REVERT: C 75 MET cc_start: 0.8563 (mtm) cc_final: 0.8362 (mtp) REVERT: E 473 MET cc_start: 0.9169 (tpp) cc_final: 0.8906 (tpp) REVERT: L 96 TRP cc_start: 0.8491 (OUTLIER) cc_final: 0.7209 (m-10) outliers start: 22 outliers final: 12 residues processed: 71 average time/residue: 0.3004 time to fit residues: 38.4817 Evaluate side-chains 64 residues out of total 2595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 51 time to evaluate : 2.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain F residue 626 MET Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 59 TYR Chi-restraints excluded: chain I residue 197 ASN Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain L residue 96 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 148 optimal weight: 10.0000 chunk 82 optimal weight: 9.9990 chunk 222 optimal weight: 10.0000 chunk 181 optimal weight: 9.9990 chunk 73 optimal weight: 1.9990 chunk 267 optimal weight: 0.0270 chunk 288 optimal weight: 20.0000 chunk 238 optimal weight: 5.9990 chunk 265 optimal weight: 4.9990 chunk 91 optimal weight: 7.9990 chunk 214 optimal weight: 10.0000 overall best weight: 4.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN D 38 HIS ** E 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 GLN F 625 ASN H 32 ASN H 38 HIS H 92 ASN ** I 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 280 ASN ** K 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.3595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 24549 Z= 0.278 Angle : 0.654 8.392 33322 Z= 0.327 Chirality : 0.047 0.465 3954 Planarity : 0.004 0.039 4158 Dihedral : 10.990 80.253 4557 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.59 % Favored : 94.38 % Rotamer: Outliers : 1.16 % Allowed : 9.07 % Favored : 89.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.16), residues: 2916 helix: 1.25 (0.28), residues: 396 sheet: -1.17 (0.16), residues: 989 loop : -1.29 (0.16), residues: 1531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 631 HIS 0.006 0.001 HIS A 374 PHE 0.021 0.002 PHE F 519 TYR 0.024 0.002 TYR L 49 ARG 0.002 0.000 ARG A 298 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5832 Ramachandran restraints generated. 2916 Oldfield, 0 Emsley, 2916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5832 Ramachandran restraints generated. 2916 Oldfield, 0 Emsley, 2916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 2595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 53 time to evaluate : 3.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 624 ASP cc_start: 0.9089 (OUTLIER) cc_final: 0.8363 (p0) REVERT: B 626 MET cc_start: 0.7390 (mtt) cc_final: 0.7107 (mmp) REVERT: E 473 MET cc_start: 0.9052 (tpp) cc_final: 0.8792 (tpp) REVERT: H 96 TRP cc_start: 0.7975 (OUTLIER) cc_final: 0.6705 (m100) REVERT: L 96 TRP cc_start: 0.8341 (OUTLIER) cc_final: 0.7141 (m-10) outliers start: 30 outliers final: 15 residues processed: 79 average time/residue: 0.3164 time to fit residues: 45.4713 Evaluate side-chains 69 residues out of total 2595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 51 time to evaluate : 2.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain H residue 96 TRP Chi-restraints excluded: chain I residue 197 ASN Chi-restraints excluded: chain I residue 373 THR Chi-restraints excluded: chain I residue 427 TRP Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain K residue 80 MET Chi-restraints excluded: chain K residue 89 MET Chi-restraints excluded: chain L residue 96 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 264 optimal weight: 8.9990 chunk 201 optimal weight: 10.0000 chunk 138 optimal weight: 0.9980 chunk 29 optimal weight: 10.0000 chunk 127 optimal weight: 9.9990 chunk 179 optimal weight: 9.9990 chunk 268 optimal weight: 9.9990 chunk 284 optimal weight: 5.9990 chunk 140 optimal weight: 8.9990 chunk 254 optimal weight: 3.9990 chunk 76 optimal weight: 9.9990 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 334 ASN ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 ASN ** I 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 658 GLN ** K 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.4575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 24549 Z= 0.385 Angle : 0.723 8.981 33322 Z= 0.362 Chirality : 0.048 0.447 3954 Planarity : 0.005 0.042 4158 Dihedral : 10.194 72.166 4557 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.16 % Favored : 91.80 % Rotamer: Outliers : 2.70 % Allowed : 10.53 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.16), residues: 2916 helix: 1.27 (0.29), residues: 396 sheet: -1.31 (0.17), residues: 936 loop : -1.33 (0.15), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP J 631 HIS 0.010 0.002 HIS G 100D PHE 0.018 0.002 PHE D 87 TYR 0.022 0.002 TYR L 49 ARG 0.006 0.000 ARG C 3 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5832 Ramachandran restraints generated. 2916 Oldfield, 0 Emsley, 2916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5832 Ramachandran restraints generated. 2916 Oldfield, 0 Emsley, 2916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 2595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 51 time to evaluate : 2.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 624 ASP cc_start: 0.9159 (OUTLIER) cc_final: 0.8385 (p0) REVERT: B 626 MET cc_start: 0.7476 (mtt) cc_final: 0.7203 (mmt) REVERT: E 473 MET cc_start: 0.9027 (tpp) cc_final: 0.8775 (tpp) REVERT: G 2 VAL cc_start: 0.9440 (OUTLIER) cc_final: 0.9097 (p) REVERT: G 102 HIS cc_start: 0.8472 (OUTLIER) cc_final: 0.8106 (t-90) REVERT: H 96 TRP cc_start: 0.8098 (OUTLIER) cc_final: 0.7052 (m-10) REVERT: J 529 THR cc_start: 0.7563 (OUTLIER) cc_final: 0.7279 (t) REVERT: K 75 MET cc_start: 0.8547 (mtm) cc_final: 0.8244 (mtp) REVERT: K 89 MET cc_start: 0.8778 (OUTLIER) cc_final: 0.8273 (tmm) REVERT: L 96 TRP cc_start: 0.8377 (OUTLIER) cc_final: 0.7243 (m-10) outliers start: 70 outliers final: 36 residues processed: 115 average time/residue: 0.2790 time to fit residues: 57.8586 Evaluate side-chains 94 residues out of total 2595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 51 time to evaluate : 2.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 427 TRP Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain E residue 494 VAL Chi-restraints excluded: chain F residue 576 LEU Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 102 HIS Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 96 TRP Chi-restraints excluded: chain I residue 42 VAL Chi-restraints excluded: chain I residue 197 ASN Chi-restraints excluded: chain I residue 236 THR Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 373 THR Chi-restraints excluded: chain I residue 427 TRP Chi-restraints excluded: chain J residue 529 THR Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 80 MET Chi-restraints excluded: chain K residue 89 MET Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 96 TRP Chi-restraints excluded: chain L residue 109 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 236 optimal weight: 8.9990 chunk 161 optimal weight: 2.9990 chunk 4 optimal weight: 20.0000 chunk 211 optimal weight: 10.0000 chunk 117 optimal weight: 9.9990 chunk 242 optimal weight: 0.0270 chunk 196 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 145 optimal weight: 8.9990 chunk 255 optimal weight: 0.0670 chunk 71 optimal weight: 30.0000 overall best weight: 3.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 651 ASN H 38 HIS ** I 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 100DHIS ** K 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.4770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 24549 Z= 0.257 Angle : 0.619 9.855 33322 Z= 0.308 Chirality : 0.045 0.429 3954 Planarity : 0.004 0.038 4158 Dihedral : 9.695 70.010 4557 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 2.16 % Allowed : 11.84 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.16), residues: 2916 helix: 1.50 (0.29), residues: 396 sheet: -1.15 (0.17), residues: 948 loop : -1.23 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 631 HIS 0.005 0.001 HIS A 374 PHE 0.013 0.001 PHE L 87 TYR 0.025 0.001 TYR L 49 ARG 0.002 0.000 ARG E 273 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5832 Ramachandran restraints generated. 2916 Oldfield, 0 Emsley, 2916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5832 Ramachandran restraints generated. 2916 Oldfield, 0 Emsley, 2916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 2595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 51 time to evaluate : 2.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 624 ASP cc_start: 0.9093 (OUTLIER) cc_final: 0.8512 (p0) REVERT: B 626 MET cc_start: 0.7440 (mtt) cc_final: 0.7101 (mpp) REVERT: H 96 TRP cc_start: 0.8086 (OUTLIER) cc_final: 0.7174 (m100) REVERT: I 143 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8324 (tp30) REVERT: K 75 MET cc_start: 0.8568 (mtm) cc_final: 0.8333 (mtp) REVERT: L 48 ILE cc_start: 0.8344 (OUTLIER) cc_final: 0.8027 (mt) REVERT: L 96 TRP cc_start: 0.8342 (OUTLIER) cc_final: 0.7210 (m-10) outliers start: 56 outliers final: 29 residues processed: 101 average time/residue: 0.2949 time to fit residues: 53.2675 Evaluate side-chains 85 residues out of total 2595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 51 time to evaluate : 2.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 427 TRP Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 482 TYR Chi-restraints excluded: chain F residue 651 ASN Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain H residue 96 TRP Chi-restraints excluded: chain I residue 143 GLU Chi-restraints excluded: chain I residue 197 ASN Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 260 LEU Chi-restraints excluded: chain I residue 261 LEU Chi-restraints excluded: chain I residue 373 THR Chi-restraints excluded: chain I residue 427 TRP Chi-restraints excluded: chain I residue 430 VAL Chi-restraints excluded: chain J residue 576 LEU Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain K residue 80 MET Chi-restraints excluded: chain K residue 89 MET Chi-restraints excluded: chain K residue 197 ASN Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 96 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 95 optimal weight: 10.0000 chunk 255 optimal weight: 0.0770 chunk 56 optimal weight: 10.0000 chunk 166 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 chunk 284 optimal weight: 1.9990 chunk 236 optimal weight: 1.9990 chunk 131 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 chunk 94 optimal weight: 5.9990 chunk 149 optimal weight: 8.9990 overall best weight: 2.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 653 GLN ** K 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.4889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 24549 Z= 0.171 Angle : 0.572 8.146 33322 Z= 0.283 Chirality : 0.044 0.407 3954 Planarity : 0.004 0.040 4158 Dihedral : 9.142 66.712 4557 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 1.89 % Allowed : 11.81 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.16), residues: 2916 helix: 1.67 (0.29), residues: 396 sheet: -0.95 (0.17), residues: 945 loop : -1.11 (0.16), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 628 HIS 0.006 0.001 HIS I 374 PHE 0.009 0.001 PHE H 71 TYR 0.022 0.001 TYR L 49 ARG 0.002 0.000 ARG A 456 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5832 Ramachandran restraints generated. 2916 Oldfield, 0 Emsley, 2916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5832 Ramachandran restraints generated. 2916 Oldfield, 0 Emsley, 2916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 2595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 52 time to evaluate : 2.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 259 LEU cc_start: 0.7420 (OUTLIER) cc_final: 0.7160 (pp) REVERT: B 624 ASP cc_start: 0.9079 (OUTLIER) cc_final: 0.8286 (p0) REVERT: B 626 MET cc_start: 0.7393 (mtt) cc_final: 0.7081 (mpp) REVERT: H 96 TRP cc_start: 0.8012 (OUTLIER) cc_final: 0.7252 (m100) REVERT: K 75 MET cc_start: 0.8576 (mtm) cc_final: 0.8355 (mtp) REVERT: K 89 MET cc_start: 0.8704 (OUTLIER) cc_final: 0.8286 (tmm) REVERT: L 48 ILE cc_start: 0.8288 (OUTLIER) cc_final: 0.7993 (mt) REVERT: L 96 TRP cc_start: 0.8263 (OUTLIER) cc_final: 0.7120 (m-10) outliers start: 49 outliers final: 34 residues processed: 93 average time/residue: 0.2982 time to fit residues: 49.9475 Evaluate side-chains 90 residues out of total 2595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 50 time to evaluate : 2.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 427 TRP Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 482 TYR Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain H residue 96 TRP Chi-restraints excluded: chain I residue 42 VAL Chi-restraints excluded: chain I residue 197 ASN Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 260 LEU Chi-restraints excluded: chain I residue 261 LEU Chi-restraints excluded: chain I residue 315 GLN Chi-restraints excluded: chain I residue 373 THR Chi-restraints excluded: chain I residue 427 TRP Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 80 MET Chi-restraints excluded: chain K residue 89 MET Chi-restraints excluded: chain K residue 197 ASN Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 96 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 274 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 chunk 162 optimal weight: 5.9990 chunk 207 optimal weight: 7.9990 chunk 160 optimal weight: 3.9990 chunk 239 optimal weight: 10.0000 chunk 158 optimal weight: 0.9980 chunk 283 optimal weight: 2.9990 chunk 177 optimal weight: 0.9990 chunk 172 optimal weight: 30.0000 chunk 130 optimal weight: 9.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.5018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 24549 Z= 0.211 Angle : 0.578 8.138 33322 Z= 0.285 Chirality : 0.044 0.411 3954 Planarity : 0.004 0.037 4158 Dihedral : 9.064 65.221 4557 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 2.62 % Allowed : 11.84 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % 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: -0.99 (0.16), residues: 2916 helix: 1.78 (0.29), residues: 396 sheet: -0.91 (0.17), residues: 903 loop : -1.11 (0.15), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 628 HIS 0.021 0.001 HIS A 72 PHE 0.011 0.001 PHE D 87 TYR 0.022 0.001 TYR L 49 ARG 0.002 0.000 ARG A 298 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5832 Ramachandran restraints generated. 2916 Oldfield, 0 Emsley, 2916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5832 Ramachandran restraints generated. 2916 Oldfield, 0 Emsley, 2916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 2595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 51 time to evaluate : 2.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 259 LEU cc_start: 0.7459 (OUTLIER) cc_final: 0.7217 (pp) REVERT: B 624 ASP cc_start: 0.9090 (OUTLIER) cc_final: 0.8292 (p0) REVERT: B 626 MET cc_start: 0.7375 (mtt) cc_final: 0.7042 (mpp) REVERT: H 96 TRP cc_start: 0.8090 (OUTLIER) cc_final: 0.7264 (m100) REVERT: K 75 MET cc_start: 0.8595 (mtm) cc_final: 0.8331 (mtp) REVERT: L 96 TRP cc_start: 0.8308 (OUTLIER) cc_final: 0.7173 (m-10) outliers start: 68 outliers final: 50 residues processed: 110 average time/residue: 0.2938 time to fit residues: 58.2503 Evaluate side-chains 104 residues out of total 2595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 50 time to evaluate : 2.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 427 TRP Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 482 TYR Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 576 LEU Chi-restraints excluded: chain F residue 626 MET Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 96 TRP Chi-restraints excluded: chain I residue 42 VAL Chi-restraints excluded: chain I residue 197 ASN Chi-restraints excluded: chain I residue 236 THR Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 260 LEU Chi-restraints excluded: chain I residue 261 LEU Chi-restraints excluded: chain I residue 315 GLN Chi-restraints excluded: chain I residue 373 THR Chi-restraints excluded: chain I residue 427 TRP Chi-restraints excluded: chain I residue 430 VAL Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 80 MET Chi-restraints excluded: chain K residue 89 MET Chi-restraints excluded: chain K residue 197 ASN Chi-restraints excluded: chain L residue 96 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 175 optimal weight: 2.9990 chunk 113 optimal weight: 8.9990 chunk 169 optimal weight: 20.0000 chunk 85 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 54 optimal weight: 9.9990 chunk 180 optimal weight: 9.9990 chunk 193 optimal weight: 30.0000 chunk 140 optimal weight: 2.9990 chunk 26 optimal weight: 8.9990 chunk 222 optimal weight: 20.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 ASN ** E 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.5399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 24549 Z= 0.338 Angle : 0.657 8.895 33322 Z= 0.325 Chirality : 0.046 0.423 3954 Planarity : 0.004 0.048 4158 Dihedral : 9.388 64.275 4557 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 2.51 % Allowed : 12.42 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.16), residues: 2916 helix: 1.69 (0.29), residues: 393 sheet: -0.94 (0.17), residues: 914 loop : -1.23 (0.15), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 628 HIS 0.008 0.002 HIS G 100D PHE 0.018 0.002 PHE D 87 TYR 0.023 0.002 TYR L 49 ARG 0.003 0.000 ARG E 273 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5832 Ramachandran restraints generated. 2916 Oldfield, 0 Emsley, 2916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5832 Ramachandran restraints generated. 2916 Oldfield, 0 Emsley, 2916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 2595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 50 time to evaluate : 2.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 259 LEU cc_start: 0.7528 (OUTLIER) cc_final: 0.7160 (pp) REVERT: B 624 ASP cc_start: 0.9121 (OUTLIER) cc_final: 0.8320 (p0) REVERT: B 626 MET cc_start: 0.7367 (mtt) cc_final: 0.7023 (mpp) REVERT: H 96 TRP cc_start: 0.8158 (OUTLIER) cc_final: 0.7383 (m-10) REVERT: K 75 MET cc_start: 0.8646 (mtm) cc_final: 0.8305 (mtp) REVERT: L 96 TRP cc_start: 0.8348 (OUTLIER) cc_final: 0.7203 (m-10) outliers start: 65 outliers final: 50 residues processed: 106 average time/residue: 0.2877 time to fit residues: 55.1668 Evaluate side-chains 104 residues out of total 2595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 50 time to evaluate : 2.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 427 TRP Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 482 TYR Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 576 LEU Chi-restraints excluded: chain F residue 626 MET Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 96 TRP Chi-restraints excluded: chain I residue 42 VAL Chi-restraints excluded: chain I residue 197 ASN Chi-restraints excluded: chain I residue 236 THR Chi-restraints excluded: chain I residue 260 LEU Chi-restraints excluded: chain I residue 261 LEU Chi-restraints excluded: chain I residue 315 GLN Chi-restraints excluded: chain I residue 373 THR Chi-restraints excluded: chain I residue 427 TRP Chi-restraints excluded: chain I residue 430 VAL Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 80 MET Chi-restraints excluded: chain K residue 89 MET Chi-restraints excluded: chain L residue 96 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 257 optimal weight: 0.7980 chunk 271 optimal weight: 20.0000 chunk 247 optimal weight: 0.0970 chunk 264 optimal weight: 7.9990 chunk 158 optimal weight: 0.9990 chunk 115 optimal weight: 5.9990 chunk 207 optimal weight: 9.9990 chunk 81 optimal weight: 1.9990 chunk 238 optimal weight: 7.9990 chunk 249 optimal weight: 9.9990 chunk 263 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 ASN ** I 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 540 GLN ** K 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.5419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 24549 Z= 0.143 Angle : 0.562 9.272 33322 Z= 0.276 Chirality : 0.044 0.391 3954 Planarity : 0.004 0.038 4158 Dihedral : 8.783 61.787 4557 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 1.50 % Allowed : 13.00 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % 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: -0.91 (0.16), residues: 2916 helix: 1.78 (0.29), residues: 396 sheet: -0.76 (0.17), residues: 900 loop : -1.10 (0.15), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 96 HIS 0.036 0.001 HIS A 72 PHE 0.009 0.001 PHE L 98 TYR 0.022 0.001 TYR L 49 ARG 0.002 0.000 ARG F 588 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5832 Ramachandran restraints generated. 2916 Oldfield, 0 Emsley, 2916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5832 Ramachandran restraints generated. 2916 Oldfield, 0 Emsley, 2916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 2595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 53 time to evaluate : 2.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 259 LEU cc_start: 0.7465 (OUTLIER) cc_final: 0.7137 (pp) REVERT: B 626 MET cc_start: 0.7274 (mtt) cc_final: 0.6967 (mpp) REVERT: K 75 MET cc_start: 0.8620 (mtm) cc_final: 0.8379 (mtp) REVERT: K 89 MET cc_start: 0.8699 (OUTLIER) cc_final: 0.8222 (tmm) outliers start: 39 outliers final: 32 residues processed: 85 average time/residue: 0.2999 time to fit residues: 45.7780 Evaluate side-chains 84 residues out of total 2595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 50 time to evaluate : 2.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 427 TRP Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain E residue 482 TYR Chi-restraints excluded: chain F residue 626 MET Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain I residue 42 VAL Chi-restraints excluded: chain I residue 197 ASN Chi-restraints excluded: chain I residue 236 THR Chi-restraints excluded: chain I residue 260 LEU Chi-restraints excluded: chain I residue 261 LEU Chi-restraints excluded: chain I residue 315 GLN Chi-restraints excluded: chain I residue 427 TRP Chi-restraints excluded: chain K residue 89 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 173 optimal weight: 9.9990 chunk 279 optimal weight: 10.0000 chunk 170 optimal weight: 2.9990 chunk 132 optimal weight: 30.0000 chunk 194 optimal weight: 30.0000 chunk 292 optimal weight: 8.9990 chunk 269 optimal weight: 6.9990 chunk 233 optimal weight: 0.0170 chunk 24 optimal weight: 10.0000 chunk 180 optimal weight: 10.0000 chunk 143 optimal weight: 9.9990 overall best weight: 5.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.5668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 24549 Z= 0.368 Angle : 0.664 8.843 33322 Z= 0.328 Chirality : 0.046 0.419 3954 Planarity : 0.004 0.044 4158 Dihedral : 9.262 61.715 4557 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 1.85 % Allowed : 12.85 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.16), residues: 2916 helix: 1.74 (0.29), residues: 393 sheet: -0.91 (0.18), residues: 914 loop : -1.18 (0.15), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 96 HIS 0.008 0.002 HIS G 100D PHE 0.020 0.002 PHE L 87 TYR 0.024 0.002 TYR L 49 ARG 0.003 0.000 ARG D 24 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5832 Ramachandran restraints generated. 2916 Oldfield, 0 Emsley, 2916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5832 Ramachandran restraints generated. 2916 Oldfield, 0 Emsley, 2916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 2595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 50 time to evaluate : 2.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 259 LEU cc_start: 0.7518 (OUTLIER) cc_final: 0.7159 (pp) REVERT: B 624 ASP cc_start: 0.9129 (OUTLIER) cc_final: 0.8322 (p0) REVERT: B 626 MET cc_start: 0.7314 (mtt) cc_final: 0.6976 (mpp) REVERT: K 75 MET cc_start: 0.8625 (mtm) cc_final: 0.8273 (mtp) outliers start: 48 outliers final: 42 residues processed: 91 average time/residue: 0.2886 time to fit residues: 47.7787 Evaluate side-chains 94 residues out of total 2595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 50 time to evaluate : 2.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 427 TRP Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain E residue 482 TYR Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 576 LEU Chi-restraints excluded: chain F residue 626 MET Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain I residue 197 ASN Chi-restraints excluded: chain I residue 236 THR Chi-restraints excluded: chain I residue 260 LEU Chi-restraints excluded: chain I residue 261 LEU Chi-restraints excluded: chain I residue 315 GLN Chi-restraints excluded: chain I residue 427 TRP Chi-restraints excluded: chain I residue 430 VAL Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 80 MET Chi-restraints excluded: chain K residue 89 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 185 optimal weight: 0.9990 chunk 248 optimal weight: 7.9990 chunk 71 optimal weight: 30.0000 chunk 215 optimal weight: 10.0000 chunk 34 optimal weight: 20.0000 chunk 64 optimal weight: 0.8980 chunk 233 optimal weight: 0.0010 chunk 97 optimal weight: 1.9990 chunk 239 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 43 optimal weight: 9.9990 overall best weight: 1.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.041279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.031840 restraints weight = 217707.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.032606 restraints weight = 117213.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.033061 restraints weight = 82643.902| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.5688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 24549 Z= 0.157 Angle : 0.563 8.938 33322 Z= 0.276 Chirality : 0.044 0.393 3954 Planarity : 0.004 0.040 4158 Dihedral : 8.774 59.858 4557 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 1.62 % Allowed : 13.00 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % 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: -0.88 (0.16), residues: 2916 helix: 1.85 (0.29), residues: 393 sheet: -0.77 (0.18), residues: 901 loop : -1.08 (0.15), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 628 HIS 0.005 0.001 HIS I 374 PHE 0.007 0.001 PHE L 98 TYR 0.023 0.001 TYR L 49 ARG 0.002 0.000 ARG B 588 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3046.28 seconds wall clock time: 58 minutes 14.90 seconds (3494.90 seconds total)