Starting phenix.real_space_refine on Mon Mar 18 08:04:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6orn_20175/03_2024/6orn_20175.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6orn_20175/03_2024/6orn_20175.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6orn_20175/03_2024/6orn_20175.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6orn_20175/03_2024/6orn_20175.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6orn_20175/03_2024/6orn_20175.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6orn_20175/03_2024/6orn_20175.pdb" } resolution = 4.05 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= 0.012 sd= 0.158 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 123 5.16 5 C 12729 2.51 5 N 3402 2.21 5 O 4084 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 327": "NH1" <-> "NH2" Residue "G ARG 456": "NH1" <-> "NH2" Residue "G ARG 469": "NH1" <-> "NH2" Residue "K PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 327": "NH1" <-> "NH2" Residue "K PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 456": "NH1" <-> "NH2" Residue "K ARG 469": "NH1" <-> "NH2" Residue "R PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 327": "NH1" <-> "NH2" Residue "R ARG 456": "NH1" <-> "NH2" Residue "R ARG 469": "NH1" <-> "NH2" Residue "A ARG 96": "NH1" <-> "NH2" Residue "F ARG 96": "NH1" <-> "NH2" Residue "O ARG 96": "NH1" <-> "NH2" Residue "B ARG 9": "NH1" <-> "NH2" Residue "B ARG 20": "NH1" <-> "NH2" Residue "B ARG 70": "NH1" <-> "NH2" Residue "B ARG 94": "NH1" <-> "NH2" Residue "I ARG 9": "NH1" <-> "NH2" Residue "I ARG 20": "NH1" <-> "NH2" Residue "I ARG 70": "NH1" <-> "NH2" Residue "I ARG 94": "NH1" <-> "NH2" Residue "P ARG 9": "NH1" <-> "NH2" Residue "P ARG 20": "NH1" <-> "NH2" Residue "P ARG 70": "NH1" <-> "NH2" Residue "P ARG 94": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 20338 Number of models: 1 Model: "" Number of chains: 39 Chain: "C" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "G" Number of atoms: 3485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3485 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 22, 'TRANS': 419} Chain breaks: 4 Chain: "J" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "K" Number of atoms: 3485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3485 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 22, 'TRANS': 419} Chain breaks: 4 Chain: "Q" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "R" Number of atoms: 3485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3485 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 22, 'TRANS': 419} Chain breaks: 4 Chain: "A" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1041 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 5, 'TRANS': 127} Chain: "F" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1041 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 5, 'TRANS': 127} Chain: "O" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1041 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 5, 'TRANS': 127} Chain: "B" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "I" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "P" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} 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: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "L" 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: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "V" 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: "W" 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: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 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: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 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: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "J" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "Q" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 10.76, per 1000 atoms: 0.53 Number of scatterers: 20338 At special positions: 0 Unit cell: (150.78, 157.96, 159.396, 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 123 16.00 O 4084 8.00 N 3402 7.00 C 12729 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 605 " - pdb=" SG CYS G 501 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.03 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.05 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.02 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.03 Simple disulfide: pdb=" SG CYS J 605 " - pdb=" SG CYS K 501 " distance=2.03 Simple disulfide: pdb=" SG CYS K 54 " - pdb=" SG CYS K 74 " distance=2.03 Simple disulfide: pdb=" SG CYS K 119 " - pdb=" SG CYS K 205 " distance=2.03 Simple disulfide: pdb=" SG CYS K 126 " - pdb=" SG CYS K 196 " distance=2.03 Simple disulfide: pdb=" SG CYS K 131 " - pdb=" SG CYS K 157 " distance=2.03 Simple disulfide: pdb=" SG CYS K 218 " - pdb=" SG CYS K 247 " distance=2.06 Simple disulfide: pdb=" SG CYS K 228 " - pdb=" SG CYS K 239 " distance=2.03 Simple disulfide: pdb=" SG CYS K 296 " - pdb=" SG CYS K 331 " distance=2.03 Simple disulfide: pdb=" SG CYS K 378 " - pdb=" SG CYS K 445 " distance=2.02 Simple disulfide: pdb=" SG CYS K 385 " - pdb=" SG CYS K 418 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 598 " - pdb=" SG CYS Q 604 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 605 " - pdb=" SG CYS R 501 " distance=2.03 Simple disulfide: pdb=" SG CYS R 54 " - pdb=" SG CYS R 74 " distance=2.03 Simple disulfide: pdb=" SG CYS R 119 " - pdb=" SG CYS R 205 " distance=2.03 Simple disulfide: pdb=" SG CYS R 126 " - pdb=" SG CYS R 196 " distance=2.03 Simple disulfide: pdb=" SG CYS R 131 " - pdb=" SG CYS R 157 " distance=2.03 Simple disulfide: pdb=" SG CYS R 218 " - pdb=" SG CYS R 247 " distance=2.06 Simple disulfide: pdb=" SG CYS R 228 " - pdb=" SG CYS R 239 " distance=2.03 Simple disulfide: pdb=" SG CYS R 296 " - pdb=" SG CYS R 331 " distance=2.03 Simple disulfide: pdb=" SG CYS R 378 " - pdb=" SG CYS R 445 " distance=2.02 Simple disulfide: pdb=" SG CYS R 385 " - pdb=" SG CYS R 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 92 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN D 4 " - " MAN D 5 " " MAN H 4 " - " MAN H 5 " " MAN U 4 " - " MAN U 5 " " MAN W 4 " - " MAN W 5 " " MAN b 4 " - " MAN b 5 " ALPHA1-3 " BMA D 3 " - " MAN D 4 " " BMA H 3 " - " MAN H 4 " " MAN H 6 " - " MAN H 7 " " BMA U 3 " - " MAN U 4 " " MAN U 6 " - " MAN U 7 " " BMA W 3 " - " MAN W 4 " " BMA b 3 " - " MAN b 4 " " BMA e 3 " - " MAN e 6 " ALPHA1-6 " BMA D 3 " - " MAN D 6 " " BMA H 3 " - " MAN H 6 " " BMA U 3 " - " MAN U 6 " " BMA W 3 " - " MAN W 6 " " BMA b 3 " - " MAN b 6 " " BMA e 3 " - " MAN e 4 " " MAN e 4 " - " MAN e 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " NAG-ASN " NAG C 701 " - " ASN C 637 " " NAG C 702 " - " ASN C 618 " " NAG C 703 " - " ASN C 611 " " NAG D 1 " - " ASN G 262 " " NAG E 1 " - " ASN G 276 " " NAG G 601 " - " ASN G 88 " " NAG G 602 " - " ASN G 160 " " NAG G 603 " - " ASN G 197 " " NAG G 604 " - " ASN G 234 " " NAG G 614 " - " ASN G 295 " " NAG G 615 " - " ASN G 301 " " NAG G 623 " - " ASN G 339 " " NAG G 624 " - " ASN G 355 " " NAG G 628 " - " ASN G 392 " " NAG H 1 " - " ASN G 332 " " NAG J 701 " - " ASN J 611 " " NAG J 702 " - " ASN J 618 " " NAG J 703 " - " ASN J 637 " " NAG K 601 " - " ASN K 448 " " NAG K 608 " - " ASN K 234 " " NAG K 619 " - " ASN K 295 " " NAG K 620 " - " ASN K 301 " " NAG K 627 " - " ASN K 339 " " NAG K 628 " - " ASN K 355 " " NAG K 631 " - " ASN K 392 " " NAG L 1 " - " ASN G 386 " " NAG M 1 " - " ASN G 448 " " NAG N 1 " - " ASN K 88 " " NAG Q 701 " - " ASN Q 611 " " NAG Q 702 " - " ASN Q 618 " " NAG Q 703 " - " ASN Q 637 " " NAG R 607 " - " ASN R 234 " " NAG R 616 " - " ASN R 295 " " NAG R 625 " - " ASN R 339 " " NAG R 626 " - " ASN R 355 " " NAG R 629 " - " ASN R 392 " " NAG S 1 " - " ASN K 160 " " NAG T 1 " - " ASN K 197 " " NAG U 1 " - " ASN K 262 " " NAG V 1 " - " ASN K 276 " " NAG W 1 " - " ASN K 332 " " NAG X 1 " - " ASN K 386 " " NAG Y 1 " - " ASN R 88 " " NAG Z 1 " - " ASN R 160 " " NAG a 1 " - " ASN R 197 " " NAG b 1 " - " ASN R 262 " " NAG c 1 " - " ASN R 276 " " NAG d 1 " - " ASN R 301 " " NAG e 1 " - " ASN R 332 " " NAG f 1 " - " ASN R 386 " " NAG g 1 " - " ASN R 448 " Time building additional restraints: 9.85 Conformation dependent library (CDL) restraints added in 3.7 seconds 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4476 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 41 sheets defined 16.5% alpha, 25.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.35 Creating SS restraints... Processing helix chain 'C' and resid 529 through 534 Processing helix chain 'C' and resid 537 through 543 removed outlier: 3.677A pdb=" N ALA C 541 " --> pdb=" O LEU C 537 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASN C 543 " --> pdb=" O VAL C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 596 removed outlier: 3.604A pdb=" N ALA C 578 " --> pdb=" O LYS C 574 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ARG C 579 " --> pdb=" O GLN C 575 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU C 581 " --> pdb=" O GLN C 577 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N VAL C 583 " --> pdb=" O ARG C 579 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU C 584 " --> pdb=" O VAL C 580 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N HIS C 585 " --> pdb=" O LEU C 581 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASP C 589 " --> pdb=" O HIS C 585 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TRP C 596 " --> pdb=" O LEU C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 636 removed outlier: 4.253A pdb=" N LYS C 633 " --> pdb=" O LEU C 629 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N GLU C 634 " --> pdb=" O GLN C 630 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE C 635 " --> pdb=" O TRP C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 638 through 662 removed outlier: 3.631A pdb=" N GLU C 647 " --> pdb=" O TYR C 643 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER C 649 " --> pdb=" O LEU C 645 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN C 650 " --> pdb=" O LEU C 646 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ASN C 651 " --> pdb=" O GLU C 647 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLN C 652 " --> pdb=" O GLU C 648 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASN C 656 " --> pdb=" O GLN C 652 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLU C 657 " --> pdb=" O GLN C 653 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLN C 658 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASP C 659 " --> pdb=" O LYS C 655 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 115 removed outlier: 3.631A pdb=" N GLU G 106 " --> pdb=" O GLU G 102 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ILE G 109 " --> pdb=" O HIS G 105 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU G 111 " --> pdb=" O ASP G 107 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER G 115 " --> pdb=" O LEU G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 179 No H-bonds generated for 'chain 'G' and resid 177 through 179' Processing helix chain 'G' and resid 335 through 350 removed outlier: 3.506A pdb=" N LYS G 347 " --> pdb=" O GLY G 343 " (cutoff:3.500A) Processing helix chain 'G' and resid 351 through 353 No H-bonds generated for 'chain 'G' and resid 351 through 353' Processing helix chain 'G' and resid 368 through 373 removed outlier: 3.583A pdb=" N THR G 373 " --> pdb=" O LEU G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 387 through 391 removed outlier: 3.694A pdb=" N LEU G 390 " --> pdb=" O THR G 387 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N PHE G 391 " --> pdb=" O SER G 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 387 through 391' Processing helix chain 'G' and resid 425 through 429 removed outlier: 4.044A pdb=" N GLN G 428 " --> pdb=" O ASN G 425 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ARG G 429 " --> pdb=" O MET G 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 425 through 429' Processing helix chain 'G' and resid 476 through 481 Processing helix chain 'J' and resid 529 through 534 Processing helix chain 'J' and resid 537 through 543 removed outlier: 3.676A pdb=" N ALA J 541 " --> pdb=" O LEU J 537 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASN J 543 " --> pdb=" O VAL J 539 " (cutoff:3.500A) Processing helix chain 'J' and resid 573 through 596 removed outlier: 3.604A pdb=" N ALA J 578 " --> pdb=" O LYS J 574 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ARG J 579 " --> pdb=" O GLN J 575 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU J 581 " --> pdb=" O GLN J 577 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N VAL J 583 " --> pdb=" O ARG J 579 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU J 584 " --> pdb=" O VAL J 580 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N HIS J 585 " --> pdb=" O LEU J 581 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASP J 589 " --> pdb=" O HIS J 585 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TRP J 596 " --> pdb=" O LEU J 592 " (cutoff:3.500A) Processing helix chain 'J' and resid 627 through 636 removed outlier: 4.253A pdb=" N LYS J 633 " --> pdb=" O LEU J 629 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N GLU J 634 " --> pdb=" O GLN J 630 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE J 635 " --> pdb=" O TRP J 631 " (cutoff:3.500A) Processing helix chain 'J' and resid 638 through 662 removed outlier: 3.632A pdb=" N GLU J 647 " --> pdb=" O TYR J 643 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER J 649 " --> pdb=" O LEU J 645 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN J 650 " --> pdb=" O LEU J 646 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ASN J 651 " --> pdb=" O GLU J 647 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLN J 652 " --> pdb=" O GLU J 648 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASN J 656 " --> pdb=" O GLN J 652 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLU J 657 " --> pdb=" O GLN J 653 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLN J 658 " --> pdb=" O GLU J 654 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASP J 659 " --> pdb=" O LYS J 655 " (cutoff:3.500A) Processing helix chain 'K' and resid 99 through 115 removed outlier: 3.559A pdb=" N GLU K 106 " --> pdb=" O GLU K 102 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE K 109 " --> pdb=" O HIS K 105 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU K 111 " --> pdb=" O ASP K 107 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER K 115 " --> pdb=" O LEU K 111 " (cutoff:3.500A) Processing helix chain 'K' and resid 177 through 179 No H-bonds generated for 'chain 'K' and resid 177 through 179' Processing helix chain 'K' and resid 335 through 350 removed outlier: 3.610A pdb=" N LYS K 347 " --> pdb=" O GLY K 343 " (cutoff:3.500A) Processing helix chain 'K' and resid 351 through 353 No H-bonds generated for 'chain 'K' and resid 351 through 353' Processing helix chain 'K' and resid 368 through 373 removed outlier: 3.668A pdb=" N THR K 373 " --> pdb=" O LEU K 369 " (cutoff:3.500A) Processing helix chain 'K' and resid 387 through 391 removed outlier: 3.759A pdb=" N LEU K 390 " --> pdb=" O THR K 387 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N PHE K 391 " --> pdb=" O SER K 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 387 through 391' Processing helix chain 'K' and resid 425 through 429 removed outlier: 4.056A pdb=" N GLN K 428 " --> pdb=" O ASN K 425 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ARG K 429 " --> pdb=" O MET K 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 425 through 429' Processing helix chain 'K' and resid 476 through 481 Processing helix chain 'Q' and resid 529 through 534 Processing helix chain 'Q' and resid 537 through 543 removed outlier: 3.676A pdb=" N ALA Q 541 " --> pdb=" O LEU Q 537 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASN Q 543 " --> pdb=" O VAL Q 539 " (cutoff:3.500A) Processing helix chain 'Q' and resid 573 through 596 removed outlier: 3.604A pdb=" N ALA Q 578 " --> pdb=" O LYS Q 574 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ARG Q 579 " --> pdb=" O GLN Q 575 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU Q 581 " --> pdb=" O GLN Q 577 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N VAL Q 583 " --> pdb=" O ARG Q 579 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU Q 584 " --> pdb=" O VAL Q 580 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N HIS Q 585 " --> pdb=" O LEU Q 581 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASP Q 589 " --> pdb=" O HIS Q 585 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TRP Q 596 " --> pdb=" O LEU Q 592 " (cutoff:3.500A) Processing helix chain 'Q' and resid 627 through 636 removed outlier: 4.253A pdb=" N LYS Q 633 " --> pdb=" O LEU Q 629 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N GLU Q 634 " --> pdb=" O GLN Q 630 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ILE Q 635 " --> pdb=" O TRP Q 631 " (cutoff:3.500A) Processing helix chain 'Q' and resid 638 through 662 removed outlier: 3.633A pdb=" N GLU Q 647 " --> pdb=" O TYR Q 643 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER Q 649 " --> pdb=" O LEU Q 645 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN Q 650 " --> pdb=" O LEU Q 646 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ASN Q 651 " --> pdb=" O GLU Q 647 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLN Q 652 " --> pdb=" O GLU Q 648 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASN Q 656 " --> pdb=" O GLN Q 652 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLU Q 657 " --> pdb=" O GLN Q 653 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLN Q 658 " --> pdb=" O GLU Q 654 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP Q 659 " --> pdb=" O LYS Q 655 " (cutoff:3.500A) Processing helix chain 'R' and resid 99 through 115 removed outlier: 3.561A pdb=" N GLN R 103 " --> pdb=" O ASN R 99 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU R 106 " --> pdb=" O GLU R 102 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE R 109 " --> pdb=" O HIS R 105 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU R 111 " --> pdb=" O ASP R 107 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLN R 114 " --> pdb=" O SER R 110 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SER R 115 " --> pdb=" O LEU R 111 " (cutoff:3.500A) Processing helix chain 'R' and resid 177 through 179 No H-bonds generated for 'chain 'R' and resid 177 through 179' Processing helix chain 'R' and resid 335 through 350 removed outlier: 3.501A pdb=" N LYS R 347 " --> pdb=" O GLY R 343 " (cutoff:3.500A) Processing helix chain 'R' and resid 351 through 353 No H-bonds generated for 'chain 'R' and resid 351 through 353' Processing helix chain 'R' and resid 368 through 373 removed outlier: 3.525A pdb=" N THR R 373 " --> pdb=" O LEU R 369 " (cutoff:3.500A) Processing helix chain 'R' and resid 387 through 391 removed outlier: 3.633A pdb=" N LEU R 390 " --> pdb=" O THR R 387 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE R 391 " --> pdb=" O SER R 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 387 through 391' Processing helix chain 'R' and resid 425 through 429 removed outlier: 4.164A pdb=" N GLN R 428 " --> pdb=" O ASN R 425 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ARG R 429 " --> pdb=" O MET R 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 425 through 429' Processing helix chain 'R' and resid 476 through 481 Processing sheet with id=AA1, first strand: chain 'G' and resid 35 through 40 Processing sheet with id=AA2, first strand: chain 'G' and resid 45 through 46 removed outlier: 3.801A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 91 through 94 removed outlier: 3.838A pdb=" N GLU G 91 " --> pdb=" O CYS G 239 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY G 237 " --> pdb=" O PHE G 93 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 169 through 176 removed outlier: 3.604A pdb=" N VAL G 172 " --> pdb=" O PHE G 159 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE G 159 " --> pdb=" O VAL G 172 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N CYS G 131 " --> pdb=" O LYS G 189 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LYS G 189 " --> pdb=" O CYS G 131 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 199 through 203 removed outlier: 6.384A pdb=" N ALA G 200 " --> pdb=" O ALA G 433 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N TYR G 435 " --> pdb=" O ALA G 200 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N THR G 202 " --> pdb=" O TYR G 435 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'G' and resid 271 through 273 Processing sheet with id=AA7, first strand: chain 'G' and resid 384 through 385 removed outlier: 4.699A pdb=" N SER G 334 " --> pdb=" O GLN G 293 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N GLN G 293 " --> pdb=" O SER G 334 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N VAL G 292 " --> pdb=" O ILE G 449 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE G 294 " --> pdb=" O SER G 447 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE G 443 " --> pdb=" O ARG G 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 304 through 307 removed outlier: 3.753A pdb=" N LYS G 305 " --> pdb=" O TYR G 319 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR G 319 " --> pdb=" O LYS G 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 377 through 378 removed outlier: 3.590A pdb=" N GLU G 381 " --> pdb=" O CYS G 378 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 35 through 40 Processing sheet with id=AB2, first strand: chain 'K' and resid 45 through 46 removed outlier: 3.693A pdb=" N ILE K 225 " --> pdb=" O VAL K 245 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 91 through 94 removed outlier: 3.758A pdb=" N GLU K 91 " --> pdb=" O CYS K 239 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY K 237 " --> pdb=" O PHE K 93 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 169 through 176 removed outlier: 3.533A pdb=" N VAL K 172 " --> pdb=" O PHE K 159 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE K 159 " --> pdb=" O VAL K 172 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N CYS K 131 " --> pdb=" O LYS K 189 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS K 189 " --> pdb=" O CYS K 131 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 200 through 203 removed outlier: 4.045A pdb=" N ALA K 433 " --> pdb=" O ALA K 200 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 259 through 261 removed outlier: 4.883A pdb=" N LEU K 260 " --> pdb=" O THR K 450 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE K 358 " --> pdb=" O GLU K 466 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N PHE K 468 " --> pdb=" O ILE K 358 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ARG K 360 " --> pdb=" O PHE K 468 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'K' and resid 271 through 273 removed outlier: 3.503A pdb=" N VAL K 286 " --> pdb=" O LEU K 452 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU K 452 " --> pdb=" O VAL K 286 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ILE K 443 " --> pdb=" O ARG K 298 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER K 447 " --> pdb=" O ILE K 294 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE K 294 " --> pdb=" O SER K 447 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL K 292 " --> pdb=" O ILE K 449 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N GLN K 293 " --> pdb=" O SER K 334 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N SER K 334 " --> pdb=" O GLN K 293 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N HIS K 330 " --> pdb=" O THR K 297 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU K 381 " --> pdb=" O CYS K 378 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N CYS K 378 " --> pdb=" O GLU K 381 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE K 376 " --> pdb=" O PHE K 383 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'K' and resid 302 through 307 removed outlier: 6.637A pdb=" N THR K 303 " --> pdb=" O GLY K 321 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS K 305 " --> pdb=" O TYR K 319 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR K 319 " --> pdb=" O LYS K 305 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'R' and resid 35 through 40 Processing sheet with id=AC1, first strand: chain 'R' and resid 45 through 46 removed outlier: 3.754A pdb=" N ILE R 225 " --> pdb=" O VAL R 245 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'R' and resid 91 through 94 removed outlier: 3.825A pdb=" N GLU R 91 " --> pdb=" O CYS R 239 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY R 237 " --> pdb=" O PHE R 93 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'R' and resid 169 through 176 removed outlier: 3.608A pdb=" N VAL R 172 " --> pdb=" O PHE R 159 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE R 159 " --> pdb=" O VAL R 172 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS R 189 " --> pdb=" O CYS R 131 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'R' and resid 200 through 203 removed outlier: 6.798A pdb=" N ALA R 200 " --> pdb=" O ALA R 433 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N TYR R 435 " --> pdb=" O ALA R 200 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N THR R 202 " --> pdb=" O TYR R 435 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'R' and resid 271 through 273 Processing sheet with id=AC6, first strand: chain 'R' and resid 374 through 378 removed outlier: 3.732A pdb=" N PHE R 376 " --> pdb=" O PHE R 383 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N HIS R 330 " --> pdb=" O THR R 297 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N SER R 334 " --> pdb=" O GLN R 293 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N GLN R 293 " --> pdb=" O SER R 334 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL R 292 " --> pdb=" O ILE R 449 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE R 294 " --> pdb=" O SER R 447 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE R 443 " --> pdb=" O ARG R 298 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'R' and resid 302 through 307 removed outlier: 6.495A pdb=" N THR R 303 " --> pdb=" O GLY R 321 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LYS R 305 " --> pdb=" O TYR R 319 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TYR R 319 " --> pdb=" O LYS R 305 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'R' and resid 360 through 361 removed outlier: 6.645A pdb=" N ARG R 360 " --> pdb=" O PHE R 468 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'A' and resid 3 through 7 removed outlier: 3.520A pdb=" N LEU A 78 " --> pdb=" O CYS A 22 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 11 through 12 removed outlier: 3.500A pdb=" N VAL A 12 " --> pdb=" O THR A 129 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR A 126 " --> pdb=" O TYR A 90 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL A 128 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL A 89 " --> pdb=" O GLN A 39 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA A 93 " --> pdb=" O THR A 35 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N TRP A 34 " --> pdb=" O TYR A 50 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N TYR A 50 " --> pdb=" O TRP A 34 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N TRP A 36 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR A 50 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR A 58 " --> pdb=" O TYR A 50 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 11 through 12 removed outlier: 3.500A pdb=" N VAL A 12 " --> pdb=" O THR A 129 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR A 126 " --> pdb=" O TYR A 90 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL A 128 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE A 100K" --> pdb=" O ARG A 100 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 3 through 7 removed outlier: 3.520A pdb=" N LEU F 78 " --> pdb=" O CYS F 22 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.501A pdb=" N VAL F 12 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR F 107 " --> pdb=" O TYR F 90 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL F 109 " --> pdb=" O ALA F 88 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL F 89 " --> pdb=" O GLN F 39 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA F 93 " --> pdb=" O THR F 35 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N TRP F 34 " --> pdb=" O TYR F 50 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N TYR F 50 " --> pdb=" O TRP F 34 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N TRP F 36 " --> pdb=" O ILE F 48 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR F 50 " --> pdb=" O THR F 58 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR F 58 " --> pdb=" O TYR F 50 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.501A pdb=" N VAL F 12 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR F 107 " --> pdb=" O TYR F 90 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL F 109 " --> pdb=" O ALA F 88 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE F 100K" --> pdb=" O ARG F 100 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'O' and resid 3 through 7 removed outlier: 3.520A pdb=" N LEU O 78 " --> pdb=" O CYS O 22 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'O' and resid 11 through 12 removed outlier: 3.500A pdb=" N VAL O 12 " --> pdb=" O THR O 110 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR O 107 " --> pdb=" O TYR O 90 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL O 109 " --> pdb=" O ALA O 88 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL O 89 " --> pdb=" O GLN O 39 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA O 93 " --> pdb=" O THR O 35 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N TRP O 34 " --> pdb=" O TYR O 50 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N TYR O 50 " --> pdb=" O TRP O 34 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N TRP O 36 " --> pdb=" O ILE O 48 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR O 50 " --> pdb=" O THR O 58 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR O 58 " --> pdb=" O TYR O 50 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'O' and resid 11 through 12 removed outlier: 3.500A pdb=" N VAL O 12 " --> pdb=" O THR O 110 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR O 107 " --> pdb=" O TYR O 90 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL O 109 " --> pdb=" O ALA O 88 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE O 100K" --> pdb=" O ARG O 100 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 9 through 11 removed outlier: 6.499A pdb=" N ARG B 9 " --> pdb=" O ARG B 103 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR B 102 " --> pdb=" O TYR B 86 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP B 85 " --> pdb=" O HIS B 38 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TYR B 87 " --> pdb=" O TYR B 36 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR B 36 " --> pdb=" O TYR B 87 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 19 through 22 Processing sheet with id=AE2, first strand: chain 'I' and resid 9 through 11 removed outlier: 6.500A pdb=" N ARG I 9 " --> pdb=" O ARG I 103 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR I 102 " --> pdb=" O TYR I 86 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASP I 85 " --> pdb=" O HIS I 38 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR I 87 " --> pdb=" O TYR I 36 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR I 36 " --> pdb=" O TYR I 87 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 19 through 22 Processing sheet with id=AE4, first strand: chain 'P' and resid 9 through 11 removed outlier: 6.500A pdb=" N ARG P 9 " --> pdb=" O ARG P 103 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR P 102 " --> pdb=" O TYR P 86 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP P 85 " --> pdb=" O HIS P 38 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR P 87 " --> pdb=" O TYR P 36 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR P 36 " --> pdb=" O TYR P 87 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N TRP P 35 " --> pdb=" O LEU P 47 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'P' and resid 19 through 22 473 hydrogen bonds defined for protein. 1251 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: 6.63 Time building geometry restraints manager: 10.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5907 1.33 - 1.46: 5361 1.46 - 1.58: 9311 1.58 - 1.71: 5 1.71 - 1.84: 168 Bond restraints: 20752 Sorted by residual: bond pdb=" C1 MAN W 6 " pdb=" O5 MAN W 6 " ideal model delta sigma weight residual 1.399 1.485 -0.086 2.00e-02 2.50e+03 1.85e+01 bond pdb=" C5 MAN W 6 " pdb=" O5 MAN W 6 " ideal model delta sigma weight residual 1.418 1.496 -0.078 2.00e-02 2.50e+03 1.54e+01 bond pdb=" C1 MAN e 6 " pdb=" C2 MAN e 6 " ideal model delta sigma weight residual 1.526 1.602 -0.076 2.00e-02 2.50e+03 1.45e+01 bond pdb=" C1 NAG S 1 " pdb=" O5 NAG S 1 " ideal model delta sigma weight residual 1.406 1.331 0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" C5 MAN H 5 " pdb=" O5 MAN H 5 " ideal model delta sigma weight residual 1.418 1.483 -0.065 2.00e-02 2.50e+03 1.04e+01 ... (remaining 20747 not shown) Histogram of bond angle deviations from ideal: 88.82 - 98.06: 1 98.06 - 107.30: 916 107.30 - 116.55: 14456 116.55 - 125.79: 12318 125.79 - 135.04: 485 Bond angle restraints: 28176 Sorted by residual: angle pdb=" C ASN C 618 " pdb=" CA ASN C 618 " pdb=" CB ASN C 618 " ideal model delta sigma weight residual 109.46 88.82 20.64 1.84e+00 2.95e-01 1.26e+02 angle pdb=" N ASN G 302 " pdb=" CA ASN G 302 " pdb=" C ASN G 302 " ideal model delta sigma weight residual 110.91 117.78 -6.87 1.17e+00 7.31e-01 3.44e+01 angle pdb=" CA GLU C 584 " pdb=" CB GLU C 584 " pdb=" CG GLU C 584 " ideal model delta sigma weight residual 114.10 125.34 -11.24 2.00e+00 2.50e-01 3.16e+01 angle pdb=" CA GLU Q 584 " pdb=" CB GLU Q 584 " pdb=" CG GLU Q 584 " ideal model delta sigma weight residual 114.10 125.31 -11.21 2.00e+00 2.50e-01 3.14e+01 angle pdb=" CA GLU J 584 " pdb=" CB GLU J 584 " pdb=" CG GLU J 584 " ideal model delta sigma weight residual 114.10 125.31 -11.21 2.00e+00 2.50e-01 3.14e+01 ... (remaining 28171 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.92: 12919 21.92 - 43.84: 515 43.84 - 65.75: 149 65.75 - 87.67: 67 87.67 - 109.59: 44 Dihedral angle restraints: 13694 sinusoidal: 6737 harmonic: 6957 Sorted by residual: dihedral pdb=" C ASN C 618 " pdb=" N ASN C 618 " pdb=" CA ASN C 618 " pdb=" CB ASN C 618 " ideal model delta harmonic sigma weight residual -122.60 -96.33 -26.27 0 2.50e+00 1.60e-01 1.10e+02 dihedral pdb=" CA ASN R 386 " pdb=" C ASN R 386 " pdb=" N THR R 387 " pdb=" CA THR R 387 " ideal model delta harmonic sigma weight residual -180.00 -127.74 -52.26 0 5.00e+00 4.00e-02 1.09e+02 dihedral pdb=" CA LEU R 261 " pdb=" C LEU R 261 " pdb=" N ASN R 262 " pdb=" CA ASN R 262 " ideal model delta harmonic sigma weight residual -180.00 -134.34 -45.66 0 5.00e+00 4.00e-02 8.34e+01 ... (remaining 13691 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.158: 3336 0.158 - 0.315: 85 0.315 - 0.473: 14 0.473 - 0.630: 0 0.630 - 0.788: 1 Chirality restraints: 3436 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN G 262 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.61 -0.79 2.00e-01 2.50e+01 1.55e+01 chirality pdb=" CA ASN C 618 " pdb=" N ASN C 618 " pdb=" C ASN C 618 " pdb=" CB ASN C 618 " both_signs ideal model delta sigma weight residual False 2.51 2.95 -0.44 2.00e-01 2.50e+01 4.93e+00 chirality pdb=" C1 NAG J 702 " pdb=" ND2 ASN J 618 " pdb=" C2 NAG J 702 " pdb=" O5 NAG J 702 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 4.03e+00 ... (remaining 3433 not shown) Planarity restraints: 3498 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 702 " -0.391 2.00e-02 2.50e+03 3.31e-01 1.37e+03 pdb=" C7 NAG C 702 " 0.100 2.00e-02 2.50e+03 pdb=" C8 NAG C 702 " -0.100 2.00e-02 2.50e+03 pdb=" N2 NAG C 702 " 0.581 2.00e-02 2.50e+03 pdb=" O7 NAG C 702 " -0.191 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 703 " 0.044 2.00e-02 2.50e+03 3.62e-02 1.64e+01 pdb=" C7 NAG C 703 " -0.011 2.00e-02 2.50e+03 pdb=" C8 NAG C 703 " 0.033 2.00e-02 2.50e+03 pdb=" N2 NAG C 703 " -0.058 2.00e-02 2.50e+03 pdb=" O7 NAG C 703 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN R 386 " -0.017 2.00e-02 2.50e+03 3.35e-02 1.12e+01 pdb=" C ASN R 386 " 0.058 2.00e-02 2.50e+03 pdb=" O ASN R 386 " -0.021 2.00e-02 2.50e+03 pdb=" N THR R 387 " -0.020 2.00e-02 2.50e+03 ... (remaining 3495 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 4669 2.79 - 3.31: 17379 3.31 - 3.84: 31083 3.84 - 4.37: 32362 4.37 - 4.90: 57173 Nonbonded interactions: 142666 Sorted by model distance: nonbonded pdb=" OG1 THR R 278 " pdb=" O7 NAG c 1 " model vdw 2.257 2.440 nonbonded pdb=" O TRP Q 571 " pdb=" NE2 GLN Q 575 " model vdw 2.298 2.520 nonbonded pdb=" O TRP J 571 " pdb=" NE2 GLN J 575 " model vdw 2.299 2.520 nonbonded pdb=" O TRP C 571 " pdb=" NE2 GLN C 575 " model vdw 2.299 2.520 nonbonded pdb=" O4 MAN e 6 " pdb=" O6 MAN e 6 " model vdw 2.335 2.440 ... (remaining 142661 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' selection = chain 'O' } ncs_group { reference = chain 'B' selection = chain 'I' selection = chain 'P' } ncs_group { reference = chain 'C' selection = chain 'J' selection = chain 'Q' } ncs_group { reference = (chain 'D' and (resid 1 or resid 4 through 6)) selection = (chain 'H' and (resid 2 or resid 5 through 7)) selection = (chain 'U' and (resid 2 or resid 5 through 7)) selection = (chain 'W' and (resid 1 or resid 4 through 6)) selection = (chain 'b' and (resid 1 or resid 4 through 6)) selection = (chain 'e' and (resid 1 or resid 4 through 6)) } ncs_group { reference = chain 'E' selection = chain 'L' selection = chain 'V' } ncs_group { reference = (chain 'G' and (resid 31 through 505 or resid 601 through 614)) selection = (chain 'K' and (resid 31 through 505 or resid 601 through 627)) selection = chain 'R' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'S' selection = chain 'T' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'c' selection = chain 'd' selection = chain 'f' selection = chain 'g' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 3.360 Check model and map are aligned: 0.350 Set scattering table: 0.210 Process input model: 56.380 Find NCS groups from input model: 1.580 Set up NCS constraints: 0.340 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 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 : 0.008 0.086 20752 Z= 0.471 Angle : 1.136 20.643 28176 Z= 0.578 Chirality : 0.068 0.788 3436 Planarity : 0.009 0.331 3447 Dihedral : 15.034 109.588 9101 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.45 % Favored : 92.39 % Rotamer: Outliers : 0.62 % Allowed : 3.03 % Favored : 96.35 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.01 % Twisted General : 0.22 % 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: -4.42 (0.14), residues: 2364 helix: -4.07 (0.15), residues: 351 sheet: -2.00 (0.20), residues: 558 loop : -3.17 (0.13), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP R 96 HIS 0.004 0.001 HIS I 38 PHE 0.022 0.003 PHE R 53 TYR 0.014 0.002 TYR K 319 ARG 0.047 0.001 ARG O 54 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 2109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 476 time to evaluate : 2.055 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: C 573 ILE cc_start: 0.9088 (mm) cc_final: 0.8508 (tp) REVERT: C 575 GLN cc_start: 0.8690 (mp-120) cc_final: 0.8077 (mp-120) REVERT: C 576 LEU cc_start: 0.9637 (OUTLIER) cc_final: 0.9394 (mt) REVERT: C 590 GLN cc_start: 0.9436 (tp-100) cc_final: 0.9020 (tp-100) REVERT: C 632 ASP cc_start: 0.8763 (t70) cc_final: 0.7897 (t70) REVERT: C 654 GLU cc_start: 0.9580 (mm-30) cc_final: 0.9241 (mm-30) REVERT: G 95 MET cc_start: 0.9154 (ptt) cc_final: 0.8806 (ptt) REVERT: G 161 MET cc_start: 0.8726 (tpp) cc_final: 0.8289 (tpt) REVERT: G 322 ILE cc_start: 0.9199 (mm) cc_final: 0.8981 (mm) REVERT: J 543 ASN cc_start: 0.9006 (m-40) cc_final: 0.8721 (t0) REVERT: J 576 LEU cc_start: 0.9615 (OUTLIER) cc_final: 0.9399 (mt) REVERT: J 577 GLN cc_start: 0.9158 (mt0) cc_final: 0.8528 (mt0) REVERT: J 588 ARG cc_start: 0.8766 (ttm-80) cc_final: 0.8520 (ttm170) REVERT: J 632 ASP cc_start: 0.8923 (t70) cc_final: 0.8578 (t70) REVERT: J 654 GLU cc_start: 0.9421 (mm-30) cc_final: 0.9186 (mm-30) REVERT: K 475 MET cc_start: 0.8699 (mmm) cc_final: 0.8427 (tpp) REVERT: K 482 GLU cc_start: 0.8916 (tp30) cc_final: 0.8364 (tp30) REVERT: K 492 GLU cc_start: 0.8563 (tm-30) cc_final: 0.7889 (tm-30) REVERT: Q 530 MET cc_start: 0.9067 (mtp) cc_final: 0.8815 (ttm) REVERT: Q 573 ILE cc_start: 0.8993 (mm) cc_final: 0.8481 (tp) REVERT: Q 575 GLN cc_start: 0.9041 (mp-120) cc_final: 0.8659 (mp10) REVERT: Q 576 LEU cc_start: 0.9591 (OUTLIER) cc_final: 0.9370 (mt) REVERT: Q 577 GLN cc_start: 0.9121 (mt0) cc_final: 0.8877 (mt0) REVERT: Q 601 LYS cc_start: 0.9158 (mppt) cc_final: 0.8938 (mmtt) REVERT: Q 632 ASP cc_start: 0.8835 (t70) cc_final: 0.8404 (t70) REVERT: R 99 ASN cc_start: 0.9493 (m-40) cc_final: 0.9246 (m-40) REVERT: R 377 ASN cc_start: 0.9314 (p0) cc_final: 0.8584 (t0) REVERT: R 434 MET cc_start: 0.8836 (ttm) cc_final: 0.8381 (ttm) REVERT: R 492 GLU cc_start: 0.8735 (tm-30) cc_final: 0.8079 (tm-30) REVERT: A 13 LYS cc_start: 0.8996 (pmtt) cc_final: 0.8655 (mmmt) REVERT: A 29 MET cc_start: 0.6694 (ptm) cc_final: 0.5535 (ptp) REVERT: A 34 TRP cc_start: 0.8817 (m100) cc_final: 0.8444 (m100) REVERT: A 37 ILE cc_start: 0.9483 (mm) cc_final: 0.9279 (mm) REVERT: A 46 GLU cc_start: 0.8887 (tt0) cc_final: 0.8573 (tm-30) REVERT: A 64 ASN cc_start: 0.8945 (m-40) cc_final: 0.8718 (m110) REVERT: A 78 LEU cc_start: 0.9118 (mt) cc_final: 0.8709 (mt) REVERT: A 81 LYS cc_start: 0.9437 (mttt) cc_final: 0.9063 (mtpp) REVERT: A 91 TYR cc_start: 0.9160 (m-80) cc_final: 0.8639 (m-80) REVERT: A 100 GLU cc_start: 0.8658 (tt0) cc_final: 0.8294 (tt0) REVERT: F 1 GLN cc_start: 0.7273 (tp40) cc_final: 0.6471 (tm-30) REVERT: F 3 GLN cc_start: 0.9348 (mm110) cc_final: 0.9009 (mm110) REVERT: F 13 LYS cc_start: 0.9360 (pmtt) cc_final: 0.9111 (tppt) REVERT: F 29 MET cc_start: 0.6131 (ptm) cc_final: 0.5534 (ptm) REVERT: F 46 GLU cc_start: 0.8640 (tt0) cc_final: 0.8421 (tm-30) REVERT: F 77 GLN cc_start: 0.8757 (mm-40) cc_final: 0.8428 (tp40) REVERT: F 78 LEU cc_start: 0.9126 (mt) cc_final: 0.8725 (mt) REVERT: F 80 LEU cc_start: 0.8559 (mt) cc_final: 0.7335 (mt) REVERT: F 81 LYS cc_start: 0.9531 (mttt) cc_final: 0.8982 (mmmm) REVERT: F 105 LYS cc_start: 0.8776 (ptmt) cc_final: 0.8295 (mtmm) REVERT: O 3 GLN cc_start: 0.9350 (mm110) cc_final: 0.8758 (mp10) REVERT: O 13 LYS cc_start: 0.9110 (pmtt) cc_final: 0.8751 (tppt) REVERT: O 29 MET cc_start: 0.5098 (ptm) cc_final: 0.4725 (ptp) REVERT: O 46 GLU cc_start: 0.8703 (tt0) cc_final: 0.8488 (tm-30) REVERT: O 77 GLN cc_start: 0.9002 (mm-40) cc_final: 0.8702 (tp40) REVERT: O 78 LEU cc_start: 0.9193 (mt) cc_final: 0.8549 (mt) REVERT: O 81 LYS cc_start: 0.9449 (mttt) cc_final: 0.9008 (mmmm) REVERT: O 82 ASN cc_start: 0.9019 (m-40) cc_final: 0.8668 (p0) REVERT: O 100 GLU cc_start: 0.8568 (tt0) cc_final: 0.8024 (tt0) REVERT: B 26 GLN cc_start: 0.8623 (mm-40) cc_final: 0.8245 (tp-100) REVERT: B 42 GLN cc_start: 0.8329 (mp10) cc_final: 0.8047 (mp10) REVERT: B 47 LEU cc_start: 0.9690 (mt) cc_final: 0.9471 (mp) REVERT: B 70 ARG cc_start: 0.7924 (mmm160) cc_final: 0.6501 (tpt90) REVERT: B 83 GLU cc_start: 0.7642 (tp30) cc_final: 0.7315 (tp30) REVERT: B 85 ASP cc_start: 0.8270 (m-30) cc_final: 0.7730 (p0) REVERT: B 104 LEU cc_start: 0.8741 (tp) cc_final: 0.8086 (tp) REVERT: I 37 GLN cc_start: 0.8835 (tt0) cc_final: 0.8514 (tm-30) REVERT: I 42 GLN cc_start: 0.8453 (mp10) cc_final: 0.8091 (mp10) REVERT: I 47 LEU cc_start: 0.9626 (mt) cc_final: 0.9120 (mp) REVERT: I 70 ARG cc_start: 0.7944 (mmm160) cc_final: 0.7006 (mmt180) REVERT: I 83 GLU cc_start: 0.7915 (tp30) cc_final: 0.7518 (tp30) REVERT: I 85 ASP cc_start: 0.8388 (m-30) cc_final: 0.8040 (p0) REVERT: I 92 ASP cc_start: 0.8807 (p0) cc_final: 0.8561 (p0) REVERT: I 104 LEU cc_start: 0.8637 (tp) cc_final: 0.8072 (tp) REVERT: P 18 THR cc_start: 0.9108 (p) cc_final: 0.8883 (t) REVERT: P 33 VAL cc_start: 0.9416 (m) cc_final: 0.8921 (m) REVERT: P 37 GLN cc_start: 0.9017 (tt0) cc_final: 0.8427 (tp40) REVERT: P 42 GLN cc_start: 0.8172 (mp10) cc_final: 0.7879 (mp10) REVERT: P 47 LEU cc_start: 0.9637 (mt) cc_final: 0.9342 (mp) REVERT: P 53 ASP cc_start: 0.9030 (m-30) cc_final: 0.8738 (t0) REVERT: P 70 ARG cc_start: 0.7818 (mmm160) cc_final: 0.6338 (tpt90) REVERT: P 83 GLU cc_start: 0.7863 (tp30) cc_final: 0.7535 (tp30) REVERT: P 85 ASP cc_start: 0.8192 (m-30) cc_final: 0.7741 (p0) REVERT: P 104 LEU cc_start: 0.8701 (tp) cc_final: 0.8500 (tp) outliers start: 13 outliers final: 6 residues processed: 482 average time/residue: 0.3607 time to fit residues: 251.2055 Evaluate side-chains 317 residues out of total 2109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 308 time to evaluate : 2.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 200 optimal weight: 0.0010 chunk 179 optimal weight: 3.9990 chunk 99 optimal weight: 0.1980 chunk 61 optimal weight: 2.9990 chunk 121 optimal weight: 0.9990 chunk 95 optimal weight: 5.9990 chunk 185 optimal weight: 6.9990 chunk 71 optimal weight: 9.9990 chunk 112 optimal weight: 10.0000 chunk 138 optimal weight: 10.0000 chunk 215 optimal weight: 5.9990 overall best weight: 1.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 590 GLN G 103 GLN G 133 ASN G 137 ASN G 188 ASN G 352 HIS ** J 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 103 GLN K 133 ASN K 302 ASN Q 590 GLN ** Q 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 103 GLN R 133 ASN R 188 ASN R 300 ASN R 478 ASN ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 HIS I 89 HIS P 89 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 20752 Z= 0.197 Angle : 0.728 15.819 28176 Z= 0.350 Chirality : 0.049 0.484 3436 Planarity : 0.004 0.041 3447 Dihedral : 13.459 105.629 4667 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.54 % Favored : 94.33 % Rotamer: Outliers : 0.09 % Allowed : 2.42 % Favored : 97.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.65 (0.15), residues: 2364 helix: -2.86 (0.20), residues: 369 sheet: -1.53 (0.21), residues: 543 loop : -2.79 (0.14), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP G 69 HIS 0.003 0.001 HIS G 330 PHE 0.013 0.001 PHE K 320 TYR 0.017 0.001 TYR B 86 ARG 0.009 0.001 ARG I 31 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 425 time to evaluate : 2.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 543 ASN cc_start: 0.8544 (t0) cc_final: 0.8288 (t0) REVERT: C 577 GLN cc_start: 0.8871 (mt0) cc_final: 0.8539 (mt0) REVERT: C 580 VAL cc_start: 0.9421 (p) cc_final: 0.8965 (p) REVERT: C 584 GLU cc_start: 0.9281 (pm20) cc_final: 0.8852 (pm20) REVERT: C 647 GLU cc_start: 0.8741 (tm-30) cc_final: 0.8391 (tm-30) REVERT: G 49 GLU cc_start: 0.8770 (pp20) cc_final: 0.8521 (pp20) REVERT: G 95 MET cc_start: 0.9172 (ptt) cc_final: 0.8688 (ptt) REVERT: G 164 GLU cc_start: 0.8156 (tt0) cc_final: 0.7923 (tt0) REVERT: G 322 ILE cc_start: 0.9236 (mm) cc_final: 0.9012 (mm) REVERT: J 543 ASN cc_start: 0.9040 (m-40) cc_final: 0.8681 (t0) REVERT: J 574 LYS cc_start: 0.9186 (mmtm) cc_final: 0.8748 (mttp) REVERT: J 577 GLN cc_start: 0.8949 (mt0) cc_final: 0.8495 (mt0) REVERT: J 624 ASP cc_start: 0.8894 (m-30) cc_final: 0.8520 (p0) REVERT: J 632 ASP cc_start: 0.8905 (t70) cc_final: 0.8510 (t70) REVERT: K 475 MET cc_start: 0.8702 (mmm) cc_final: 0.8502 (mmm) REVERT: Q 543 ASN cc_start: 0.8671 (t0) cc_final: 0.8414 (t0) REVERT: Q 573 ILE cc_start: 0.9100 (mm) cc_final: 0.8742 (tp) REVERT: Q 577 GLN cc_start: 0.8904 (mt0) cc_final: 0.8482 (mt0) REVERT: Q 584 GLU cc_start: 0.9275 (pm20) cc_final: 0.8931 (pm20) REVERT: Q 591 GLN cc_start: 0.9696 (tm-30) cc_final: 0.9321 (tm-30) REVERT: Q 601 LYS cc_start: 0.9023 (mppt) cc_final: 0.8761 (mmtt) REVERT: Q 624 ASP cc_start: 0.9052 (m-30) cc_final: 0.8775 (p0) REVERT: Q 632 ASP cc_start: 0.8856 (t70) cc_final: 0.8549 (t70) REVERT: Q 639 THR cc_start: 0.9562 (p) cc_final: 0.9352 (p) REVERT: Q 643 TYR cc_start: 0.9469 (m-10) cc_final: 0.9183 (m-80) REVERT: R 95 MET cc_start: 0.9198 (ptt) cc_final: 0.8334 (ptt) REVERT: R 377 ASN cc_start: 0.9309 (p0) cc_final: 0.8582 (t0) REVERT: R 434 MET cc_start: 0.8971 (ttm) cc_final: 0.8675 (ttm) REVERT: R 492 GLU cc_start: 0.8764 (tm-30) cc_final: 0.7931 (tm-30) REVERT: R 494 LEU cc_start: 0.9298 (tp) cc_final: 0.8730 (tt) REVERT: A 29 MET cc_start: 0.6627 (ptm) cc_final: 0.5337 (ptp) REVERT: A 34 TRP cc_start: 0.8678 (m100) cc_final: 0.7903 (m100) REVERT: A 48 ILE cc_start: 0.9147 (mt) cc_final: 0.8623 (mp) REVERT: A 64 ASN cc_start: 0.8974 (m-40) cc_final: 0.8746 (m110) REVERT: A 81 LYS cc_start: 0.9521 (mttt) cc_final: 0.9178 (tptt) REVERT: A 82 LEU cc_start: 0.8808 (mp) cc_final: 0.8260 (mp) REVERT: A 86 ASP cc_start: 0.8879 (t70) cc_final: 0.8596 (p0) REVERT: A 91 TYR cc_start: 0.9030 (m-80) cc_final: 0.8638 (m-80) REVERT: F 1 GLN cc_start: 0.7338 (tp40) cc_final: 0.6429 (tm-30) REVERT: F 3 GLN cc_start: 0.9277 (mm110) cc_final: 0.8869 (mm110) REVERT: F 13 LYS cc_start: 0.9381 (pttm) cc_final: 0.9178 (tppt) REVERT: F 48 ILE cc_start: 0.9148 (mt) cc_final: 0.8665 (mp) REVERT: F 80 LEU cc_start: 0.8491 (mt) cc_final: 0.7449 (mt) REVERT: F 81 LYS cc_start: 0.9544 (mttt) cc_final: 0.8972 (mmmm) REVERT: F 82 ASN cc_start: 0.8925 (m-40) cc_final: 0.8686 (p0) REVERT: F 86 ASP cc_start: 0.8862 (t70) cc_final: 0.8615 (p0) REVERT: F 91 TYR cc_start: 0.8831 (m-80) cc_final: 0.8575 (m-80) REVERT: O 3 GLN cc_start: 0.9254 (mm110) cc_final: 0.8637 (mp10) REVERT: O 13 LYS cc_start: 0.9193 (pttm) cc_final: 0.8941 (tppt) REVERT: O 46 GLU cc_start: 0.8854 (tt0) cc_final: 0.8390 (tm-30) REVERT: O 77 GLN cc_start: 0.8996 (mm-40) cc_final: 0.8665 (mm-40) REVERT: O 80 LEU cc_start: 0.8681 (mt) cc_final: 0.8412 (mt) REVERT: O 81 LYS cc_start: 0.9518 (mttt) cc_final: 0.9037 (mmmm) REVERT: O 82 ASN cc_start: 0.8960 (m-40) cc_final: 0.8649 (p0) REVERT: O 99 GLN cc_start: 0.8595 (pp30) cc_final: 0.8314 (pp30) REVERT: O 100 GLU cc_start: 0.8625 (tt0) cc_final: 0.8014 (tt0) REVERT: B 37 GLN cc_start: 0.8202 (tp40) cc_final: 0.7519 (tp-100) REVERT: B 42 GLN cc_start: 0.8372 (mp10) cc_final: 0.8075 (mp10) REVERT: B 70 ARG cc_start: 0.7982 (mmm160) cc_final: 0.6509 (tpt170) REVERT: B 85 ASP cc_start: 0.8207 (m-30) cc_final: 0.7830 (p0) REVERT: B 90 MET cc_start: 0.9071 (tpp) cc_final: 0.8811 (tpp) REVERT: I 31 ARG cc_start: 0.8851 (mtm110) cc_final: 0.8250 (ptp90) REVERT: I 37 GLN cc_start: 0.8876 (tt0) cc_final: 0.8661 (tm-30) REVERT: I 42 GLN cc_start: 0.8545 (mp10) cc_final: 0.8184 (mp10) REVERT: I 47 LEU cc_start: 0.9721 (mt) cc_final: 0.9258 (mp) REVERT: I 70 ARG cc_start: 0.7816 (mmm160) cc_final: 0.7108 (mmt180) REVERT: I 83 GLU cc_start: 0.7984 (tp30) cc_final: 0.7676 (mm-30) REVERT: I 85 ASP cc_start: 0.8364 (m-30) cc_final: 0.8002 (p0) REVERT: I 92 ASP cc_start: 0.8801 (p0) cc_final: 0.8594 (p0) REVERT: P 18 THR cc_start: 0.9042 (p) cc_final: 0.8819 (t) REVERT: P 31 ARG cc_start: 0.8635 (mtm110) cc_final: 0.8224 (ptp-110) REVERT: P 33 VAL cc_start: 0.9348 (m) cc_final: 0.9012 (m) REVERT: P 37 GLN cc_start: 0.8905 (tt0) cc_final: 0.8539 (tp40) REVERT: P 42 GLN cc_start: 0.8426 (mp10) cc_final: 0.8140 (mp10) REVERT: P 47 LEU cc_start: 0.9689 (mt) cc_final: 0.9344 (mp) REVERT: P 48 ILE cc_start: 0.9558 (mm) cc_final: 0.9347 (mm) REVERT: P 53 ASP cc_start: 0.8931 (m-30) cc_final: 0.8728 (t0) REVERT: P 70 ARG cc_start: 0.7677 (mmm160) cc_final: 0.7096 (mmt180) REVERT: P 83 GLU cc_start: 0.7907 (tp30) cc_final: 0.7621 (tp30) REVERT: P 85 ASP cc_start: 0.8038 (m-30) cc_final: 0.7465 (p0) REVERT: P 104 LEU cc_start: 0.8593 (tp) cc_final: 0.8354 (tp) outliers start: 2 outliers final: 0 residues processed: 425 average time/residue: 0.3324 time to fit residues: 210.8662 Evaluate side-chains 315 residues out of total 2109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 315 time to evaluate : 2.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 119 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 chunk 179 optimal weight: 9.9990 chunk 146 optimal weight: 0.9990 chunk 59 optimal weight: 7.9990 chunk 215 optimal weight: 0.9990 chunk 232 optimal weight: 9.9990 chunk 192 optimal weight: 10.0000 chunk 213 optimal weight: 9.9990 chunk 73 optimal weight: 9.9990 chunk 172 optimal weight: 9.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 590 GLN Q 616 ASN ** Q 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 52 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20752 Z= 0.216 Angle : 0.690 13.209 28176 Z= 0.330 Chirality : 0.048 0.453 3436 Planarity : 0.004 0.036 3447 Dihedral : 12.048 105.036 4667 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.30 % Favored : 93.61 % Rotamer: Outliers : 0.05 % Allowed : 3.08 % Favored : 96.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.18 (0.15), residues: 2364 helix: -1.94 (0.24), residues: 336 sheet: -1.35 (0.20), residues: 597 loop : -2.60 (0.14), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP K 69 HIS 0.005 0.001 HIS K 330 PHE 0.012 0.001 PHE K 320 TYR 0.016 0.001 TYR C 643 ARG 0.004 0.000 ARG B 103 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 398 time to evaluate : 2.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 543 ASN cc_start: 0.8663 (t0) cc_final: 0.8335 (t0) REVERT: C 574 LYS cc_start: 0.9172 (mttm) cc_final: 0.8819 (mtmt) REVERT: C 577 GLN cc_start: 0.8928 (mt0) cc_final: 0.8589 (mt0) REVERT: C 584 GLU cc_start: 0.9204 (pm20) cc_final: 0.8656 (pm20) REVERT: C 647 GLU cc_start: 0.8540 (tm-30) cc_final: 0.8264 (tm-30) REVERT: C 657 GLU cc_start: 0.9532 (mm-30) cc_final: 0.9309 (mm-30) REVERT: G 95 MET cc_start: 0.9230 (ptt) cc_final: 0.8736 (ptt) REVERT: J 543 ASN cc_start: 0.9054 (m-40) cc_final: 0.8752 (t0) REVERT: J 574 LYS cc_start: 0.9152 (mmtm) cc_final: 0.8774 (mttm) REVERT: J 577 GLN cc_start: 0.8998 (mt0) cc_final: 0.8535 (mt0) REVERT: J 624 ASP cc_start: 0.8949 (m-30) cc_final: 0.8608 (p0) REVERT: J 632 ASP cc_start: 0.8981 (t70) cc_final: 0.8640 (t70) REVERT: K 217 TYR cc_start: 0.8764 (m-80) cc_final: 0.8219 (m-80) REVERT: K 256 SER cc_start: 0.9417 (p) cc_final: 0.9187 (p) REVERT: K 475 MET cc_start: 0.8807 (mmm) cc_final: 0.8551 (mmm) REVERT: Q 543 ASN cc_start: 0.8776 (t0) cc_final: 0.8401 (t0) REVERT: Q 573 ILE cc_start: 0.9183 (mm) cc_final: 0.8617 (tp) REVERT: Q 577 GLN cc_start: 0.8973 (mt0) cc_final: 0.8569 (mt0) REVERT: Q 584 GLU cc_start: 0.9211 (pm20) cc_final: 0.8872 (pm20) REVERT: Q 591 GLN cc_start: 0.9699 (tm-30) cc_final: 0.9318 (tm-30) REVERT: Q 601 LYS cc_start: 0.9105 (mppt) cc_final: 0.8895 (mmtt) REVERT: Q 624 ASP cc_start: 0.9075 (m-30) cc_final: 0.8775 (p0) REVERT: Q 626 MET cc_start: 0.8115 (ptm) cc_final: 0.7730 (ptm) REVERT: Q 632 ASP cc_start: 0.9041 (t70) cc_final: 0.8729 (t70) REVERT: R 95 MET cc_start: 0.9188 (ptt) cc_final: 0.8319 (ptt) REVERT: R 377 ASN cc_start: 0.9335 (p0) cc_final: 0.8590 (t0) REVERT: R 434 MET cc_start: 0.9050 (ttm) cc_final: 0.8782 (ttm) REVERT: R 492 GLU cc_start: 0.8672 (tm-30) cc_final: 0.8360 (tm-30) REVERT: R 494 LEU cc_start: 0.9306 (tp) cc_final: 0.8991 (tt) REVERT: A 16 GLU cc_start: 0.7882 (pt0) cc_final: 0.7655 (mm-30) REVERT: A 64 ASN cc_start: 0.8991 (m-40) cc_final: 0.8761 (m110) REVERT: A 81 LYS cc_start: 0.9550 (mttt) cc_final: 0.9187 (tptt) REVERT: A 82 LEU cc_start: 0.8831 (mp) cc_final: 0.8237 (mp) REVERT: A 86 ASP cc_start: 0.8889 (t70) cc_final: 0.8535 (t0) REVERT: A 91 TYR cc_start: 0.9081 (m-80) cc_final: 0.8837 (m-80) REVERT: A 124 LYS cc_start: 0.8833 (ptpp) cc_final: 0.8365 (ptpp) REVERT: F 1 GLN cc_start: 0.7281 (tp40) cc_final: 0.6462 (tm-30) REVERT: F 3 GLN cc_start: 0.9280 (mm110) cc_final: 0.8882 (mm110) REVERT: F 13 LYS cc_start: 0.9364 (pttm) cc_final: 0.9154 (tppt) REVERT: F 48 ILE cc_start: 0.9082 (mt) cc_final: 0.8752 (mp) REVERT: F 80 LEU cc_start: 0.8550 (mt) cc_final: 0.7552 (mt) REVERT: F 81 LYS cc_start: 0.9552 (mttt) cc_final: 0.9024 (mmmm) REVERT: F 82 ASN cc_start: 0.8912 (m-40) cc_final: 0.8699 (p0) REVERT: F 86 ASP cc_start: 0.8890 (t70) cc_final: 0.8193 (p0) REVERT: O 3 GLN cc_start: 0.9242 (mm110) cc_final: 0.8621 (mp10) REVERT: O 13 LYS cc_start: 0.9203 (pttm) cc_final: 0.8970 (tppt) REVERT: O 46 GLU cc_start: 0.8699 (tt0) cc_final: 0.8286 (tm-30) REVERT: O 77 GLN cc_start: 0.8998 (mm-40) cc_final: 0.8606 (mm-40) REVERT: O 80 LEU cc_start: 0.8756 (mt) cc_final: 0.8365 (mt) REVERT: O 81 LYS cc_start: 0.9496 (mttt) cc_final: 0.9026 (mmmm) REVERT: O 82 ASN cc_start: 0.8910 (m-40) cc_final: 0.8665 (p0) REVERT: O 86 ASP cc_start: 0.8984 (t0) cc_final: 0.8475 (p0) REVERT: O 99 GLN cc_start: 0.8706 (pp30) cc_final: 0.8400 (pp30) REVERT: O 100 GLU cc_start: 0.8585 (tt0) cc_final: 0.7948 (tt0) REVERT: O 105 LYS cc_start: 0.8727 (ptpp) cc_final: 0.8332 (pttm) REVERT: B 26 GLN cc_start: 0.8951 (tp-100) cc_final: 0.8750 (tp-100) REVERT: B 37 GLN cc_start: 0.8336 (tp40) cc_final: 0.7498 (tp40) REVERT: B 42 GLN cc_start: 0.8390 (mp10) cc_final: 0.8059 (mp10) REVERT: B 70 ARG cc_start: 0.7825 (mmm160) cc_final: 0.6596 (tpt170) REVERT: B 85 ASP cc_start: 0.8282 (m-30) cc_final: 0.7888 (p0) REVERT: B 90 MET cc_start: 0.9034 (tpp) cc_final: 0.8760 (tpp) REVERT: I 42 GLN cc_start: 0.8568 (mp10) cc_final: 0.8147 (mp10) REVERT: I 47 LEU cc_start: 0.9727 (mt) cc_final: 0.9444 (mp) REVERT: I 70 ARG cc_start: 0.7814 (mmm160) cc_final: 0.6981 (mmt180) REVERT: I 83 GLU cc_start: 0.8099 (tp30) cc_final: 0.7799 (mm-30) REVERT: I 85 ASP cc_start: 0.8428 (m-30) cc_final: 0.7993 (p0) REVERT: I 104 LEU cc_start: 0.8510 (tp) cc_final: 0.8297 (tp) REVERT: P 18 THR cc_start: 0.9021 (p) cc_final: 0.8773 (t) REVERT: P 33 VAL cc_start: 0.9370 (m) cc_final: 0.9057 (m) REVERT: P 37 GLN cc_start: 0.8958 (tt0) cc_final: 0.8462 (tm-30) REVERT: P 42 GLN cc_start: 0.8470 (mp10) cc_final: 0.8161 (mp10) REVERT: P 47 LEU cc_start: 0.9674 (mt) cc_final: 0.9364 (mp) REVERT: P 70 ARG cc_start: 0.7614 (mmm160) cc_final: 0.7153 (mmt180) REVERT: P 83 GLU cc_start: 0.7981 (tp30) cc_final: 0.7694 (tp30) REVERT: P 85 ASP cc_start: 0.8117 (m-30) cc_final: 0.7569 (p0) REVERT: P 104 LEU cc_start: 0.8553 (tp) cc_final: 0.8277 (tp) outliers start: 1 outliers final: 0 residues processed: 398 average time/residue: 0.3209 time to fit residues: 193.3212 Evaluate side-chains 301 residues out of total 2109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 301 time to evaluate : 2.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 213 optimal weight: 9.9990 chunk 162 optimal weight: 5.9990 chunk 111 optimal weight: 6.9990 chunk 23 optimal weight: 8.9990 chunk 102 optimal weight: 5.9990 chunk 144 optimal weight: 1.9990 chunk 216 optimal weight: 2.9990 chunk 229 optimal weight: 1.9990 chunk 113 optimal weight: 10.0000 chunk 205 optimal weight: 6.9990 chunk 61 optimal weight: 0.0870 overall best weight: 2.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 99 ASN J 575 GLN ** J 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 575 GLN Q 590 GLN ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20752 Z= 0.225 Angle : 0.686 10.103 28176 Z= 0.325 Chirality : 0.049 0.576 3436 Planarity : 0.003 0.034 3447 Dihedral : 10.997 105.704 4667 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.98 % Favored : 92.94 % Rotamer: Outliers : 0.05 % Allowed : 2.37 % Favored : 97.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.16), residues: 2364 helix: -1.35 (0.26), residues: 342 sheet: -1.13 (0.20), residues: 591 loop : -2.44 (0.15), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 112 HIS 0.005 0.001 HIS K 330 PHE 0.012 0.001 PHE K 320 TYR 0.018 0.001 TYR J 586 ARG 0.012 0.000 ARG I 31 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 396 time to evaluate : 2.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 530 MET cc_start: 0.9225 (ttm) cc_final: 0.8575 (mmm) REVERT: C 540 GLN cc_start: 0.9036 (mp10) cc_final: 0.8834 (mp10) REVERT: C 543 ASN cc_start: 0.8810 (t0) cc_final: 0.8414 (t0) REVERT: C 574 LYS cc_start: 0.9293 (mttm) cc_final: 0.8950 (mtmt) REVERT: C 575 GLN cc_start: 0.9094 (mp10) cc_final: 0.8670 (mp10) REVERT: C 577 GLN cc_start: 0.8938 (mt0) cc_final: 0.8587 (mt0) REVERT: C 584 GLU cc_start: 0.9084 (pm20) cc_final: 0.8555 (pm20) REVERT: C 590 GLN cc_start: 0.9503 (tp40) cc_final: 0.9034 (tp40) REVERT: C 591 GLN cc_start: 0.9627 (tm-30) cc_final: 0.9223 (tm-30) REVERT: C 654 GLU cc_start: 0.9372 (mm-30) cc_final: 0.9130 (mm-30) REVERT: C 657 GLU cc_start: 0.9541 (mm-30) cc_final: 0.9285 (mm-30) REVERT: G 49 GLU cc_start: 0.8724 (pp20) cc_final: 0.8444 (pp20) REVERT: G 95 MET cc_start: 0.9252 (ptt) cc_final: 0.8516 (ptt) REVERT: G 106 GLU cc_start: 0.8666 (tm-30) cc_final: 0.8419 (tm-30) REVERT: J 543 ASN cc_start: 0.9050 (m-40) cc_final: 0.8725 (t0) REVERT: J 574 LYS cc_start: 0.9178 (mmtm) cc_final: 0.8783 (mttm) REVERT: J 577 GLN cc_start: 0.9004 (mt0) cc_final: 0.8533 (mt0) REVERT: J 624 ASP cc_start: 0.8873 (m-30) cc_final: 0.8599 (p0) REVERT: J 632 ASP cc_start: 0.9022 (t70) cc_final: 0.8698 (t70) REVERT: J 647 GLU cc_start: 0.8981 (pp20) cc_final: 0.8752 (pp20) REVERT: K 478 ASN cc_start: 0.9154 (m110) cc_final: 0.8941 (m110) REVERT: Q 543 ASN cc_start: 0.8875 (t0) cc_final: 0.8443 (t0) REVERT: Q 573 ILE cc_start: 0.8825 (mm) cc_final: 0.8600 (tp) REVERT: Q 577 GLN cc_start: 0.9027 (mt0) cc_final: 0.8611 (mt0) REVERT: Q 584 GLU cc_start: 0.9084 (pm20) cc_final: 0.8829 (pm20) REVERT: Q 591 GLN cc_start: 0.9711 (tm-30) cc_final: 0.9325 (tm-30) REVERT: Q 624 ASP cc_start: 0.9016 (m-30) cc_final: 0.8704 (m-30) REVERT: Q 632 ASP cc_start: 0.9043 (t70) cc_final: 0.8781 (t70) REVERT: Q 643 TYR cc_start: 0.9465 (m-10) cc_final: 0.9167 (m-10) REVERT: R 95 MET cc_start: 0.9223 (ptt) cc_final: 0.8366 (ptt) REVERT: R 377 ASN cc_start: 0.9295 (p0) cc_final: 0.8645 (t0) REVERT: R 434 MET cc_start: 0.9050 (ttm) cc_final: 0.8758 (ttm) REVERT: R 492 GLU cc_start: 0.8714 (tm-30) cc_final: 0.8359 (tm-30) REVERT: R 494 LEU cc_start: 0.9306 (tp) cc_final: 0.8988 (tt) REVERT: A 64 ASN cc_start: 0.9006 (m-40) cc_final: 0.8774 (m110) REVERT: A 81 LYS cc_start: 0.9528 (mttt) cc_final: 0.9213 (tptt) REVERT: A 82 LEU cc_start: 0.8843 (mp) cc_final: 0.8266 (mp) REVERT: A 86 ASP cc_start: 0.8931 (t70) cc_final: 0.8434 (t0) REVERT: F 1 GLN cc_start: 0.7306 (tp40) cc_final: 0.6360 (tm-30) REVERT: F 3 GLN cc_start: 0.9280 (mm110) cc_final: 0.8908 (mm110) REVERT: F 16 GLU cc_start: 0.8435 (mm-30) cc_final: 0.8072 (mm-30) REVERT: F 48 ILE cc_start: 0.9172 (mt) cc_final: 0.8891 (mp) REVERT: F 77 GLN cc_start: 0.8703 (mm-40) cc_final: 0.8388 (tp40) REVERT: F 80 LEU cc_start: 0.8560 (mt) cc_final: 0.7394 (mt) REVERT: F 81 LYS cc_start: 0.9565 (mttt) cc_final: 0.8980 (mmmm) REVERT: F 86 ASP cc_start: 0.8775 (t70) cc_final: 0.8060 (p0) REVERT: O 3 GLN cc_start: 0.9233 (mm110) cc_final: 0.8603 (mp-120) REVERT: O 13 LYS cc_start: 0.9208 (pttm) cc_final: 0.8971 (tppt) REVERT: O 46 GLU cc_start: 0.8719 (tt0) cc_final: 0.8368 (tm-30) REVERT: O 77 GLN cc_start: 0.8997 (mm-40) cc_final: 0.8577 (mm-40) REVERT: O 80 LEU cc_start: 0.8821 (mt) cc_final: 0.8433 (mt) REVERT: O 81 LYS cc_start: 0.9502 (mttt) cc_final: 0.9033 (mmmm) REVERT: O 82 ASN cc_start: 0.8977 (m-40) cc_final: 0.8690 (p0) REVERT: O 86 ASP cc_start: 0.8876 (t0) cc_final: 0.8428 (p0) REVERT: O 99 GLN cc_start: 0.8732 (pp30) cc_final: 0.8387 (pp30) REVERT: O 100 GLU cc_start: 0.8434 (tt0) cc_final: 0.7780 (tt0) REVERT: O 105 LYS cc_start: 0.8728 (ptpp) cc_final: 0.8320 (pttm) REVERT: B 26 GLN cc_start: 0.8978 (tp-100) cc_final: 0.8721 (tp-100) REVERT: B 37 GLN cc_start: 0.8231 (tp40) cc_final: 0.7460 (tp40) REVERT: B 42 GLN cc_start: 0.8396 (mp10) cc_final: 0.8049 (mp10) REVERT: B 47 LEU cc_start: 0.9683 (mp) cc_final: 0.9389 (mp) REVERT: B 70 ARG cc_start: 0.7835 (mmm160) cc_final: 0.6894 (tpt170) REVERT: B 85 ASP cc_start: 0.8354 (m-30) cc_final: 0.7978 (p0) REVERT: B 90 MET cc_start: 0.9043 (tpp) cc_final: 0.8759 (tpp) REVERT: I 31 ARG cc_start: 0.9188 (mtm110) cc_final: 0.8347 (ptp-110) REVERT: I 42 GLN cc_start: 0.8540 (mp10) cc_final: 0.8122 (mp10) REVERT: I 47 LEU cc_start: 0.9687 (mt) cc_final: 0.9405 (mp) REVERT: I 70 ARG cc_start: 0.7804 (mmm160) cc_final: 0.7052 (mmt180) REVERT: I 83 GLU cc_start: 0.8176 (tp30) cc_final: 0.7892 (mm-30) REVERT: I 85 ASP cc_start: 0.8430 (m-30) cc_final: 0.7811 (p0) REVERT: P 18 THR cc_start: 0.8979 (p) cc_final: 0.8770 (t) REVERT: P 31 ARG cc_start: 0.9036 (mtm110) cc_final: 0.8729 (ptp-110) REVERT: P 33 VAL cc_start: 0.9420 (m) cc_final: 0.9081 (m) REVERT: P 37 GLN cc_start: 0.8943 (tt0) cc_final: 0.8431 (tm-30) REVERT: P 42 GLN cc_start: 0.8425 (mp10) cc_final: 0.8082 (mp10) REVERT: P 47 LEU cc_start: 0.9670 (mt) cc_final: 0.9334 (mp) REVERT: P 70 ARG cc_start: 0.7602 (mmm160) cc_final: 0.7275 (mmt180) REVERT: P 83 GLU cc_start: 0.8084 (tp30) cc_final: 0.7843 (mm-30) REVERT: P 85 ASP cc_start: 0.8261 (m-30) cc_final: 0.7671 (p0) REVERT: P 104 LEU cc_start: 0.8572 (tp) cc_final: 0.8348 (tp) outliers start: 1 outliers final: 0 residues processed: 397 average time/residue: 0.3210 time to fit residues: 192.4861 Evaluate side-chains 312 residues out of total 2109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 312 time to evaluate : 2.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 190 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 170 optimal weight: 20.0000 chunk 94 optimal weight: 7.9990 chunk 195 optimal weight: 30.0000 chunk 158 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 116 optimal weight: 0.9980 chunk 205 optimal weight: 6.9990 chunk 57 optimal weight: 9.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 590 GLN R 300 ASN ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 20752 Z= 0.389 Angle : 0.769 10.871 28176 Z= 0.368 Chirality : 0.050 0.560 3436 Planarity : 0.004 0.034 3447 Dihedral : 10.747 99.508 4667 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.04 % Favored : 91.88 % Rotamer: Outliers : 0.05 % Allowed : 2.75 % Favored : 97.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.16), residues: 2364 helix: -1.15 (0.26), residues: 366 sheet: -1.18 (0.20), residues: 621 loop : -2.40 (0.15), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP R 112 HIS 0.008 0.001 HIS K 330 PHE 0.016 0.002 PHE K 320 TYR 0.019 0.002 TYR J 586 ARG 0.008 0.001 ARG F 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 377 time to evaluate : 2.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 535 MET cc_start: 0.8816 (mmp) cc_final: 0.8379 (mmm) REVERT: C 540 GLN cc_start: 0.9096 (mp10) cc_final: 0.8871 (mp10) REVERT: C 543 ASN cc_start: 0.9036 (t0) cc_final: 0.8624 (t0) REVERT: C 574 LYS cc_start: 0.9329 (mttm) cc_final: 0.9016 (mtmt) REVERT: C 575 GLN cc_start: 0.8905 (mp10) cc_final: 0.8578 (mp10) REVERT: C 584 GLU cc_start: 0.8948 (pm20) cc_final: 0.8645 (pm20) REVERT: C 590 GLN cc_start: 0.9519 (tp40) cc_final: 0.9081 (tp40) REVERT: C 591 GLN cc_start: 0.9684 (tm-30) cc_final: 0.9308 (tm-30) REVERT: C 654 GLU cc_start: 0.9381 (mm-30) cc_final: 0.9160 (mm-30) REVERT: C 657 GLU cc_start: 0.9544 (mm-30) cc_final: 0.9275 (mm-30) REVERT: G 49 GLU cc_start: 0.8730 (pp20) cc_final: 0.8442 (pp20) REVERT: G 95 MET cc_start: 0.9286 (ptt) cc_final: 0.8709 (ptt) REVERT: G 106 GLU cc_start: 0.8860 (tm-30) cc_final: 0.8626 (tm-30) REVERT: G 180 ASP cc_start: 0.9050 (t0) cc_final: 0.8806 (t0) REVERT: J 540 GLN cc_start: 0.8667 (mp10) cc_final: 0.8464 (mp10) REVERT: J 543 ASN cc_start: 0.9100 (m-40) cc_final: 0.8791 (t0) REVERT: J 577 GLN cc_start: 0.8982 (mt0) cc_final: 0.8590 (mt0) REVERT: J 591 GLN cc_start: 0.9789 (tm-30) cc_final: 0.9333 (tm-30) REVERT: J 624 ASP cc_start: 0.8906 (m-30) cc_final: 0.8675 (p0) REVERT: J 632 ASP cc_start: 0.9163 (t70) cc_final: 0.8874 (t70) REVERT: J 647 GLU cc_start: 0.9012 (pp20) cc_final: 0.8810 (pp20) REVERT: J 654 GLU cc_start: 0.8835 (mp0) cc_final: 0.8409 (mp0) REVERT: K 150 MET cc_start: 0.9054 (mtt) cc_final: 0.8781 (mtt) REVERT: K 475 MET cc_start: 0.8972 (mmm) cc_final: 0.8631 (mmm) REVERT: Q 543 ASN cc_start: 0.9078 (t0) cc_final: 0.8708 (t0) REVERT: Q 584 GLU cc_start: 0.9089 (pm20) cc_final: 0.8807 (pm20) REVERT: Q 624 ASP cc_start: 0.8999 (m-30) cc_final: 0.8685 (m-30) REVERT: Q 632 ASP cc_start: 0.9206 (t70) cc_final: 0.8942 (t70) REVERT: Q 643 TYR cc_start: 0.9509 (m-10) cc_final: 0.9221 (m-80) REVERT: Q 647 GLU cc_start: 0.8899 (tm-30) cc_final: 0.8627 (tm-30) REVERT: Q 659 ASP cc_start: 0.9348 (t0) cc_final: 0.9140 (t0) REVERT: R 95 MET cc_start: 0.9319 (ptt) cc_final: 0.8470 (ptt) REVERT: R 377 ASN cc_start: 0.9403 (p0) cc_final: 0.8698 (t0) REVERT: A 46 GLU cc_start: 0.8480 (tm-30) cc_final: 0.8087 (tm-30) REVERT: A 64 ASN cc_start: 0.9054 (m-40) cc_final: 0.8811 (m110) REVERT: A 81 LYS cc_start: 0.9552 (mttt) cc_final: 0.9235 (tptt) REVERT: A 82 LEU cc_start: 0.8696 (mp) cc_final: 0.8195 (mp) REVERT: A 86 ASP cc_start: 0.8756 (t70) cc_final: 0.8305 (t0) REVERT: F 1 GLN cc_start: 0.7304 (tp40) cc_final: 0.6359 (tm-30) REVERT: F 16 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7742 (mm-30) REVERT: F 80 LEU cc_start: 0.8748 (mt) cc_final: 0.7716 (mt) REVERT: F 81 LYS cc_start: 0.9608 (mttt) cc_final: 0.9008 (mmmm) REVERT: F 86 ASP cc_start: 0.8498 (t70) cc_final: 0.8190 (p0) REVERT: O 3 GLN cc_start: 0.9255 (mm110) cc_final: 0.8989 (mm110) REVERT: O 13 LYS cc_start: 0.9268 (pttm) cc_final: 0.8968 (tppp) REVERT: O 46 GLU cc_start: 0.8835 (tt0) cc_final: 0.8496 (tm-30) REVERT: O 77 GLN cc_start: 0.9048 (mm-40) cc_final: 0.8587 (tp40) REVERT: O 78 LEU cc_start: 0.9077 (mt) cc_final: 0.8522 (mt) REVERT: O 80 LEU cc_start: 0.8858 (mt) cc_final: 0.7845 (mt) REVERT: O 81 LYS cc_start: 0.9527 (mttt) cc_final: 0.8978 (mmmm) REVERT: O 82 ASN cc_start: 0.8974 (m-40) cc_final: 0.8663 (p0) REVERT: O 99 GLN cc_start: 0.8890 (pp30) cc_final: 0.8604 (pp30) REVERT: O 100 GLU cc_start: 0.8494 (tt0) cc_final: 0.7760 (tt0) REVERT: O 105 LYS cc_start: 0.8750 (ptpp) cc_final: 0.8429 (pttm) REVERT: B 26 GLN cc_start: 0.9023 (tp-100) cc_final: 0.8675 (tp-100) REVERT: B 37 GLN cc_start: 0.8373 (tp40) cc_final: 0.7621 (tp-100) REVERT: B 42 GLN cc_start: 0.8449 (mp10) cc_final: 0.7982 (mp10) REVERT: B 47 LEU cc_start: 0.9646 (mp) cc_final: 0.9354 (mp) REVERT: B 70 ARG cc_start: 0.7825 (mmm160) cc_final: 0.6998 (tpt170) REVERT: B 85 ASP cc_start: 0.8410 (m-30) cc_final: 0.8005 (p0) REVERT: B 90 MET cc_start: 0.8981 (tpp) cc_final: 0.8697 (tpp) REVERT: I 31 ARG cc_start: 0.9225 (mtm110) cc_final: 0.8489 (ptp90) REVERT: I 42 GLN cc_start: 0.8337 (mp10) cc_final: 0.7831 (mp10) REVERT: I 47 LEU cc_start: 0.9628 (mt) cc_final: 0.9217 (mp) REVERT: I 70 ARG cc_start: 0.7738 (mmm160) cc_final: 0.7009 (mmt180) REVERT: I 83 GLU cc_start: 0.8123 (tp30) cc_final: 0.7742 (tp30) REVERT: I 85 ASP cc_start: 0.8404 (m-30) cc_final: 0.7863 (p0) REVERT: I 104 LEU cc_start: 0.8546 (tp) cc_final: 0.7868 (tp) REVERT: P 18 THR cc_start: 0.9069 (p) cc_final: 0.8812 (t) REVERT: P 31 ARG cc_start: 0.9137 (mtm110) cc_final: 0.8730 (ptp90) REVERT: P 37 GLN cc_start: 0.8978 (tt0) cc_final: 0.8509 (tm-30) REVERT: P 42 GLN cc_start: 0.8562 (mp10) cc_final: 0.8315 (mp10) REVERT: P 47 LEU cc_start: 0.9669 (mt) cc_final: 0.9415 (mp) REVERT: P 70 ARG cc_start: 0.7586 (mmm160) cc_final: 0.7225 (mmt180) REVERT: P 83 GLU cc_start: 0.8064 (tp30) cc_final: 0.7804 (mm-30) REVERT: P 85 ASP cc_start: 0.8335 (m-30) cc_final: 0.7697 (p0) outliers start: 1 outliers final: 0 residues processed: 378 average time/residue: 0.3280 time to fit residues: 184.9685 Evaluate side-chains 291 residues out of total 2109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 291 time to evaluate : 2.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 77 optimal weight: 3.9990 chunk 206 optimal weight: 5.9990 chunk 45 optimal weight: 7.9990 chunk 134 optimal weight: 9.9990 chunk 56 optimal weight: 10.0000 chunk 229 optimal weight: 10.0000 chunk 190 optimal weight: 7.9990 chunk 106 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 75 optimal weight: 7.9990 chunk 120 optimal weight: 3.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 616 ASN G 422 GLN ** J 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 20752 Z= 0.379 Angle : 0.763 10.561 28176 Z= 0.367 Chirality : 0.050 0.515 3436 Planarity : 0.004 0.035 3447 Dihedral : 10.514 96.870 4667 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.80 % Favored : 91.12 % Rotamer: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.16), residues: 2364 helix: -1.00 (0.26), residues: 366 sheet: -1.14 (0.19), residues: 662 loop : -2.43 (0.16), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP K 69 HIS 0.008 0.001 HIS K 330 PHE 0.013 0.002 PHE K 320 TYR 0.018 0.002 TYR C 643 ARG 0.005 0.000 ARG I 9 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 354 time to evaluate : 2.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 530 MET cc_start: 0.9184 (ttm) cc_final: 0.8537 (mmm) REVERT: C 535 MET cc_start: 0.8815 (mmp) cc_final: 0.8367 (mmm) REVERT: C 540 GLN cc_start: 0.9084 (mp10) cc_final: 0.8856 (mp10) REVERT: C 543 ASN cc_start: 0.9106 (t0) cc_final: 0.8712 (t0) REVERT: C 574 LYS cc_start: 0.9333 (mttm) cc_final: 0.9069 (mttt) REVERT: C 575 GLN cc_start: 0.8923 (mp10) cc_final: 0.8541 (mp10) REVERT: C 590 GLN cc_start: 0.9511 (tp40) cc_final: 0.9098 (tp40) REVERT: C 591 GLN cc_start: 0.9709 (tm-30) cc_final: 0.9314 (tm-30) REVERT: C 624 ASP cc_start: 0.8964 (m-30) cc_final: 0.8728 (p0) REVERT: C 654 GLU cc_start: 0.9393 (mm-30) cc_final: 0.9167 (mm-30) REVERT: C 657 GLU cc_start: 0.9573 (mm-30) cc_final: 0.9272 (mm-30) REVERT: G 49 GLU cc_start: 0.8663 (pp20) cc_final: 0.8376 (pp20) REVERT: G 95 MET cc_start: 0.9315 (ptt) cc_final: 0.8667 (ptt) REVERT: G 106 GLU cc_start: 0.8939 (tm-30) cc_final: 0.8695 (tm-30) REVERT: J 543 ASN cc_start: 0.9070 (m-40) cc_final: 0.8735 (t0) REVERT: J 573 ILE cc_start: 0.9131 (mm) cc_final: 0.8882 (tp) REVERT: J 632 ASP cc_start: 0.9316 (t70) cc_final: 0.9017 (t70) REVERT: J 647 GLU cc_start: 0.9057 (pp20) cc_final: 0.8731 (pp20) REVERT: K 150 MET cc_start: 0.9001 (mtt) cc_final: 0.8707 (mtt) REVERT: K 475 MET cc_start: 0.8996 (mmm) cc_final: 0.8616 (mmm) REVERT: Q 543 ASN cc_start: 0.9119 (t0) cc_final: 0.8713 (t0) REVERT: Q 584 GLU cc_start: 0.9008 (pm20) cc_final: 0.8779 (pm20) REVERT: Q 624 ASP cc_start: 0.8959 (m-30) cc_final: 0.8652 (m-30) REVERT: Q 632 ASP cc_start: 0.9218 (t70) cc_final: 0.8962 (t70) REVERT: Q 643 TYR cc_start: 0.9522 (m-10) cc_final: 0.9216 (m-80) REVERT: Q 659 ASP cc_start: 0.9375 (t0) cc_final: 0.9120 (t0) REVERT: R 95 MET cc_start: 0.9319 (ptt) cc_final: 0.8297 (ptt) REVERT: R 377 ASN cc_start: 0.9308 (p0) cc_final: 0.9076 (p0) REVERT: R 434 MET cc_start: 0.8950 (ttm) cc_final: 0.8585 (ttm) REVERT: A 64 ASN cc_start: 0.9094 (m-40) cc_final: 0.8855 (m110) REVERT: A 81 LYS cc_start: 0.9588 (mttt) cc_final: 0.9267 (tptt) REVERT: A 82 LEU cc_start: 0.8719 (mp) cc_final: 0.8253 (mp) REVERT: A 86 ASP cc_start: 0.8570 (t70) cc_final: 0.8112 (t0) REVERT: F 1 GLN cc_start: 0.7550 (tp40) cc_final: 0.6521 (tm-30) REVERT: F 16 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7774 (mm-30) REVERT: F 46 GLU cc_start: 0.8206 (tm-30) cc_final: 0.7982 (tm-30) REVERT: F 80 LEU cc_start: 0.8709 (mt) cc_final: 0.7686 (mt) REVERT: F 81 LYS cc_start: 0.9622 (mttt) cc_final: 0.9181 (mmtm) REVERT: F 99 GLN cc_start: 0.8792 (pp30) cc_final: 0.8575 (pp30) REVERT: O 3 GLN cc_start: 0.9248 (mm110) cc_final: 0.8944 (mm110) REVERT: O 46 GLU cc_start: 0.8918 (tt0) cc_final: 0.8480 (tm-30) REVERT: O 80 LEU cc_start: 0.8890 (mt) cc_final: 0.7868 (mt) REVERT: O 81 LYS cc_start: 0.9539 (mttt) cc_final: 0.8972 (mmmm) REVERT: O 86 ASP cc_start: 0.8706 (t0) cc_final: 0.8377 (p0) REVERT: O 99 GLN cc_start: 0.8927 (pp30) cc_final: 0.8614 (pp30) REVERT: O 105 LYS cc_start: 0.8775 (ptpp) cc_final: 0.8450 (pttm) REVERT: B 26 GLN cc_start: 0.9061 (tp-100) cc_final: 0.8648 (tp-100) REVERT: B 37 GLN cc_start: 0.8398 (tp40) cc_final: 0.7876 (tp-100) REVERT: B 42 GLN cc_start: 0.8243 (mp10) cc_final: 0.7834 (mp10) REVERT: B 47 LEU cc_start: 0.9635 (mp) cc_final: 0.9305 (mp) REVERT: B 70 ARG cc_start: 0.7769 (mmm160) cc_final: 0.6990 (tpt170) REVERT: B 85 ASP cc_start: 0.8372 (m-30) cc_final: 0.8111 (p0) REVERT: B 90 MET cc_start: 0.9038 (tpp) cc_final: 0.8763 (tpp) REVERT: I 26 GLN cc_start: 0.9230 (tp-100) cc_final: 0.8749 (tp-100) REVERT: I 42 GLN cc_start: 0.8390 (mp10) cc_final: 0.7872 (mp10) REVERT: I 47 LEU cc_start: 0.9604 (mt) cc_final: 0.9314 (mp) REVERT: I 70 ARG cc_start: 0.7714 (mmm160) cc_final: 0.6853 (tpt90) REVERT: I 83 GLU cc_start: 0.8171 (tp30) cc_final: 0.7867 (tp30) REVERT: I 85 ASP cc_start: 0.8488 (m-30) cc_final: 0.8048 (p0) REVERT: I 104 LEU cc_start: 0.8606 (tp) cc_final: 0.7913 (tp) REVERT: P 18 THR cc_start: 0.9102 (p) cc_final: 0.8877 (t) REVERT: P 37 GLN cc_start: 0.8941 (tt0) cc_final: 0.8482 (tm-30) REVERT: P 42 GLN cc_start: 0.8462 (mp10) cc_final: 0.8216 (mp10) REVERT: P 47 LEU cc_start: 0.9656 (mt) cc_final: 0.9361 (mp) REVERT: P 48 ILE cc_start: 0.9539 (mm) cc_final: 0.9201 (mm) REVERT: P 70 ARG cc_start: 0.7506 (mmm160) cc_final: 0.6908 (tpt170) REVERT: P 83 GLU cc_start: 0.8098 (tp30) cc_final: 0.7747 (tp30) REVERT: P 85 ASP cc_start: 0.8359 (m-30) cc_final: 0.7652 (p0) outliers start: 0 outliers final: 0 residues processed: 354 average time/residue: 0.3366 time to fit residues: 180.4311 Evaluate side-chains 279 residues out of total 2109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 279 time to evaluate : 2.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 221 optimal weight: 10.0000 chunk 25 optimal weight: 0.0970 chunk 130 optimal weight: 2.9990 chunk 167 optimal weight: 2.9990 chunk 129 optimal weight: 4.9990 chunk 193 optimal weight: 10.0000 chunk 128 optimal weight: 8.9990 chunk 228 optimal weight: 6.9990 chunk 142 optimal weight: 5.9990 chunk 139 optimal weight: 0.0570 chunk 105 optimal weight: 0.9990 overall best weight: 1.4302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 258 GLN ** R 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 82AASN ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 20752 Z= 0.166 Angle : 0.673 11.592 28176 Z= 0.319 Chirality : 0.049 0.605 3436 Planarity : 0.004 0.038 3447 Dihedral : 9.932 105.031 4667 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.84 % Favored : 94.12 % Rotamer: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.16), residues: 2364 helix: -0.67 (0.28), residues: 348 sheet: -0.81 (0.21), residues: 577 loop : -2.18 (0.15), residues: 1439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 112 HIS 0.004 0.001 HIS I 38 PHE 0.008 0.001 PHE R 320 TYR 0.019 0.001 TYR C 643 ARG 0.013 0.000 ARG I 31 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 383 time to evaluate : 2.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 530 MET cc_start: 0.9139 (ttm) cc_final: 0.8503 (mmm) REVERT: C 543 ASN cc_start: 0.8969 (t0) cc_final: 0.8583 (t0) REVERT: C 574 LYS cc_start: 0.9315 (mttm) cc_final: 0.9030 (mttt) REVERT: C 584 GLU cc_start: 0.8973 (pm20) cc_final: 0.8746 (pm20) REVERT: C 621 GLU cc_start: 0.8612 (pt0) cc_final: 0.7956 (pt0) REVERT: C 654 GLU cc_start: 0.9378 (mm-30) cc_final: 0.9104 (mm-30) REVERT: C 657 GLU cc_start: 0.9544 (mm-30) cc_final: 0.9237 (mm-30) REVERT: G 49 GLU cc_start: 0.8641 (pp20) cc_final: 0.8344 (pp20) REVERT: G 69 TRP cc_start: 0.7461 (p90) cc_final: 0.7235 (p-90) REVERT: G 95 MET cc_start: 0.9268 (ptt) cc_final: 0.8698 (ptt) REVERT: G 106 GLU cc_start: 0.8793 (tm-30) cc_final: 0.8535 (tm-30) REVERT: G 161 MET cc_start: 0.8449 (tpp) cc_final: 0.8053 (tpt) REVERT: J 543 ASN cc_start: 0.9067 (m-40) cc_final: 0.8650 (t0) REVERT: J 590 GLN cc_start: 0.9575 (tp40) cc_final: 0.9309 (tp40) REVERT: J 632 ASP cc_start: 0.9185 (t70) cc_final: 0.8888 (t70) REVERT: J 647 GLU cc_start: 0.9112 (pp20) cc_final: 0.8777 (pp20) REVERT: K 194 ILE cc_start: 0.9328 (tp) cc_final: 0.8969 (tp) REVERT: K 217 TYR cc_start: 0.8752 (m-80) cc_final: 0.8346 (m-80) REVERT: Q 543 ASN cc_start: 0.9039 (t0) cc_final: 0.8644 (t0) REVERT: Q 584 GLU cc_start: 0.9082 (pm20) cc_final: 0.8693 (pm20) REVERT: Q 624 ASP cc_start: 0.8968 (m-30) cc_final: 0.8679 (m-30) REVERT: Q 626 MET cc_start: 0.8347 (ptp) cc_final: 0.8030 (ptp) REVERT: Q 632 ASP cc_start: 0.9111 (t70) cc_final: 0.8854 (t70) REVERT: Q 659 ASP cc_start: 0.9345 (t0) cc_final: 0.9078 (t0) REVERT: R 69 TRP cc_start: 0.7309 (p-90) cc_final: 0.6978 (p-90) REVERT: R 95 MET cc_start: 0.9185 (ptt) cc_final: 0.8223 (ptt) REVERT: R 377 ASN cc_start: 0.9221 (p0) cc_final: 0.8413 (t0) REVERT: R 434 MET cc_start: 0.8933 (ttm) cc_final: 0.8592 (ttm) REVERT: A 64 ASN cc_start: 0.9136 (m-40) cc_final: 0.8896 (m110) REVERT: A 81 LYS cc_start: 0.9575 (mttt) cc_final: 0.9249 (tptt) REVERT: A 82 LEU cc_start: 0.8676 (mp) cc_final: 0.8217 (mp) REVERT: A 86 ASP cc_start: 0.8782 (t70) cc_final: 0.8306 (t0) REVERT: F 1 GLN cc_start: 0.7519 (tp40) cc_final: 0.6552 (tm-30) REVERT: F 3 GLN cc_start: 0.9269 (mm110) cc_final: 0.8882 (mm110) REVERT: F 37 ILE cc_start: 0.9543 (mm) cc_final: 0.9321 (mm) REVERT: F 80 LEU cc_start: 0.8678 (mt) cc_final: 0.7709 (mt) REVERT: F 81 LYS cc_start: 0.9615 (mttt) cc_final: 0.9157 (mmtm) REVERT: F 99 GLN cc_start: 0.8811 (pp30) cc_final: 0.8540 (pp30) REVERT: O 3 GLN cc_start: 0.9254 (mm110) cc_final: 0.8639 (mp10) REVERT: O 13 LYS cc_start: 0.9180 (pttm) cc_final: 0.8891 (tppp) REVERT: O 46 GLU cc_start: 0.8899 (tt0) cc_final: 0.8482 (tm-30) REVERT: O 80 LEU cc_start: 0.8981 (mt) cc_final: 0.8110 (mt) REVERT: O 81 LYS cc_start: 0.9557 (mttt) cc_final: 0.8987 (mmmm) REVERT: O 82 ASN cc_start: 0.9073 (m-40) cc_final: 0.8727 (p0) REVERT: O 99 GLN cc_start: 0.8865 (pp30) cc_final: 0.8527 (pp30) REVERT: O 101 ASP cc_start: 0.9258 (p0) cc_final: 0.8793 (p0) REVERT: O 105 LYS cc_start: 0.8759 (ptpp) cc_final: 0.8267 (pttm) REVERT: B 37 GLN cc_start: 0.8497 (tp40) cc_final: 0.7773 (tp-100) REVERT: B 42 GLN cc_start: 0.8383 (mp10) cc_final: 0.7984 (mp10) REVERT: B 47 LEU cc_start: 0.9658 (mp) cc_final: 0.9391 (mp) REVERT: B 70 ARG cc_start: 0.7951 (mmm160) cc_final: 0.7244 (mmt180) REVERT: B 85 ASP cc_start: 0.8407 (m-30) cc_final: 0.8041 (p0) REVERT: I 26 GLN cc_start: 0.9213 (tp-100) cc_final: 0.8626 (tp-100) REVERT: I 31 ARG cc_start: 0.9121 (mtm110) cc_final: 0.8286 (ptp90) REVERT: I 42 GLN cc_start: 0.8272 (mp10) cc_final: 0.7831 (mp10) REVERT: I 47 LEU cc_start: 0.9630 (mt) cc_final: 0.9407 (mp) REVERT: I 70 ARG cc_start: 0.7820 (mmm160) cc_final: 0.7154 (tpt170) REVERT: I 83 GLU cc_start: 0.8047 (tp30) cc_final: 0.7767 (tp30) REVERT: I 85 ASP cc_start: 0.8480 (m-30) cc_final: 0.8000 (p0) REVERT: I 104 LEU cc_start: 0.8510 (tp) cc_final: 0.7809 (tp) REVERT: P 18 THR cc_start: 0.9083 (p) cc_final: 0.8880 (t) REVERT: P 31 ARG cc_start: 0.8980 (mtm110) cc_final: 0.8613 (ptp90) REVERT: P 37 GLN cc_start: 0.8918 (tt0) cc_final: 0.8317 (tm-30) REVERT: P 42 GLN cc_start: 0.8530 (mp10) cc_final: 0.8214 (mp10) REVERT: P 47 LEU cc_start: 0.9665 (mt) cc_final: 0.9409 (mp) REVERT: P 70 ARG cc_start: 0.7603 (mmm160) cc_final: 0.7280 (mmt180) REVERT: P 83 GLU cc_start: 0.8131 (tp30) cc_final: 0.7821 (tp30) REVERT: P 85 ASP cc_start: 0.8350 (m-30) cc_final: 0.7621 (p0) outliers start: 0 outliers final: 0 residues processed: 383 average time/residue: 0.3241 time to fit residues: 188.4530 Evaluate side-chains 301 residues out of total 2109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 301 time to evaluate : 2.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 141 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 136 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 44 optimal weight: 8.9990 chunk 145 optimal weight: 7.9990 chunk 155 optimal weight: 9.9990 chunk 112 optimal weight: 10.0000 chunk 21 optimal weight: 0.7980 chunk 179 optimal weight: 3.9990 chunk 207 optimal weight: 4.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20752 Z= 0.222 Angle : 0.687 12.938 28176 Z= 0.324 Chirality : 0.048 0.547 3436 Planarity : 0.004 0.046 3447 Dihedral : 9.706 101.283 4667 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.45 % Favored : 92.47 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.17), residues: 2364 helix: -0.50 (0.28), residues: 345 sheet: -0.80 (0.20), residues: 638 loop : -2.18 (0.16), residues: 1381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP K 69 HIS 0.004 0.001 HIS K 330 PHE 0.012 0.001 PHE K 320 TYR 0.021 0.001 TYR J 586 ARG 0.010 0.000 ARG P 31 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 370 time to evaluate : 2.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 535 MET cc_start: 0.8825 (mmp) cc_final: 0.8363 (mmm) REVERT: C 543 ASN cc_start: 0.9047 (t0) cc_final: 0.8651 (t0) REVERT: C 574 LYS cc_start: 0.9310 (mttm) cc_final: 0.9053 (mttt) REVERT: C 584 GLU cc_start: 0.8918 (pm20) cc_final: 0.8686 (pm20) REVERT: C 621 GLU cc_start: 0.8482 (pt0) cc_final: 0.7872 (pt0) REVERT: C 654 GLU cc_start: 0.9386 (mm-30) cc_final: 0.9122 (mm-30) REVERT: C 657 GLU cc_start: 0.9547 (mm-30) cc_final: 0.9209 (mm-30) REVERT: G 69 TRP cc_start: 0.7498 (p90) cc_final: 0.7210 (p-90) REVERT: G 95 MET cc_start: 0.9208 (ptt) cc_final: 0.8544 (ptt) REVERT: G 106 GLU cc_start: 0.8842 (tm-30) cc_final: 0.8572 (tm-30) REVERT: J 530 MET cc_start: 0.9402 (ttm) cc_final: 0.8658 (tpp) REVERT: J 543 ASN cc_start: 0.9104 (m-40) cc_final: 0.8671 (t0) REVERT: J 632 ASP cc_start: 0.9187 (t70) cc_final: 0.8905 (t70) REVERT: J 647 GLU cc_start: 0.9145 (pp20) cc_final: 0.8771 (pp20) REVERT: J 654 GLU cc_start: 0.9251 (mt-10) cc_final: 0.8953 (mt-10) REVERT: K 217 TYR cc_start: 0.8749 (m-80) cc_final: 0.8239 (m-80) REVERT: K 475 MET cc_start: 0.9177 (mmm) cc_final: 0.8888 (mmm) REVERT: Q 543 ASN cc_start: 0.9079 (t0) cc_final: 0.8699 (t0) REVERT: Q 624 ASP cc_start: 0.8940 (m-30) cc_final: 0.8652 (m-30) REVERT: Q 626 MET cc_start: 0.8350 (ptp) cc_final: 0.8013 (ptp) REVERT: Q 632 ASP cc_start: 0.9198 (t70) cc_final: 0.8961 (t70) REVERT: Q 659 ASP cc_start: 0.9345 (t0) cc_final: 0.9067 (t0) REVERT: R 69 TRP cc_start: 0.7238 (p-90) cc_final: 0.6196 (p-90) REVERT: R 95 MET cc_start: 0.9177 (ptt) cc_final: 0.8546 (ptt) REVERT: R 377 ASN cc_start: 0.9184 (p0) cc_final: 0.8408 (t0) REVERT: R 434 MET cc_start: 0.8971 (ttm) cc_final: 0.8646 (ttm) REVERT: A 64 ASN cc_start: 0.9061 (m-40) cc_final: 0.8821 (m110) REVERT: A 81 LYS cc_start: 0.9581 (mttt) cc_final: 0.9259 (tptt) REVERT: A 82 LEU cc_start: 0.8713 (mp) cc_final: 0.8248 (mp) REVERT: A 86 ASP cc_start: 0.8697 (t70) cc_final: 0.8241 (t0) REVERT: F 1 GLN cc_start: 0.7666 (tp40) cc_final: 0.6785 (tm-30) REVERT: F 80 LEU cc_start: 0.8803 (mt) cc_final: 0.7955 (mt) REVERT: F 81 LYS cc_start: 0.9620 (mttt) cc_final: 0.9204 (mmtm) REVERT: F 82 ASN cc_start: 0.8931 (m-40) cc_final: 0.8685 (p0) REVERT: F 99 GLN cc_start: 0.8877 (pp30) cc_final: 0.8615 (pp30) REVERT: O 3 GLN cc_start: 0.9240 (mm110) cc_final: 0.8943 (mm110) REVERT: O 5 GLN cc_start: 0.9180 (tp-100) cc_final: 0.8928 (tp-100) REVERT: O 13 LYS cc_start: 0.9187 (pttm) cc_final: 0.8894 (tppp) REVERT: O 46 GLU cc_start: 0.8938 (tt0) cc_final: 0.8575 (tm-30) REVERT: O 77 GLN cc_start: 0.8963 (mm-40) cc_final: 0.8468 (mm-40) REVERT: O 80 LEU cc_start: 0.9034 (mt) cc_final: 0.8166 (mt) REVERT: O 81 LYS cc_start: 0.9560 (mttt) cc_final: 0.8995 (mmmm) REVERT: O 82 ASN cc_start: 0.8972 (m-40) cc_final: 0.8669 (p0) REVERT: O 99 GLN cc_start: 0.8911 (pp30) cc_final: 0.8556 (pp30) REVERT: O 101 ASP cc_start: 0.9259 (p0) cc_final: 0.8796 (p0) REVERT: B 37 GLN cc_start: 0.8498 (tp40) cc_final: 0.7785 (tp-100) REVERT: B 42 GLN cc_start: 0.8386 (mp10) cc_final: 0.7990 (mp10) REVERT: B 47 LEU cc_start: 0.9641 (mp) cc_final: 0.9344 (mp) REVERT: B 70 ARG cc_start: 0.7868 (mmm160) cc_final: 0.7311 (mmt180) REVERT: B 85 ASP cc_start: 0.8329 (m-30) cc_final: 0.7876 (p0) REVERT: I 26 GLN cc_start: 0.9239 (tp-100) cc_final: 0.8814 (tp-100) REVERT: I 31 ARG cc_start: 0.9102 (mtm110) cc_final: 0.8159 (ptp90) REVERT: I 42 GLN cc_start: 0.8295 (mp10) cc_final: 0.7815 (mp10) REVERT: I 47 LEU cc_start: 0.9608 (mt) cc_final: 0.9339 (mp) REVERT: I 70 ARG cc_start: 0.7767 (mmm160) cc_final: 0.7005 (tpt90) REVERT: I 83 GLU cc_start: 0.8096 (tp30) cc_final: 0.7816 (tp30) REVERT: I 85 ASP cc_start: 0.8446 (m-30) cc_final: 0.8042 (p0) REVERT: I 104 LEU cc_start: 0.8597 (tp) cc_final: 0.7929 (tp) REVERT: P 31 ARG cc_start: 0.9002 (mtm110) cc_final: 0.8680 (ptp90) REVERT: P 37 GLN cc_start: 0.8901 (tt0) cc_final: 0.8317 (tm-30) REVERT: P 42 GLN cc_start: 0.8508 (mp10) cc_final: 0.8186 (mp10) REVERT: P 47 LEU cc_start: 0.9647 (mt) cc_final: 0.9342 (mp) REVERT: P 48 ILE cc_start: 0.9498 (mm) cc_final: 0.9194 (mm) REVERT: P 70 ARG cc_start: 0.7586 (mmm160) cc_final: 0.7108 (tpt170) REVERT: P 83 GLU cc_start: 0.8086 (tp30) cc_final: 0.7739 (tp30) REVERT: P 85 ASP cc_start: 0.8385 (m-30) cc_final: 0.7672 (p0) outliers start: 0 outliers final: 0 residues processed: 370 average time/residue: 0.3548 time to fit residues: 200.8337 Evaluate side-chains 301 residues out of total 2109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 301 time to evaluate : 2.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 218 optimal weight: 5.9990 chunk 199 optimal weight: 7.9990 chunk 212 optimal weight: 5.9990 chunk 128 optimal weight: 7.9990 chunk 92 optimal weight: 4.9990 chunk 167 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 192 optimal weight: 9.9990 chunk 201 optimal weight: 4.9990 chunk 139 optimal weight: 0.6980 chunk 225 optimal weight: 3.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 5 GLN ** F 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 20752 Z= 0.242 Angle : 0.699 13.033 28176 Z= 0.330 Chirality : 0.048 0.524 3436 Planarity : 0.004 0.042 3447 Dihedral : 9.597 100.213 4667 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.28 % Favored : 92.64 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.17), residues: 2364 helix: -0.50 (0.28), residues: 348 sheet: -0.83 (0.20), residues: 629 loop : -2.13 (0.16), residues: 1387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 112 HIS 0.005 0.001 HIS K 330 PHE 0.011 0.001 PHE K 320 TYR 0.021 0.001 TYR Q 586 ARG 0.009 0.000 ARG P 31 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 373 time to evaluate : 2.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 535 MET cc_start: 0.8820 (mmp) cc_final: 0.8361 (mmm) REVERT: C 543 ASN cc_start: 0.9082 (t0) cc_final: 0.8682 (t0) REVERT: C 574 LYS cc_start: 0.9310 (mttm) cc_final: 0.9046 (mttt) REVERT: C 584 GLU cc_start: 0.8917 (pm20) cc_final: 0.8679 (pm20) REVERT: C 621 GLU cc_start: 0.8645 (pt0) cc_final: 0.8201 (pt0) REVERT: C 654 GLU cc_start: 0.9385 (mm-30) cc_final: 0.9124 (mm-30) REVERT: C 657 GLU cc_start: 0.9526 (mm-30) cc_final: 0.9208 (mm-30) REVERT: G 49 GLU cc_start: 0.8646 (pp20) cc_final: 0.8359 (pp20) REVERT: G 69 TRP cc_start: 0.7481 (p90) cc_final: 0.7215 (p-90) REVERT: G 95 MET cc_start: 0.9217 (ptt) cc_final: 0.8550 (ptt) REVERT: G 106 GLU cc_start: 0.8950 (tm-30) cc_final: 0.8672 (tm-30) REVERT: G 161 MET cc_start: 0.8411 (tpp) cc_final: 0.8073 (tpt) REVERT: J 543 ASN cc_start: 0.9127 (m-40) cc_final: 0.8670 (t0) REVERT: J 590 GLN cc_start: 0.9572 (tp40) cc_final: 0.9311 (tp40) REVERT: J 632 ASP cc_start: 0.9187 (t70) cc_final: 0.8919 (t70) REVERT: J 647 GLU cc_start: 0.9136 (pp20) cc_final: 0.8769 (pp20) REVERT: J 654 GLU cc_start: 0.9189 (mt-10) cc_final: 0.8938 (mt-10) REVERT: K 217 TYR cc_start: 0.8773 (m-80) cc_final: 0.8304 (m-80) REVERT: K 475 MET cc_start: 0.9190 (mmm) cc_final: 0.8895 (mmm) REVERT: Q 530 MET cc_start: 0.9340 (ttm) cc_final: 0.8654 (mmm) REVERT: Q 535 MET cc_start: 0.9124 (tpp) cc_final: 0.8782 (tmm) REVERT: Q 543 ASN cc_start: 0.9101 (t0) cc_final: 0.8713 (t0) REVERT: Q 584 GLU cc_start: 0.9136 (pm20) cc_final: 0.8833 (pm20) REVERT: Q 624 ASP cc_start: 0.8934 (m-30) cc_final: 0.8640 (m-30) REVERT: Q 626 MET cc_start: 0.8250 (ptp) cc_final: 0.7857 (ptp) REVERT: Q 632 ASP cc_start: 0.9210 (t70) cc_final: 0.8976 (t70) REVERT: Q 659 ASP cc_start: 0.9341 (t0) cc_final: 0.9066 (t0) REVERT: R 69 TRP cc_start: 0.7152 (p-90) cc_final: 0.6355 (p-90) REVERT: R 377 ASN cc_start: 0.9213 (p0) cc_final: 0.8467 (t0) REVERT: R 434 MET cc_start: 0.8974 (ttm) cc_final: 0.8689 (ttm) REVERT: A 46 GLU cc_start: 0.8529 (tm-30) cc_final: 0.8283 (tm-30) REVERT: A 64 ASN cc_start: 0.9142 (m-40) cc_final: 0.8902 (m110) REVERT: A 81 LYS cc_start: 0.9605 (mttt) cc_final: 0.9285 (tptt) REVERT: A 82 LEU cc_start: 0.8689 (mp) cc_final: 0.8234 (mp) REVERT: A 86 ASP cc_start: 0.8694 (t70) cc_final: 0.8235 (t0) REVERT: F 1 GLN cc_start: 0.7682 (tp40) cc_final: 0.6780 (tm-30) REVERT: F 46 GLU cc_start: 0.8240 (tm-30) cc_final: 0.8001 (tm-30) REVERT: F 80 LEU cc_start: 0.8829 (mt) cc_final: 0.7748 (mt) REVERT: F 81 LYS cc_start: 0.9618 (mttt) cc_final: 0.9015 (mmmm) REVERT: F 99 GLN cc_start: 0.8886 (pp30) cc_final: 0.8605 (pp30) REVERT: O 3 GLN cc_start: 0.9269 (mm110) cc_final: 0.8987 (mm110) REVERT: O 29 MET cc_start: 0.4755 (ptp) cc_final: 0.4550 (ptp) REVERT: O 46 GLU cc_start: 0.8960 (tt0) cc_final: 0.8576 (tm-30) REVERT: O 77 GLN cc_start: 0.8944 (mm-40) cc_final: 0.8486 (mm-40) REVERT: O 80 LEU cc_start: 0.9050 (mt) cc_final: 0.8189 (mt) REVERT: O 81 LYS cc_start: 0.9562 (mttt) cc_final: 0.8998 (mmmm) REVERT: O 82 ASN cc_start: 0.8973 (m-40) cc_final: 0.8667 (p0) REVERT: O 99 GLN cc_start: 0.8934 (pp30) cc_final: 0.8586 (pp30) REVERT: O 101 ASP cc_start: 0.9257 (p0) cc_final: 0.8794 (p0) REVERT: B 37 GLN cc_start: 0.8502 (tp40) cc_final: 0.7770 (tp-100) REVERT: B 42 GLN cc_start: 0.8261 (mp10) cc_final: 0.7846 (mp10) REVERT: B 47 LEU cc_start: 0.9610 (mp) cc_final: 0.9326 (mp) REVERT: B 70 ARG cc_start: 0.7871 (mmm160) cc_final: 0.7318 (mmt180) REVERT: B 85 ASP cc_start: 0.8363 (m-30) cc_final: 0.7827 (p0) REVERT: I 26 GLN cc_start: 0.9249 (tp-100) cc_final: 0.8850 (tp-100) REVERT: I 42 GLN cc_start: 0.8311 (mp10) cc_final: 0.7819 (mp10) REVERT: I 47 LEU cc_start: 0.9627 (mt) cc_final: 0.9410 (mp) REVERT: I 70 ARG cc_start: 0.7897 (mmm160) cc_final: 0.7129 (tpt90) REVERT: I 83 GLU cc_start: 0.8117 (tp30) cc_final: 0.7831 (tp30) REVERT: I 85 ASP cc_start: 0.8478 (m-30) cc_final: 0.8058 (p0) REVERT: I 104 LEU cc_start: 0.8610 (tp) cc_final: 0.7942 (tp) REVERT: P 31 ARG cc_start: 0.8973 (mtm110) cc_final: 0.8531 (ptp90) REVERT: P 37 GLN cc_start: 0.8895 (tt0) cc_final: 0.8352 (tm-30) REVERT: P 42 GLN cc_start: 0.8516 (mp10) cc_final: 0.8196 (mp10) REVERT: P 47 LEU cc_start: 0.9647 (mt) cc_final: 0.9347 (mp) REVERT: P 70 ARG cc_start: 0.7621 (mmm160) cc_final: 0.7156 (tpt170) REVERT: P 83 GLU cc_start: 0.8088 (tp30) cc_final: 0.7769 (tp30) REVERT: P 85 ASP cc_start: 0.8397 (m-30) cc_final: 0.7635 (p0) outliers start: 0 outliers final: 0 residues processed: 373 average time/residue: 0.3257 time to fit residues: 182.9577 Evaluate side-chains 302 residues out of total 2109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 302 time to evaluate : 2.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 137 optimal weight: 8.9990 chunk 106 optimal weight: 8.9990 chunk 156 optimal weight: 9.9990 chunk 236 optimal weight: 4.9990 chunk 217 optimal weight: 0.4980 chunk 188 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 145 optimal weight: 6.9990 chunk 115 optimal weight: 8.9990 chunk 149 optimal weight: 6.9990 chunk 200 optimal weight: 2.9990 overall best weight: 4.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 20752 Z= 0.335 Angle : 0.760 14.264 28176 Z= 0.360 Chirality : 0.049 0.563 3436 Planarity : 0.004 0.041 3447 Dihedral : 9.730 100.130 4667 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.01 % Favored : 90.91 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.17), residues: 2364 helix: -0.21 (0.29), residues: 330 sheet: -0.83 (0.20), residues: 684 loop : -2.31 (0.16), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP R 112 HIS 0.008 0.001 HIS G 330 PHE 0.012 0.001 PHE K 320 TYR 0.021 0.001 TYR J 586 ARG 0.014 0.001 ARG I 31 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 360 time to evaluate : 2.538 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: C 530 MET cc_start: 0.9221 (ttm) cc_final: 0.8809 (mmm) REVERT: C 535 MET cc_start: 0.8818 (mmp) cc_final: 0.8362 (mmm) REVERT: C 543 ASN cc_start: 0.9187 (t0) cc_final: 0.8783 (t0) REVERT: C 574 LYS cc_start: 0.9307 (mttm) cc_final: 0.9051 (mttt) REVERT: C 584 GLU cc_start: 0.8912 (pm20) cc_final: 0.8690 (pm20) REVERT: C 654 GLU cc_start: 0.9393 (mm-30) cc_final: 0.9139 (mm-30) REVERT: C 657 GLU cc_start: 0.9455 (mm-30) cc_final: 0.9168 (mm-30) REVERT: G 49 GLU cc_start: 0.8664 (pp20) cc_final: 0.8383 (pp20) REVERT: G 95 MET cc_start: 0.9252 (ptt) cc_final: 0.8536 (ptt) REVERT: G 106 GLU cc_start: 0.8996 (tm-30) cc_final: 0.8719 (tm-30) REVERT: G 161 MET cc_start: 0.8376 (tpp) cc_final: 0.7961 (tpt) REVERT: G 328 MET cc_start: 0.8238 (mmp) cc_final: 0.7518 (mmp) REVERT: J 530 MET cc_start: 0.9379 (ttm) cc_final: 0.8661 (tpp) REVERT: J 543 ASN cc_start: 0.9153 (m-40) cc_final: 0.8754 (t0) REVERT: J 632 ASP cc_start: 0.9187 (t70) cc_final: 0.8890 (t70) REVERT: J 647 GLU cc_start: 0.9095 (pp20) cc_final: 0.8716 (pp20) REVERT: K 217 TYR cc_start: 0.8949 (m-80) cc_final: 0.8503 (m-80) REVERT: K 475 MET cc_start: 0.9170 (mmm) cc_final: 0.8862 (mmm) REVERT: Q 535 MET cc_start: 0.9131 (tpp) cc_final: 0.8829 (tmm) REVERT: Q 543 ASN cc_start: 0.9157 (t0) cc_final: 0.8759 (t0) REVERT: Q 584 GLU cc_start: 0.9092 (pm20) cc_final: 0.8860 (pm20) REVERT: Q 624 ASP cc_start: 0.8944 (m-30) cc_final: 0.8661 (m-30) REVERT: Q 626 MET cc_start: 0.8431 (ptp) cc_final: 0.8094 (ptp) REVERT: Q 632 ASP cc_start: 0.9253 (t70) cc_final: 0.9015 (t70) REVERT: Q 647 GLU cc_start: 0.9004 (tm-30) cc_final: 0.8791 (tm-30) REVERT: Q 659 ASP cc_start: 0.9398 (t0) cc_final: 0.9130 (t0) REVERT: R 69 TRP cc_start: 0.7116 (p-90) cc_final: 0.6321 (p-90) REVERT: R 150 MET cc_start: 0.8804 (mpp) cc_final: 0.8295 (mtt) REVERT: R 377 ASN cc_start: 0.9258 (p0) cc_final: 0.8473 (t0) REVERT: A 46 GLU cc_start: 0.8527 (tm-30) cc_final: 0.8203 (tm-30) REVERT: A 64 ASN cc_start: 0.9094 (m-40) cc_final: 0.8853 (m110) REVERT: A 81 LYS cc_start: 0.9574 (mttt) cc_final: 0.9264 (tptt) REVERT: A 82 LEU cc_start: 0.8713 (mp) cc_final: 0.8304 (mp) REVERT: A 86 ASP cc_start: 0.8526 (t70) cc_final: 0.8100 (t0) REVERT: A 99 GLN cc_start: 0.8852 (pp30) cc_final: 0.8649 (pp30) REVERT: F 1 GLN cc_start: 0.7736 (tp40) cc_final: 0.6797 (tm-30) REVERT: F 80 LEU cc_start: 0.8710 (mt) cc_final: 0.7484 (mt) REVERT: F 81 LYS cc_start: 0.9615 (mttt) cc_final: 0.9016 (mmmm) REVERT: O 3 GLN cc_start: 0.9262 (mm110) cc_final: 0.8829 (mm110) REVERT: O 29 MET cc_start: 0.4707 (ptp) cc_final: 0.4501 (ptp) REVERT: O 46 GLU cc_start: 0.8985 (tt0) cc_final: 0.8617 (tm-30) REVERT: O 77 GLN cc_start: 0.8959 (mm-40) cc_final: 0.8497 (mm-40) REVERT: O 80 LEU cc_start: 0.9080 (mt) cc_final: 0.8265 (mt) REVERT: O 81 LYS cc_start: 0.9575 (mttt) cc_final: 0.8996 (mmmm) REVERT: O 99 GLN cc_start: 0.8963 (pp30) cc_final: 0.8619 (pp30) REVERT: O 101 ASP cc_start: 0.9241 (p0) cc_final: 0.8788 (p0) REVERT: B 37 GLN cc_start: 0.8509 (tp40) cc_final: 0.7805 (tp-100) REVERT: B 42 GLN cc_start: 0.8284 (mp10) cc_final: 0.7848 (mp10) REVERT: B 47 LEU cc_start: 0.9605 (mp) cc_final: 0.9302 (mp) REVERT: B 70 ARG cc_start: 0.7811 (mmm160) cc_final: 0.7250 (mmt180) REVERT: B 85 ASP cc_start: 0.8395 (m-30) cc_final: 0.7888 (p0) REVERT: I 31 ARG cc_start: 0.9205 (mtm110) cc_final: 0.8335 (ptp90) REVERT: I 42 GLN cc_start: 0.8362 (mp10) cc_final: 0.7844 (mp10) REVERT: I 47 LEU cc_start: 0.9602 (mt) cc_final: 0.9316 (mp) REVERT: I 70 ARG cc_start: 0.7825 (mmm160) cc_final: 0.7174 (mmt180) REVERT: I 83 GLU cc_start: 0.8202 (tp30) cc_final: 0.7917 (tp30) REVERT: I 85 ASP cc_start: 0.8484 (m-30) cc_final: 0.8095 (p0) REVERT: I 104 LEU cc_start: 0.8584 (tp) cc_final: 0.7919 (tp) REVERT: P 31 ARG cc_start: 0.9053 (mtm110) cc_final: 0.8732 (ptp90) REVERT: P 37 GLN cc_start: 0.8930 (tt0) cc_final: 0.8347 (tm-30) REVERT: P 42 GLN cc_start: 0.8448 (mp10) cc_final: 0.8166 (mp10) REVERT: P 47 LEU cc_start: 0.9613 (mt) cc_final: 0.9406 (mp) REVERT: P 70 ARG cc_start: 0.7517 (mmm160) cc_final: 0.7189 (tpt170) REVERT: P 83 GLU cc_start: 0.8184 (tp30) cc_final: 0.7892 (tp30) REVERT: P 85 ASP cc_start: 0.8447 (m-30) cc_final: 0.7743 (p0) outliers start: 0 outliers final: 0 residues processed: 360 average time/residue: 0.3253 time to fit residues: 175.9315 Evaluate side-chains 287 residues out of total 2109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 287 time to evaluate : 2.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 57 optimal weight: 9.9990 chunk 173 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 188 optimal weight: 9.9990 chunk 78 optimal weight: 6.9990 chunk 193 optimal weight: 7.9990 chunk 23 optimal weight: 0.0670 chunk 34 optimal weight: 6.9990 chunk 165 optimal weight: 0.9990 chunk 10 optimal weight: 7.9990 overall best weight: 2.3924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 650 GLN ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 77 GLN O 82AASN ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.070940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.052419 restraints weight = 70816.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.054513 restraints weight = 34583.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.055924 restraints weight = 22233.870| |-----------------------------------------------------------------------------| r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.3506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20752 Z= 0.213 Angle : 0.696 13.241 28176 Z= 0.329 Chirality : 0.048 0.508 3436 Planarity : 0.004 0.046 3447 Dihedral : 9.498 102.036 4667 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.73 % Favored : 93.23 % Rotamer: Outliers : 0.05 % Allowed : 0.05 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.17), residues: 2364 helix: -0.44 (0.28), residues: 348 sheet: -0.77 (0.20), residues: 679 loop : -2.09 (0.16), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 112 HIS 0.004 0.001 HIS K 330 PHE 0.011 0.001 PHE K 320 TYR 0.019 0.001 TYR C 643 ARG 0.013 0.000 ARG I 31 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4211.63 seconds wall clock time: 77 minutes 11.41 seconds (4631.41 seconds total)