Starting phenix.real_space_refine on Mon Mar 18 10:26:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6um5_20817/03_2024/6um5_20817_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6um5_20817/03_2024/6um5_20817.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6um5_20817/03_2024/6um5_20817.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6um5_20817/03_2024/6um5_20817.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6um5_20817/03_2024/6um5_20817_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6um5_20817/03_2024/6um5_20817_neut.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.091 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 135 5.16 5 C 12822 2.51 5 N 3381 2.21 5 O 4224 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 293": "OE1" <-> "OE2" Residue "A GLU 381": "OE1" <-> "OE2" Residue "A TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 10": "OE1" <-> "OE2" Residue "C TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 293": "OE1" <-> "OE2" Residue "E GLU 381": "OE1" <-> "OE2" Residue "E TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 10": "OE1" <-> "OE2" Residue "G TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 293": "OE1" <-> "OE2" Residue "I GLU 381": "OE1" <-> "OE2" Residue "I TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 10": "OE1" <-> "OE2" Residue "K TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 20562 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 3615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3615 Classifications: {'peptide': 462} Link IDs: {'CIS': 4, 'PCIS': 2, 'PTRANS': 21, 'TRANS': 434} Chain: "B" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1030 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 1, 'TRANS': 129} Chain breaks: 1 Chain: "C" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 989 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "D" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 796 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "E" Number of atoms: 3615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3615 Classifications: {'peptide': 462} Link IDs: {'CIS': 4, 'PCIS': 2, 'PTRANS': 21, 'TRANS': 434} Chain: "F" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1030 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 1, 'TRANS': 129} Chain breaks: 1 Chain: "G" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 989 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "H" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 796 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "I" Number of atoms: 3615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3615 Classifications: {'peptide': 462} Link IDs: {'CIS': 4, 'PCIS': 2, 'PTRANS': 21, 'TRANS': 434} Chain: "J" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1030 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 1, 'TRANS': 129} Chain breaks: 1 Chain: "K" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 989 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "L" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 796 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} 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: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 2, 'MAN': 3, '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: "O" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 53 Unusual residues: {'BMA': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "P" Number of atoms: 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: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 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: "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': 2, 'MAN': 3, '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: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 53 Unusual residues: {'BMA': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 2, 'MAN': 3, '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: "c" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 53 Unusual residues: {'BMA': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "d" 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: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 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: "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: "A" 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: "E" 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: "I" 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 Time building chain proxies: 11.08, per 1000 atoms: 0.54 Number of scatterers: 20562 At special positions: 0 Unit cell: (157.68, 160.92, 140.4, 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 135 16.00 O 4224 8.00 N 3381 7.00 C 12822 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.12 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=1.98 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=1.86 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 155 " distance=2.09 Simple disulfide: pdb=" SG CYS A 200 " - pdb=" SG CYS A 433 " distance=2.05 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.01 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.15 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=1.99 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.00 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.15 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.25 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 90 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.12 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=1.98 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=1.86 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 155 " distance=2.09 Simple disulfide: pdb=" SG CYS E 200 " - pdb=" SG CYS E 433 " distance=2.05 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.01 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.15 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=1.99 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.00 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.15 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.25 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 90 " distance=2.03 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 74 " distance=2.12 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=1.98 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=1.86 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 155 " distance=2.09 Simple disulfide: pdb=" SG CYS I 200 " - pdb=" SG CYS I 433 " distance=2.05 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.01 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.15 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=1.99 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.03 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.00 Simple disulfide: pdb=" SG CYS I 501 " - pdb=" SG CYS J 605 " distance=2.15 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.02 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.25 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " 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 Atom "HETATM20210 O5 NAG A 618 .*. O " rejected from bonding due to valence issues. Atom "HETATM20336 O5 NAG E 618 .*. O " rejected from bonding due to valence issues. Atom "HETATM20462 O5 NAG I 618 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN N 4 " - " MAN N 5 " " MAN U 4 " - " MAN U 5 " " MAN b 4 " - " MAN b 5 " ALPHA1-3 " BMA N 3 " - " MAN N 4 " " BMA U 3 " - " MAN U 4 " " BMA b 3 " - " MAN b 4 " ALPHA1-6 " BMA N 6 " - " MAN N 7 " " BMA U 6 " - " MAN U 7 " " BMA b 6 " - " MAN b 7 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " BMA O 3 " - " NAG O 4 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " 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 " " BMA V 3 " - " NAG V 4 " " 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 Y 2 " - " BMA Y 3 " " 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 c 2 " - " BMA c 3 " " BMA c 3 " - " NAG c 4 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " BETA1-6 " BMA N 3 " - " BMA N 6 " " BMA U 3 " - " BMA U 6 " " BMA b 3 " - " BMA b 6 " NAG-ASN " NAG A 617 " - " ASN A 262 " " NAG A 618 " - " ASN A 386 " " NAG A 619 " - " ASN A 392 " " NAG A 622 " - " ASN A 158 " " NAG A 626 " - " ASN A 362 " " NAG A 627 " - " ASN A 276 " " NAG A 630 " - " ASN A 88 " " NAG A 631 " - " ASN A 241 " " NAG A 632 " - " ASN A 448 " " NAG E 617 " - " ASN E 262 " " NAG E 618 " - " ASN E 386 " " NAG E 619 " - " ASN E 392 " " NAG E 622 " - " ASN E 158 " " NAG E 626 " - " ASN E 362 " " NAG E 627 " - " ASN E 276 " " NAG E 630 " - " ASN E 88 " " NAG E 631 " - " ASN E 241 " " NAG E 632 " - " ASN E 448 " " NAG I 617 " - " ASN I 262 " " NAG I 618 " - " ASN I 386 " " NAG I 619 " - " ASN I 392 " " NAG I 622 " - " ASN I 158 " " NAG I 626 " - " ASN I 362 " " NAG I 627 " - " ASN I 276 " " NAG I 630 " - " ASN I 88 " " NAG I 631 " - " ASN I 241 " " NAG I 632 " - " ASN I 448 " " NAG M 1 " - " ASN A 154 " " NAG N 1 " - " ASN A 332 " " NAG O 1 " - " ASN A 300 " " NAG P 1 " - " ASN A 442 " " NAG Q 1 " - " ASN A 197 " " NAG R 1 " - " ASN A 339 " " NAG S 1 " - " ASN A 234 " " NAG T 1 " - " ASN E 154 " " NAG U 1 " - " ASN E 332 " " NAG V 1 " - " ASN E 300 " " NAG W 1 " - " ASN E 442 " " NAG X 1 " - " ASN E 197 " " NAG Y 1 " - " ASN E 339 " " NAG Z 1 " - " ASN E 234 " " NAG a 1 " - " ASN I 154 " " NAG b 1 " - " ASN I 332 " " NAG c 1 " - " ASN I 300 " " NAG d 1 " - " ASN I 442 " " NAG e 1 " - " ASN I 197 " " NAG f 1 " - " ASN I 339 " " NAG g 1 " - " ASN I 234 " Time building additional restraints: 7.93 Conformation dependent library (CDL) restraints added in 3.1 seconds 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4572 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 48 sheets defined 21.5% alpha, 29.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.52 Creating SS restraints... Processing helix chain 'A' and resid 57 through 61 Processing helix chain 'A' and resid 68 through 74 removed outlier: 4.168A pdb=" N HIS A 72 " --> pdb=" O VAL A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 116 removed outlier: 4.346A pdb=" N ASP A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 335 through 350 removed outlier: 3.511A pdb=" N GLY A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 474 through 483 removed outlier: 4.018A pdb=" N ASN A 478 " --> pdb=" O ASP A 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 525 removed outlier: 3.823A pdb=" N LEU B 523 " --> pdb=" O LEU B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 543 removed outlier: 3.626A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 596 removed outlier: 4.266A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ARG B 579 " --> pdb=" O GLN B 575 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TRP B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 615 Processing helix chain 'B' and resid 618 through 626 Processing helix chain 'B' and resid 627 through 636 removed outlier: 3.731A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 664 removed outlier: 4.265A pdb=" N ASP B 664 " --> pdb=" O LEU B 660 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 30 No H-bonds generated for 'chain 'C' and resid 28 through 30' Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'D' and resid 81 through 85 Processing helix chain 'E' and resid 57 through 61 Processing helix chain 'E' and resid 68 through 74 removed outlier: 4.168A pdb=" N HIS E 72 " --> pdb=" O VAL E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 116 removed outlier: 4.347A pdb=" N ASP E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU E 116 " --> pdb=" O TRP E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 198 Processing helix chain 'E' and resid 335 through 350 removed outlier: 3.512A pdb=" N GLY E 346 " --> pdb=" O LEU E 342 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 474 through 483 removed outlier: 4.019A pdb=" N ASN E 478 " --> pdb=" O ASP E 474 " (cutoff:3.500A) Processing helix chain 'F' and resid 520 through 525 removed outlier: 3.823A pdb=" N LEU F 523 " --> pdb=" O LEU F 520 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 543 removed outlier: 3.625A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 596 removed outlier: 4.266A pdb=" N LYS F 574 " --> pdb=" O VAL F 570 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ARG F 579 " --> pdb=" O GLN F 575 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TRP F 596 " --> pdb=" O LEU F 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 611 through 615 Processing helix chain 'F' and resid 618 through 626 Processing helix chain 'F' and resid 627 through 636 removed outlier: 3.730A pdb=" N LYS F 633 " --> pdb=" O LEU F 629 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU F 634 " --> pdb=" O GLN F 630 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 664 removed outlier: 4.265A pdb=" N ASP F 664 " --> pdb=" O LEU F 660 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 30 No H-bonds generated for 'chain 'G' and resid 28 through 30' Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'H' and resid 81 through 85 Processing helix chain 'I' and resid 57 through 61 Processing helix chain 'I' and resid 68 through 74 removed outlier: 4.168A pdb=" N HIS I 72 " --> pdb=" O VAL I 68 " (cutoff:3.500A) Processing helix chain 'I' and resid 98 through 116 removed outlier: 4.346A pdb=" N ASP I 102 " --> pdb=" O ASN I 98 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU I 116 " --> pdb=" O TRP I 112 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 198 Processing helix chain 'I' and resid 335 through 350 removed outlier: 3.511A pdb=" N GLY I 346 " --> pdb=" O LEU I 342 " (cutoff:3.500A) Processing helix chain 'I' and resid 368 through 373 Processing helix chain 'I' and resid 474 through 483 removed outlier: 4.019A pdb=" N ASN I 478 " --> pdb=" O ASP I 474 " (cutoff:3.500A) Processing helix chain 'J' and resid 520 through 525 removed outlier: 3.823A pdb=" N LEU J 523 " --> pdb=" O LEU J 520 " (cutoff:3.500A) Processing helix chain 'J' and resid 529 through 534 Processing helix chain 'J' and resid 536 through 543 removed outlier: 3.626A pdb=" N ASN J 543 " --> pdb=" O VAL J 539 " (cutoff:3.500A) Processing helix chain 'J' and resid 570 through 596 removed outlier: 4.266A pdb=" N LYS J 574 " --> pdb=" O VAL J 570 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ARG J 579 " --> pdb=" O GLN J 575 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TRP J 596 " --> pdb=" O LEU J 592 " (cutoff:3.500A) Processing helix chain 'J' and resid 611 through 615 Processing helix chain 'J' and resid 618 through 626 Processing helix chain 'J' and resid 627 through 636 removed outlier: 3.731A pdb=" N LYS J 633 " --> pdb=" O LEU J 629 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU J 634 " --> pdb=" O GLN J 630 " (cutoff:3.500A) Processing helix chain 'J' and resid 638 through 664 removed outlier: 4.265A pdb=" N ASP J 664 " --> pdb=" O LEU J 660 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 30 No H-bonds generated for 'chain 'K' and resid 28 through 30' Processing helix chain 'K' and resid 87 through 91 Processing helix chain 'L' and resid 81 through 85 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.405A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR B 606 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 removed outlier: 6.690A pdb=" N CYS A 54 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N TYR A 217 " --> pdb=" O HIS A 249 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N HIS A 249 " --> pdb=" O TYR A 217 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.850A pdb=" N PHE A 93 " --> pdb=" O GLY A 237 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 130 through 136 removed outlier: 9.744A pdb=" N ILE A 130 " --> pdb=" O LYS A 153 " (cutoff:3.500A) removed outlier: 9.581A pdb=" N LYS A 153 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 11.531A pdb=" N SER A 132 " --> pdb=" O GLU A 151 " (cutoff:3.500A) removed outlier: 9.641A pdb=" N GLU A 151 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ALA A 134 " --> pdb=" O VAL A 149 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLU A 170 " --> pdb=" O PHE A 157 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 179 through 180 Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 260 removed outlier: 4.086A pdb=" N GLY A 451 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 259 through 260 removed outlier: 4.086A pdb=" N GLY A 451 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE A 358 " --> pdb=" O TYR A 395 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR A 361 " --> pdb=" O GLY A 393 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLY A 393 " --> pdb=" O TYR A 361 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 374 through 378 removed outlier: 4.770A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS A 421 " --> pdb=" O PHE A 382 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 304 through 309 Processing sheet with id=AB2, first strand: chain 'A' and resid 423 through 424 Processing sheet with id=AB3, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AB4, first strand: chain 'C' and resid 10 through 12 removed outlier: 4.560A pdb=" N TYR C 33 " --> pdb=" O GLY C 99 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 9 through 10 removed outlier: 6.246A pdb=" N TRP D 37 " --> pdb=" O MET D 49 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 9 through 10 removed outlier: 6.081A pdb=" N THR D 98 " --> pdb=" O ALA D 94 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 18 through 23 Processing sheet with id=AB8, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.405A pdb=" N VAL E 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR F 606 " --> pdb=" O VAL E 36 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AC1, first strand: chain 'E' and resid 75 through 76 removed outlier: 6.690A pdb=" N CYS E 54 " --> pdb=" O VAL E 75 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N TYR E 217 " --> pdb=" O HIS E 249 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N HIS E 249 " --> pdb=" O TYR E 217 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 91 through 94 removed outlier: 3.850A pdb=" N PHE E 93 " --> pdb=" O GLY E 237 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 130 through 136 removed outlier: 9.744A pdb=" N ILE E 130 " --> pdb=" O LYS E 153 " (cutoff:3.500A) removed outlier: 9.581A pdb=" N LYS E 153 " --> pdb=" O ILE E 130 " (cutoff:3.500A) removed outlier: 11.531A pdb=" N SER E 132 " --> pdb=" O GLU E 151 " (cutoff:3.500A) removed outlier: 9.641A pdb=" N GLU E 151 " --> pdb=" O SER E 132 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ALA E 134 " --> pdb=" O VAL E 149 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLU E 170 " --> pdb=" O PHE E 157 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 179 through 180 Processing sheet with id=AC5, first strand: chain 'E' and resid 259 through 260 removed outlier: 4.086A pdb=" N GLY E 451 " --> pdb=" O LEU E 260 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 259 through 260 removed outlier: 4.086A pdb=" N GLY E 451 " --> pdb=" O LEU E 260 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE E 358 " --> pdb=" O TYR E 395 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR E 361 " --> pdb=" O GLY E 393 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLY E 393 " --> pdb=" O TYR E 361 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 374 through 378 removed outlier: 4.770A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS E 421 " --> pdb=" O PHE E 382 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 304 through 309 Processing sheet with id=AC9, first strand: chain 'E' and resid 423 through 424 Processing sheet with id=AD1, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AD2, first strand: chain 'G' and resid 10 through 12 removed outlier: 4.561A pdb=" N TYR G 33 " --> pdb=" O GLY G 99 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 9 through 10 removed outlier: 6.246A pdb=" N TRP H 37 " --> pdb=" O MET H 49 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 9 through 10 removed outlier: 6.081A pdb=" N THR H 98 " --> pdb=" O ALA H 94 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 18 through 23 Processing sheet with id=AD6, first strand: chain 'I' and resid 494 through 499 removed outlier: 5.405A pdb=" N VAL I 36 " --> pdb=" O THR J 606 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR J 606 " --> pdb=" O VAL I 36 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 45 through 47 Processing sheet with id=AD8, first strand: chain 'I' and resid 75 through 76 removed outlier: 6.689A pdb=" N CYS I 54 " --> pdb=" O VAL I 75 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N TYR I 217 " --> pdb=" O HIS I 249 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N HIS I 249 " --> pdb=" O TYR I 217 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 91 through 94 removed outlier: 3.851A pdb=" N PHE I 93 " --> pdb=" O GLY I 237 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 130 through 136 removed outlier: 9.744A pdb=" N ILE I 130 " --> pdb=" O LYS I 153 " (cutoff:3.500A) removed outlier: 9.581A pdb=" N LYS I 153 " --> pdb=" O ILE I 130 " (cutoff:3.500A) removed outlier: 11.531A pdb=" N SER I 132 " --> pdb=" O GLU I 151 " (cutoff:3.500A) removed outlier: 9.641A pdb=" N GLU I 151 " --> pdb=" O SER I 132 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ALA I 134 " --> pdb=" O VAL I 149 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLU I 170 " --> pdb=" O PHE I 157 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 179 through 180 Processing sheet with id=AE3, first strand: chain 'I' and resid 259 through 260 removed outlier: 4.087A pdb=" N GLY I 451 " --> pdb=" O LEU I 260 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 259 through 260 removed outlier: 4.087A pdb=" N GLY I 451 " --> pdb=" O LEU I 260 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE I 358 " --> pdb=" O TYR I 395 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR I 361 " --> pdb=" O GLY I 393 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLY I 393 " --> pdb=" O TYR I 361 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 374 through 378 removed outlier: 4.770A pdb=" N PHE I 382 " --> pdb=" O LYS I 421 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS I 421 " --> pdb=" O PHE I 382 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 304 through 309 Processing sheet with id=AE7, first strand: chain 'I' and resid 423 through 424 Processing sheet with id=AE8, first strand: chain 'K' and resid 3 through 6 Processing sheet with id=AE9, first strand: chain 'K' and resid 10 through 12 removed outlier: 4.560A pdb=" N TYR K 33 " --> pdb=" O GLY K 99 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 9 through 10 removed outlier: 6.246A pdb=" N TRP L 37 " --> pdb=" O MET L 49 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 9 through 10 removed outlier: 6.081A pdb=" N THR L 98 " --> pdb=" O ALA L 94 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 18 through 23 750 hydrogen bonds defined for protein. 1872 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: 6.77 Time building geometry restraints manager: 8.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 3310 1.31 - 1.44: 5955 1.44 - 1.57: 11525 1.57 - 1.70: 0 1.70 - 1.83: 186 Bond restraints: 20976 Sorted by residual: bond pdb=" N PRO I 354 " pdb=" CA PRO I 354 " ideal model delta sigma weight residual 1.469 1.702 -0.234 1.28e-02 6.10e+03 3.33e+02 bond pdb=" N PRO A 354 " pdb=" CA PRO A 354 " ideal model delta sigma weight residual 1.469 1.702 -0.234 1.28e-02 6.10e+03 3.33e+02 bond pdb=" N PRO E 354 " pdb=" CA PRO E 354 " ideal model delta sigma weight residual 1.469 1.702 -0.233 1.28e-02 6.10e+03 3.31e+02 bond pdb=" N PRO I 220 " pdb=" CD PRO I 220 " ideal model delta sigma weight residual 1.473 1.395 0.078 1.40e-02 5.10e+03 3.13e+01 bond pdb=" N PRO E 220 " pdb=" CD PRO E 220 " ideal model delta sigma weight residual 1.473 1.395 0.078 1.40e-02 5.10e+03 3.11e+01 ... (remaining 20971 not shown) Histogram of bond angle deviations from ideal: 87.84 - 98.08: 18 98.08 - 108.32: 1619 108.32 - 118.56: 15764 118.56 - 128.80: 10904 128.80 - 139.04: 204 Bond angle restraints: 28509 Sorted by residual: angle pdb=" C PHE I 353 " pdb=" N PRO I 354 " pdb=" CA PRO I 354 " ideal model delta sigma weight residual 119.84 139.04 -19.20 1.25e+00 6.40e-01 2.36e+02 angle pdb=" C PHE E 353 " pdb=" N PRO E 354 " pdb=" CA PRO E 354 " ideal model delta sigma weight residual 119.84 139.03 -19.19 1.25e+00 6.40e-01 2.36e+02 angle pdb=" C PHE A 353 " pdb=" N PRO A 354 " pdb=" CA PRO A 354 " ideal model delta sigma weight residual 119.84 139.02 -19.18 1.25e+00 6.40e-01 2.35e+02 angle pdb=" C ASN E 197 " pdb=" CA ASN E 197 " pdb=" CB ASN E 197 " ideal model delta sigma weight residual 110.79 91.24 19.55 1.66e+00 3.63e-01 1.39e+02 angle pdb=" C ASN I 197 " pdb=" CA ASN I 197 " pdb=" CB ASN I 197 " ideal model delta sigma weight residual 110.79 91.26 19.53 1.66e+00 3.63e-01 1.38e+02 ... (remaining 28504 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.00: 12768 23.00 - 46.01: 663 46.01 - 69.01: 189 69.01 - 92.02: 87 92.02 - 115.02: 60 Dihedral angle restraints: 13767 sinusoidal: 6615 harmonic: 7152 Sorted by residual: dihedral pdb=" C HIS I 249 " pdb=" N HIS I 249 " pdb=" CA HIS I 249 " pdb=" CB HIS I 249 " ideal model delta harmonic sigma weight residual -122.60 -93.20 -29.40 0 2.50e+00 1.60e-01 1.38e+02 dihedral pdb=" C HIS E 249 " pdb=" N HIS E 249 " pdb=" CA HIS E 249 " pdb=" CB HIS E 249 " ideal model delta harmonic sigma weight residual -122.60 -93.23 -29.37 0 2.50e+00 1.60e-01 1.38e+02 dihedral pdb=" C HIS A 249 " pdb=" N HIS A 249 " pdb=" CA HIS A 249 " pdb=" CB HIS A 249 " ideal model delta harmonic sigma weight residual -122.60 -93.24 -29.36 0 2.50e+00 1.60e-01 1.38e+02 ... (remaining 13764 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.271: 3360 0.271 - 0.541: 96 0.541 - 0.812: 15 0.812 - 1.082: 3 1.082 - 1.353: 6 Chirality restraints: 3480 Sorted by residual: chirality pdb=" C1 MAN U 7 " pdb=" O6 BMA U 6 " pdb=" C2 MAN U 7 " pdb=" O5 MAN U 7 " both_signs ideal model delta sigma weight residual False 2.40 1.05 1.35 2.00e-02 2.50e+03 4.57e+03 chirality pdb=" C1 MAN N 7 " pdb=" O6 BMA N 6 " pdb=" C2 MAN N 7 " pdb=" O5 MAN N 7 " both_signs ideal model delta sigma weight residual False 2.40 1.05 1.35 2.00e-02 2.50e+03 4.56e+03 chirality pdb=" C1 MAN b 7 " pdb=" O6 BMA b 6 " pdb=" C2 MAN b 7 " pdb=" O5 MAN b 7 " both_signs ideal model delta sigma weight residual False 2.40 1.05 1.35 2.00e-02 2.50e+03 4.56e+03 ... (remaining 3477 not shown) Planarity restraints: 3549 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG I 622 " -0.317 2.00e-02 2.50e+03 2.63e-01 8.65e+02 pdb=" C7 NAG I 622 " 0.100 2.00e-02 2.50e+03 pdb=" C8 NAG I 622 " -0.207 2.00e-02 2.50e+03 pdb=" N2 NAG I 622 " 0.439 2.00e-02 2.50e+03 pdb=" O7 NAG I 622 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 622 " 0.316 2.00e-02 2.50e+03 2.63e-01 8.64e+02 pdb=" C7 NAG A 622 " -0.100 2.00e-02 2.50e+03 pdb=" C8 NAG A 622 " 0.207 2.00e-02 2.50e+03 pdb=" N2 NAG A 622 " -0.438 2.00e-02 2.50e+03 pdb=" O7 NAG A 622 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 622 " -0.316 2.00e-02 2.50e+03 2.63e-01 8.64e+02 pdb=" C7 NAG E 622 " 0.101 2.00e-02 2.50e+03 pdb=" C8 NAG E 622 " -0.207 2.00e-02 2.50e+03 pdb=" N2 NAG E 622 " 0.438 2.00e-02 2.50e+03 pdb=" O7 NAG E 622 " -0.015 2.00e-02 2.50e+03 ... (remaining 3546 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 330 2.60 - 3.17: 17866 3.17 - 3.75: 29267 3.75 - 4.32: 40517 4.32 - 4.90: 65542 Nonbonded interactions: 153522 Sorted by model distance: nonbonded pdb=" O3 NAG A 630 " pdb=" O7 NAG A 630 " model vdw 2.022 2.440 nonbonded pdb=" O3 NAG E 630 " pdb=" O7 NAG E 630 " model vdw 2.022 2.440 nonbonded pdb=" O3 NAG I 630 " pdb=" O7 NAG I 630 " model vdw 2.022 2.440 nonbonded pdb=" O4 NAG I 626 " pdb=" O6 NAG I 626 " model vdw 2.029 2.440 nonbonded pdb=" O4 NAG A 626 " pdb=" O6 NAG A 626 " model vdw 2.029 2.440 ... (remaining 153517 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 'E' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'X' selection = chain 'Z' selection = chain 'a' selection = chain 'e' selection = chain 'g' } ncs_group { reference = chain 'N' selection = chain 'U' selection = chain 'b' } ncs_group { reference = chain 'O' selection = chain 'V' selection = chain 'c' } ncs_group { reference = chain 'P' selection = chain 'R' selection = chain 'W' selection = chain 'Y' selection = chain 'd' selection = chain 'f' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 8.090 Check model and map are aligned: 0.340 Set scattering table: 0.210 Process input model: 57.600 Find NCS groups from input model: 1.460 Set up NCS constraints: 0.310 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6688 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 : 0.010 0.234 20976 Z= 0.657 Angle : 1.575 23.463 28509 Z= 0.814 Chirality : 0.118 1.353 3480 Planarity : 0.022 0.263 3501 Dihedral : 17.842 115.020 9069 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 1.22 % Allowed : 5.98 % Favored : 92.80 % Rotamer: Outliers : 4.06 % Allowed : 6.57 % Favored : 89.37 % Cbeta Deviations : 1.18 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.51 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.16), residues: 2457 helix: -0.81 (0.24), residues: 393 sheet: -0.30 (0.18), residues: 717 loop : -1.98 (0.16), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP J 596 HIS 0.005 0.002 HIS A 249 PHE 0.025 0.003 PHE I 353 TYR 0.013 0.002 TYR G 95 ARG 0.005 0.001 ARG K 98 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 438 time to evaluate : 2.427 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 SER cc_start: 0.6814 (t) cc_final: 0.6559 (p) REVERT: B 584 GLU cc_start: 0.7722 (tm-30) cc_final: 0.7452 (tm-30) REVERT: F 584 GLU cc_start: 0.7684 (tm-30) cc_final: 0.7333 (tm-30) REVERT: I 99 ASP cc_start: 0.5812 (p0) cc_final: 0.5534 (p0) REVERT: J 584 GLU cc_start: 0.7792 (tm-30) cc_final: 0.7514 (tm-30) outliers start: 87 outliers final: 31 residues processed: 510 average time/residue: 0.3417 time to fit residues: 262.2146 Evaluate side-chains 234 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 203 time to evaluate : 1.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 207 optimal weight: 3.9990 chunk 186 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 125 optimal weight: 0.7980 chunk 99 optimal weight: 0.9990 chunk 192 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 117 optimal weight: 7.9990 chunk 143 optimal weight: 0.9990 chunk 223 optimal weight: 10.0000 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 203 GLN A 249 HIS A 404 ASN ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 GLN D 6 GLN ** E 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 ASN E 203 GLN E 249 HIS E 404 ASN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 652 GLN G 1 GLN G 39 GLN H 6 GLN ** I 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 186 ASN I 203 GLN I 249 HIS I 404 ASN ** J 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN L 6 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6713 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 20976 Z= 0.248 Angle : 0.914 12.702 28509 Z= 0.442 Chirality : 0.064 0.820 3480 Planarity : 0.005 0.070 3501 Dihedral : 15.391 91.802 4641 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.49 % Allowed : 6.67 % Favored : 92.84 % Rotamer: Outliers : 0.14 % Allowed : 2.89 % Favored : 96.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.51 % Twisted Proline : 3.03 % Twisted General : 0.34 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.16), residues: 2457 helix: -0.30 (0.24), residues: 423 sheet: 0.11 (0.19), residues: 702 loop : -2.02 (0.16), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 37 HIS 0.007 0.001 HIS E 249 PHE 0.037 0.003 PHE E 157 TYR 0.012 0.001 TYR A 223 ARG 0.009 0.001 ARG G 85 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 312 time to evaluate : 2.387 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASP cc_start: 0.5938 (p0) cc_final: 0.5620 (p0) REVERT: A 434 MET cc_start: 0.7061 (mtm) cc_final: 0.6718 (mtm) REVERT: B 584 GLU cc_start: 0.8437 (tm-30) cc_final: 0.8123 (tm-30) REVERT: E 369 MET cc_start: 0.6653 (mtp) cc_final: 0.5999 (ttm) REVERT: F 584 GLU cc_start: 0.8373 (tm-30) cc_final: 0.8090 (tm-30) REVERT: J 584 GLU cc_start: 0.8351 (tm-30) cc_final: 0.8107 (tm-30) outliers start: 3 outliers final: 0 residues processed: 315 average time/residue: 0.2942 time to fit residues: 146.1034 Evaluate side-chains 195 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 2.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 124 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 chunk 185 optimal weight: 4.9990 chunk 152 optimal weight: 0.2980 chunk 61 optimal weight: 1.9990 chunk 223 optimal weight: 9.9990 chunk 241 optimal weight: 9.9990 chunk 199 optimal weight: 20.0000 chunk 221 optimal weight: 0.9990 chunk 76 optimal weight: 7.9990 chunk 179 optimal weight: 5.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 651 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6892 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 20976 Z= 0.289 Angle : 0.832 11.409 28509 Z= 0.415 Chirality : 0.058 0.583 3480 Planarity : 0.005 0.070 3501 Dihedral : 13.231 79.255 4641 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.49 % Favored : 92.14 % Rotamer: Outliers : 0.33 % Allowed : 3.17 % Favored : 96.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.51 % Twisted Proline : 3.03 % Twisted General : 0.38 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.16), residues: 2457 helix: -0.42 (0.24), residues: 408 sheet: -0.01 (0.20), residues: 651 loop : -1.69 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP J 596 HIS 0.006 0.001 HIS E 249 PHE 0.030 0.003 PHE E 157 TYR 0.013 0.002 TYR A 40 ARG 0.017 0.001 ARG A 164 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 252 time to evaluate : 2.556 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: symmetry clash revert: symmetry clash REVERT: A 369 MET cc_start: 0.6452 (mtp) cc_final: 0.6182 (ttm) REVERT: A 434 MET cc_start: 0.6813 (mtm) cc_final: 0.6388 (mtm) REVERT: B 584 GLU cc_start: 0.8554 (tm-30) cc_final: 0.8235 (tm-30) REVERT: E 369 MET cc_start: 0.6610 (mtp) cc_final: 0.5960 (ttm) REVERT: F 584 GLU cc_start: 0.8465 (tm-30) cc_final: 0.8231 (tm-30) REVERT: J 584 GLU cc_start: 0.8429 (tm-30) cc_final: 0.8134 (tm-30) outliers start: 7 outliers final: 3 residues processed: 256 average time/residue: 0.2896 time to fit residues: 119.9080 Evaluate side-chains 173 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 170 time to evaluate : 2.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 221 optimal weight: 5.9990 chunk 168 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 chunk 106 optimal weight: 9.9990 chunk 150 optimal weight: 9.9990 chunk 224 optimal weight: 20.0000 chunk 237 optimal weight: 0.8980 chunk 117 optimal weight: 8.9990 chunk 212 optimal weight: 9.9990 chunk 64 optimal weight: 3.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 289 HIS ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 640 GLN B 651 ASN ** E 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 289 HIS ** E 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 640 GLN F 651 ASN ** I 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 289 HIS ** I 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 591 GLN J 640 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 moved from start: 0.4617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 20976 Z= 0.341 Angle : 0.823 11.549 28509 Z= 0.417 Chirality : 0.055 0.459 3480 Planarity : 0.005 0.072 3501 Dihedral : 12.335 70.077 4641 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.37 % Allowed : 8.91 % Favored : 90.72 % Rotamer: Outliers : 0.14 % Allowed : 3.96 % Favored : 95.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.51 % Twisted Proline : 3.03 % Twisted General : 0.38 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.16), residues: 2457 helix: -0.27 (0.24), residues: 408 sheet: -0.25 (0.19), residues: 678 loop : -1.85 (0.16), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 45 HIS 0.005 0.001 HIS A 287 PHE 0.023 0.002 PHE E 157 TYR 0.017 0.002 TYR K 94 ARG 0.014 0.001 ARG G 85 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 246 time to evaluate : 2.487 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: symmetry clash REVERT: A 369 MET cc_start: 0.6384 (mtp) cc_final: 0.6129 (ttm) REVERT: A 434 MET cc_start: 0.6740 (mtm) cc_final: 0.6161 (mtm) REVERT: B 584 GLU cc_start: 0.8600 (tm-30) cc_final: 0.8292 (tm-30) REVERT: C 83 LEU cc_start: 0.7434 (mm) cc_final: 0.7229 (mm) REVERT: E 369 MET cc_start: 0.6562 (mtp) cc_final: 0.6218 (ttm) REVERT: E 434 MET cc_start: 0.7109 (mtm) cc_final: 0.6471 (mtt) REVERT: J 584 GLU cc_start: 0.8465 (tm-30) cc_final: 0.8160 (tm-30) REVERT: J 589 ASP cc_start: 0.8411 (t70) cc_final: 0.7415 (t0) outliers start: 3 outliers final: 3 residues processed: 246 average time/residue: 0.2892 time to fit residues: 114.6511 Evaluate side-chains 165 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 162 time to evaluate : 2.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 198 optimal weight: 1.9990 chunk 134 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 177 optimal weight: 5.9990 chunk 98 optimal weight: 0.9980 chunk 202 optimal weight: 4.9990 chunk 164 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 121 optimal weight: 4.9990 chunk 213 optimal weight: 5.9990 chunk 60 optimal weight: 20.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 HIS ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 GLN ** E 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 591 GLN ** I 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.5036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 20976 Z= 0.330 Angle : 0.822 11.467 28509 Z= 0.412 Chirality : 0.056 0.569 3480 Planarity : 0.005 0.077 3501 Dihedral : 12.491 94.022 4641 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.37 % Allowed : 8.79 % Favored : 90.84 % Rotamer: Outliers : 0.05 % Allowed : 2.61 % Favored : 97.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.51 % Twisted Proline : 0.00 % Twisted General : 0.34 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.16), residues: 2457 helix: -0.32 (0.24), residues: 408 sheet: -0.36 (0.19), residues: 678 loop : -1.82 (0.16), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 112 HIS 0.003 0.001 HIS A 287 PHE 0.040 0.003 PHE A 157 TYR 0.021 0.002 TYR K 95 ARG 0.010 0.001 ARG C 85 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 241 time to evaluate : 2.285 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: A 369 MET cc_start: 0.6261 (mtp) cc_final: 0.6015 (ttm) REVERT: A 434 MET cc_start: 0.6899 (mtm) cc_final: 0.6125 (mtm) REVERT: B 584 GLU cc_start: 0.8646 (tm-30) cc_final: 0.8279 (tm-30) REVERT: C 90 ASP cc_start: 0.8443 (m-30) cc_final: 0.8232 (m-30) REVERT: E 369 MET cc_start: 0.6472 (mtp) cc_final: 0.6104 (ttm) REVERT: E 434 MET cc_start: 0.7197 (mtm) cc_final: 0.6635 (mtt) REVERT: F 589 ASP cc_start: 0.8454 (t70) cc_final: 0.8017 (t70) REVERT: I 369 MET cc_start: 0.6391 (mtp) cc_final: 0.6160 (ttm) REVERT: J 584 GLU cc_start: 0.8458 (tm-30) cc_final: 0.8159 (tm-30) REVERT: J 589 ASP cc_start: 0.8507 (t70) cc_final: 0.8098 (t0) REVERT: J 626 MET cc_start: 0.7797 (tpp) cc_final: 0.7520 (tmm) REVERT: K 90 ASP cc_start: 0.8539 (m-30) cc_final: 0.8316 (m-30) outliers start: 1 outliers final: 1 residues processed: 241 average time/residue: 0.2952 time to fit residues: 114.5957 Evaluate side-chains 160 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 159 time to evaluate : 2.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 80 optimal weight: 9.9990 chunk 214 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 139 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 238 optimal weight: 10.0000 chunk 197 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 19 optimal weight: 10.0000 chunk 78 optimal weight: 20.0000 chunk 124 optimal weight: 20.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 HIS ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 287 HIS ** E 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.5309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 20976 Z= 0.269 Angle : 0.769 11.264 28509 Z= 0.387 Chirality : 0.054 0.502 3480 Planarity : 0.004 0.057 3501 Dihedral : 11.791 82.058 4641 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.59 % Favored : 91.17 % Rotamer: Outliers : 0.05 % Allowed : 2.42 % Favored : 97.53 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 4.04 % Cis-general : 0.51 % Twisted Proline : 2.02 % Twisted General : 0.38 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.16), residues: 2457 helix: -0.13 (0.25), residues: 408 sheet: -0.29 (0.19), residues: 672 loop : -1.88 (0.16), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP F 596 HIS 0.004 0.001 HIS I 287 PHE 0.015 0.002 PHE I 157 TYR 0.018 0.001 TYR G 94 ARG 0.009 0.001 ARG G 85 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 240 time to evaluate : 1.816 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: A 434 MET cc_start: 0.6921 (mtm) cc_final: 0.6188 (mtm) REVERT: B 584 GLU cc_start: 0.8572 (tm-30) cc_final: 0.8194 (tm-30) REVERT: E 369 MET cc_start: 0.6387 (mtp) cc_final: 0.6135 (ttm) REVERT: E 434 MET cc_start: 0.7266 (mtm) cc_final: 0.6696 (mtm) REVERT: F 589 ASP cc_start: 0.8271 (t70) cc_final: 0.8061 (t70) REVERT: I 107 ASP cc_start: 0.4652 (t0) cc_final: 0.4404 (t0) REVERT: I 369 MET cc_start: 0.6389 (mtp) cc_final: 0.6179 (ttm) REVERT: J 584 GLU cc_start: 0.8476 (tm-30) cc_final: 0.8154 (tm-30) REVERT: J 589 ASP cc_start: 0.8472 (t70) cc_final: 0.8164 (t0) REVERT: J 626 MET cc_start: 0.7515 (tpp) cc_final: 0.7159 (tmm) REVERT: K 90 ASP cc_start: 0.8513 (m-30) cc_final: 0.8308 (m-30) outliers start: 1 outliers final: 1 residues processed: 241 average time/residue: 0.2869 time to fit residues: 111.4361 Evaluate side-chains 170 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 169 time to evaluate : 2.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 229 optimal weight: 9.9990 chunk 26 optimal weight: 10.0000 chunk 135 optimal weight: 2.9990 chunk 173 optimal weight: 3.9990 chunk 134 optimal weight: 0.7980 chunk 200 optimal weight: 0.0040 chunk 132 optimal weight: 5.9990 chunk 237 optimal weight: 8.9990 chunk 148 optimal weight: 10.0000 chunk 144 optimal weight: 4.9990 chunk 109 optimal weight: 7.9990 overall best weight: 2.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 350 GLN ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 350 GLN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 350 GLN ** J 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.5523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 20976 Z= 0.253 Angle : 0.755 11.193 28509 Z= 0.383 Chirality : 0.053 0.485 3480 Planarity : 0.004 0.061 3501 Dihedral : 11.314 76.193 4641 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.75 % Favored : 90.96 % Rotamer: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.51 % Twisted Proline : 0.00 % Twisted General : 0.38 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.16), residues: 2457 helix: -0.06 (0.25), residues: 390 sheet: -0.30 (0.19), residues: 684 loop : -1.83 (0.16), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP F 596 HIS 0.003 0.001 HIS E 330 PHE 0.018 0.002 PHE J 519 TYR 0.015 0.001 TYR G 94 ARG 0.008 0.001 ARG C 85 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 238 time to evaluate : 2.406 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: A 286 VAL cc_start: 0.8552 (t) cc_final: 0.8290 (t) REVERT: B 584 GLU cc_start: 0.8541 (tm-30) cc_final: 0.8159 (tm-30) REVERT: B 589 ASP cc_start: 0.8503 (t0) cc_final: 0.8021 (t0) REVERT: B 648 GLU cc_start: 0.8925 (pm20) cc_final: 0.8720 (pm20) REVERT: C 90 ASP cc_start: 0.8533 (m-30) cc_final: 0.8315 (m-30) REVERT: E 369 MET cc_start: 0.6460 (mtp) cc_final: 0.6192 (ttm) REVERT: E 434 MET cc_start: 0.7111 (mtm) cc_final: 0.6308 (mtm) REVERT: F 589 ASP cc_start: 0.8441 (t70) cc_final: 0.8146 (t70) REVERT: I 434 MET cc_start: 0.6801 (ttm) cc_final: 0.6553 (ttm) REVERT: J 584 GLU cc_start: 0.8446 (tm-30) cc_final: 0.8194 (tm-30) REVERT: J 589 ASP cc_start: 0.8615 (t70) cc_final: 0.8199 (t0) REVERT: J 626 MET cc_start: 0.7679 (tpp) cc_final: 0.7358 (tmm) outliers start: 0 outliers final: 0 residues processed: 238 average time/residue: 0.3079 time to fit residues: 117.3602 Evaluate side-chains 166 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 2.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 146 optimal weight: 0.9990 chunk 94 optimal weight: 0.5980 chunk 141 optimal weight: 10.0000 chunk 71 optimal weight: 0.9990 chunk 46 optimal weight: 9.9990 chunk 45 optimal weight: 0.9980 chunk 150 optimal weight: 9.9990 chunk 161 optimal weight: 9.9990 chunk 117 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 186 optimal weight: 6.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN ** E 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.5661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 20976 Z= 0.228 Angle : 0.743 11.121 28509 Z= 0.377 Chirality : 0.052 0.459 3480 Planarity : 0.004 0.063 3501 Dihedral : 11.008 68.538 4641 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.14 % Favored : 91.58 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.51 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.16), residues: 2457 helix: -0.14 (0.25), residues: 408 sheet: -0.16 (0.20), residues: 642 loop : -1.81 (0.16), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 112 HIS 0.003 0.001 HIS E 330 PHE 0.023 0.002 PHE E 157 TYR 0.017 0.001 TYR I 40 ARG 0.008 0.001 ARG F 585 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 232 time to evaluate : 2.514 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: B 584 GLU cc_start: 0.8577 (tm-30) cc_final: 0.8110 (tm-30) REVERT: B 589 ASP cc_start: 0.8351 (t0) cc_final: 0.7860 (t0) REVERT: E 369 MET cc_start: 0.6459 (mtp) cc_final: 0.6251 (ttm) REVERT: E 434 MET cc_start: 0.7088 (mtm) cc_final: 0.6286 (mtm) REVERT: F 648 GLU cc_start: 0.8874 (pm20) cc_final: 0.8653 (pm20) REVERT: J 584 GLU cc_start: 0.8465 (tm-30) cc_final: 0.8196 (tm-30) REVERT: J 589 ASP cc_start: 0.8379 (t70) cc_final: 0.8017 (t0) REVERT: J 626 MET cc_start: 0.7723 (tpp) cc_final: 0.7322 (tmm) outliers start: 0 outliers final: 0 residues processed: 232 average time/residue: 0.2782 time to fit residues: 103.8644 Evaluate side-chains 160 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 2.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 215 optimal weight: 0.9990 chunk 227 optimal weight: 0.0980 chunk 207 optimal weight: 2.9990 chunk 220 optimal weight: 0.6980 chunk 132 optimal weight: 0.8980 chunk 96 optimal weight: 4.9990 chunk 173 optimal weight: 0.9990 chunk 67 optimal weight: 6.9990 chunk 199 optimal weight: 3.9990 chunk 208 optimal weight: 5.9990 chunk 145 optimal weight: 0.2980 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 GLN D 39 GLN ** E 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 HIS ** E 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 540 GLN ** I 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 540 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6937 moved from start: 0.5785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20976 Z= 0.167 Angle : 0.719 10.856 28509 Z= 0.362 Chirality : 0.052 0.421 3480 Planarity : 0.004 0.066 3501 Dihedral : 10.599 60.179 4641 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.90 % Favored : 91.86 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.51 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.16), residues: 2457 helix: -0.04 (0.25), residues: 408 sheet: -0.14 (0.20), residues: 639 loop : -1.71 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 112 HIS 0.004 0.001 HIS I 374 PHE 0.018 0.002 PHE A 157 TYR 0.016 0.001 TYR C 95 ARG 0.007 0.000 ARG G 85 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 241 time to evaluate : 2.359 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: B 584 GLU cc_start: 0.8550 (tm-30) cc_final: 0.8137 (tm-30) REVERT: B 589 ASP cc_start: 0.8233 (t0) cc_final: 0.7804 (t0) REVERT: C 90 ASP cc_start: 0.8526 (m-30) cc_final: 0.8316 (m-30) REVERT: E 369 MET cc_start: 0.6448 (mtp) cc_final: 0.6215 (ttm) REVERT: E 434 MET cc_start: 0.7101 (mtm) cc_final: 0.6315 (mtm) REVERT: F 589 ASP cc_start: 0.8317 (t70) cc_final: 0.7987 (t70) REVERT: J 584 GLU cc_start: 0.8376 (tm-30) cc_final: 0.8066 (tm-30) REVERT: J 589 ASP cc_start: 0.8277 (t70) cc_final: 0.7944 (t0) REVERT: J 626 MET cc_start: 0.7465 (tpp) cc_final: 0.7220 (tmm) outliers start: 0 outliers final: 0 residues processed: 241 average time/residue: 0.2935 time to fit residues: 114.1640 Evaluate side-chains 163 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 2.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 233 optimal weight: 7.9990 chunk 142 optimal weight: 20.0000 chunk 110 optimal weight: 8.9990 chunk 162 optimal weight: 9.9990 chunk 245 optimal weight: 10.0000 chunk 225 optimal weight: 5.9990 chunk 195 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 150 optimal weight: 10.0000 chunk 119 optimal weight: 3.9990 chunk 155 optimal weight: 0.6980 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.5941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 20976 Z= 0.363 Angle : 0.792 11.377 28509 Z= 0.407 Chirality : 0.053 0.462 3480 Planarity : 0.005 0.071 3501 Dihedral : 10.715 59.813 4641 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 15.76 Ramachandran Plot: Outliers : 0.33 % Allowed : 9.36 % Favored : 90.31 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.51 % Twisted Proline : 0.00 % Twisted General : 0.34 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.16), residues: 2457 helix: -0.33 (0.25), residues: 393 sheet: -0.35 (0.20), residues: 666 loop : -1.80 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP J 596 HIS 0.003 0.001 HIS E 352 PHE 0.024 0.002 PHE I 157 TYR 0.021 0.002 TYR K 116 ARG 0.008 0.001 ARG G 85 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 219 time to evaluate : 2.301 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: B 584 GLU cc_start: 0.8600 (tm-30) cc_final: 0.8180 (tm-30) REVERT: B 589 ASP cc_start: 0.8453 (t0) cc_final: 0.7975 (t0) REVERT: E 369 MET cc_start: 0.6557 (mtp) cc_final: 0.6204 (ttm) REVERT: E 434 MET cc_start: 0.7330 (mtm) cc_final: 0.6291 (mtm) REVERT: F 589 ASP cc_start: 0.8392 (t70) cc_final: 0.8043 (t70) REVERT: G 90 ASP cc_start: 0.8749 (m-30) cc_final: 0.8515 (m-30) REVERT: J 584 GLU cc_start: 0.8470 (tm-30) cc_final: 0.8136 (tm-30) REVERT: J 589 ASP cc_start: 0.8534 (t70) cc_final: 0.8224 (t0) REVERT: J 626 MET cc_start: 0.7756 (tpp) cc_final: 0.7420 (tmm) outliers start: 0 outliers final: 0 residues processed: 219 average time/residue: 0.2787 time to fit residues: 100.5928 Evaluate side-chains 150 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 2.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 207 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 chunk 179 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 54 optimal weight: 8.9990 chunk 195 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 200 optimal weight: 20.0000 chunk 24 optimal weight: 2.9990 chunk 36 optimal weight: 20.0000 chunk 171 optimal weight: 0.8980 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.049713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.039137 restraints weight = 137213.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.040441 restraints weight = 82474.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.041332 restraints weight = 58816.322| |-----------------------------------------------------------------------------| r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.6089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 20976 Z= 0.273 Angle : 0.747 11.176 28509 Z= 0.386 Chirality : 0.052 0.435 3480 Planarity : 0.004 0.072 3501 Dihedral : 10.513 56.884 4641 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.04 % Favored : 90.72 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.51 % Twisted Proline : 0.00 % Twisted General : 0.34 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.16), residues: 2457 helix: -0.29 (0.24), residues: 411 sheet: -0.26 (0.20), residues: 627 loop : -1.83 (0.16), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP J 596 HIS 0.003 0.001 HIS A 330 PHE 0.021 0.002 PHE E 157 TYR 0.021 0.002 TYR C 95 ARG 0.009 0.001 ARG E 164 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3696.91 seconds wall clock time: 70 minutes 11.73 seconds (4211.73 seconds total)