Starting phenix.real_space_refine on Sun Feb 18 03:41:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gje_40088/02_2024/8gje_40088.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gje_40088/02_2024/8gje_40088.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gje_40088/02_2024/8gje_40088.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gje_40088/02_2024/8gje_40088.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gje_40088/02_2024/8gje_40088.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gje_40088/02_2024/8gje_40088.pdb" } resolution = 3.4 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= -0.001 sd= 0.096 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 123 5.16 5 C 12855 2.51 5 N 3414 2.21 5 O 4221 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 20613 Number of models: 1 Model: "" Number of chains: 48 Chain: "A" Number of atoms: 3569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3569 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 22, 'TRANS': 429} Chain breaks: 1 Chain: "B" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 975 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "H" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 985 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "L" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 783 Classifications: {'peptide': 98} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 92} Chain: "C" Number of atoms: 3569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3569 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 22, 'TRANS': 429} Chain breaks: 1 Chain: "E" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 975 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "G" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 985 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "J" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 783 Classifications: {'peptide': 98} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 92} Chain: "D" Number of atoms: 3569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3569 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 22, 'TRANS': 429} Chain breaks: 1 Chain: "F" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 975 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "I" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 985 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "K" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 783 Classifications: {'peptide': 98} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 92} Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 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: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} 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: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} 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: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} 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: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} 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: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} 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: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 11.88, per 1000 atoms: 0.58 Number of scatterers: 20613 At special positions: 0 Unit cell: (141.48, 145.41, 121.83, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 123 16.00 O 4221 8.00 N 3414 7.00 C 12855 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.04 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.04 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.04 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.04 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.04 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.04 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.04 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS E 605 " distance=2.03 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.04 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.04 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.03 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.04 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 157 " distance=2.04 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.03 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.03 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.04 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.04 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.03 Simple disulfide: pdb=" SG CYS D 501 " - pdb=" SG CYS F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.04 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN R 4 " - " MAN R 5 " " MAN R 5 " - " MAN R 6 " " MAN a 4 " - " MAN a 5 " " MAN a 5 " - " MAN a 6 " " MAN j 4 " - " MAN j 5 " " MAN j 5 " - " MAN j 6 " ALPHA1-3 " BMA R 3 " - " MAN R 4 " " MAN R 7 " - " MAN R 8 " " BMA U 3 " - " MAN U 7 " " MAN U 4 " - " MAN U 5 " " BMA a 3 " - " MAN a 4 " " MAN a 7 " - " MAN a 8 " " BMA d 3 " - " MAN d 7 " " MAN d 4 " - " MAN d 5 " " BMA j 3 " - " MAN j 4 " " MAN j 7 " - " MAN j 8 " " BMA m 3 " - " MAN m 7 " " MAN m 4 " - " MAN m 5 " ALPHA1-6 " BMA R 3 " - " MAN R 7 " " MAN R 7 " - " MAN R 9 " " BMA U 3 " - " MAN U 4 " " MAN U 4 " - " MAN U 6 " " BMA a 3 " - " MAN a 7 " " MAN a 7 " - " MAN a 9 " " BMA d 3 " - " MAN d 4 " " MAN d 4 " - " MAN d 6 " " BMA j 3 " - " MAN j 7 " " MAN j 7 " - " MAN j 9 " " BMA m 3 " - " MAN m 4 " " MAN m 4 " - " MAN m 6 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " 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 W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " BETA1-6 " NAG O 1 " - " FUC O 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG X 1 " - " FUC X 4 " " NAG g 1 " - " FUC g 4 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 133 " " NAG A 603 " - " ASN A 289 " " NAG A 604 " - " ASN A 301 " " NAG A 605 " - " ASN A 339 " " NAG A 606 " - " ASN A 442 " " NAG A 607 " - " ASN A 448 " " NAG B 700 " - " ASN B 611 " " NAG B 701 " - " ASN B 625 " " NAG B 702 " - " ASN B 637 " " NAG C 601 " - " ASN C 88 " " NAG C 602 " - " ASN C 133 " " NAG C 603 " - " ASN C 289 " " NAG C 604 " - " ASN C 301 " " NAG C 605 " - " ASN C 339 " " NAG C 606 " - " ASN C 442 " " NAG C 607 " - " ASN C 448 " " NAG D 601 " - " ASN D 88 " " NAG D 602 " - " ASN D 133 " " NAG D 603 " - " ASN D 289 " " NAG D 604 " - " ASN D 301 " " NAG D 605 " - " ASN D 339 " " NAG D 606 " - " ASN D 442 " " NAG D 607 " - " ASN D 448 " " NAG E 700 " - " ASN E 611 " " NAG E 701 " - " ASN E 625 " " NAG E 702 " - " ASN E 637 " " NAG F 700 " - " ASN F 611 " " NAG F 701 " - " ASN F 625 " " NAG F 702 " - " ASN F 637 " " NAG J 600 " - " ASN J 72 " " NAG K 600 " - " ASN K 72 " " NAG L 600 " - " ASN L 72 " " NAG M 1 " - " ASN A 156 " " NAG N 1 " - " ASN A 160 " " NAG O 1 " - " ASN A 197 " " NAG P 1 " - " ASN A 230 " " NAG Q 1 " - " ASN A 241 " " NAG R 1 " - " ASN A 262 " " NAG S 1 " - " ASN A 332 " " NAG T 1 " - " ASN A 386 " " NAG U 1 " - " ASN A 276 " " NAG V 1 " - " ASN C 156 " " NAG W 1 " - " ASN C 160 " " NAG X 1 " - " ASN C 197 " " NAG Y 1 " - " ASN C 230 " " NAG Z 1 " - " ASN C 241 " " NAG a 1 " - " ASN C 262 " " NAG b 1 " - " ASN C 332 " " NAG c 1 " - " ASN C 386 " " NAG d 1 " - " ASN C 276 " " NAG e 1 " - " ASN D 156 " " NAG f 1 " - " ASN D 160 " " NAG g 1 " - " ASN D 197 " " NAG h 1 " - " ASN D 230 " " NAG i 1 " - " ASN D 241 " " NAG j 1 " - " ASN D 262 " " NAG k 1 " - " ASN D 332 " " NAG l 1 " - " ASN D 386 " " NAG m 1 " - " ASN D 276 " Time building additional restraints: 10.21 Conformation dependent library (CDL) restraints added in 3.3 seconds 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4446 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 45 sheets defined 22.3% alpha, 32.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.51 Creating SS restraints... Processing helix chain 'A' and resid 69 through 74 removed outlier: 3.690A pdb=" N HIS A 72 " --> pdb=" O TRP A 69 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N CYS A 74 " --> pdb=" O THR A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 117 Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 143 through 152 removed outlier: 3.574A pdb=" N LYS A 152 " --> pdb=" O ASP A 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 143 through 152' Processing helix chain 'A' and resid 185E through 189 removed outlier: 3.513A pdb=" N SER A 189 " --> pdb=" O SER A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 352 removed outlier: 3.531A pdb=" N ASN A 352 " --> pdb=" O LYS A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 474 through 484 removed outlier: 4.055A pdb=" N ASN A 478 " --> pdb=" O ASN A 474 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 removed outlier: 3.557A pdb=" N SER B 534 " --> pdb=" O MET B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 542 Processing helix chain 'B' and resid 570 through 596 Processing helix chain 'B' and resid 618 through 626 removed outlier: 3.758A pdb=" N MET B 626 " --> pdb=" O ILE B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 653 Processing helix chain 'B' and resid 658 through 663 removed outlier: 3.507A pdb=" N LEU B 663 " --> pdb=" O ASP B 659 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 60 through 64 Processing helix chain 'H' and resid 71D through 73 No H-bonds generated for 'chain 'H' and resid 71D through 73' Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.602A pdb=" N THR H 87 " --> pdb=" O SER H 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'C' and resid 69 through 74 removed outlier: 3.690A pdb=" N HIS C 72 " --> pdb=" O TRP C 69 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N CYS C 74 " --> pdb=" O THR C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 117 Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 143 through 152 removed outlier: 3.574A pdb=" N LYS C 152 " --> pdb=" O ASP C 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 143 through 152' Processing helix chain 'C' and resid 185E through 189 removed outlier: 3.513A pdb=" N SER C 189 " --> pdb=" O SER C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 352 removed outlier: 3.531A pdb=" N ASN C 352 " --> pdb=" O LYS C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 474 through 484 removed outlier: 4.055A pdb=" N ASN C 478 " --> pdb=" O ASN C 474 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 534 removed outlier: 3.557A pdb=" N SER E 534 " --> pdb=" O MET E 530 " (cutoff:3.500A) Processing helix chain 'E' and resid 536 through 542 Processing helix chain 'E' and resid 570 through 596 Processing helix chain 'E' and resid 618 through 626 removed outlier: 3.759A pdb=" N MET E 626 " --> pdb=" O ILE E 622 " (cutoff:3.500A) Processing helix chain 'E' and resid 627 through 635 Processing helix chain 'E' and resid 638 through 653 Processing helix chain 'E' and resid 658 through 663 removed outlier: 3.507A pdb=" N LEU E 663 " --> pdb=" O ASP E 659 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 32 Processing helix chain 'G' and resid 60 through 64 Processing helix chain 'G' and resid 71D through 73 No H-bonds generated for 'chain 'G' and resid 71D through 73' Processing helix chain 'G' and resid 83 through 87 removed outlier: 3.602A pdb=" N THR G 87 " --> pdb=" O SER G 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 79 through 83 Processing helix chain 'D' and resid 69 through 74 removed outlier: 3.690A pdb=" N HIS D 72 " --> pdb=" O TRP D 69 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N CYS D 74 " --> pdb=" O THR D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 117 Processing helix chain 'D' and resid 122 through 126 Processing helix chain 'D' and resid 143 through 152 removed outlier: 3.574A pdb=" N LYS D 152 " --> pdb=" O ASP D 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 143 through 152' Processing helix chain 'D' and resid 185E through 189 removed outlier: 3.513A pdb=" N SER D 189 " --> pdb=" O SER D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 352 removed outlier: 3.531A pdb=" N ASN D 352 " --> pdb=" O LYS D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 474 through 484 removed outlier: 4.054A pdb=" N ASN D 478 " --> pdb=" O ASN D 474 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLU D 482 " --> pdb=" O ASN D 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 removed outlier: 3.557A pdb=" N SER F 534 " --> pdb=" O MET F 530 " (cutoff:3.500A) Processing helix chain 'F' and resid 536 through 542 Processing helix chain 'F' and resid 570 through 596 Processing helix chain 'F' and resid 618 through 626 removed outlier: 3.758A pdb=" N MET F 626 " --> pdb=" O ILE F 622 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 653 Processing helix chain 'F' and resid 658 through 663 removed outlier: 3.507A pdb=" N LEU F 663 " --> pdb=" O ASP F 659 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 32 Processing helix chain 'I' and resid 60 through 64 Processing helix chain 'I' and resid 71D through 73 No H-bonds generated for 'chain 'I' and resid 71D through 73' Processing helix chain 'I' and resid 83 through 87 removed outlier: 3.602A pdb=" N THR I 87 " --> pdb=" O SER I 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.210A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.644A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.578A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.945A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.623A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 removed outlier: 5.424A pdb=" N ILE A 215 " --> pdb=" O GLY A 250 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLY A 250 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N TYR A 217 " --> pdb=" O THR A 248 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 129 through 133 Processing sheet with id=AA6, first strand: chain 'A' and resid 181 through 184 Processing sheet with id=AA7, first strand: chain 'A' and resid 201 through 203 Processing sheet with id=AA8, first strand: chain 'A' and resid 259 through 261 removed outlier: 3.522A pdb=" N GLY A 451 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 10.216A pdb=" N THR A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.614A pdb=" N ILE A 294 " --> pdb=" O THR A 444 " (cutoff:3.500A) removed outlier: 9.803A pdb=" N LYS A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.924A pdb=" N VAL A 292 " --> pdb=" O LYS A 446 " (cutoff:3.500A) removed outlier: 9.522A pdb=" N ASN A 448 " --> pdb=" O LYS A 290 " (cutoff:3.500A) removed outlier: 10.158A pdb=" N LYS A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 284 through 298 current: chain 'A' and resid 358 through 361 Processing sheet with id=AA9, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.879A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.158A pdb=" N LYS A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.522A pdb=" N ASN A 448 " --> pdb=" O LYS A 290 " (cutoff:3.500A) removed outlier: 10.924A pdb=" N VAL A 292 " --> pdb=" O LYS A 446 " (cutoff:3.500A) removed outlier: 9.803A pdb=" N LYS A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.614A pdb=" N ILE A 294 " --> pdb=" O THR A 444 " (cutoff:3.500A) removed outlier: 10.216A pdb=" N THR A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 443 through 456 current: chain 'A' and resid 413 through 421 removed outlier: 4.152A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 303 through 312 removed outlier: 6.850A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AB3, first strand: chain 'H' and resid 10 through 11 removed outlier: 4.054A pdb=" N PHE H 33 " --> pdb=" O GLN H 95 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 10 through 11 removed outlier: 5.012A pdb=" N VAL H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB6, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.586A pdb=" N LEU L 11 " --> pdb=" O ASP L 105 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N CYS L 88 " --> pdb=" O VAL L 99 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLY L 101 " --> pdb=" O TYR L 86 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N TYR L 86 " --> pdb=" O GLY L 101 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.210A pdb=" N VAL E 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 8.644A pdb=" N VAL C 38 " --> pdb=" O THR E 606 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N THR E 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 8.578A pdb=" N TYR C 40 " --> pdb=" O CYS E 604 " (cutoff:3.500A) removed outlier: 8.945A pdb=" N CYS E 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.623A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 53 through 55 removed outlier: 5.423A pdb=" N ILE C 215 " --> pdb=" O GLY C 250 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLY C 250 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N TYR C 217 " --> pdb=" O THR C 248 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AC2, first strand: chain 'C' and resid 129 through 133 Processing sheet with id=AC3, first strand: chain 'C' and resid 181 through 184 Processing sheet with id=AC4, first strand: chain 'C' and resid 201 through 203 Processing sheet with id=AC5, first strand: chain 'C' and resid 259 through 261 removed outlier: 3.522A pdb=" N GLY C 451 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 10.215A pdb=" N THR C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.614A pdb=" N ILE C 294 " --> pdb=" O THR C 444 " (cutoff:3.500A) removed outlier: 9.803A pdb=" N LYS C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.924A pdb=" N VAL C 292 " --> pdb=" O LYS C 446 " (cutoff:3.500A) removed outlier: 9.522A pdb=" N ASN C 448 " --> pdb=" O LYS C 290 " (cutoff:3.500A) removed outlier: 10.158A pdb=" N LYS C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 284 through 298 current: chain 'C' and resid 358 through 361 Processing sheet with id=AC6, first strand: chain 'C' and resid 271 through 273 removed outlier: 6.879A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 10.158A pdb=" N LYS C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.522A pdb=" N ASN C 448 " --> pdb=" O LYS C 290 " (cutoff:3.500A) removed outlier: 10.924A pdb=" N VAL C 292 " --> pdb=" O LYS C 446 " (cutoff:3.500A) removed outlier: 9.803A pdb=" N LYS C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.614A pdb=" N ILE C 294 " --> pdb=" O THR C 444 " (cutoff:3.500A) removed outlier: 10.215A pdb=" N THR C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 443 through 456 current: chain 'C' and resid 413 through 421 removed outlier: 4.152A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 303 through 312 removed outlier: 6.850A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AC9, first strand: chain 'G' and resid 10 through 11 removed outlier: 4.055A pdb=" N PHE G 33 " --> pdb=" O GLN G 95 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE G 34 " --> pdb=" O TRP G 50 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N TRP G 50 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 10 through 11 removed outlier: 5.013A pdb=" N VAL G 102 " --> pdb=" O ARG G 94 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AD3, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.587A pdb=" N LEU J 11 " --> pdb=" O ASP J 105 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N CYS J 88 " --> pdb=" O VAL J 99 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLY J 101 " --> pdb=" O TYR J 86 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N TYR J 86 " --> pdb=" O GLY J 101 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 494 through 499 removed outlier: 5.210A pdb=" N VAL F 608 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 8.643A pdb=" N VAL D 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N THR F 606 " --> pdb=" O VAL D 38 " (cutoff:3.500A) removed outlier: 8.578A pdb=" N TYR D 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.945A pdb=" N CYS F 604 " --> pdb=" O TYR D 40 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 45 through 47 removed outlier: 4.623A pdb=" N VAL D 242 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 53 through 55 removed outlier: 5.423A pdb=" N ILE D 215 " --> pdb=" O GLY D 250 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLY D 250 " --> pdb=" O ILE D 215 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N TYR D 217 " --> pdb=" O THR D 248 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 91 through 94 Processing sheet with id=AD8, first strand: chain 'D' and resid 129 through 133 Processing sheet with id=AD9, first strand: chain 'D' and resid 181 through 184 Processing sheet with id=AE1, first strand: chain 'D' and resid 201 through 203 Processing sheet with id=AE2, first strand: chain 'D' and resid 259 through 261 removed outlier: 3.522A pdb=" N GLY D 451 " --> pdb=" O LEU D 260 " (cutoff:3.500A) removed outlier: 10.215A pdb=" N THR D 444 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 11.614A pdb=" N ILE D 294 " --> pdb=" O THR D 444 " (cutoff:3.500A) removed outlier: 9.803A pdb=" N LYS D 446 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 10.925A pdb=" N VAL D 292 " --> pdb=" O LYS D 446 " (cutoff:3.500A) removed outlier: 9.522A pdb=" N ASN D 448 " --> pdb=" O LYS D 290 " (cutoff:3.500A) removed outlier: 10.158A pdb=" N LYS D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N THR D 450 " --> pdb=" O LEU D 288 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 284 through 298 current: chain 'D' and resid 358 through 361 Processing sheet with id=AE3, first strand: chain 'D' and resid 271 through 273 removed outlier: 6.879A pdb=" N THR D 450 " --> pdb=" O LEU D 288 " (cutoff:3.500A) removed outlier: 10.158A pdb=" N LYS D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 9.522A pdb=" N ASN D 448 " --> pdb=" O LYS D 290 " (cutoff:3.500A) removed outlier: 10.925A pdb=" N VAL D 292 " --> pdb=" O LYS D 446 " (cutoff:3.500A) removed outlier: 9.803A pdb=" N LYS D 446 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 11.614A pdb=" N ILE D 294 " --> pdb=" O THR D 444 " (cutoff:3.500A) removed outlier: 10.215A pdb=" N THR D 444 " --> pdb=" O ILE D 294 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 443 through 456 current: chain 'D' and resid 413 through 421 removed outlier: 4.152A pdb=" N PHE D 382 " --> pdb=" O LYS D 421 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 303 through 312 removed outlier: 6.850A pdb=" N THR D 303 " --> pdb=" O GLY D 321 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N GLN D 315 " --> pdb=" O ILE D 309 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AE6, first strand: chain 'I' and resid 10 through 11 removed outlier: 4.054A pdb=" N PHE I 33 " --> pdb=" O GLN I 95 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE I 34 " --> pdb=" O TRP I 50 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N TRP I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 10 through 11 removed outlier: 5.012A pdb=" N VAL I 102 " --> pdb=" O ARG I 94 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AE9, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.586A pdb=" N LEU K 11 " --> pdb=" O ASP K 105 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N CYS K 88 " --> pdb=" O VAL K 99 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLY K 101 " --> pdb=" O TYR K 86 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N TYR K 86 " --> pdb=" O GLY K 101 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) 705 hydrogen bonds defined for protein. 1809 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: 7.38 Time building geometry restraints manager: 10.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6308 1.34 - 1.46: 5422 1.46 - 1.59: 9126 1.59 - 1.71: 3 1.71 - 1.84: 168 Bond restraints: 21027 Sorted by residual: bond pdb=" C1 FUC g 4 " pdb=" C2 FUC g 4 " ideal model delta sigma weight residual 1.528 1.657 -0.129 2.00e-02 2.50e+03 4.18e+01 bond pdb=" C1 FUC O 4 " pdb=" C2 FUC O 4 " ideal model delta sigma weight residual 1.528 1.657 -0.129 2.00e-02 2.50e+03 4.18e+01 bond pdb=" C1 FUC X 4 " pdb=" C2 FUC X 4 " ideal model delta sigma weight residual 1.528 1.657 -0.129 2.00e-02 2.50e+03 4.17e+01 bond pdb=" C1 FUC g 4 " pdb=" O5 FUC g 4 " ideal model delta sigma weight residual 1.400 1.494 -0.094 2.00e-02 2.50e+03 2.21e+01 bond pdb=" C1 FUC O 4 " pdb=" O5 FUC O 4 " ideal model delta sigma weight residual 1.400 1.494 -0.094 2.00e-02 2.50e+03 2.21e+01 ... (remaining 21022 not shown) Histogram of bond angle deviations from ideal: 99.04 - 106.08: 483 106.08 - 113.11: 11954 113.11 - 120.15: 7362 120.15 - 127.19: 8452 127.19 - 134.22: 309 Bond angle restraints: 28560 Sorted by residual: angle pdb=" N ALA D 70 " pdb=" CA ALA D 70 " pdb=" C ALA D 70 " ideal model delta sigma weight residual 108.08 114.78 -6.70 1.69e+00 3.50e-01 1.57e+01 angle pdb=" N ASN C 138 " pdb=" CA ASN C 138 " pdb=" C ASN C 138 " ideal model delta sigma weight residual 107.37 115.55 -8.18 2.07e+00 2.33e-01 1.56e+01 angle pdb=" N ALA C 70 " pdb=" CA ALA C 70 " pdb=" C ALA C 70 " ideal model delta sigma weight residual 108.08 114.75 -6.67 1.69e+00 3.50e-01 1.56e+01 angle pdb=" N ASN D 138 " pdb=" CA ASN D 138 " pdb=" C ASN D 138 " ideal model delta sigma weight residual 107.37 115.52 -8.15 2.07e+00 2.33e-01 1.55e+01 angle pdb=" N ALA A 70 " pdb=" CA ALA A 70 " pdb=" C ALA A 70 " ideal model delta sigma weight residual 108.08 114.73 -6.65 1.69e+00 3.50e-01 1.55e+01 ... (remaining 28555 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.21: 13577 21.21 - 42.42: 406 42.42 - 63.62: 168 63.62 - 84.83: 72 84.83 - 106.04: 45 Dihedral angle restraints: 14268 sinusoidal: 7374 harmonic: 6894 Sorted by residual: dihedral pdb=" CA PHE D 376 " pdb=" C PHE D 376 " pdb=" N ASN D 377 " pdb=" CA ASN D 377 " ideal model delta harmonic sigma weight residual 180.00 159.74 20.26 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA PHE A 376 " pdb=" C PHE A 376 " pdb=" N ASN A 377 " pdb=" CA ASN A 377 " ideal model delta harmonic sigma weight residual 180.00 159.74 20.26 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA PHE C 376 " pdb=" C PHE C 376 " pdb=" N ASN C 377 " pdb=" CA ASN C 377 " ideal model delta harmonic sigma weight residual 180.00 159.75 20.25 0 5.00e+00 4.00e-02 1.64e+01 ... (remaining 14265 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 2873 0.078 - 0.156: 587 0.156 - 0.234: 53 0.234 - 0.311: 24 0.311 - 0.389: 6 Chirality restraints: 3543 Sorted by residual: chirality pdb=" C1 NAG U 2 " pdb=" O4 NAG U 1 " pdb=" C2 NAG U 2 " pdb=" O5 NAG U 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-02 2.50e+03 1.42e+02 chirality pdb=" C1 NAG d 2 " pdb=" O4 NAG d 1 " pdb=" C2 NAG d 2 " pdb=" O5 NAG d 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-02 2.50e+03 1.41e+02 chirality pdb=" C1 NAG m 2 " pdb=" O4 NAG m 1 " pdb=" C2 NAG m 2 " pdb=" O5 NAG m 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-02 2.50e+03 1.39e+02 ... (remaining 3540 not shown) Planarity restraints: 3534 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG d 1 " 0.039 2.00e-02 2.50e+03 3.19e-02 1.28e+01 pdb=" C7 NAG d 1 " -0.012 2.00e-02 2.50e+03 pdb=" C8 NAG d 1 " 0.030 2.00e-02 2.50e+03 pdb=" N2 NAG d 1 " -0.050 2.00e-02 2.50e+03 pdb=" O7 NAG d 1 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG U 1 " 0.039 2.00e-02 2.50e+03 3.19e-02 1.28e+01 pdb=" C7 NAG U 1 " -0.012 2.00e-02 2.50e+03 pdb=" C8 NAG U 1 " 0.030 2.00e-02 2.50e+03 pdb=" N2 NAG U 1 " -0.050 2.00e-02 2.50e+03 pdb=" O7 NAG U 1 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG m 1 " 0.039 2.00e-02 2.50e+03 3.19e-02 1.28e+01 pdb=" C7 NAG m 1 " -0.012 2.00e-02 2.50e+03 pdb=" C8 NAG m 1 " 0.030 2.00e-02 2.50e+03 pdb=" N2 NAG m 1 " -0.050 2.00e-02 2.50e+03 pdb=" O7 NAG m 1 " -0.007 2.00e-02 2.50e+03 ... (remaining 3531 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.28: 9 2.28 - 2.94: 9028 2.94 - 3.59: 26930 3.59 - 4.25: 47408 4.25 - 4.90: 77014 Nonbonded interactions: 160389 Sorted by model distance: nonbonded pdb=" OD1 ASN A 67 " pdb=" CB ASN A 209 " model vdw 1.626 3.440 nonbonded pdb=" OD1 ASN D 67 " pdb=" CB ASN D 209 " model vdw 1.626 3.440 nonbonded pdb=" OD1 ASN C 67 " pdb=" CB ASN C 209 " model vdw 1.626 3.440 nonbonded pdb=" OD1 ASN A 67 " pdb=" CG ASN A 209 " model vdw 2.133 3.270 nonbonded pdb=" OD1 ASN D 67 " pdb=" CG ASN D 209 " model vdw 2.133 3.270 ... (remaining 160384 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 'C' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'b' selection = chain 'c' selection = chain 'e' selection = chain 'f' selection = chain 'h' selection = chain 'i' selection = chain 'k' selection = chain 'l' } ncs_group { reference = chain 'O' selection = chain 'X' selection = chain 'g' } ncs_group { reference = chain 'R' selection = chain 'a' selection = chain 'j' } ncs_group { reference = chain 'U' selection = chain 'd' selection = chain 'm' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.260 Check model and map are aligned: 0.310 Set scattering table: 0.190 Process input model: 58.340 Find NCS groups from input model: 1.410 Set up NCS constraints: 0.390 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 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 : 0.007 0.129 21027 Z= 0.441 Angle : 1.058 10.391 28560 Z= 0.559 Chirality : 0.066 0.389 3543 Planarity : 0.007 0.115 3474 Dihedral : 14.032 106.041 9705 Min Nonbonded Distance : 1.626 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.29 % Allowed : 2.00 % Favored : 97.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.17), residues: 2343 helix: 1.22 (0.27), residues: 381 sheet: 0.76 (0.19), residues: 681 loop : 0.58 (0.17), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP I 50 HIS 0.007 0.002 HIS C 130 PHE 0.035 0.003 PHE A 233 TYR 0.029 0.003 TYR K 71 ARG 0.009 0.001 ARG A 298 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 654 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 648 time to evaluate : 2.396 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 53 PHE cc_start: 0.7269 (m-80) cc_final: 0.6447 (m-10) REVERT: A 150 MET cc_start: 0.8296 (mmm) cc_final: 0.8030 (tpp) REVERT: A 376 PHE cc_start: 0.7755 (m-80) cc_final: 0.7069 (m-80) REVERT: B 584 GLU cc_start: 0.8547 (mt-10) cc_final: 0.8150 (mt-10) REVERT: B 589 ASP cc_start: 0.8391 (m-30) cc_final: 0.8118 (m-30) REVERT: B 625 ASN cc_start: 0.7866 (OUTLIER) cc_final: 0.7592 (t0) REVERT: B 639 THR cc_start: 0.8929 (m) cc_final: 0.8701 (p) REVERT: B 648 ASP cc_start: 0.8761 (m-30) cc_final: 0.8462 (t0) REVERT: B 652 GLN cc_start: 0.8391 (tp40) cc_final: 0.7949 (tp40) REVERT: H 83 ARG cc_start: 0.8094 (mtm180) cc_final: 0.7783 (mtm180) REVERT: H 84 SER cc_start: 0.9109 (p) cc_final: 0.8711 (t) REVERT: L 70 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7786 (pt0) REVERT: L 73 LEU cc_start: 0.6773 (tp) cc_final: 0.6261 (tp) REVERT: C 42 VAL cc_start: 0.8322 (t) cc_final: 0.7975 (p) REVERT: C 53 PHE cc_start: 0.7583 (m-80) cc_final: 0.6812 (m-10) REVERT: C 152 LYS cc_start: 0.8970 (mttt) cc_final: 0.8751 (mtmm) REVERT: C 185 LYS cc_start: 0.8622 (mttt) cc_final: 0.8250 (tptp) REVERT: C 302 ASN cc_start: 0.8101 (m110) cc_final: 0.7806 (m110) REVERT: C 432 ARG cc_start: 0.8518 (mtt90) cc_final: 0.8300 (mtm-85) REVERT: E 584 GLU cc_start: 0.8720 (mt-10) cc_final: 0.8317 (mt-10) REVERT: E 652 GLN cc_start: 0.8413 (tp40) cc_final: 0.7920 (tp40) REVERT: G 84 SER cc_start: 0.8805 (p) cc_final: 0.8339 (t) REVERT: J 50 ASP cc_start: 0.6066 (t0) cc_final: 0.5819 (t0) REVERT: J 53 LYS cc_start: 0.8086 (mttt) cc_final: 0.7805 (mttt) REVERT: J 61 ARG cc_start: 0.7790 (mtm-85) cc_final: 0.7090 (ptp90) REVERT: J 70 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7878 (pt0) REVERT: J 82 ASP cc_start: 0.6310 (m-30) cc_final: 0.5851 (m-30) REVERT: D 53 PHE cc_start: 0.7677 (m-80) cc_final: 0.6891 (m-10) REVERT: D 111 LEU cc_start: 0.8905 (mt) cc_final: 0.8595 (mt) REVERT: D 150 MET cc_start: 0.8068 (mmm) cc_final: 0.7763 (tpp) REVERT: D 349 LEU cc_start: 0.9324 (mt) cc_final: 0.9007 (mt) REVERT: D 432 ARG cc_start: 0.8677 (mtt90) cc_final: 0.8376 (mtm-85) REVERT: F 584 GLU cc_start: 0.8697 (mt-10) cc_final: 0.8100 (mt-10) REVERT: F 589 ASP cc_start: 0.8636 (m-30) cc_final: 0.8358 (m-30) REVERT: F 625 ASN cc_start: 0.7881 (OUTLIER) cc_final: 0.7655 (t0) REVERT: F 639 THR cc_start: 0.8850 (m) cc_final: 0.8618 (p) REVERT: K 61 ARG cc_start: 0.7975 (mtm-85) cc_final: 0.7156 (ptp90) REVERT: K 70 GLU cc_start: 0.8435 (mt-10) cc_final: 0.8083 (pt0) REVERT: K 104 LEU cc_start: 0.7746 (tt) cc_final: 0.7403 (tp) outliers start: 6 outliers final: 3 residues processed: 654 average time/residue: 0.4045 time to fit residues: 380.3213 Evaluate side-chains 346 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 341 time to evaluate : 2.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain D residue 276 ASN Chi-restraints excluded: chain F residue 625 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 0.7980 chunk 177 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 119 optimal weight: 0.6980 chunk 94 optimal weight: 4.9990 chunk 183 optimal weight: 3.9990 chunk 70 optimal weight: 10.0000 chunk 111 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 212 optimal weight: 0.7980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN A 425 ASN ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 GLN L 24 GLN C 114 GLN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 ASN J 24 GLN D 114 GLN D 138 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 425 ASN D 428 GLN F 543 GLN F 577 GLN F 619 GLN I 62 GLN K 77 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 21027 Z= 0.306 Angle : 0.696 9.066 28560 Z= 0.350 Chirality : 0.049 0.292 3543 Planarity : 0.004 0.037 3474 Dihedral : 10.744 71.293 5197 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.61 % Allowed : 8.89 % Favored : 87.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.17), residues: 2343 helix: 1.61 (0.26), residues: 390 sheet: 0.59 (0.18), residues: 738 loop : 0.36 (0.18), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 571 HIS 0.007 0.001 HIS D 374 PHE 0.018 0.002 PHE J 62 TYR 0.028 0.002 TYR L 49 ARG 0.007 0.001 ARG C 480 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 348 time to evaluate : 2.577 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 95 MET cc_start: 0.8817 (ptm) cc_final: 0.8526 (ptm) REVERT: A 150 MET cc_start: 0.8424 (mmm) cc_final: 0.8145 (tpp) REVERT: A 376 PHE cc_start: 0.8077 (m-80) cc_final: 0.7190 (m-80) REVERT: B 584 GLU cc_start: 0.8774 (mt-10) cc_final: 0.8234 (mt-10) REVERT: B 589 ASP cc_start: 0.8420 (m-30) cc_final: 0.8024 (m-30) REVERT: B 625 ASN cc_start: 0.7801 (OUTLIER) cc_final: 0.7486 (t0) REVERT: B 648 ASP cc_start: 0.8720 (m-30) cc_final: 0.8358 (t0) REVERT: H 82 LYS cc_start: 0.9070 (mttm) cc_final: 0.8653 (mtpp) REVERT: H 84 SER cc_start: 0.9127 (p) cc_final: 0.8656 (t) REVERT: L 50 ASP cc_start: 0.7135 (t0) cc_final: 0.5989 (t0) REVERT: L 70 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7721 (pt0) REVERT: C 98 ASN cc_start: 0.8860 (OUTLIER) cc_final: 0.8492 (t0) REVERT: C 185 LYS cc_start: 0.8551 (mttt) cc_final: 0.8179 (tptp) REVERT: E 577 GLN cc_start: 0.9012 (tp40) cc_final: 0.8808 (tp40) REVERT: G 84 SER cc_start: 0.8773 (p) cc_final: 0.8300 (t) REVERT: J 50 ASP cc_start: 0.6949 (t0) cc_final: 0.6736 (t0) REVERT: J 53 LYS cc_start: 0.8182 (mttt) cc_final: 0.7958 (mttm) REVERT: J 70 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7799 (pt0) REVERT: J 82 ASP cc_start: 0.7332 (m-30) cc_final: 0.7035 (m-30) REVERT: D 53 PHE cc_start: 0.7580 (m-80) cc_final: 0.7187 (m-10) REVERT: D 150 MET cc_start: 0.8319 (mmm) cc_final: 0.8089 (tpp) REVERT: D 486 TYR cc_start: 0.8077 (OUTLIER) cc_final: 0.7419 (p90) REVERT: F 576 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8755 (mm) REVERT: F 584 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8130 (mt-10) REVERT: F 589 ASP cc_start: 0.8643 (m-30) cc_final: 0.8430 (m-30) REVERT: F 625 ASN cc_start: 0.7961 (OUTLIER) cc_final: 0.7680 (t0) REVERT: I 27 TYR cc_start: 0.8471 (p90) cc_final: 0.8253 (p90) REVERT: K 50 ASP cc_start: 0.7243 (t0) cc_final: 0.6033 (t0) REVERT: K 70 GLU cc_start: 0.8392 (mt-10) cc_final: 0.7991 (pt0) outliers start: 76 outliers final: 43 residues processed: 403 average time/residue: 0.3697 time to fit residues: 219.0846 Evaluate side-chains 339 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 291 time to evaluate : 2.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 444 THR Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 276 ASN Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 365 SER Chi-restraints excluded: chain D residue 428 GLN Chi-restraints excluded: chain D residue 486 TYR Chi-restraints excluded: chain D residue 490 GLU Chi-restraints excluded: chain F residue 574 LYS Chi-restraints excluded: chain F residue 576 LEU Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 625 ASN Chi-restraints excluded: chain F residue 647 GLU Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 99 TYR Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 63 SER Chi-restraints excluded: chain K residue 69 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 118 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 176 optimal weight: 1.9990 chunk 144 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 212 optimal weight: 0.8980 chunk 229 optimal weight: 0.7980 chunk 189 optimal weight: 1.9990 chunk 211 optimal weight: 0.9980 chunk 72 optimal weight: 6.9990 chunk 170 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 HIS B 575 GLN ** B 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 24 GLN C 130 HIS C 425 ASN J 24 GLN D 130 HIS D 425 ASN ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 GLN K 24 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 21027 Z= 0.224 Angle : 0.627 9.161 28560 Z= 0.312 Chirality : 0.047 0.290 3543 Planarity : 0.004 0.041 3474 Dihedral : 9.397 64.721 5197 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.19 % Allowed : 11.36 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.17), residues: 2343 helix: 1.81 (0.26), residues: 390 sheet: 0.46 (0.18), residues: 735 loop : 0.29 (0.18), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 571 HIS 0.004 0.001 HIS C 105 PHE 0.016 0.001 PHE D 376 TYR 0.024 0.001 TYR L 49 ARG 0.005 0.001 ARG J 40 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 308 time to evaluate : 2.329 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: A 42 VAL cc_start: 0.8443 (t) cc_final: 0.8084 (p) REVERT: A 150 MET cc_start: 0.8475 (mmm) cc_final: 0.8267 (tpp) REVERT: A 376 PHE cc_start: 0.8159 (m-80) cc_final: 0.7344 (m-80) REVERT: B 589 ASP cc_start: 0.8307 (m-30) cc_final: 0.7960 (m-30) REVERT: B 625 ASN cc_start: 0.7802 (OUTLIER) cc_final: 0.7461 (t0) REVERT: B 648 ASP cc_start: 0.8607 (m-30) cc_final: 0.8247 (t0) REVERT: B 653 GLN cc_start: 0.7500 (OUTLIER) cc_final: 0.6958 (tt0) REVERT: H 19 ARG cc_start: 0.8630 (ttm170) cc_final: 0.8339 (ttt-90) REVERT: H 84 SER cc_start: 0.9121 (p) cc_final: 0.8636 (t) REVERT: L 3 GLN cc_start: 0.8251 (pp30) cc_final: 0.7936 (pp30) REVERT: L 50 ASP cc_start: 0.7949 (t0) cc_final: 0.7477 (t0) REVERT: L 70 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7738 (pt0) REVERT: C 98 ASN cc_start: 0.8916 (OUTLIER) cc_final: 0.8529 (t0) REVERT: C 185 LYS cc_start: 0.8535 (mttt) cc_final: 0.8143 (tptp) REVERT: C 434 MET cc_start: 0.8927 (ttp) cc_final: 0.8718 (ttp) REVERT: E 579 ARG cc_start: 0.8894 (OUTLIER) cc_final: 0.8499 (mpp80) REVERT: G 53 LYS cc_start: 0.8988 (mtmt) cc_final: 0.8703 (mtmm) REVERT: G 84 SER cc_start: 0.8774 (p) cc_final: 0.8313 (t) REVERT: J 50 ASP cc_start: 0.7319 (t0) cc_final: 0.7087 (t0) REVERT: J 70 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7842 (pt0) REVERT: D 53 PHE cc_start: 0.7692 (m-80) cc_final: 0.7237 (m-10) REVERT: D 320 THR cc_start: 0.9292 (m) cc_final: 0.8960 (p) REVERT: D 425 ASN cc_start: 0.8512 (OUTLIER) cc_final: 0.8036 (p0) REVERT: D 486 TYR cc_start: 0.8115 (OUTLIER) cc_final: 0.7482 (p90) REVERT: F 575 GLN cc_start: 0.9135 (mm-40) cc_final: 0.8771 (mm-40) REVERT: F 577 GLN cc_start: 0.8747 (tp-100) cc_final: 0.8101 (mm-40) REVERT: F 584 GLU cc_start: 0.8540 (mt-10) cc_final: 0.8081 (mt-10) REVERT: F 589 ASP cc_start: 0.8569 (m-30) cc_final: 0.8349 (m-30) REVERT: F 625 ASN cc_start: 0.7821 (OUTLIER) cc_final: 0.7584 (t0) REVERT: F 638 TYR cc_start: 0.8786 (m-10) cc_final: 0.8555 (m-10) REVERT: K 50 ASP cc_start: 0.8067 (t0) cc_final: 0.7549 (t0) REVERT: K 70 GLU cc_start: 0.8362 (mt-10) cc_final: 0.7969 (pt0) outliers start: 67 outliers final: 44 residues processed: 347 average time/residue: 0.3714 time to fit residues: 189.2163 Evaluate side-chains 332 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 281 time to evaluate : 2.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain B residue 653 GLN Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 545 LEU Chi-restraints excluded: chain E residue 579 ARG Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 621 ASP Chi-restraints excluded: chain G residue 99 TYR Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain D residue 69 TRP Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 276 ASN Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 425 ASN Chi-restraints excluded: chain D residue 482 GLU Chi-restraints excluded: chain D residue 486 TYR Chi-restraints excluded: chain F residue 574 LYS Chi-restraints excluded: chain F residue 588 LYS Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 625 ASN Chi-restraints excluded: chain F residue 647 GLU Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 99 TYR Chi-restraints excluded: chain K residue 69 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 210 optimal weight: 0.9980 chunk 160 optimal weight: 0.7980 chunk 110 optimal weight: 0.6980 chunk 23 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 142 optimal weight: 5.9990 chunk 213 optimal weight: 5.9990 chunk 226 optimal weight: 6.9990 chunk 111 optimal weight: 0.8980 chunk 202 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 653 GLN H 43 GLN L 24 GLN C 229 ASN C 425 ASN E 577 GLN D 229 ASN D 425 ASN F 619 GLN I 3 GLN K 24 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 21027 Z= 0.261 Angle : 0.616 9.205 28560 Z= 0.305 Chirality : 0.047 0.292 3543 Planarity : 0.004 0.034 3474 Dihedral : 8.148 54.835 5197 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.61 % Allowed : 12.22 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.17), residues: 2343 helix: 1.73 (0.27), residues: 390 sheet: 0.37 (0.18), residues: 735 loop : 0.19 (0.18), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP I 71D HIS 0.003 0.001 HIS C 216 PHE 0.011 0.001 PHE A 176 TYR 0.022 0.002 TYR L 49 ARG 0.005 0.000 ARG E 542 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 300 time to evaluate : 2.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 303 THR cc_start: 0.8677 (OUTLIER) cc_final: 0.8411 (p) REVERT: A 376 PHE cc_start: 0.8153 (m-80) cc_final: 0.7310 (m-80) REVERT: B 589 ASP cc_start: 0.8346 (m-30) cc_final: 0.7893 (m-30) REVERT: B 625 ASN cc_start: 0.7770 (OUTLIER) cc_final: 0.7404 (t0) REVERT: B 648 ASP cc_start: 0.8525 (m-30) cc_final: 0.8142 (t0) REVERT: H 19 ARG cc_start: 0.8682 (ttm170) cc_final: 0.8106 (ttt180) REVERT: H 84 SER cc_start: 0.9111 (p) cc_final: 0.8634 (t) REVERT: L 3 GLN cc_start: 0.8251 (pp30) cc_final: 0.7923 (pp30) REVERT: L 50 ASP cc_start: 0.8559 (t0) cc_final: 0.8065 (t0) REVERT: L 70 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7702 (pt0) REVERT: C 185 LYS cc_start: 0.8564 (mttt) cc_final: 0.8172 (tptp) REVERT: E 579 ARG cc_start: 0.8692 (OUTLIER) cc_final: 0.8453 (mpp80) REVERT: G 84 SER cc_start: 0.8760 (p) cc_final: 0.8302 (t) REVERT: J 50 ASP cc_start: 0.8201 (t0) cc_final: 0.7810 (t0) REVERT: J 70 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7813 (pt0) REVERT: D 53 PHE cc_start: 0.7726 (m-80) cc_final: 0.7452 (m-10) REVERT: D 150 MET cc_start: 0.8251 (tpp) cc_final: 0.8045 (tpp) REVERT: D 320 THR cc_start: 0.9314 (m) cc_final: 0.8988 (p) REVERT: D 486 TYR cc_start: 0.8273 (OUTLIER) cc_final: 0.7642 (p90) REVERT: F 575 GLN cc_start: 0.9137 (mt0) cc_final: 0.8698 (mm-40) REVERT: F 577 GLN cc_start: 0.8823 (tp-100) cc_final: 0.8226 (mm-40) REVERT: F 584 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8100 (mt-10) REVERT: F 589 ASP cc_start: 0.8573 (m-30) cc_final: 0.8335 (m-30) REVERT: F 626 MET cc_start: 0.8176 (ttt) cc_final: 0.7716 (ttt) REVERT: F 651 THR cc_start: 0.7690 (m) cc_final: 0.7417 (p) REVERT: K 70 GLU cc_start: 0.8349 (mt-10) cc_final: 0.7909 (pt0) outliers start: 76 outliers final: 49 residues processed: 344 average time/residue: 0.3726 time to fit residues: 188.0634 Evaluate side-chains 320 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 267 time to evaluate : 2.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 545 LEU Chi-restraints excluded: chain E residue 579 ARG Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 621 ASP Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 80 MET Chi-restraints excluded: chain G residue 83 ARG Chi-restraints excluded: chain G residue 99 TYR Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain D residue 69 TRP Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 276 ASN Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 365 SER Chi-restraints excluded: chain D residue 486 TYR Chi-restraints excluded: chain F residue 574 LYS Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 647 GLU Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 99 TYR Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 63 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 188 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 168 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 chunk 193 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 115 optimal weight: 0.2980 chunk 203 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 24 GLN C 425 ASN E 577 GLN ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 619 GLN I 58 ASN K 24 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.3929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 21027 Z= 0.301 Angle : 0.634 9.378 28560 Z= 0.314 Chirality : 0.047 0.389 3543 Planarity : 0.004 0.039 3474 Dihedral : 7.310 55.486 5195 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 4.04 % Allowed : 12.93 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.17), residues: 2343 helix: 1.70 (0.27), residues: 393 sheet: 0.15 (0.18), residues: 747 loop : -0.04 (0.18), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP H 71D HIS 0.005 0.001 HIS D 374 PHE 0.012 0.002 PHE D 176 TYR 0.020 0.002 TYR K 49 ARG 0.008 0.001 ARG I 94 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 282 time to evaluate : 2.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.8136 (tp30) REVERT: A 303 THR cc_start: 0.8750 (OUTLIER) cc_final: 0.8450 (p) REVERT: B 589 ASP cc_start: 0.8356 (m-30) cc_final: 0.7905 (m-30) REVERT: B 625 ASN cc_start: 0.7794 (OUTLIER) cc_final: 0.7421 (t0) REVERT: B 648 ASP cc_start: 0.8559 (m-30) cc_final: 0.8170 (t0) REVERT: H 19 ARG cc_start: 0.8680 (ttm170) cc_final: 0.8333 (tpp80) REVERT: H 43 GLN cc_start: 0.8759 (OUTLIER) cc_final: 0.8061 (mp10) REVERT: H 84 SER cc_start: 0.9109 (p) cc_final: 0.8636 (t) REVERT: L 3 GLN cc_start: 0.8302 (pp30) cc_final: 0.8022 (pp30) REVERT: L 49 TYR cc_start: 0.8721 (p90) cc_final: 0.8393 (p90) REVERT: L 50 ASP cc_start: 0.8872 (t0) cc_final: 0.8415 (t0) REVERT: L 70 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7664 (pt0) REVERT: C 114 GLN cc_start: 0.8622 (OUTLIER) cc_final: 0.8200 (mp10) REVERT: C 185 LYS cc_start: 0.8575 (mttt) cc_final: 0.8148 (tptp) REVERT: E 579 ARG cc_start: 0.8906 (OUTLIER) cc_final: 0.8527 (mpp80) REVERT: E 625 ASN cc_start: 0.7522 (OUTLIER) cc_final: 0.7273 (t0) REVERT: G 84 SER cc_start: 0.8753 (p) cc_final: 0.8242 (t) REVERT: J 50 ASP cc_start: 0.8690 (t0) cc_final: 0.8408 (t0) REVERT: J 70 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7820 (pt0) REVERT: D 53 PHE cc_start: 0.7723 (m-80) cc_final: 0.7077 (m-10) REVERT: D 275 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8053 (tp30) REVERT: D 320 THR cc_start: 0.9312 (m) cc_final: 0.9022 (p) REVERT: D 482 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.8088 (mm-30) REVERT: D 486 TYR cc_start: 0.8308 (OUTLIER) cc_final: 0.7579 (p90) REVERT: F 575 GLN cc_start: 0.9048 (mt0) cc_final: 0.8484 (mm-40) REVERT: F 577 GLN cc_start: 0.8980 (tp-100) cc_final: 0.8430 (mm-40) REVERT: F 584 GLU cc_start: 0.8601 (mt-10) cc_final: 0.8140 (mt-10) REVERT: F 589 ASP cc_start: 0.8580 (m-30) cc_final: 0.8346 (m-30) REVERT: F 626 MET cc_start: 0.8357 (ttt) cc_final: 0.7971 (ttt) REVERT: I 38 ARG cc_start: 0.8819 (OUTLIER) cc_final: 0.7333 (ttp80) REVERT: K 70 GLU cc_start: 0.8363 (mt-10) cc_final: 0.7905 (pt0) outliers start: 85 outliers final: 55 residues processed: 343 average time/residue: 0.3678 time to fit residues: 186.5083 Evaluate side-chains 323 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 257 time to evaluate : 2.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 43 GLN Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 545 LEU Chi-restraints excluded: chain E residue 579 ARG Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 625 ASN Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 80 MET Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 96 GLU Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 69 TRP Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 275 GLU Chi-restraints excluded: chain D residue 276 ASN Chi-restraints excluded: chain D residue 365 SER Chi-restraints excluded: chain D residue 482 GLU Chi-restraints excluded: chain D residue 486 TYR Chi-restraints excluded: chain F residue 574 LYS Chi-restraints excluded: chain F residue 588 LYS Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 620 THR Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 647 GLU Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 38 ARG Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 99 TYR Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 63 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 76 optimal weight: 5.9990 chunk 203 optimal weight: 6.9990 chunk 44 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 226 optimal weight: 9.9990 chunk 187 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 74 optimal weight: 0.8980 chunk 118 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 425 ASN I 95 GLN K 24 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.4074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21027 Z= 0.182 Angle : 0.585 9.059 28560 Z= 0.288 Chirality : 0.046 0.346 3543 Planarity : 0.003 0.037 3474 Dihedral : 6.846 53.918 5195 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.57 % Allowed : 14.27 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.17), residues: 2343 helix: 1.75 (0.27), residues: 393 sheet: 0.18 (0.18), residues: 744 loop : -0.09 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP I 71D HIS 0.003 0.001 HIS D 374 PHE 0.010 0.001 PHE A 376 TYR 0.021 0.001 TYR K 49 ARG 0.006 0.000 ARG E 542 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 283 time to evaluate : 2.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.8222 (t) cc_final: 0.7879 (p) REVERT: A 376 PHE cc_start: 0.8278 (m-80) cc_final: 0.7611 (m-80) REVERT: B 577 GLN cc_start: 0.8731 (OUTLIER) cc_final: 0.8241 (tm-30) REVERT: B 589 ASP cc_start: 0.8333 (m-30) cc_final: 0.7858 (m-30) REVERT: B 625 ASN cc_start: 0.7759 (OUTLIER) cc_final: 0.7425 (t0) REVERT: B 648 ASP cc_start: 0.8302 (m-30) cc_final: 0.7983 (t0) REVERT: H 43 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.7994 (mp10) REVERT: H 84 SER cc_start: 0.9091 (p) cc_final: 0.8590 (t) REVERT: L 3 GLN cc_start: 0.8267 (pp30) cc_final: 0.7947 (pp30) REVERT: L 49 TYR cc_start: 0.8713 (p90) cc_final: 0.8433 (p90) REVERT: L 50 ASP cc_start: 0.8883 (t0) cc_final: 0.8446 (t0) REVERT: L 70 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7655 (pt0) REVERT: C 66 HIS cc_start: 0.7641 (OUTLIER) cc_final: 0.7265 (t-90) REVERT: C 114 GLN cc_start: 0.8590 (OUTLIER) cc_final: 0.8147 (mp10) REVERT: C 185 LYS cc_start: 0.8553 (mttt) cc_final: 0.8333 (tptp) REVERT: E 579 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.8354 (mpp80) REVERT: E 625 ASN cc_start: 0.7680 (OUTLIER) cc_final: 0.7389 (t0) REVERT: G 84 SER cc_start: 0.8847 (p) cc_final: 0.8496 (t) REVERT: J 50 ASP cc_start: 0.8658 (t0) cc_final: 0.8413 (t0) REVERT: J 70 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7807 (pt0) REVERT: D 53 PHE cc_start: 0.7598 (m-80) cc_final: 0.6974 (m-10) REVERT: D 217 TYR cc_start: 0.9134 (m-80) cc_final: 0.8781 (m-80) REVERT: D 275 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.8002 (tp30) REVERT: D 320 THR cc_start: 0.9301 (m) cc_final: 0.8995 (p) REVERT: D 482 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.8063 (mm-30) REVERT: D 486 TYR cc_start: 0.8245 (OUTLIER) cc_final: 0.7565 (p90) REVERT: F 575 GLN cc_start: 0.9016 (mt0) cc_final: 0.8535 (mm-40) REVERT: F 577 GLN cc_start: 0.8933 (tp-100) cc_final: 0.8410 (mm-40) REVERT: F 584 GLU cc_start: 0.8652 (mt-10) cc_final: 0.8216 (mt-10) REVERT: I 38 ARG cc_start: 0.8693 (OUTLIER) cc_final: 0.7173 (ttp80) REVERT: K 70 GLU cc_start: 0.8349 (mt-10) cc_final: 0.7863 (pt0) REVERT: K 82 ASP cc_start: 0.7436 (m-30) cc_final: 0.7049 (m-30) outliers start: 75 outliers final: 47 residues processed: 331 average time/residue: 0.3635 time to fit residues: 177.7560 Evaluate side-chains 319 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 261 time to evaluate : 2.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain B residue 577 GLN Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 43 GLN Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 17 ASP Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 96 GLU Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 545 LEU Chi-restraints excluded: chain E residue 579 ARG Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 625 ASN Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 80 MET Chi-restraints excluded: chain G residue 83 ARG Chi-restraints excluded: chain G residue 99 TYR Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain D residue 69 TRP Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 275 GLU Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 482 GLU Chi-restraints excluded: chain D residue 486 TYR Chi-restraints excluded: chain F residue 574 LYS Chi-restraints excluded: chain F residue 588 LYS Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 620 THR Chi-restraints excluded: chain F residue 647 GLU Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 38 ARG Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 99 TYR Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain K residue 54 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 218 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 165 optimal weight: 3.9990 chunk 190 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 chunk 225 optimal weight: 4.9990 chunk 141 optimal weight: 0.9990 chunk 137 optimal weight: 7.9990 chunk 104 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 GLN B 653 GLN C 425 ASN ** C 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 46 GLN J 24 GLN ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.4294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 21027 Z= 0.327 Angle : 0.642 9.666 28560 Z= 0.317 Chirality : 0.047 0.316 3543 Planarity : 0.004 0.039 3474 Dihedral : 6.828 55.176 5193 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 3.71 % Allowed : 14.98 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.17), residues: 2343 helix: 1.66 (0.27), residues: 393 sheet: 0.13 (0.18), residues: 744 loop : -0.21 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP I 71D HIS 0.007 0.001 HIS D 374 PHE 0.011 0.002 PHE A 176 TYR 0.019 0.002 TYR K 49 ARG 0.006 0.001 ARG E 542 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 267 time to evaluate : 2.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.8498 (t) cc_final: 0.8230 (p) REVERT: A 303 THR cc_start: 0.8820 (OUTLIER) cc_final: 0.8582 (p) REVERT: B 589 ASP cc_start: 0.8369 (m-30) cc_final: 0.7916 (m-30) REVERT: B 625 ASN cc_start: 0.7777 (OUTLIER) cc_final: 0.7467 (t0) REVERT: B 648 ASP cc_start: 0.8340 (m-30) cc_final: 0.8010 (t0) REVERT: H 43 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.8064 (mp10) REVERT: H 84 SER cc_start: 0.9156 (p) cc_final: 0.8725 (t) REVERT: L 3 GLN cc_start: 0.8276 (pp30) cc_final: 0.7983 (pp30) REVERT: L 49 TYR cc_start: 0.8753 (p90) cc_final: 0.8547 (p90) REVERT: L 50 ASP cc_start: 0.8942 (t0) cc_final: 0.8619 (t0) REVERT: L 70 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7565 (pt0) REVERT: C 66 HIS cc_start: 0.7360 (OUTLIER) cc_final: 0.7049 (t-90) REVERT: C 114 GLN cc_start: 0.8616 (OUTLIER) cc_final: 0.8186 (mp10) REVERT: C 185 LYS cc_start: 0.8611 (mttt) cc_final: 0.8313 (tptp) REVERT: E 575 GLN cc_start: 0.9031 (mt0) cc_final: 0.8711 (mt0) REVERT: E 579 ARG cc_start: 0.8693 (OUTLIER) cc_final: 0.8278 (mpp80) REVERT: E 625 ASN cc_start: 0.7489 (OUTLIER) cc_final: 0.7242 (t0) REVERT: G 84 SER cc_start: 0.8885 (p) cc_final: 0.8544 (t) REVERT: J 50 ASP cc_start: 0.8799 (t0) cc_final: 0.8576 (t0) REVERT: J 70 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7801 (pt0) REVERT: D 275 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8096 (tp30) REVERT: D 320 THR cc_start: 0.9301 (m) cc_final: 0.9030 (p) REVERT: D 482 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.8112 (mm-30) REVERT: D 486 TYR cc_start: 0.8403 (OUTLIER) cc_final: 0.7521 (p90) REVERT: F 577 GLN cc_start: 0.8972 (tp-100) cc_final: 0.8438 (mm-40) REVERT: F 584 GLU cc_start: 0.8692 (mt-10) cc_final: 0.8266 (mt-10) REVERT: F 638 TYR cc_start: 0.8909 (m-10) cc_final: 0.8566 (m-10) REVERT: I 38 ARG cc_start: 0.8811 (OUTLIER) cc_final: 0.7321 (ttp80) REVERT: I 72 ASP cc_start: 0.7703 (m-30) cc_final: 0.7474 (m-30) REVERT: K 50 ASP cc_start: 0.8581 (t0) cc_final: 0.7925 (t0) REVERT: K 70 GLU cc_start: 0.8415 (mt-10) cc_final: 0.7937 (pt0) outliers start: 78 outliers final: 57 residues processed: 319 average time/residue: 0.3509 time to fit residues: 166.1803 Evaluate side-chains 325 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 257 time to evaluate : 2.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 43 GLN Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 17 ASP Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 96 GLU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 545 LEU Chi-restraints excluded: chain E residue 579 ARG Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 625 ASN Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain G residue 80 MET Chi-restraints excluded: chain G residue 83 ARG Chi-restraints excluded: chain G residue 99 TYR Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain J residue 17 ASP Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 69 TRP Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 275 GLU Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 365 SER Chi-restraints excluded: chain D residue 426 MET Chi-restraints excluded: chain D residue 482 GLU Chi-restraints excluded: chain D residue 486 TYR Chi-restraints excluded: chain D residue 490 GLU Chi-restraints excluded: chain F residue 574 LYS Chi-restraints excluded: chain F residue 588 LYS Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 620 THR Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 647 GLU Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 38 ARG Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 63 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 90 optimal weight: 0.8980 chunk 134 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 143 optimal weight: 0.9980 chunk 153 optimal weight: 0.6980 chunk 111 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 177 optimal weight: 2.9990 chunk 205 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 425 ASN J 24 GLN D 407 ASN ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.4405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21027 Z= 0.208 Angle : 0.592 10.620 28560 Z= 0.292 Chirality : 0.046 0.293 3543 Planarity : 0.003 0.038 3474 Dihedral : 6.476 53.318 5193 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.52 % Allowed : 15.12 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.17), residues: 2343 helix: 1.67 (0.27), residues: 396 sheet: 0.11 (0.18), residues: 744 loop : -0.23 (0.18), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP I 71D HIS 0.004 0.001 HIS D 216 PHE 0.013 0.001 PHE A 376 TYR 0.022 0.001 TYR K 49 ARG 0.007 0.000 ARG J 56 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 282 time to evaluate : 2.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.8476 (t) cc_final: 0.8187 (p) REVERT: A 303 THR cc_start: 0.8748 (OUTLIER) cc_final: 0.8509 (p) REVERT: B 589 ASP cc_start: 0.8359 (m-30) cc_final: 0.7912 (m-30) REVERT: B 625 ASN cc_start: 0.7675 (OUTLIER) cc_final: 0.7358 (t0) REVERT: B 647 GLU cc_start: 0.8444 (tp30) cc_final: 0.8208 (tp30) REVERT: B 648 ASP cc_start: 0.8268 (m-30) cc_final: 0.8029 (t0) REVERT: H 43 GLN cc_start: 0.8606 (OUTLIER) cc_final: 0.8052 (mp10) REVERT: H 84 SER cc_start: 0.9140 (p) cc_final: 0.8703 (t) REVERT: L 3 GLN cc_start: 0.8262 (pp30) cc_final: 0.7965 (pp30) REVERT: L 50 ASP cc_start: 0.8966 (t0) cc_final: 0.8655 (t0) REVERT: L 70 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7617 (pt0) REVERT: C 66 HIS cc_start: 0.7100 (OUTLIER) cc_final: 0.6815 (t-90) REVERT: C 114 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.8120 (mp10) REVERT: C 185 LYS cc_start: 0.8550 (mttt) cc_final: 0.8330 (tptp) REVERT: E 575 GLN cc_start: 0.8988 (mt0) cc_final: 0.8693 (mt0) REVERT: E 579 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.8459 (mpp80) REVERT: E 625 ASN cc_start: 0.7590 (OUTLIER) cc_final: 0.7334 (t0) REVERT: G 84 SER cc_start: 0.8877 (p) cc_final: 0.8537 (t) REVERT: J 50 ASP cc_start: 0.8769 (t0) cc_final: 0.8531 (t0) REVERT: J 70 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7754 (pt0) REVERT: D 217 TYR cc_start: 0.9130 (m-80) cc_final: 0.8836 (m-80) REVERT: D 275 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.8016 (tp30) REVERT: D 320 THR cc_start: 0.9296 (m) cc_final: 0.9001 (p) REVERT: D 482 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.8095 (mm-30) REVERT: D 486 TYR cc_start: 0.8345 (OUTLIER) cc_final: 0.7421 (p90) REVERT: F 577 GLN cc_start: 0.8937 (tp-100) cc_final: 0.8383 (mm-40) REVERT: F 584 GLU cc_start: 0.8676 (mt-10) cc_final: 0.8296 (mt-10) REVERT: F 638 TYR cc_start: 0.8857 (m-10) cc_final: 0.8551 (m-10) REVERT: I 38 ARG cc_start: 0.8742 (OUTLIER) cc_final: 0.7311 (ttp80) REVERT: K 50 ASP cc_start: 0.8551 (t0) cc_final: 0.7873 (t0) REVERT: K 62 PHE cc_start: 0.7242 (m-80) cc_final: 0.7033 (m-80) REVERT: K 70 GLU cc_start: 0.8377 (mt-10) cc_final: 0.7867 (pt0) outliers start: 74 outliers final: 54 residues processed: 333 average time/residue: 0.3832 time to fit residues: 190.2787 Evaluate side-chains 327 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 262 time to evaluate : 2.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 43 GLN Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 17 ASP Chi-restraints excluded: chain L residue 96 GLU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 545 LEU Chi-restraints excluded: chain E residue 579 ARG Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 625 ASN Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain G residue 80 MET Chi-restraints excluded: chain G residue 99 TYR Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain D residue 69 TRP Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 275 GLU Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 365 SER Chi-restraints excluded: chain D residue 482 GLU Chi-restraints excluded: chain D residue 486 TYR Chi-restraints excluded: chain D residue 490 GLU Chi-restraints excluded: chain F residue 574 LYS Chi-restraints excluded: chain F residue 588 LYS Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 620 THR Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 647 GLU Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 38 ARG Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 99 TYR Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 63 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 2.9990 chunk 197 optimal weight: 0.0570 chunk 210 optimal weight: 0.9990 chunk 126 optimal weight: 1.9990 chunk 91 optimal weight: 0.0370 chunk 165 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 189 optimal weight: 0.6980 chunk 198 optimal weight: 0.7980 chunk 209 optimal weight: 0.8980 chunk 138 optimal weight: 4.9990 overall best weight: 0.4976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN C 425 ASN J 24 GLN ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.4487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 21027 Z= 0.155 Angle : 0.578 11.319 28560 Z= 0.285 Chirality : 0.045 0.288 3543 Planarity : 0.003 0.042 3474 Dihedral : 6.014 52.188 5193 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.19 % Allowed : 16.31 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.17), residues: 2343 helix: 1.73 (0.27), residues: 396 sheet: 0.13 (0.18), residues: 744 loop : -0.22 (0.18), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP I 71D HIS 0.005 0.001 HIS C 374 PHE 0.011 0.001 PHE A 376 TYR 0.023 0.001 TYR K 49 ARG 0.008 0.000 ARG E 542 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 295 time to evaluate : 2.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.8266 (t) cc_final: 0.7949 (p) REVERT: A 95 MET cc_start: 0.8935 (ptm) cc_final: 0.8687 (ptm) REVERT: A 486 TYR cc_start: 0.8155 (OUTLIER) cc_final: 0.6464 (p90) REVERT: B 589 ASP cc_start: 0.8363 (m-30) cc_final: 0.7875 (m-30) REVERT: H 43 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.8023 (mp10) REVERT: H 84 SER cc_start: 0.9104 (p) cc_final: 0.8651 (t) REVERT: L 3 GLN cc_start: 0.8318 (pp30) cc_final: 0.8055 (pp30) REVERT: L 40 ARG cc_start: 0.7742 (mmp80) cc_final: 0.7489 (mmp80) REVERT: L 50 ASP cc_start: 0.9015 (t0) cc_final: 0.8671 (t0) REVERT: L 53 LYS cc_start: 0.8318 (mttm) cc_final: 0.8021 (mttm) REVERT: C 66 HIS cc_start: 0.7099 (OUTLIER) cc_final: 0.6860 (t-90) REVERT: C 114 GLN cc_start: 0.8565 (OUTLIER) cc_final: 0.8108 (mp10) REVERT: C 150 MET cc_start: 0.8265 (mmm) cc_final: 0.7686 (mmt) REVERT: C 320 THR cc_start: 0.9312 (m) cc_final: 0.9060 (p) REVERT: E 575 GLN cc_start: 0.8988 (mt0) cc_final: 0.8655 (mt0) REVERT: E 577 GLN cc_start: 0.8931 (tp40) cc_final: 0.8548 (mm-40) REVERT: E 579 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.8289 (mpp80) REVERT: E 584 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8153 (mt-10) REVERT: E 625 ASN cc_start: 0.7569 (OUTLIER) cc_final: 0.7317 (t0) REVERT: E 626 MET cc_start: 0.8414 (ttm) cc_final: 0.8038 (ttt) REVERT: G 84 SER cc_start: 0.8845 (p) cc_final: 0.8498 (t) REVERT: J 50 ASP cc_start: 0.8704 (t0) cc_final: 0.8458 (t0) REVERT: J 70 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7767 (pt0) REVERT: D 217 TYR cc_start: 0.9060 (m-80) cc_final: 0.8762 (m-80) REVERT: D 275 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7973 (tp30) REVERT: D 320 THR cc_start: 0.9278 (m) cc_final: 0.8947 (p) REVERT: D 486 TYR cc_start: 0.8377 (OUTLIER) cc_final: 0.7574 (p90) REVERT: F 577 GLN cc_start: 0.8899 (tp-100) cc_final: 0.8337 (mm-40) REVERT: F 584 GLU cc_start: 0.8655 (mt-10) cc_final: 0.8273 (mt-10) REVERT: F 626 MET cc_start: 0.8234 (ttt) cc_final: 0.7921 (ttt) REVERT: F 634 GLU cc_start: 0.8785 (tp30) cc_final: 0.8505 (tt0) REVERT: F 638 TYR cc_start: 0.8763 (m-10) cc_final: 0.8555 (m-10) REVERT: F 655 LYS cc_start: 0.7664 (ptpt) cc_final: 0.7353 (ptpt) REVERT: K 50 ASP cc_start: 0.8527 (t0) cc_final: 0.7884 (t0) REVERT: K 70 GLU cc_start: 0.8345 (mt-10) cc_final: 0.7883 (pt0) outliers start: 67 outliers final: 49 residues processed: 337 average time/residue: 0.3522 time to fit residues: 176.9110 Evaluate side-chains 334 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 276 time to evaluate : 2.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 486 TYR Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 43 GLN Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 17 ASP Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 545 LEU Chi-restraints excluded: chain E residue 579 ARG Chi-restraints excluded: chain E residue 584 GLU Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 625 ASN Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain G residue 80 MET Chi-restraints excluded: chain G residue 99 TYR Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 96 GLU Chi-restraints excluded: chain D residue 69 TRP Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 275 GLU Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 365 SER Chi-restraints excluded: chain D residue 486 TYR Chi-restraints excluded: chain F residue 574 LYS Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 620 THR Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 647 GLU Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 99 TYR Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 85 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 222 optimal weight: 3.9990 chunk 135 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 chunk 154 optimal weight: 3.9990 chunk 233 optimal weight: 3.9990 chunk 214 optimal weight: 0.9990 chunk 185 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 143 optimal weight: 0.9980 chunk 113 optimal weight: 3.9990 chunk 147 optimal weight: 0.0270 overall best weight: 0.8044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN B 575 GLN C 425 ASN E 619 GLN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 24 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.4577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21027 Z= 0.181 Angle : 0.588 12.170 28560 Z= 0.290 Chirality : 0.046 0.401 3543 Planarity : 0.003 0.037 3474 Dihedral : 5.816 52.248 5189 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.95 % Allowed : 16.64 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.17), residues: 2343 helix: 1.76 (0.27), residues: 396 sheet: 0.14 (0.19), residues: 744 loop : -0.22 (0.18), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP I 71D HIS 0.006 0.001 HIS A 374 PHE 0.015 0.001 PHE A 376 TYR 0.023 0.001 TYR K 49 ARG 0.010 0.000 ARG J 56 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 281 time to evaluate : 2.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.8348 (t) cc_final: 0.8041 (p) REVERT: A 95 MET cc_start: 0.8957 (ptm) cc_final: 0.8719 (ptm) REVERT: A 486 TYR cc_start: 0.8154 (OUTLIER) cc_final: 0.6419 (p90) REVERT: B 543 GLN cc_start: 0.8620 (mm-40) cc_final: 0.8163 (tm-30) REVERT: B 589 ASP cc_start: 0.8344 (m-30) cc_final: 0.7909 (m-30) REVERT: H 3 GLN cc_start: 0.8608 (tt0) cc_final: 0.8391 (tt0) REVERT: H 43 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.8026 (mp10) REVERT: H 84 SER cc_start: 0.9083 (p) cc_final: 0.8641 (t) REVERT: L 3 GLN cc_start: 0.8377 (pp30) cc_final: 0.8086 (pp30) REVERT: L 50 ASP cc_start: 0.8984 (t0) cc_final: 0.8696 (t0) REVERT: C 66 HIS cc_start: 0.7250 (OUTLIER) cc_final: 0.6977 (t-90) REVERT: C 114 GLN cc_start: 0.8573 (OUTLIER) cc_final: 0.8114 (mp10) REVERT: E 575 GLN cc_start: 0.8986 (mt0) cc_final: 0.8660 (mt0) REVERT: E 579 ARG cc_start: 0.8683 (OUTLIER) cc_final: 0.8387 (mpp80) REVERT: E 625 ASN cc_start: 0.7591 (OUTLIER) cc_final: 0.7339 (t0) REVERT: E 626 MET cc_start: 0.8322 (ttm) cc_final: 0.8033 (ttt) REVERT: G 84 SER cc_start: 0.8799 (p) cc_final: 0.8442 (t) REVERT: J 50 ASP cc_start: 0.8717 (t0) cc_final: 0.8454 (t0) REVERT: J 70 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7788 (pt0) REVERT: D 217 TYR cc_start: 0.9085 (m-80) cc_final: 0.8788 (m-80) REVERT: D 275 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7996 (tp30) REVERT: D 320 THR cc_start: 0.9251 (m) cc_final: 0.8892 (p) REVERT: D 486 TYR cc_start: 0.8305 (OUTLIER) cc_final: 0.7494 (p90) REVERT: F 577 GLN cc_start: 0.8909 (tp-100) cc_final: 0.8344 (mm-40) REVERT: F 584 GLU cc_start: 0.8658 (mt-10) cc_final: 0.8277 (mt-10) REVERT: F 626 MET cc_start: 0.8250 (ttt) cc_final: 0.7974 (ttt) REVERT: F 634 GLU cc_start: 0.8709 (tp30) cc_final: 0.8457 (tt0) REVERT: K 50 ASP cc_start: 0.8567 (t0) cc_final: 0.8155 (t0) REVERT: K 70 GLU cc_start: 0.8342 (mt-10) cc_final: 0.7896 (pt0) outliers start: 62 outliers final: 47 residues processed: 320 average time/residue: 0.3535 time to fit residues: 167.9839 Evaluate side-chains 329 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 274 time to evaluate : 2.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 486 TYR Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 43 GLN Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 545 LEU Chi-restraints excluded: chain E residue 579 ARG Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 625 ASN Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 80 MET Chi-restraints excluded: chain G residue 99 TYR Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 96 GLU Chi-restraints excluded: chain D residue 69 TRP Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 275 GLU Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 365 SER Chi-restraints excluded: chain D residue 426 MET Chi-restraints excluded: chain D residue 486 TYR Chi-restraints excluded: chain F residue 574 LYS Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 620 THR Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 647 GLU Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 99 TYR Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 85 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 171 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 51 optimal weight: 0.0020 chunk 185 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 190 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 163 optimal weight: 4.9990 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.098032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.079949 restraints weight = 44125.101| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.96 r_work: 0.3117 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.4636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21027 Z= 0.167 Angle : 0.586 12.128 28560 Z= 0.289 Chirality : 0.046 0.355 3543 Planarity : 0.003 0.037 3474 Dihedral : 5.588 52.163 5187 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.71 % Allowed : 17.21 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.17), residues: 2343 helix: 1.85 (0.27), residues: 393 sheet: 0.18 (0.19), residues: 744 loop : -0.23 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP I 71D HIS 0.007 0.001 HIS A 374 PHE 0.012 0.001 PHE A 376 TYR 0.048 0.001 TYR F 638 ARG 0.009 0.000 ARG L 56 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4630.22 seconds wall clock time: 85 minutes 4.00 seconds (5104.00 seconds total)