Starting phenix.real_space_refine on Sun Mar 17 22:58:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mar_9062/03_2024/6mar_9062_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mar_9062/03_2024/6mar_9062.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mar_9062/03_2024/6mar_9062.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mar_9062/03_2024/6mar_9062.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mar_9062/03_2024/6mar_9062_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mar_9062/03_2024/6mar_9062_updated.pdb" } resolution = 4.5 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= 0.000 sd= 0.005 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 116 5.16 5 C 12000 2.51 5 N 3158 2.21 5 O 3937 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "N TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 19211 Number of models: 1 Model: "" Number of chains: 47 Chain: "M" Number of atoms: 1067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1067 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain: "N" Number of atoms: 866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 866 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 105} Chain: "H" Number of atoms: 1073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1073 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain: "L" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 881 Classifications: {'peptide': 114} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 107} Chain: "A" Number of atoms: 3464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3464 Classifications: {'peptide': 440} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 417} Chain breaks: 3 Chain: "B" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1050 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 1, 'TRANS': 132} Chain breaks: 1 Chain: "D" Number of atoms: 1149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1149 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 1, 'TRANS': 144} Chain breaks: 1 Chain: "C" Number of atoms: 3493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3493 Classifications: {'peptide': 444} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 421} Chain breaks: 3 Chain: "E" Number of atoms: 3448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3448 Classifications: {'peptide': 438} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 415} Chain breaks: 3 Chain: "F" Number of atoms: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1009 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 1, 'TRANS': 125} Chain breaks: 1 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 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: "K" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 135 Unusual residues: {'BMA': 1, 'FUC': 1, 'GAL': 2, 'MAN': 2, 'NAG': 5} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "U" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 124 Unusual residues: {'BMA': 1, 'FUC': 1, 'GAL': 1, 'MAN': 2, 'NAG': 5} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 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: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 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: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 121 Unusual residues: {'BMA': 1, 'FUC': 1, 'GAL': 2, 'MAN': 2, 'NAG': 4} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "o" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 124 Unusual residues: {'BMA': 1, 'FUC': 1, 'GAL': 1, 'MAN': 2, 'NAG': 5} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: "D" 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: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "F" Number of atoms: 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: 10.30, per 1000 atoms: 0.54 Number of scatterers: 19211 At special positions: 0 Unit cell: (158.4, 142.8, 128.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 116 16.00 O 3937 8.00 N 3158 7.00 C 12000 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " 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 A 54 " - pdb=" SG CYS A 74 " distance=2.04 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.04 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 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=2.02 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.04 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 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 K 4 " - " MAN K 5 " " MAN h 4 " - " MAN h 5 " ALPHA1-3 " BMA K 3 " - " MAN K 4 " " BMA T 3 " - " MAN T 9 " " BMA U 3 " - " MAN U 4 " " BMA e 3 " - " MAN e 4 " " BMA h 3 " - " MAN h 4 " " MAN h 6 " - " MAN h 7 " " BMA n 3 " - " MAN n 9 " " BMA o 3 " - " MAN o 4 " ALPHA1-6 " BMA K 3 " - " MAN K 6 " " BMA T 3 " - " MAN T 4 " " BMA U 3 " - " MAN U 8 " " BMA h 3 " - " MAN h 6 " " BMA n 3 " - " MAN n 4 " " BMA o 3 " - " MAN o 8 " BETA1-2 " MAN T 4 " - " NAG T 5 " " MAN T 9 " - " NAG T 10 " " MAN U 4 " - " NAG U 5 " " MAN U 8 " - " NAG U 9 " " MAN n 4 " - " NAG n 5 " " MAN o 4 " - " NAG o 5 " " MAN o 8 " - " NAG o 9 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG T 5 " - " GAL T 6 " " NAG T 7 " - " GAL T 8 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " MAN U 4 " - " NAG U 7 " " NAG U 5 " - " GAL U 6 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " 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 n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG n 5 " - " GAL n 6 " " NAG n 7 " - " GAL n 8 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " MAN o 4 " - " NAG o 7 " " NAG o 5 " - " GAL o 6 " BETA1-6 " NAG T 1 " - " FUC T 11 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " MAN T 4 " - " NAG T 7 " " NAG U 1 " - " FUC U 10 " " NAG n 1 " - " FUC n 10 " " MAN n 4 " - " NAG n 7 " " NAG o 1 " - " FUC o 10 " NAG-ASN " NAG A1000 " - " ASN A 295 " " NAG A1015 " - " ASN A 355 " " NAG A1018 " - " ASN A 392 " " NAG A1022 " - " ASN A 234 " " NAG A1023 " - " ASN A 276 " " NAG B 801 " - " ASN B 625 " " NAG B 802 " - " ASN B 618 " " NAG C 601 " - " ASN C 295 " " NAG C 610 " - " ASN C 355 " " NAG C 611 " - " ASN C 88 " " NAG C 612 " - " ASN C 392 " " NAG C 615 " - " ASN C 234 " " NAG D1000 " - " ASN D 625 " " NAG D1001 " - " ASN D 618 " " NAG D1004 " - " ASN D 637 " " NAG E1000 " - " ASN E 295 " " NAG E1001 " - " ASN E 301 " " NAG E1015 " - " ASN E 355 " " NAG E1016 " - " ASN E 88 " " NAG E1017 " - " ASN E 392 " " NAG E1021 " - " ASN E 234 " " NAG F1000 " - " ASN F 618 " " NAG G 1 " - " ASN A 301 " " NAG I 1 " - " ASN A 156 " " NAG J 1 " - " ASN A 197 " " NAG K 1 " - " ASN A 262 " " NAG O 1 " - " ASN A 448 " " NAG P 1 " - " ASN A 88 " " NAG Q 1 " - " ASN A 386 " " NAG R 1 " - " ASN A 160 " " NAG S 1 " - " ASN A 363 " " NAG T 1 " - " ASN B 611 " " NAG U 1 " - " ASN B 637 " " NAG V 1 " - " ASN D 611 " " NAG W 1 " - " ASN C 301 " " NAG X 1 " - " ASN C 156 " " NAG Y 1 " - " ASN C 197 " " NAG Z 1 " - " ASN C 448 " " NAG a 1 " - " ASN C 386 " " NAG b 1 " - " ASN C 276 " " NAG c 1 " - " ASN C 160 " " NAG d 1 " - " ASN C 363 " " NAG e 1 " - " ASN C 262 " " NAG f 1 " - " ASN E 156 " " NAG g 1 " - " ASN E 197 " " NAG h 1 " - " ASN E 262 " " NAG i 1 " - " ASN E 448 " " NAG j 1 " - " ASN E 386 " " NAG k 1 " - " ASN E 276 " " NAG l 1 " - " ASN E 160 " " NAG m 1 " - " ASN E 363 " " NAG n 1 " - " ASN F 611 " " NAG o 1 " - " ASN F 637 " Time building additional restraints: 9.43 Conformation dependent library (CDL) restraints added in 3.4 seconds 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4124 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 48 helices and 39 sheets defined 17.6% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.56 Creating SS restraints... Processing helix chain 'M' and resid 29 through 31 No H-bonds generated for 'chain 'M' and resid 29 through 31' Processing helix chain 'M' and resid 84 through 86 No H-bonds generated for 'chain 'M' and resid 84 through 86' Processing helix chain 'N' and resid 80 through 82 No H-bonds generated for 'chain 'N' and resid 80 through 82' Processing helix chain 'H' and resid 84 through 86 No H-bonds generated for 'chain 'H' and resid 84 through 86' Processing helix chain 'A' and resid 99 through 115 Processing helix chain 'A' and resid 123 through 125 No H-bonds generated for 'chain 'A' and resid 123 through 125' Processing helix chain 'A' and resid 140 through 142 No H-bonds generated for 'chain 'A' and resid 140 through 142' Processing helix chain 'A' and resid 178 through 180 No H-bonds generated for 'chain 'A' and resid 178 through 180' Processing helix chain 'A' and resid 336 through 351 removed outlier: 4.065A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 372 No H-bonds generated for 'chain 'A' and resid 369 through 372' Processing helix chain 'A' and resid 378 through 380 No H-bonds generated for 'chain 'A' and resid 378 through 380' Processing helix chain 'A' and resid 475 through 482 removed outlier: 4.093A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 527 removed outlier: 4.133A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 524 through 527' Processing helix chain 'B' and resid 530 through 535 removed outlier: 5.566A pdb=" N MET B 535 " --> pdb=" O GLY B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 543 removed outlier: 4.124A pdb=" N ALA B 541 " --> pdb=" O LEU B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 595 Processing helix chain 'B' and resid 628 through 635 Processing helix chain 'B' and resid 639 through 651 Processing helix chain 'B' and resid 656 through 661 Processing helix chain 'D' and resid 530 through 535 removed outlier: 5.795A pdb=" N MET D 535 " --> pdb=" O GLY D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 544 removed outlier: 4.263A pdb=" N ASN D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N LEU D 544 " --> pdb=" O GLN D 540 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 564 Processing helix chain 'D' and resid 570 through 595 Processing helix chain 'D' and resid 619 through 622 No H-bonds generated for 'chain 'D' and resid 619 through 622' Processing helix chain 'D' and resid 628 through 635 Processing helix chain 'D' and resid 639 through 651 Processing helix chain 'D' and resid 656 through 660 Processing helix chain 'C' and resid 68 through 70 No H-bonds generated for 'chain 'C' and resid 68 through 70' Processing helix chain 'C' and resid 99 through 115 removed outlier: 3.623A pdb=" N GLN C 103 " --> pdb=" O ASN C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 126 removed outlier: 3.854A pdb=" N CYS C 126 " --> pdb=" O THR C 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 123 through 126' Processing helix chain 'C' and resid 336 through 349 Processing helix chain 'C' and resid 378 through 380 No H-bonds generated for 'chain 'C' and resid 378 through 380' Processing helix chain 'C' and resid 475 through 480 Processing helix chain 'E' and resid 100 through 117 removed outlier: 3.847A pdb=" N LEU E 116 " --> pdb=" O TRP E 112 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LYS E 117 " --> pdb=" O ASP E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 126 removed outlier: 3.961A pdb=" N CYS E 126 " --> pdb=" O THR E 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 123 through 126' Processing helix chain 'E' and resid 140 through 142 No H-bonds generated for 'chain 'E' and resid 140 through 142' Processing helix chain 'E' and resid 178 through 180 No H-bonds generated for 'chain 'E' and resid 178 through 180' Processing helix chain 'E' and resid 336 through 351 removed outlier: 3.892A pdb=" N ARG E 350 " --> pdb=" O VAL E 346 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N LYS E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 372 No H-bonds generated for 'chain 'E' and resid 369 through 372' Processing helix chain 'E' and resid 378 through 380 No H-bonds generated for 'chain 'E' and resid 378 through 380' Processing helix chain 'E' and resid 388 through 391 removed outlier: 3.550A pdb=" N PHE E 391 " --> pdb=" O SER E 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 388 through 391' Processing helix chain 'E' and resid 477 through 485 removed outlier: 4.136A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LYS E 485 " --> pdb=" O SER E 481 " (cutoff:3.500A) Processing helix chain 'F' and resid 537 through 543 Processing helix chain 'F' and resid 570 through 595 removed outlier: 3.724A pdb=" N LYS F 574 " --> pdb=" O VAL F 570 " (cutoff:3.500A) Processing helix chain 'F' and resid 619 through 624 Processing helix chain 'F' and resid 628 through 635 Processing helix chain 'F' and resid 639 through 651 Processing helix chain 'F' and resid 656 through 662 Processing sheet with id= A, first strand: chain 'M' and resid 10 through 12 removed outlier: 3.514A pdb=" N GLY M 10 " --> pdb=" O THR M 108 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N VAL M 109 " --> pdb=" O ALA M 88 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ALA M 88 " --> pdb=" O VAL M 109 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG M 91 " --> pdb=" O VAL M 37 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL M 37 " --> pdb=" O ARG M 91 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N MET M 34 " --> pdb=" O ILE M 51 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N ARG M 38 " --> pdb=" O TRP M 47 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N TRP M 47 " --> pdb=" O ARG M 38 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ALA M 40 " --> pdb=" O LEU M 45 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU M 45 " --> pdb=" O ALA M 40 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'M' and resid 20 through 23 Processing sheet with id= C, first strand: chain 'N' and resid 5 through 7 removed outlier: 3.508A pdb=" N THR N 7 " --> pdb=" O SER N 22 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'N' and resid 85 through 90 removed outlier: 3.501A pdb=" N TYR N 87 " --> pdb=" O TYR N 36 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N ARG N 37 " --> pdb=" O LEU N 46 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N LEU N 46 " --> pdb=" O ARG N 37 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'N' and resid 63 through 66 removed outlier: 3.764A pdb=" N VAL N 63 " --> pdb=" O ARG N 74 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ARG N 74 " --> pdb=" O VAL N 63 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N SER N 65 " --> pdb=" O THR N 72 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR N 72 " --> pdb=" O SER N 65 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.719A pdb=" N ARG H 91 " --> pdb=" O VAL H 37 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ALA H 93 " --> pdb=" O TYR H 35 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N TYR H 35 " --> pdb=" O ALA H 93 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'H' and resid 17 through 22 removed outlier: 3.633A pdb=" N MET H 82 " --> pdb=" O VAL H 18 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU H 80 " --> pdb=" O LEU H 20 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N CYS H 22 " --> pdb=" O LEU H 78 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'H' and resid 93 through 95 removed outlier: 3.535A pdb=" N ARG H 94 " --> pdb=" O VAL H 102 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N VAL H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'L' and resid 21 through 24 removed outlier: 3.507A pdb=" N SER L 65 " --> pdb=" O THR L 72 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'L' and resid 102 through 104 removed outlier: 3.689A pdb=" N TRP L 35 " --> pdb=" O VAL L 48 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ARG L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N LEU L 46 " --> pdb=" O ARG L 37 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 35 through 40 removed outlier: 4.042A pdb=" N GLY A 495 " --> pdb=" O TYR A 39 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 91 through 93 removed outlier: 4.180A pdb=" N GLY A 237 " --> pdb=" O PHE A 93 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 130 through 133 removed outlier: 3.792A pdb=" N MET A 161 " --> pdb=" O GLN A 170 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 181 through 183 Processing sheet with id= O, first strand: chain 'A' and resid 487 through 490 removed outlier: 3.819A pdb=" N LYS A 487 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL A 245 " --> pdb=" O ILE A 225 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'A' and resid 271 through 274 removed outlier: 6.380A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'A' and resid 443 through 447 removed outlier: 3.883A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N HIS A 330 " --> pdb=" O THR A 297 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL A 333 " --> pdb=" O ILE A 414 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'A' and resid 359 through 361 removed outlier: 6.175A pdb=" N GLU A 466 " --> pdb=" O ARG A 360 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'A' and resid 383 through 385 Processing sheet with id= T, first strand: chain 'A' and resid 307 through 312 removed outlier: 6.702A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 35 through 39 Processing sheet with id= V, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.609A pdb=" N LYS C 487 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL C 245 " --> pdb=" O ILE C 225 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 53 through 56 removed outlier: 3.843A pdb=" N PHE C 53 " --> pdb=" O CYS C 218 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'C' and resid 91 through 94 removed outlier: 3.778A pdb=" N PHE C 93 " --> pdb=" O GLY C 237 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLY C 237 " --> pdb=" O PHE C 93 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'C' and resid 130 through 133 removed outlier: 3.522A pdb=" N MET C 161 " --> pdb=" O GLN C 170 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'C' and resid 181 through 183 Processing sheet with id= AA, first strand: chain 'C' and resid 271 through 273 removed outlier: 3.921A pdb=" N SER C 393 " --> pdb=" O PHE C 361 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'C' and resid 444 through 447 removed outlier: 3.532A pdb=" N SER C 447 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR C 297 " --> pdb=" O HIS C 330 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N HIS C 330 " --> pdb=" O THR C 297 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL C 333 " --> pdb=" O ILE C 414 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE C 414 " --> pdb=" O VAL C 333 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'C' and resid 383 through 385 Processing sheet with id= AD, first strand: chain 'C' and resid 307 through 312 removed outlier: 6.590A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'E' and resid 35 through 40 Processing sheet with id= AF, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.696A pdb=" N THR E 244 " --> pdb=" O ILE E 84 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE E 84 " --> pdb=" O THR E 244 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'E' and resid 130 through 133 removed outlier: 3.780A pdb=" N GLN E 130 " --> pdb=" O SER E 158 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'E' and resid 181 through 183 Processing sheet with id= AI, first strand: chain 'E' and resid 271 through 273 removed outlier: 3.629A pdb=" N MET E 271 " --> pdb=" O GLN E 287 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'E' and resid 443 through 447 removed outlier: 3.765A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N HIS E 330 " --> pdb=" O THR E 297 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'E' and resid 359 through 361 removed outlier: 5.885A pdb=" N GLU E 466 " --> pdb=" O ARG E 360 " (cutoff:3.500A) No H-bonds generated for sheet with id= AK Processing sheet with id= AL, first strand: chain 'E' and resid 374 through 376 removed outlier: 3.962A pdb=" N PHE E 376 " --> pdb=" O PHE E 383 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE E 383 " --> pdb=" O PHE E 376 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'E' and resid 307 through 312 removed outlier: 6.782A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) 431 hydrogen bonds defined for protein. 1158 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: 5.40 Time building geometry restraints manager: 10.05 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: 5901 1.34 - 1.46: 4949 1.46 - 1.59: 8558 1.59 - 1.71: 2 1.71 - 1.83: 164 Bond restraints: 19574 Sorted by residual: bond pdb=" C LYS E 117 " pdb=" N PRO E 118 " ideal model delta sigma weight residual 1.334 1.379 -0.045 8.40e-03 1.42e+04 2.91e+01 bond pdb=" C1 NAG g 1 " pdb=" O5 NAG g 1 " ideal model delta sigma weight residual 1.406 1.501 -0.095 2.00e-02 2.50e+03 2.24e+01 bond pdb=" C1 NAG j 1 " pdb=" O5 NAG j 1 " ideal model delta sigma weight residual 1.406 1.497 -0.091 2.00e-02 2.50e+03 2.09e+01 bond pdb=" C THR E 123 " pdb=" N PRO E 124 " ideal model delta sigma weight residual 1.334 1.368 -0.034 8.40e-03 1.42e+04 1.67e+01 bond pdb=" C1 BMA o 3 " pdb=" C2 BMA o 3 " ideal model delta sigma weight residual 1.519 1.595 -0.076 2.00e-02 2.50e+03 1.45e+01 ... (remaining 19569 not shown) Histogram of bond angle deviations from ideal: 98.65 - 105.75: 401 105.75 - 112.85: 11299 112.85 - 119.94: 6149 119.94 - 127.04: 8475 127.04 - 134.14: 240 Bond angle restraints: 26564 Sorted by residual: angle pdb=" C MET C 426 " pdb=" N TRP C 427 " pdb=" CA TRP C 427 " ideal model delta sigma weight residual 121.19 128.68 -7.49 1.59e+00 3.96e-01 2.22e+01 angle pdb=" C ALA C 70 " pdb=" N THR C 71 " pdb=" CA THR C 71 " ideal model delta sigma weight residual 122.46 128.87 -6.41 1.41e+00 5.03e-01 2.07e+01 angle pdb=" N SER A 199 " pdb=" CA SER A 199 " pdb=" C SER A 199 " ideal model delta sigma weight residual 110.24 115.31 -5.07 1.30e+00 5.92e-01 1.52e+01 angle pdb=" C THR A 198 " pdb=" N SER A 199 " pdb=" CA SER A 199 " ideal model delta sigma weight residual 120.82 126.54 -5.72 1.47e+00 4.63e-01 1.52e+01 angle pdb=" C ALA A 70 " pdb=" N THR A 71 " pdb=" CA THR A 71 " ideal model delta sigma weight residual 122.41 130.50 -8.09 2.09e+00 2.29e-01 1.50e+01 ... (remaining 26559 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.09: 12721 24.09 - 48.18: 429 48.18 - 72.26: 111 72.26 - 96.35: 69 96.35 - 120.44: 72 Dihedral angle restraints: 13402 sinusoidal: 7006 harmonic: 6396 Sorted by residual: dihedral pdb=" CB CYS E 54 " pdb=" SG CYS E 54 " pdb=" SG CYS E 74 " pdb=" CB CYS E 74 " ideal model delta sinusoidal sigma weight residual -86.00 -155.18 69.18 1 1.00e+01 1.00e-02 6.19e+01 dihedral pdb=" CB CYS E 119 " pdb=" SG CYS E 119 " pdb=" SG CYS E 205 " pdb=" CB CYS E 205 " ideal model delta sinusoidal sigma weight residual -86.00 -153.59 67.59 1 1.00e+01 1.00e-02 5.94e+01 dihedral pdb=" CB CYS A 54 " pdb=" SG CYS A 54 " pdb=" SG CYS A 74 " pdb=" CB CYS A 74 " ideal model delta sinusoidal sigma weight residual -86.00 -152.29 66.29 1 1.00e+01 1.00e-02 5.74e+01 ... (remaining 13399 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.115: 3167 0.115 - 0.230: 173 0.230 - 0.345: 16 0.345 - 0.461: 9 0.461 - 0.576: 3 Chirality restraints: 3368 Sorted by residual: chirality pdb=" C1 NAG E1015 " pdb=" ND2 ASN E 355 " pdb=" C2 NAG E1015 " pdb=" O5 NAG E1015 " both_signs ideal model delta sigma weight residual False -2.40 -1.82 -0.58 2.00e-01 2.50e+01 8.29e+00 chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN A 88 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.87 -0.53 2.00e-01 2.50e+01 7.04e+00 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN A 301 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.37e+00 ... (remaining 3365 not shown) Planarity restraints: 3253 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 497 " 0.051 5.00e-02 4.00e+02 7.71e-02 9.50e+00 pdb=" N PRO C 498 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO C 498 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 498 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR M 32 " 0.050 5.00e-02 4.00e+02 7.52e-02 9.05e+00 pdb=" N PRO M 33 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO M 33 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO M 33 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG E 469 " -0.048 5.00e-02 4.00e+02 7.28e-02 8.47e+00 pdb=" N PRO E 470 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO E 470 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO E 470 " -0.040 5.00e-02 4.00e+02 ... (remaining 3250 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 276 2.60 - 3.18: 15792 3.18 - 3.75: 27591 3.75 - 4.33: 37204 4.33 - 4.90: 58440 Nonbonded interactions: 139303 Sorted by model distance: nonbonded pdb=" OE1 GLU N 50 " pdb=" ND2 ASN N 53 " model vdw 2.031 2.520 nonbonded pdb=" O ILE A 424 " pdb=" O ASN A 425 " model vdw 2.035 3.040 nonbonded pdb=" CE2 TRP H 55 " pdb=" O7 NAG T 5 " model vdw 2.078 3.260 nonbonded pdb=" CZ3 TRP H 55 " pdb=" C6 BMA T 3 " model vdw 2.207 3.740 nonbonded pdb=" CD1 TRP H 55 " pdb=" OH TYR H 100M" model vdw 2.221 3.260 ... (remaining 139298 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 32 through 56 or resid 67 through 396 or resid 412 through \ 505 or resid 1000 through 1023)) selection = (chain 'C' and (resid 32 through 56 or resid 67 through 396 or resid 412 through \ 505 or resid 601 through 615)) selection = (chain 'E' and (resid 32 through 505 or resid 1000 through 1017)) } ncs_group { reference = (chain 'B' and (resid 521 through 664 or resid 801)) selection = (chain 'D' and (resid 521 through 549 or resid 569 through 664 or resid 1000)) selection = (chain 'F' and (resid 521 through 549 or resid 569 through 664 or resid 1000)) } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'f' selection = chain 'g' selection = chain 'i' selection = chain 'k' selection = chain 'l' selection = chain 'm' } ncs_group { reference = (chain 'H' and resid 2 through 113) selection = (chain 'M' and resid 2 through 113) } ncs_group { reference = (chain 'K' and (resid 1 or resid 4 through 6)) selection = (chain 'h' and (resid 2 or resid 5 through 7)) } ncs_group { reference = (chain 'L' and resid 2 through 108) selection = chain 'N' } ncs_group { reference = chain 'Q' selection = chain 'j' } ncs_group { reference = (chain 'T' and (resid 2 or resid 11)) selection = (chain 'U' and (resid 1 or resid 10)) selection = (chain 'n' and (resid 1 or resid 10)) selection = (chain 'o' and (resid 1 or resid 10)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.390 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: 0.010 Extract box with map and model: 7.940 Check model and map are aligned: 0.300 Set scattering table: 0.190 Process input model: 51.720 Find NCS groups from input model: 1.390 Set up NCS constraints: 0.290 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 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 0.095 19574 Z= 0.455 Angle : 1.040 10.046 26564 Z= 0.511 Chirality : 0.065 0.576 3368 Planarity : 0.007 0.077 3200 Dihedral : 16.835 120.439 9176 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.81 % Favored : 89.96 % Rotamer: Outliers : 0.26 % Allowed : 0.61 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -3.41 (0.15), residues: 2181 helix: -1.70 (0.21), residues: 387 sheet: -1.66 (0.20), residues: 564 loop : -2.84 (0.15), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP F 614 HIS 0.008 0.002 HIS C 105 PHE 0.031 0.003 PHE A 53 TYR 0.023 0.003 TYR D 638 ARG 0.009 0.001 ARG C 298 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 279 time to evaluate : 2.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 35 TYR cc_start: 0.8259 (m-10) cc_final: 0.7972 (m-10) REVERT: N 93 ASP cc_start: 0.8573 (t0) cc_final: 0.8347 (t0) REVERT: H 31 LYS cc_start: 0.9096 (mmtt) cc_final: 0.8895 (ttmm) REVERT: H 34 MET cc_start: 0.7903 (ptp) cc_final: 0.6367 (mtm) REVERT: H 100 ASP cc_start: 0.8434 (t0) cc_final: 0.8220 (t0) REVERT: A 207 LYS cc_start: 0.9410 (mmtt) cc_final: 0.9114 (tmtt) REVERT: A 211 GLU cc_start: 0.8941 (tt0) cc_final: 0.8720 (tm-30) REVERT: A 368 ASP cc_start: 0.8222 (t0) cc_final: 0.7545 (p0) REVERT: B 530 MET cc_start: 0.7149 (mtp) cc_final: 0.6174 (mtt) REVERT: B 543 ASN cc_start: 0.9320 (m-40) cc_final: 0.8974 (m110) REVERT: B 577 GLN cc_start: 0.8459 (tp-100) cc_final: 0.7848 (tm-30) REVERT: B 584 GLU cc_start: 0.9012 (mt-10) cc_final: 0.8739 (tm-30) REVERT: D 530 MET cc_start: 0.6645 (mtm) cc_final: 0.6289 (ptp) REVERT: D 586 TYR cc_start: 0.9352 (t80) cc_final: 0.8922 (t80) REVERT: D 589 ASP cc_start: 0.8582 (m-30) cc_final: 0.8288 (p0) REVERT: C 45 TRP cc_start: 0.8839 (m-10) cc_final: 0.8615 (m-10) REVERT: C 207 LYS cc_start: 0.9339 (mmtt) cc_final: 0.8702 (tmtt) REVERT: C 424 ILE cc_start: 0.8309 (mm) cc_final: 0.8045 (mm) REVERT: E 104 MET cc_start: 0.9417 (ttm) cc_final: 0.8867 (ttt) REVERT: E 377 ASN cc_start: 0.8403 (t0) cc_final: 0.8114 (p0) REVERT: E 477 ASP cc_start: 0.9420 (m-30) cc_final: 0.8958 (p0) REVERT: F 530 MET cc_start: 0.8235 (mtm) cc_final: 0.7801 (mtm) REVERT: F 575 GLN cc_start: 0.9284 (tt0) cc_final: 0.8959 (tm-30) outliers start: 5 outliers final: 1 residues processed: 282 average time/residue: 0.3590 time to fit residues: 145.8444 Evaluate side-chains 140 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 139 time to evaluate : 2.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 184 optimal weight: 0.2980 chunk 165 optimal weight: 10.0000 chunk 91 optimal weight: 0.0670 chunk 56 optimal weight: 7.9990 chunk 111 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 170 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 127 optimal weight: 6.9990 chunk 197 optimal weight: 6.9990 overall best weight: 0.7920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 97 GLN H 100KASN L 90 GLN A 348 GLN A 352 HIS A 356 ASN A 440 GLN C 82 GLN C 348 GLN C 440 GLN F 540 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19574 Z= 0.169 Angle : 0.701 10.479 26564 Z= 0.338 Chirality : 0.049 0.437 3368 Planarity : 0.005 0.064 3200 Dihedral : 16.663 106.623 5039 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.34 % Favored : 92.62 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -2.68 (0.17), residues: 2181 helix: -0.52 (0.26), residues: 392 sheet: -1.42 (0.21), residues: 559 loop : -2.46 (0.16), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 614 HIS 0.004 0.001 HIS C 105 PHE 0.015 0.001 PHE A 53 TYR 0.014 0.001 TYR H 90 ARG 0.006 0.000 ARG L 77 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 211 time to evaluate : 2.349 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: M 35 TYR cc_start: 0.8383 (m-10) cc_final: 0.7866 (m-10) REVERT: M 100 ARG cc_start: 0.8076 (mtp85) cc_final: 0.7814 (mtp-110) REVERT: M 100 MET cc_start: 0.5828 (mtp) cc_final: 0.5455 (mtp) REVERT: N 93 ASP cc_start: 0.8590 (t0) cc_final: 0.8340 (t70) REVERT: H 100 ASP cc_start: 0.8454 (t0) cc_final: 0.8252 (t0) REVERT: A 207 LYS cc_start: 0.9422 (mmtt) cc_final: 0.9132 (tmtt) REVERT: A 368 ASP cc_start: 0.8390 (t0) cc_final: 0.7525 (p0) REVERT: A 370 GLU cc_start: 0.8870 (tm-30) cc_final: 0.8589 (tm-30) REVERT: A 479 TRP cc_start: 0.8747 (m-10) cc_final: 0.8497 (m-90) REVERT: B 530 MET cc_start: 0.7165 (mtp) cc_final: 0.6107 (mtm) REVERT: B 535 MET cc_start: 0.7534 (mpp) cc_final: 0.7313 (mpp) REVERT: B 543 ASN cc_start: 0.9207 (m-40) cc_final: 0.8909 (m110) REVERT: D 626 MET cc_start: 0.8695 (tpt) cc_final: 0.8487 (tpp) REVERT: D 655 LYS cc_start: 0.9132 (mptt) cc_final: 0.8895 (pttm) REVERT: C 207 LYS cc_start: 0.9382 (mmtt) cc_final: 0.8797 (tmtt) REVERT: E 104 MET cc_start: 0.9218 (ttm) cc_final: 0.9014 (ttm) REVERT: E 161 MET cc_start: 0.8715 (tpt) cc_final: 0.8451 (tmm) REVERT: E 420 ILE cc_start: 0.8711 (mt) cc_final: 0.8421 (tt) REVERT: E 434 MET cc_start: 0.8999 (tmm) cc_final: 0.8796 (tmm) REVERT: E 477 ASP cc_start: 0.9393 (m-30) cc_final: 0.8945 (p0) REVERT: F 575 GLN cc_start: 0.9255 (tt0) cc_final: 0.8882 (tm-30) REVERT: F 647 GLU cc_start: 0.8670 (mt-10) cc_final: 0.8425 (mt-10) outliers start: 0 outliers final: 0 residues processed: 211 average time/residue: 0.3379 time to fit residues: 106.3090 Evaluate side-chains 140 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 2.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 110 optimal weight: 4.9990 chunk 61 optimal weight: 10.0000 chunk 164 optimal weight: 6.9990 chunk 134 optimal weight: 30.0000 chunk 54 optimal weight: 6.9990 chunk 198 optimal weight: 0.0570 chunk 214 optimal weight: 0.9990 chunk 176 optimal weight: 7.9990 chunk 196 optimal weight: 1.9990 chunk 67 optimal weight: 9.9990 chunk 159 optimal weight: 1.9990 overall best weight: 2.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 97 GLN A 170 GLN A 293 GLN ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 GLN C 478 ASN E 478 ASN F 652 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19574 Z= 0.197 Angle : 0.692 11.038 26564 Z= 0.325 Chirality : 0.048 0.408 3368 Planarity : 0.004 0.060 3200 Dihedral : 14.337 99.615 5039 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.07 % Favored : 91.88 % Rotamer: Outliers : 0.05 % Allowed : 2.10 % Favored : 97.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -2.23 (0.17), residues: 2181 helix: 0.30 (0.27), residues: 383 sheet: -1.30 (0.21), residues: 564 loop : -2.23 (0.16), residues: 1234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 614 HIS 0.004 0.001 HIS A 105 PHE 0.014 0.001 PHE E 53 TYR 0.016 0.001 TYR D 643 ARG 0.003 0.000 ARG H 94 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 176 time to evaluate : 2.009 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: M 35 TYR cc_start: 0.8312 (m-10) cc_final: 0.7812 (m-10) REVERT: M 100 MET cc_start: 0.6498 (mtp) cc_final: 0.5679 (mtp) REVERT: N 93 ASP cc_start: 0.8481 (t0) cc_final: 0.8236 (t0) REVERT: H 100 ASP cc_start: 0.8520 (t0) cc_final: 0.8318 (t0) REVERT: L 14 THR cc_start: 0.7950 (m) cc_final: 0.7117 (p) REVERT: A 161 MET cc_start: 0.8783 (tmm) cc_final: 0.7807 (tmm) REVERT: A 207 LYS cc_start: 0.9388 (mmtt) cc_final: 0.9119 (tmtt) REVERT: A 368 ASP cc_start: 0.8395 (t0) cc_final: 0.7575 (p0) REVERT: A 434 MET cc_start: 0.8379 (tmm) cc_final: 0.8029 (tmm) REVERT: B 530 MET cc_start: 0.7455 (mtp) cc_final: 0.6164 (mtm) REVERT: B 535 MET cc_start: 0.7681 (mpp) cc_final: 0.7431 (mpp) REVERT: B 543 ASN cc_start: 0.9248 (m-40) cc_final: 0.8968 (m-40) REVERT: D 655 LYS cc_start: 0.9136 (mptt) cc_final: 0.8923 (pttm) REVERT: C 104 MET cc_start: 0.9291 (ttm) cc_final: 0.9056 (ttm) REVERT: C 142 MET cc_start: 0.8495 (mmm) cc_final: 0.8261 (mmt) REVERT: C 207 LYS cc_start: 0.9440 (mmtt) cc_final: 0.8851 (tmtt) REVERT: E 142 MET cc_start: 0.5557 (mmm) cc_final: 0.4350 (mpp) REVERT: E 161 MET cc_start: 0.8810 (tpt) cc_final: 0.8507 (tpt) REVERT: E 420 ILE cc_start: 0.8642 (mt) cc_final: 0.8335 (tt) REVERT: E 434 MET cc_start: 0.8745 (tmm) cc_final: 0.8430 (tpp) REVERT: E 477 ASP cc_start: 0.9451 (m-30) cc_final: 0.8978 (p0) REVERT: F 575 GLN cc_start: 0.9256 (tt0) cc_final: 0.8915 (tm-30) REVERT: F 634 GLU cc_start: 0.8295 (tm-30) cc_final: 0.8089 (tm-30) outliers start: 1 outliers final: 0 residues processed: 177 average time/residue: 0.3393 time to fit residues: 89.6401 Evaluate side-chains 134 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 1.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 195 optimal weight: 20.0000 chunk 149 optimal weight: 9.9990 chunk 102 optimal weight: 0.9990 chunk 21 optimal weight: 7.9990 chunk 94 optimal weight: 0.7980 chunk 133 optimal weight: 3.9990 chunk 199 optimal weight: 10.0000 chunk 210 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 188 optimal weight: 5.9990 chunk 56 optimal weight: 0.5980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 61 ASN N 38 GLN ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 630 GLN C 130 GLN ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19574 Z= 0.167 Angle : 0.655 11.042 26564 Z= 0.307 Chirality : 0.047 0.396 3368 Planarity : 0.004 0.055 3200 Dihedral : 12.752 95.112 5039 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.51 % Favored : 93.44 % Rotamer: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -2.01 (0.18), residues: 2181 helix: 0.50 (0.28), residues: 384 sheet: -1.11 (0.22), residues: 545 loop : -2.10 (0.17), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 479 HIS 0.004 0.001 HIS E 105 PHE 0.018 0.001 PHE H 27 TYR 0.012 0.001 TYR D 643 ARG 0.007 0.000 ARG C 273 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 2.190 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: M 35 TYR cc_start: 0.8172 (m-10) cc_final: 0.7821 (m-10) REVERT: M 100 MET cc_start: 0.6783 (mtp) cc_final: 0.6154 (mtp) REVERT: N 36 TYR cc_start: 0.6354 (p90) cc_final: 0.5402 (p90) REVERT: N 74 ARG cc_start: 0.8506 (tpt170) cc_final: 0.8301 (tmm160) REVERT: N 89 MET cc_start: 0.6378 (ttp) cc_final: 0.5187 (ttp) REVERT: N 93 ASP cc_start: 0.8540 (t0) cc_final: 0.8328 (t70) REVERT: A 142 MET cc_start: 0.8118 (mmm) cc_final: 0.7727 (mmm) REVERT: A 207 LYS cc_start: 0.9409 (mmtt) cc_final: 0.9114 (tmtt) REVERT: A 368 ASP cc_start: 0.8372 (t0) cc_final: 0.7574 (p0) REVERT: A 370 GLU cc_start: 0.8867 (tm-30) cc_final: 0.8575 (tm-30) REVERT: B 530 MET cc_start: 0.7528 (mtp) cc_final: 0.6287 (mtm) REVERT: B 535 MET cc_start: 0.7769 (mpp) cc_final: 0.7563 (mpp) REVERT: B 543 ASN cc_start: 0.9225 (m-40) cc_final: 0.8952 (m110) REVERT: C 207 LYS cc_start: 0.9446 (mmtt) cc_final: 0.8862 (tmtt) REVERT: E 95 MET cc_start: 0.9033 (ttp) cc_final: 0.8514 (ttm) REVERT: E 142 MET cc_start: 0.5926 (mmm) cc_final: 0.5159 (mpp) REVERT: E 420 ILE cc_start: 0.8615 (mt) cc_final: 0.8285 (tt) REVERT: E 477 ASP cc_start: 0.9440 (m-30) cc_final: 0.8971 (p0) REVERT: F 575 GLN cc_start: 0.9254 (tt0) cc_final: 0.8904 (tm-30) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.3287 time to fit residues: 88.8436 Evaluate side-chains 128 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 2.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 175 optimal weight: 9.9990 chunk 119 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 156 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 179 optimal weight: 6.9990 chunk 145 optimal weight: 0.2980 chunk 0 optimal weight: 10.0000 chunk 107 optimal weight: 0.0970 chunk 189 optimal weight: 4.9990 chunk 53 optimal weight: 9.9990 overall best weight: 4.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 73 ASN H 39 GLN L 45 GLN L 90 GLN A 130 GLN A 170 GLN A 356 ASN A 432 GLN B 640 GLN ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 630 GLN D 652 GLN ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 19574 Z= 0.342 Angle : 0.804 10.806 26564 Z= 0.377 Chirality : 0.050 0.419 3368 Planarity : 0.005 0.064 3200 Dihedral : 12.546 95.608 5039 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 17.09 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.77 % Favored : 89.18 % Rotamer: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.17), residues: 2181 helix: 0.32 (0.28), residues: 378 sheet: -1.28 (0.21), residues: 562 loop : -2.16 (0.16), residues: 1241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F 610 HIS 0.005 0.001 HIS A 330 PHE 0.022 0.002 PHE A 53 TYR 0.017 0.002 TYR F 586 ARG 0.005 0.001 ARG A 143 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 2.214 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: M 45 LEU cc_start: 0.8823 (tp) cc_final: 0.8576 (tp) REVERT: M 95 MET cc_start: 0.8312 (ttt) cc_final: 0.7765 (tpp) REVERT: M 100 MET cc_start: 0.6391 (mtp) cc_final: 0.5791 (mtp) REVERT: H 100 ASP cc_start: 0.8447 (t0) cc_final: 0.8191 (t0) REVERT: A 142 MET cc_start: 0.8252 (mmm) cc_final: 0.7862 (mmm) REVERT: A 207 LYS cc_start: 0.9436 (mmtt) cc_final: 0.9072 (tmtt) REVERT: A 368 ASP cc_start: 0.8464 (t0) cc_final: 0.7614 (p0) REVERT: A 370 GLU cc_start: 0.8951 (tm-30) cc_final: 0.8700 (tm-30) REVERT: B 530 MET cc_start: 0.7658 (mtp) cc_final: 0.7079 (mtm) REVERT: B 535 MET cc_start: 0.7944 (mpp) cc_final: 0.7734 (mpp) REVERT: B 647 GLU cc_start: 0.8934 (mp0) cc_final: 0.8729 (mp0) REVERT: C 207 LYS cc_start: 0.9469 (mmtt) cc_final: 0.8685 (tmtt) REVERT: E 95 MET cc_start: 0.9130 (ttp) cc_final: 0.8507 (ttm) REVERT: E 104 MET cc_start: 0.9201 (ttt) cc_final: 0.8955 (ttm) REVERT: E 477 ASP cc_start: 0.9472 (m-30) cc_final: 0.9035 (p0) REVERT: F 542 ARG cc_start: 0.8926 (mmp80) cc_final: 0.8663 (mmp80) REVERT: F 588 ARG cc_start: 0.8942 (tmm-80) cc_final: 0.8553 (tmm-80) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.3463 time to fit residues: 76.6325 Evaluate side-chains 114 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 2.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 70 optimal weight: 6.9990 chunk 189 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 123 optimal weight: 10.0000 chunk 52 optimal weight: 6.9990 chunk 210 optimal weight: 0.9990 chunk 175 optimal weight: 10.0000 chunk 97 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 chunk 110 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: M 97 GLN A 170 GLN ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 GLN C 188 ASN ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19574 Z= 0.182 Angle : 0.670 10.659 26564 Z= 0.311 Chirality : 0.047 0.404 3368 Planarity : 0.004 0.053 3200 Dihedral : 11.500 90.422 5039 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.14 % Favored : 93.81 % Rotamer: Outliers : 0.05 % Allowed : 1.23 % Favored : 98.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.86 (0.18), residues: 2181 helix: 0.78 (0.29), residues: 375 sheet: -1.07 (0.22), residues: 558 loop : -2.03 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 596 HIS 0.003 0.001 HIS A 105 PHE 0.012 0.001 PHE E 53 TYR 0.013 0.001 TYR H 32 ARG 0.007 0.000 ARG H 94 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 161 time to evaluate : 2.133 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: M 35 TYR cc_start: 0.8167 (m-10) cc_final: 0.7697 (m-10) REVERT: M 95 MET cc_start: 0.8508 (ttt) cc_final: 0.8207 (ttt) REVERT: M 100 MET cc_start: 0.6927 (mtp) cc_final: 0.6598 (mtp) REVERT: A 142 MET cc_start: 0.8171 (mmm) cc_final: 0.7774 (mmm) REVERT: A 161 MET cc_start: 0.8743 (tmm) cc_final: 0.8101 (tmm) REVERT: A 207 LYS cc_start: 0.9406 (mmtt) cc_final: 0.9089 (tmtt) REVERT: A 368 ASP cc_start: 0.8449 (t0) cc_final: 0.7626 (p0) REVERT: A 370 GLU cc_start: 0.8960 (tm-30) cc_final: 0.8757 (tm-30) REVERT: B 530 MET cc_start: 0.7674 (mtp) cc_final: 0.6356 (mtm) REVERT: C 207 LYS cc_start: 0.9475 (mmtt) cc_final: 0.8699 (tmtt) REVERT: C 426 MET cc_start: 0.8675 (tpp) cc_final: 0.8394 (tpp) REVERT: E 95 MET cc_start: 0.9116 (ttp) cc_final: 0.8357 (ttm) REVERT: E 477 ASP cc_start: 0.9445 (m-30) cc_final: 0.8951 (p0) REVERT: F 542 ARG cc_start: 0.8816 (mmp80) cc_final: 0.8613 (mmp80) REVERT: F 575 GLN cc_start: 0.9297 (tt0) cc_final: 0.8931 (tm-30) REVERT: F 588 ARG cc_start: 0.8980 (tmm-80) cc_final: 0.8539 (tmm-80) REVERT: F 647 GLU cc_start: 0.8430 (mt-10) cc_final: 0.7029 (mt-10) outliers start: 1 outliers final: 0 residues processed: 162 average time/residue: 0.3320 time to fit residues: 80.8444 Evaluate side-chains 121 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 2.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 203 optimal weight: 9.9990 chunk 23 optimal weight: 6.9990 chunk 120 optimal weight: 0.0870 chunk 154 optimal weight: 3.9990 chunk 119 optimal weight: 6.9990 chunk 177 optimal weight: 3.9990 chunk 117 optimal weight: 0.7980 chunk 210 optimal weight: 0.6980 chunk 131 optimal weight: 0.0060 chunk 128 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 overall best weight: 1.1176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 19574 Z= 0.150 Angle : 0.640 10.544 26564 Z= 0.297 Chirality : 0.047 0.389 3368 Planarity : 0.004 0.052 3200 Dihedral : 10.521 85.503 5039 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.11 % Favored : 92.85 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.66 (0.18), residues: 2181 helix: 0.81 (0.29), residues: 382 sheet: -0.91 (0.22), residues: 570 loop : -1.88 (0.17), residues: 1229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP A 479 HIS 0.003 0.001 HIS A 105 PHE 0.010 0.001 PHE C 223 TYR 0.025 0.001 TYR D 586 ARG 0.007 0.000 ARG H 94 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 1.998 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: M 35 TYR cc_start: 0.8007 (m-10) cc_final: 0.7627 (m-10) REVERT: M 95 MET cc_start: 0.8492 (ttt) cc_final: 0.8134 (ttt) REVERT: H 100 ASP cc_start: 0.8801 (t70) cc_final: 0.8540 (t0) REVERT: A 142 MET cc_start: 0.8124 (mmm) cc_final: 0.7727 (mmm) REVERT: A 207 LYS cc_start: 0.9407 (mmtt) cc_final: 0.9080 (tmtt) REVERT: A 302 ASN cc_start: 0.8377 (t0) cc_final: 0.8172 (t0) REVERT: A 368 ASP cc_start: 0.8413 (t0) cc_final: 0.7698 (p0) REVERT: B 530 MET cc_start: 0.7537 (mtp) cc_final: 0.6193 (mtm) REVERT: B 535 MET cc_start: 0.8033 (mpp) cc_final: 0.7743 (mpp) REVERT: D 530 MET cc_start: 0.8235 (mpp) cc_final: 0.7963 (mpp) REVERT: C 207 LYS cc_start: 0.9479 (mmtt) cc_final: 0.8712 (tmtt) REVERT: C 426 MET cc_start: 0.8663 (tpp) cc_final: 0.8205 (tpp) REVERT: E 95 MET cc_start: 0.9085 (ttp) cc_final: 0.8475 (ttm) REVERT: E 142 MET cc_start: 0.5472 (mmm) cc_final: 0.4480 (mpp) REVERT: E 161 MET cc_start: 0.8839 (tpt) cc_final: 0.8613 (tpp) REVERT: E 477 ASP cc_start: 0.9428 (m-30) cc_final: 0.8931 (p0) REVERT: F 542 ARG cc_start: 0.8800 (mmp80) cc_final: 0.8580 (mmp80) REVERT: F 575 GLN cc_start: 0.9249 (tt0) cc_final: 0.8934 (tm-30) REVERT: F 588 ARG cc_start: 0.8921 (tmm-80) cc_final: 0.8506 (tmm-80) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.3335 time to fit residues: 80.1201 Evaluate side-chains 121 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 2.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 129 optimal weight: 10.0000 chunk 83 optimal weight: 0.7980 chunk 125 optimal weight: 6.9990 chunk 63 optimal weight: 8.9990 chunk 41 optimal weight: 8.9990 chunk 40 optimal weight: 0.0870 chunk 133 optimal weight: 9.9990 chunk 143 optimal weight: 9.9990 chunk 103 optimal weight: 4.9990 chunk 19 optimal weight: 20.0000 chunk 165 optimal weight: 7.9990 overall best weight: 4.1764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 170 GLN ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 ASN E 130 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 19574 Z= 0.307 Angle : 0.761 10.436 26564 Z= 0.356 Chirality : 0.049 0.410 3368 Planarity : 0.004 0.055 3200 Dihedral : 10.758 87.622 5039 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 16.38 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.04 % Favored : 89.91 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.92 (0.18), residues: 2181 helix: 0.40 (0.28), residues: 384 sheet: -1.09 (0.21), residues: 578 loop : -1.98 (0.17), residues: 1219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 479 HIS 0.004 0.001 HIS C 216 PHE 0.020 0.002 PHE A 53 TYR 0.022 0.002 TYR D 586 ARG 0.008 0.001 ARG H 94 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 1.902 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: M 35 TYR cc_start: 0.8253 (m-10) cc_final: 0.7749 (m-10) REVERT: M 95 MET cc_start: 0.8579 (ttt) cc_final: 0.8229 (ttt) REVERT: H 100 ASP cc_start: 0.8936 (t70) cc_final: 0.8663 (t0) REVERT: A 142 MET cc_start: 0.8111 (mmm) cc_final: 0.7603 (mmm) REVERT: A 207 LYS cc_start: 0.9438 (mmtt) cc_final: 0.9110 (tmtt) REVERT: A 302 ASN cc_start: 0.8510 (t0) cc_final: 0.8272 (t0) REVERT: B 530 MET cc_start: 0.7644 (mtp) cc_final: 0.6343 (mtm) REVERT: B 642 ILE cc_start: 0.9725 (mt) cc_final: 0.9430 (tp) REVERT: C 207 LYS cc_start: 0.9480 (mmtt) cc_final: 0.8655 (tmtt) REVERT: C 426 MET cc_start: 0.8765 (tpp) cc_final: 0.8304 (tpp) REVERT: E 95 MET cc_start: 0.9034 (ttp) cc_final: 0.8415 (ttm) REVERT: E 142 MET cc_start: 0.4756 (mmm) cc_final: 0.3602 (mpp) REVERT: E 161 MET cc_start: 0.8831 (tpt) cc_final: 0.8599 (tpp) REVERT: E 477 ASP cc_start: 0.9470 (m-30) cc_final: 0.8990 (p0) REVERT: F 588 ARG cc_start: 0.8985 (tmm-80) cc_final: 0.8528 (tmm-80) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.3145 time to fit residues: 67.4434 Evaluate side-chains 113 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 2.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 191 optimal weight: 3.9990 chunk 201 optimal weight: 10.0000 chunk 183 optimal weight: 0.0980 chunk 195 optimal weight: 6.9990 chunk 117 optimal weight: 0.6980 chunk 85 optimal weight: 0.9990 chunk 153 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 chunk 176 optimal weight: 2.9990 chunk 185 optimal weight: 4.9990 chunk 128 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN B 650 GLN ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19574 Z= 0.159 Angle : 0.653 10.896 26564 Z= 0.303 Chirality : 0.047 0.394 3368 Planarity : 0.004 0.054 3200 Dihedral : 10.004 84.794 5039 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.60 % Favored : 93.35 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.66 (0.18), residues: 2181 helix: 0.77 (0.29), residues: 379 sheet: -0.92 (0.21), residues: 582 loop : -1.86 (0.17), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 479 HIS 0.002 0.001 HIS C 105 PHE 0.010 0.001 PHE L 71 TYR 0.024 0.001 TYR D 586 ARG 0.013 0.000 ARG M 94 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 2.098 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: M 82 MET cc_start: 0.9181 (mpp) cc_final: 0.8971 (mpp) REVERT: M 95 MET cc_start: 0.8329 (ttt) cc_final: 0.7895 (ttt) REVERT: H 100 ASP cc_start: 0.8921 (t70) cc_final: 0.8639 (t0) REVERT: A 142 MET cc_start: 0.8150 (mmm) cc_final: 0.7757 (mmm) REVERT: A 207 LYS cc_start: 0.9419 (mmtt) cc_final: 0.9098 (tmtt) REVERT: A 302 ASN cc_start: 0.8373 (t0) cc_final: 0.8149 (t0) REVERT: A 368 ASP cc_start: 0.8416 (t0) cc_final: 0.8170 (t70) REVERT: B 530 MET cc_start: 0.7590 (mtp) cc_final: 0.6221 (mtm) REVERT: B 535 MET cc_start: 0.8024 (mpp) cc_final: 0.7798 (mpp) REVERT: D 530 MET cc_start: 0.7931 (mpp) cc_final: 0.7617 (mpp) REVERT: D 624 ASP cc_start: 0.8763 (m-30) cc_final: 0.8554 (m-30) REVERT: C 207 LYS cc_start: 0.9467 (mmtt) cc_final: 0.8672 (tmtt) REVERT: C 426 MET cc_start: 0.8722 (tpp) cc_final: 0.8192 (tpp) REVERT: E 95 MET cc_start: 0.9065 (ttp) cc_final: 0.8517 (ttm) REVERT: E 142 MET cc_start: 0.5261 (mmm) cc_final: 0.4292 (mpp) REVERT: E 161 MET cc_start: 0.8824 (tpt) cc_final: 0.8572 (tpp) REVERT: E 477 ASP cc_start: 0.9438 (m-30) cc_final: 0.8931 (p0) REVERT: F 535 MET cc_start: 0.9175 (mtp) cc_final: 0.8784 (mpp) REVERT: F 575 GLN cc_start: 0.9237 (tt0) cc_final: 0.8880 (tm-30) REVERT: F 588 ARG cc_start: 0.8927 (tmm-80) cc_final: 0.8481 (tmm-80) REVERT: F 647 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8288 (pt0) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.3178 time to fit residues: 71.0076 Evaluate side-chains 116 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 2.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 207 optimal weight: 0.0770 chunk 126 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 chunk 143 optimal weight: 7.9990 chunk 217 optimal weight: 0.7980 chunk 199 optimal weight: 2.9990 chunk 172 optimal weight: 0.1980 chunk 17 optimal weight: 0.9990 chunk 133 optimal weight: 8.9990 chunk 106 optimal weight: 0.5980 chunk 137 optimal weight: 0.0570 overall best weight: 0.3456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN E 33 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 19574 Z= 0.139 Angle : 0.633 10.973 26564 Z= 0.295 Chirality : 0.047 0.372 3368 Planarity : 0.004 0.048 3200 Dihedral : 8.917 82.177 5039 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.46 (0.18), residues: 2181 helix: 0.79 (0.28), residues: 383 sheet: -0.77 (0.22), residues: 588 loop : -1.69 (0.18), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 479 HIS 0.003 0.000 HIS A 105 PHE 0.014 0.001 PHE M 27 TYR 0.022 0.001 TYR D 586 ARG 0.004 0.000 ARG M 91 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 2.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 MET cc_start: 0.8031 (mmm) cc_final: 0.7669 (mmm) REVERT: A 207 LYS cc_start: 0.9409 (mmtt) cc_final: 0.9084 (tmtt) REVERT: A 368 ASP cc_start: 0.8398 (t0) cc_final: 0.8123 (t70) REVERT: B 530 MET cc_start: 0.7504 (mtp) cc_final: 0.6088 (mtm) REVERT: B 642 ILE cc_start: 0.9707 (mt) cc_final: 0.9406 (tp) REVERT: C 207 LYS cc_start: 0.9459 (mmtt) cc_final: 0.8694 (tmtt) REVERT: C 426 MET cc_start: 0.8653 (tpp) cc_final: 0.8140 (tpp) REVERT: E 95 MET cc_start: 0.9066 (ttp) cc_final: 0.8481 (ttm) REVERT: E 142 MET cc_start: 0.5635 (mmm) cc_final: 0.4788 (mpp) REVERT: E 161 MET cc_start: 0.8830 (tpt) cc_final: 0.8374 (tpp) REVERT: E 477 ASP cc_start: 0.9425 (m-30) cc_final: 0.8945 (p0) REVERT: F 535 MET cc_start: 0.9127 (mtp) cc_final: 0.8803 (mpp) REVERT: F 575 GLN cc_start: 0.9205 (tt0) cc_final: 0.8831 (tm-30) REVERT: F 576 LEU cc_start: 0.9631 (tp) cc_final: 0.9303 (pp) REVERT: F 588 ARG cc_start: 0.8913 (tmm-80) cc_final: 0.8482 (tmm-80) REVERT: F 647 GLU cc_start: 0.8464 (mt-10) cc_final: 0.8172 (pt0) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.3270 time to fit residues: 79.6239 Evaluate side-chains 122 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 2.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 184 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 chunk 159 optimal weight: 9.9990 chunk 25 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 173 optimal weight: 6.9990 chunk 72 optimal weight: 7.9990 chunk 177 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 152 optimal weight: 9.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 90 GLN ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 630 GLN B 650 GLN ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 656 ASN ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.048491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.039225 restraints weight = 151463.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.040341 restraints weight = 91994.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.041157 restraints weight = 65268.949| |-----------------------------------------------------------------------------| r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 19574 Z= 0.342 Angle : 0.795 9.747 26564 Z= 0.377 Chirality : 0.049 0.406 3368 Planarity : 0.005 0.061 3200 Dihedral : 9.612 86.795 5039 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.49 % Favored : 90.51 % Rotamer: Outliers : 0.05 % Allowed : 0.26 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.18), residues: 2181 helix: 0.39 (0.28), residues: 381 sheet: -1.00 (0.21), residues: 607 loop : -1.84 (0.17), residues: 1193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP E 479 HIS 0.005 0.001 HIS C 216 PHE 0.025 0.002 PHE A 53 TYR 0.034 0.002 TYR H 100L ARG 0.016 0.001 ARG A 166 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3177.67 seconds wall clock time: 59 minutes 27.99 seconds (3567.99 seconds total)