Starting phenix.real_space_refine on Sun Mar 17 03:44:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t76_25735/03_2024/7t76_25735_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t76_25735/03_2024/7t76_25735.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t76_25735/03_2024/7t76_25735.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t76_25735/03_2024/7t76_25735.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t76_25735/03_2024/7t76_25735_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t76_25735/03_2024/7t76_25735_updated.pdb" } resolution = 4.43 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.093 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 106 5.16 5 C 10329 2.51 5 N 2742 2.21 5 O 3410 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 381": "OE1" <-> "OE2" Residue "C ASP 185": "OD1" <-> "OD2" Residue "C GLU 269": "OE1" <-> "OE2" Residue "C PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 186": "NH1" <-> "NH2" Residue "E GLU 269": "OE1" <-> "OE2" Residue "E GLU 381": "OE1" <-> "OE2" Residue "E TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 16587 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3494 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 22, 'TRANS': 421} Chain breaks: 2 Chain: "C" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3494 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 22, 'TRANS': 421} Chain breaks: 2 Chain: "D" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 942 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 1, 'TRANS': 117} Chain breaks: 1 Chain: "E" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3494 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 22, 'TRANS': 421} Chain breaks: 2 Chain: "F" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 942 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 1, 'TRANS': 117} Chain breaks: 1 Chain: "B" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 942 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 1, 'TRANS': 117} Chain breaks: 1 Chain: "L" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 791 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 1092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1092 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 3, 'TRANS': 132} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TYS:plan-2': 2} Unresolved non-hydrogen planarities: 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: "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: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} 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: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 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: "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: 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: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 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: 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} 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: "j" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "A" Number of atoms: 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: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "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: "E" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 8.73, per 1000 atoms: 0.53 Number of scatterers: 16587 At special positions: 0 Unit cell: (129.95, 132.25, 161, 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 106 16.00 O 3410 8.00 N 2742 7.00 C 10329 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.21 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.07 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.06 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=2.01 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.09 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.08 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.04 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.02 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 C 501 " - pdb=" SG CYS D 605 " distance=2.04 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.15 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.20 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=2.01 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=2.13 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=2.02 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM16499 O3 NAG E 607 .*. O " rejected from bonding due to valence issues. Atom "HETATM16503 O7 NAG E 607 .*. O " rejected from bonding due to valence issues. Atom "HETATM16503 O7 NAG E 607 .*. O " rejected from bonding due to valence issues. Atom "HETATM16503 O7 NAG E 607 .*. O " rejected from bonding due to valence issues. Atom "HETATM16499 O3 NAG E 607 .*. O " rejected from bonding due to valence issues. Atom "HETATM16499 O3 NAG E 607 .*. O " rejected from bonding due to valence issues. Atom "HETATM16501 O5 NAG E 607 .*. O " rejected from bonding due to valence issues. Atom "HETATM16501 O5 NAG E 607 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=2, symmetry=0 Links applied ALPHA1-3 " BMA S 3 " - " MAN S 4 " " BMA U 3 " - " MAN U 4 " " BMA Z 3 " - " MAN Z 6 " " BMA c 3 " - " MAN c 4 " " BMA i 3 " - " MAN i 4 " " BMA j 3 " - " MAN j 7 " " MAN j 4 " - " MAN j 5 " ALPHA1-6 " BMA S 3 " - " MAN S 5 " " BMA Z 3 " - " MAN Z 4 " " MAN Z 4 " - " MAN Z 5 " " BMA c 3 " - " MAN c 5 " " BMA i 3 " - " MAN i 5 " " BMA j 3 " - " MAN j 4 " " MAN j 4 " - " MAN j 6 " 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 M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " 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 Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 137 " " NAG A 603 " - " ASN A 355 " " NAG A 604 " - " ASN A 276 " " NAG A 605 " - " ASN A 133 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 618 " " NAG B 703 " - " ASN B 637 " " NAG C 601 " - " ASN C 133 " " NAG C 602 " - " ASN C 295 " " NAG C 603 " - " ASN C 355 " " NAG C 604 " - " ASN C 276 " " NAG C 605 " - " ASN C 234 " " NAG C 606 " - " ASN C 301 " " NAG C 607 " - " ASN C 88 " " NAG D 701 " - " ASN D 611 " " NAG D 702 " - " ASN D 618 " " NAG D 703 " - " ASN D 637 " " NAG E 601 " - " ASN E 133 " " NAG E 602 " - " ASN E 276 " " NAG E 603 " - " ASN E 295 " " NAG E 604 " - " ASN E 355 " " NAG E 605 " - " ASN E 462 " " NAG E 606 " - " ASN E 88 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 618 " " NAG F 703 " - " ASN F 637 " " NAG G 1 " - " ASN A 156 " " NAG I 1 " - " ASN A 160 " " NAG J 1 " - " ASN A 197 " " NAG K 1 " - " ASN A 234 " " NAG M 1 " - " ASN A 295 " " NAG N 1 " - " ASN A 301 " " NAG O 1 " - " ASN A 332 " " NAG P 1 " - " ASN A 386 " " NAG Q 1 " - " ASN A 392 " " NAG R 1 " - " ASN A 448 " " NAG S 1 " - " ASN A 262 " " NAG T 1 " - " ASN C 197 " " NAG U 1 " - " ASN C 262 " " NAG V 1 " - " ASN C 332 " " NAG W 1 " - " ASN C 386 " " NAG X 1 " - " ASN C 392 " " NAG Y 1 " - " ASN C 448 " " NAG Z 1 " - " ASN C 160 " " NAG a 1 " - " ASN C 156 " " NAG b 1 " - " ASN E 197 " " NAG c 1 " - " ASN E 262 " " NAG d 1 " - " ASN E 301 " " NAG e 1 " - " ASN E 332 " " NAG f 1 " - " ASN E 386 " " NAG g 1 " - " ASN E 392 " " NAG h 1 " - " ASN E 448 " " NAG i 1 " - " ASN E 160 " " NAG j 1 " - " ASN E 156 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.67 Conformation dependent library (CDL) restraints added in 2.6 seconds 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3594 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 49 helices and 30 sheets defined 22.1% alpha, 22.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.85 Creating SS restraints... Processing helix chain 'A' and resid 100 through 117 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 178 through 180 No H-bonds generated for 'chain 'A' and resid 178 through 180' Processing helix chain 'A' and resid 335 through 351 removed outlier: 4.007A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 371 No H-bonds generated for 'chain 'A' and resid 369 through 371' Processing helix chain 'A' and resid 387 through 390 Processing helix chain 'A' and resid 461 through 463 No H-bonds generated for 'chain 'A' and resid 461 through 463' Processing helix chain 'A' and resid 475 through 485 removed outlier: 3.657A pdb=" N TRP A 479 " --> pdb=" O ARG A 476 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ARG A 480 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N TYR A 484 " --> pdb=" O SER A 481 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LYS A 485 " --> pdb=" O GLU A 482 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 117 Processing helix chain 'C' and resid 123 through 125 No H-bonds generated for 'chain 'C' and resid 123 through 125' Processing helix chain 'C' and resid 140 through 150 No H-bonds generated for 'chain 'C' and resid 140 through 150' Processing helix chain 'C' and resid 178 through 180 No H-bonds generated for 'chain 'C' and resid 178 through 180' Processing helix chain 'C' and resid 335 through 352 removed outlier: 3.773A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 372 No H-bonds generated for 'chain 'C' and resid 369 through 372' Processing helix chain 'C' and resid 426 through 428 No H-bonds generated for 'chain 'C' and resid 426 through 428' Processing helix chain 'C' and resid 461 through 463 No H-bonds generated for 'chain 'C' and resid 461 through 463' Processing helix chain 'C' and resid 475 through 477 No H-bonds generated for 'chain 'C' and resid 475 through 477' Processing helix chain 'C' and resid 479 through 485 removed outlier: 5.200A pdb=" N TYR C 484 " --> pdb=" O SER C 481 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS C 485 " --> pdb=" O GLU C 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 543 removed outlier: 3.756A pdb=" N LEU D 537 " --> pdb=" O SER D 534 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N THR D 538 " --> pdb=" O MET D 535 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ALA D 541 " --> pdb=" O THR D 538 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASN D 543 " --> pdb=" O GLN D 540 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 595 Processing helix chain 'D' and resid 619 through 624 Processing helix chain 'D' and resid 628 through 634 Processing helix chain 'D' and resid 636 through 660 removed outlier: 5.028A pdb=" N GLN D 640 " --> pdb=" O ASN D 637 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU D 648 " --> pdb=" O LEU D 645 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N SER D 649 " --> pdb=" O LEU D 646 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN D 650 " --> pdb=" O GLU D 647 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASN D 651 " --> pdb=" O GLU D 648 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N GLN D 652 " --> pdb=" O SER D 649 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN D 653 " --> pdb=" O GLN D 650 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ASP D 659 " --> pdb=" O ASN D 656 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 117 Processing helix chain 'E' and resid 123 through 125 No H-bonds generated for 'chain 'E' and resid 123 through 125' Processing helix chain 'E' and resid 140 through 150 No H-bonds generated for 'chain 'E' and resid 140 through 150' 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 335 through 352 removed outlier: 3.871A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (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 476 through 485 removed outlier: 4.670A pdb=" N SER E 481 " --> pdb=" O ASN E 478 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N TYR E 484 " --> pdb=" O SER E 481 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LYS E 485 " --> pdb=" O GLU E 482 " (cutoff:3.500A) Processing helix chain 'F' and resid 530 through 544 removed outlier: 4.983A pdb=" N MET F 535 " --> pdb=" O GLY F 531 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N THR F 536 " --> pdb=" O ALA F 532 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU F 537 " --> pdb=" O ALA F 533 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N THR F 538 " --> pdb=" O SER F 534 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N VAL F 539 " --> pdb=" O MET F 535 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU F 544 " --> pdb=" O GLN F 540 " (cutoff:3.500A) Processing helix chain 'F' and resid 574 through 595 Processing helix chain 'F' and resid 612 through 614 No H-bonds generated for 'chain 'F' and resid 612 through 614' Processing helix chain 'F' and resid 619 through 624 Processing helix chain 'F' and resid 628 through 649 removed outlier: 5.684A pdb=" N ASN F 637 " --> pdb=" O LYS F 633 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N TYR F 638 " --> pdb=" O GLU F 634 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N THR F 639 " --> pdb=" O ILE F 635 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N GLN F 640 " --> pdb=" O SER F 636 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N ILE F 641 " --> pdb=" O ASN F 637 " (cutoff:3.500A) Processing helix chain 'F' and resid 651 through 660 removed outlier: 4.375A pdb=" N ASN F 656 " --> pdb=" O GLN F 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 544 removed outlier: 3.909A pdb=" N LEU B 537 " --> pdb=" O SER B 534 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N THR B 538 " --> pdb=" O MET B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 595 Processing helix chain 'B' and resid 612 through 614 No H-bonds generated for 'chain 'B' and resid 612 through 614' Processing helix chain 'B' and resid 619 through 623 Processing helix chain 'B' and resid 628 through 634 Processing helix chain 'B' and resid 636 through 649 removed outlier: 5.026A pdb=" N GLN B 640 " --> pdb=" O ASN B 637 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE B 642 " --> pdb=" O THR B 639 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER B 649 " --> pdb=" O LEU B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 657 Processing helix chain 'B' and resid 660 through 662 No H-bonds generated for 'chain 'B' and resid 660 through 662' Processing helix chain 'L' and resid 80 through 82 No H-bonds generated for 'chain 'L' and resid 80 through 82' Processing helix chain 'H' and resid 29 through 31 No H-bonds generated for 'chain 'H' and resid 29 through 31' Processing helix chain 'H' and resid 61 through 63 No H-bonds generated for 'chain 'H' and resid 61 through 63' Processing helix chain 'H' and resid 84 through 86 No H-bonds generated for 'chain 'H' and resid 84 through 86' Processing helix chain 'H' and resid 100J through 100L No H-bonds generated for 'chain 'H' and resid 100J through 100L' Processing sheet with id= A, first strand: chain 'A' and resid 38 through 40 Processing sheet with id= B, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.862A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 53 through 55 Processing sheet with id= D, first strand: chain 'A' and resid 130 through 133 Processing sheet with id= E, first strand: chain 'A' and resid 271 through 273 removed outlier: 3.925A pdb=" N SER A 393 " --> pdb=" O PHE A 361 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 413 through 417 removed outlier: 4.056A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 374 through 378 removed outlier: 4.461A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.618A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 35 through 40 Processing sheet with id= J, first strand: chain 'C' and resid 45 through 47 Processing sheet with id= K, first strand: chain 'C' and resid 91 through 94 Processing sheet with id= L, first strand: chain 'C' and resid 130 through 132 Processing sheet with id= M, first strand: chain 'C' and resid 271 through 273 removed outlier: 6.551A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N ALA C 362 " --> pdb=" O PRO C 470 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 413 through 417 removed outlier: 3.891A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 374 through 378 Processing sheet with id= P, first strand: chain 'C' and resid 181 through 185 removed outlier: 7.527A pdb=" N HIS C 190 " --> pdb=" O ILE C 184 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 304 through 312 removed outlier: 6.588A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 38 through 40 Processing sheet with id= S, first strand: chain 'E' and resid 45 through 47 Processing sheet with id= T, first strand: chain 'E' and resid 53 through 55 Processing sheet with id= U, first strand: chain 'E' and resid 130 through 133 Processing sheet with id= V, first strand: chain 'E' and resid 181 through 183 Processing sheet with id= W, first strand: chain 'E' and resid 271 through 273 Processing sheet with id= X, first strand: chain 'E' and resid 374 through 378 removed outlier: 4.353A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 304 through 312 removed outlier: 6.683A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.023A pdb=" N LYS L 103 " --> pdb=" O VAL L 11 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N GLY L 13 " --> pdb=" O LYS L 103 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N THR L 105 " --> pdb=" O GLY L 13 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'L' and resid 18 through 24 Processing sheet with id= AB, first strand: chain 'L' and resid 96 through 98 removed outlier: 5.878A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'H' and resid 3 through 7 Processing sheet with id= AD, first strand: chain 'H' and resid 107 through 109 removed outlier: 5.867A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) 504 hydrogen bonds defined for protein. 1257 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: 4.56 Time building geometry restraints manager: 8.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.34: 4817 1.34 - 1.49: 5235 1.49 - 1.64: 6711 1.64 - 1.79: 54 1.79 - 1.94: 88 Bond restraints: 16905 Sorted by residual: bond pdb=" NE1 TRP B 610 " pdb=" CE2 TRP B 610 " ideal model delta sigma weight residual 1.370 1.290 0.080 1.10e-02 8.26e+03 5.33e+01 bond pdb=" CB LEU D 663 " pdb=" CG LEU D 663 " ideal model delta sigma weight residual 1.530 1.656 -0.126 2.00e-02 2.50e+03 3.95e+01 bond pdb=" CB LEU B 663 " pdb=" CG LEU B 663 " ideal model delta sigma weight residual 1.530 1.651 -0.121 2.00e-02 2.50e+03 3.67e+01 bond pdb=" CA CYS A 205 " pdb=" CB CYS A 205 " ideal model delta sigma weight residual 1.522 1.564 -0.041 7.00e-03 2.04e+04 3.47e+01 bond pdb=" CB LEU F 663 " pdb=" CG LEU F 663 " ideal model delta sigma weight residual 1.530 1.644 -0.114 2.00e-02 2.50e+03 3.25e+01 ... (remaining 16900 not shown) Histogram of bond angle deviations from ideal: 97.68 - 110.83: 6636 110.83 - 123.98: 15391 123.98 - 137.14: 924 137.14 - 150.29: 0 150.29 - 163.44: 11 Bond angle restraints: 22962 Sorted by residual: angle pdb=" C2 NAG E 604 " pdb=" N2 NAG E 604 " pdb=" C7 NAG E 604 " ideal model delta sigma weight residual 124.56 163.44 -38.88 3.00e+00 1.11e-01 1.68e+02 angle pdb=" C2 NAG P 1 " pdb=" N2 NAG P 1 " pdb=" C7 NAG P 1 " ideal model delta sigma weight residual 124.56 163.08 -38.52 3.00e+00 1.11e-01 1.65e+02 angle pdb=" C2 NAG D 703 " pdb=" N2 NAG D 703 " pdb=" C7 NAG D 703 " ideal model delta sigma weight residual 124.56 162.44 -37.88 3.00e+00 1.11e-01 1.59e+02 angle pdb=" C2 NAG D 701 " pdb=" N2 NAG D 701 " pdb=" C7 NAG D 701 " ideal model delta sigma weight residual 124.56 161.76 -37.20 3.00e+00 1.11e-01 1.54e+02 angle pdb=" C2 NAG D 702 " pdb=" N2 NAG D 702 " pdb=" C7 NAG D 702 " ideal model delta sigma weight residual 124.56 161.29 -36.73 3.00e+00 1.11e-01 1.50e+02 ... (remaining 22957 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.84: 11033 21.84 - 43.67: 281 43.67 - 65.50: 77 65.50 - 87.34: 54 87.34 - 109.17: 25 Dihedral angle restraints: 11470 sinusoidal: 5892 harmonic: 5578 Sorted by residual: dihedral pdb=" CB CYS F 598 " pdb=" SG CYS F 598 " pdb=" SG CYS F 604 " pdb=" CB CYS F 604 " ideal model delta sinusoidal sigma weight residual -86.00 -171.83 85.83 1 1.00e+01 1.00e-02 8.90e+01 dihedral pdb=" CB CYS B 598 " pdb=" SG CYS B 598 " pdb=" SG CYS B 604 " pdb=" CB CYS B 604 " ideal model delta sinusoidal sigma weight residual -86.00 -169.76 83.76 1 1.00e+01 1.00e-02 8.56e+01 dihedral pdb=" CB CYS D 598 " pdb=" SG CYS D 598 " pdb=" SG CYS D 604 " pdb=" CB CYS D 604 " ideal model delta sinusoidal sigma weight residual 93.00 153.96 -60.96 1 1.00e+01 1.00e-02 4.94e+01 ... (remaining 11467 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.132: 2110 0.132 - 0.263: 499 0.263 - 0.395: 203 0.395 - 0.527: 66 0.527 - 0.659: 1 Chirality restraints: 2879 Sorted by residual: chirality pdb=" C1 BMA U 3 " pdb=" O4 NAG U 2 " pdb=" C2 BMA U 3 " pdb=" O5 BMA U 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.68 0.28 2.00e-02 2.50e+03 1.99e+02 chirality pdb=" C1 BMA S 3 " pdb=" O4 NAG S 2 " pdb=" C2 BMA S 3 " pdb=" O5 BMA S 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-02 2.50e+03 1.93e+02 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.67 0.27 2.00e-02 2.50e+03 1.85e+02 ... (remaining 2876 not shown) Planarity restraints: 2843 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG Z 1 " -0.373 2.00e-02 2.50e+03 3.18e-01 1.27e+03 pdb=" C7 NAG Z 1 " 0.092 2.00e-02 2.50e+03 pdb=" C8 NAG Z 1 " -0.066 2.00e-02 2.50e+03 pdb=" N2 NAG Z 1 " 0.557 2.00e-02 2.50e+03 pdb=" O7 NAG Z 1 " -0.210 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG S 1 " 0.354 2.00e-02 2.50e+03 3.04e-01 1.16e+03 pdb=" C7 NAG S 1 " -0.083 2.00e-02 2.50e+03 pdb=" C8 NAG S 1 " 0.073 2.00e-02 2.50e+03 pdb=" N2 NAG S 1 " -0.537 2.00e-02 2.50e+03 pdb=" O7 NAG S 1 " 0.194 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG S 2 " -0.355 2.00e-02 2.50e+03 3.03e-01 1.15e+03 pdb=" C7 NAG S 2 " 0.090 2.00e-02 2.50e+03 pdb=" C8 NAG S 2 " -0.162 2.00e-02 2.50e+03 pdb=" N2 NAG S 2 " 0.536 2.00e-02 2.50e+03 pdb=" O7 NAG S 2 " -0.109 2.00e-02 2.50e+03 ... (remaining 2840 not shown) Histogram of nonbonded interaction distances: 0.53 - 1.40: 13 1.40 - 2.28: 43 2.28 - 3.15: 13705 3.15 - 4.03: 43009 4.03 - 4.90: 75387 Warning: very small nonbonded interaction distances. Nonbonded interactions: 132157 Sorted by model distance: nonbonded pdb=" C ASN E 234 " pdb=" C2 NAG E 607 " model vdw 0.530 2.960 nonbonded pdb=" CA ASN E 234 " pdb=" C3 NAG E 607 " model vdw 0.700 3.900 nonbonded pdb=" O ASN E 234 " pdb=" N2 NAG E 607 " model vdw 0.816 2.520 nonbonded pdb=" CB PHE E 233 " pdb=" O6 NAG E 607 " model vdw 0.928 3.440 nonbonded pdb=" CA ASN E 234 " pdb=" O3 NAG E 607 " model vdw 0.962 3.470 ... (remaining 132152 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'C' and (resid 32 through 502 or resid 601 through 605)) selection = (chain 'E' and (resid 32 through 502 or resid 601 through 605)) } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'a' selection = chain 'b' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' } ncs_group { reference = chain 'S' selection = chain 'c' selection = chain 'i' } ncs_group { reference = (chain 'Z' and (resid 1 or resid 4 through 6)) selection = (chain 'j' and (resid 2 or resid 5 through 7)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.910 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: 5.460 Check model and map are aligned: 0.240 Set scattering table: 0.160 Process input model: 44.180 Find NCS groups from input model: 1.190 Set up NCS constraints: 0.280 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 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 : 0.022 0.157 16905 Z= 1.376 Angle : 1.969 38.881 22962 Z= 1.177 Chirality : 0.143 0.659 2879 Planarity : 0.017 0.318 2788 Dihedral : 12.894 109.174 7774 Min Nonbonded Distance : 0.530 Molprobity Statistics. All-atom Clashscore : 1.29 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.38 % Favored : 96.36 % Rotamer: Outliers : 0.77 % Allowed : 1.00 % Favored : 98.23 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.19), residues: 1894 helix: -0.17 (0.24), residues: 378 sheet: 0.62 (0.22), residues: 508 loop : 0.28 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.010 TRP E 96 HIS 0.017 0.003 HIS C 249 PHE 0.032 0.006 PHE E 233 TYR 0.058 0.008 TYR C 40 ARG 0.006 0.001 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 436 time to evaluate : 1.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 ILE cc_start: 0.9408 (pt) cc_final: 0.9198 (mp) REVERT: A 254 VAL cc_start: 0.9515 (t) cc_final: 0.9125 (p) REVERT: A 374 HIS cc_start: 0.7329 (t-170) cc_final: 0.6929 (t-90) REVERT: C 69 TRP cc_start: 0.8404 (m-90) cc_final: 0.7707 (m-10) REVERT: C 122 LEU cc_start: 0.9362 (mt) cc_final: 0.9132 (mp) REVERT: C 136 ASN cc_start: 0.6442 (t0) cc_final: 0.6058 (m110) REVERT: D 593 LEU cc_start: 0.9350 (mt) cc_final: 0.9149 (mm) REVERT: D 610 TRP cc_start: 0.6222 (p90) cc_final: 0.5985 (p-90) REVERT: D 655 LYS cc_start: 0.9179 (mmtm) cc_final: 0.8525 (mmmm) REVERT: E 42 VAL cc_start: 0.9298 (t) cc_final: 0.9025 (p) REVERT: E 165 LEU cc_start: 0.9258 (mt) cc_final: 0.8939 (mp) REVERT: E 180 ASP cc_start: 0.8583 (m-30) cc_final: 0.8381 (m-30) REVERT: E 186 ARG cc_start: 0.8780 (OUTLIER) cc_final: 0.8240 (ptm160) REVERT: E 373 THR cc_start: 0.9127 (p) cc_final: 0.8925 (p) REVERT: E 450 THR cc_start: 0.9263 (p) cc_final: 0.9044 (p) REVERT: F 538 THR cc_start: 0.8610 (p) cc_final: 0.8342 (p) REVERT: F 581 LEU cc_start: 0.9404 (tp) cc_final: 0.9204 (tt) REVERT: F 606 THR cc_start: 0.8958 (p) cc_final: 0.8590 (t) REVERT: F 607 ASN cc_start: 0.8474 (m-40) cc_final: 0.8109 (p0) REVERT: F 624 ASP cc_start: 0.8399 (m-30) cc_final: 0.7952 (t0) REVERT: F 652 GLN cc_start: 0.7896 (tp40) cc_final: 0.7634 (tp40) REVERT: B 543 ASN cc_start: 0.8074 (m-40) cc_final: 0.7841 (t0) REVERT: B 584 GLU cc_start: 0.8922 (tt0) cc_final: 0.8246 (tp30) REVERT: B 643 TYR cc_start: 0.8935 (m-10) cc_final: 0.8038 (m-10) REVERT: L 34 SER cc_start: 0.8990 (m) cc_final: 0.8773 (p) REVERT: L 39 HIS cc_start: 0.8878 (t-90) cc_final: 0.8579 (m-70) REVERT: L 50 GLU cc_start: 0.8511 (tt0) cc_final: 0.8065 (tm-30) REVERT: L 53 ASN cc_start: 0.8897 (m-40) cc_final: 0.8135 (m-40) REVERT: L 91 TYR cc_start: 0.7852 (t80) cc_final: 0.7552 (t80) REVERT: L 98 PHE cc_start: 0.8669 (m-80) cc_final: 0.8435 (m-80) REVERT: H 18 LEU cc_start: 0.8334 (tt) cc_final: 0.7591 (tt) REVERT: H 20 LEU cc_start: 0.9316 (mt) cc_final: 0.8906 (mt) REVERT: H 29 PHE cc_start: 0.8789 (t80) cc_final: 0.8174 (t80) REVERT: H 43 LYS cc_start: 0.8998 (mptt) cc_final: 0.8450 (pttp) REVERT: H 53 ASP cc_start: 0.8067 (OUTLIER) cc_final: 0.7671 (p0) REVERT: H 68 THR cc_start: 0.9158 (m) cc_final: 0.8738 (t) outliers start: 13 outliers final: 2 residues processed: 448 average time/residue: 0.2885 time to fit residues: 188.7237 Evaluate side-chains 227 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 223 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 158 optimal weight: 1.9990 chunk 142 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 76 optimal weight: 8.9990 chunk 147 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 chunk 170 optimal weight: 1.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN A 190 HIS C 167 ASN C 190 HIS C 363 GLN ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 HIS F 591 GLN ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 16905 Z= 0.262 Angle : 0.790 15.342 22962 Z= 0.396 Chirality : 0.054 0.815 2879 Planarity : 0.004 0.046 2788 Dihedral : 11.284 79.683 4217 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.43 % Favored : 96.41 % Rotamer: Outliers : 0.12 % Allowed : 2.18 % Favored : 97.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.19), residues: 1894 helix: 0.22 (0.26), residues: 387 sheet: 0.41 (0.22), residues: 533 loop : 0.01 (0.20), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 96 HIS 0.008 0.001 HIS A 249 PHE 0.038 0.002 PHE E 233 TYR 0.017 0.002 TYR E 435 ARG 0.009 0.001 ARG E 273 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 300 time to evaluate : 1.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 ASN cc_start: 0.8282 (t0) cc_final: 0.7484 (m-40) REVERT: A 254 VAL cc_start: 0.9366 (t) cc_final: 0.9125 (p) REVERT: A 374 HIS cc_start: 0.7198 (t-170) cc_final: 0.6904 (t-90) REVERT: C 69 TRP cc_start: 0.8638 (m-90) cc_final: 0.8231 (m-10) REVERT: C 111 LEU cc_start: 0.9408 (mm) cc_final: 0.9002 (mt) REVERT: C 122 LEU cc_start: 0.9323 (mt) cc_final: 0.9086 (mm) REVERT: C 136 ASN cc_start: 0.6439 (t0) cc_final: 0.5865 (m110) REVERT: C 210 PHE cc_start: 0.8495 (m-80) cc_final: 0.7879 (m-10) REVERT: C 369 LEU cc_start: 0.8903 (tp) cc_final: 0.8697 (mm) REVERT: D 584 GLU cc_start: 0.8796 (tp30) cc_final: 0.8176 (tm-30) REVERT: D 593 LEU cc_start: 0.9321 (mt) cc_final: 0.9094 (mm) REVERT: D 607 ASN cc_start: 0.8459 (m110) cc_final: 0.8103 (p0) REVERT: D 657 GLU cc_start: 0.9310 (mt-10) cc_final: 0.8793 (mp0) REVERT: E 180 ASP cc_start: 0.8553 (m-30) cc_final: 0.8157 (m-30) REVERT: E 435 TYR cc_start: 0.9101 (t80) cc_final: 0.8845 (t80) REVERT: F 574 LYS cc_start: 0.7118 (pttm) cc_final: 0.6660 (mmpt) REVERT: F 607 ASN cc_start: 0.8405 (m-40) cc_final: 0.7968 (p0) REVERT: F 647 GLU cc_start: 0.8221 (pt0) cc_final: 0.7831 (pt0) REVERT: B 530 MET cc_start: 0.8547 (mtp) cc_final: 0.8001 (ppp) REVERT: B 538 THR cc_start: 0.9320 (t) cc_final: 0.9069 (t) REVERT: B 543 ASN cc_start: 0.8198 (m-40) cc_final: 0.7754 (t0) REVERT: B 584 GLU cc_start: 0.8681 (tt0) cc_final: 0.8249 (tp30) REVERT: B 643 TYR cc_start: 0.8931 (m-10) cc_final: 0.8675 (m-80) REVERT: L 53 ASN cc_start: 0.8504 (m-40) cc_final: 0.8102 (m-40) REVERT: L 82 ASP cc_start: 0.6268 (m-30) cc_final: 0.6001 (m-30) REVERT: L 91 TYR cc_start: 0.7803 (t80) cc_final: 0.7432 (t80) REVERT: L 104 LEU cc_start: 0.8386 (tt) cc_final: 0.7553 (tp) REVERT: H 68 THR cc_start: 0.8793 (m) cc_final: 0.8517 (p) outliers start: 2 outliers final: 0 residues processed: 302 average time/residue: 0.2651 time to fit residues: 122.8561 Evaluate side-chains 188 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 1.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 94 optimal weight: 0.4980 chunk 52 optimal weight: 0.9990 chunk 142 optimal weight: 5.9990 chunk 116 optimal weight: 0.7980 chunk 47 optimal weight: 0.0570 chunk 171 optimal weight: 30.0000 chunk 184 optimal weight: 20.0000 chunk 152 optimal weight: 5.9990 chunk 169 optimal weight: 8.9990 chunk 58 optimal weight: 6.9990 chunk 137 optimal weight: 10.0000 overall best weight: 1.6702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN C 190 HIS ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 630 GLN E 85 HIS E 352 HIS E 422 GLN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 652 GLN ** B 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN L 39 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.3582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 16905 Z= 0.243 Angle : 0.686 14.918 22962 Z= 0.344 Chirality : 0.050 0.577 2879 Planarity : 0.004 0.037 2788 Dihedral : 9.926 71.395 4217 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.44 % Favored : 95.51 % Rotamer: Outliers : 0.06 % Allowed : 2.54 % Favored : 97.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.19), residues: 1894 helix: 0.40 (0.28), residues: 369 sheet: 0.24 (0.23), residues: 499 loop : -0.10 (0.20), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 479 HIS 0.006 0.001 HIS A 249 PHE 0.056 0.002 PHE E 233 TYR 0.024 0.001 TYR E 484 ARG 0.013 0.000 ARG H 66 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 260 time to evaluate : 1.928 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: A 69 TRP cc_start: 0.8094 (m-90) cc_final: 0.7817 (m-90) REVERT: A 180 ASP cc_start: 0.8390 (m-30) cc_final: 0.7738 (m-30) REVERT: A 254 VAL cc_start: 0.9450 (t) cc_final: 0.9153 (p) REVERT: C 69 TRP cc_start: 0.8624 (m-90) cc_final: 0.8210 (m-10) REVERT: C 111 LEU cc_start: 0.9372 (mm) cc_final: 0.8963 (mt) REVERT: C 116 LEU cc_start: 0.9452 (tt) cc_final: 0.8945 (mp) REVERT: C 122 LEU cc_start: 0.9378 (mt) cc_final: 0.9153 (mm) REVERT: C 136 ASN cc_start: 0.6557 (t0) cc_final: 0.6122 (m110) REVERT: C 210 PHE cc_start: 0.8619 (m-80) cc_final: 0.8029 (m-10) REVERT: C 260 LEU cc_start: 0.9048 (mt) cc_final: 0.8720 (mt) REVERT: C 434 MET cc_start: 0.8038 (mtm) cc_final: 0.7597 (mtm) REVERT: D 584 GLU cc_start: 0.8940 (tp30) cc_final: 0.8230 (tm-30) REVERT: D 598 CYS cc_start: 0.7729 (m) cc_final: 0.7450 (m) REVERT: D 607 ASN cc_start: 0.8528 (m110) cc_final: 0.8150 (p0) REVERT: D 648 GLU cc_start: 0.8506 (pp20) cc_final: 0.8248 (pp20) REVERT: D 657 GLU cc_start: 0.9058 (mt-10) cc_final: 0.8794 (mt-10) REVERT: E 180 ASP cc_start: 0.8660 (m-30) cc_final: 0.8041 (m-30) REVERT: F 574 LYS cc_start: 0.8194 (ptpp) cc_final: 0.7888 (mmpt) REVERT: F 576 LEU cc_start: 0.8894 (mt) cc_final: 0.8214 (tt) REVERT: F 607 ASN cc_start: 0.8563 (m-40) cc_final: 0.7871 (p0) REVERT: F 647 GLU cc_start: 0.8228 (pt0) cc_final: 0.7810 (pt0) REVERT: F 652 GLN cc_start: 0.7751 (tp40) cc_final: 0.7544 (tp-100) REVERT: B 530 MET cc_start: 0.8566 (mtp) cc_final: 0.8039 (ppp) REVERT: B 536 THR cc_start: 0.9155 (p) cc_final: 0.8870 (p) REVERT: B 538 THR cc_start: 0.9329 (t) cc_final: 0.9046 (t) REVERT: B 584 GLU cc_start: 0.8701 (tt0) cc_final: 0.8249 (tp30) REVERT: B 630 GLN cc_start: 0.9226 (mt0) cc_final: 0.8537 (mt0) REVERT: B 643 TYR cc_start: 0.8884 (m-10) cc_final: 0.8500 (m-80) REVERT: L 91 TYR cc_start: 0.7687 (t80) cc_final: 0.7373 (t80) REVERT: L 104 LEU cc_start: 0.8144 (tt) cc_final: 0.7093 (tp) REVERT: H 34 MET cc_start: 0.9307 (mmm) cc_final: 0.9051 (mmm) REVERT: H 68 THR cc_start: 0.8938 (m) cc_final: 0.8636 (p) outliers start: 1 outliers final: 1 residues processed: 261 average time/residue: 0.2688 time to fit residues: 106.8501 Evaluate side-chains 180 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 179 time to evaluate : 1.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 168 optimal weight: 20.0000 chunk 128 optimal weight: 7.9990 chunk 88 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 114 optimal weight: 8.9990 chunk 171 optimal weight: 30.0000 chunk 181 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 162 optimal weight: 4.9990 chunk 48 optimal weight: 10.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN A 328 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 607 ASN D 630 GLN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.4313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 16905 Z= 0.402 Angle : 0.793 10.145 22962 Z= 0.394 Chirality : 0.050 0.501 2879 Planarity : 0.006 0.182 2788 Dihedral : 9.470 64.522 4217 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.39 % Favored : 94.56 % Rotamer: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.19), residues: 1894 helix: 0.21 (0.28), residues: 366 sheet: -0.03 (0.21), residues: 543 loop : -0.45 (0.20), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 610 HIS 0.010 0.002 HIS A 374 PHE 0.047 0.002 PHE E 233 TYR 0.014 0.002 TYR H 100N ARG 0.009 0.001 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 221 time to evaluate : 1.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 ASN cc_start: 0.8591 (t0) cc_final: 0.7877 (m-40) REVERT: A 99 ASN cc_start: 0.9214 (p0) cc_final: 0.8520 (t0) REVERT: A 100 MET cc_start: 0.9484 (mmm) cc_final: 0.8776 (mmm) REVERT: A 180 ASP cc_start: 0.8572 (m-30) cc_final: 0.7917 (m-30) REVERT: C 69 TRP cc_start: 0.8673 (m-90) cc_final: 0.7740 (m-10) REVERT: C 136 ASN cc_start: 0.6840 (t0) cc_final: 0.6089 (m110) REVERT: C 260 LEU cc_start: 0.9174 (mt) cc_final: 0.8965 (mt) REVERT: D 584 GLU cc_start: 0.8952 (tp30) cc_final: 0.8305 (tm-30) REVERT: D 607 ASN cc_start: 0.8501 (m-40) cc_final: 0.8131 (p0) REVERT: D 653 GLN cc_start: 0.8752 (mp10) cc_final: 0.8415 (mp10) REVERT: D 657 GLU cc_start: 0.9111 (mt-10) cc_final: 0.8819 (mt-10) REVERT: E 45 TRP cc_start: 0.8114 (m-10) cc_final: 0.7896 (m-10) REVERT: E 180 ASP cc_start: 0.8616 (m-30) cc_final: 0.8092 (m-30) REVERT: F 574 LYS cc_start: 0.7989 (ptpp) cc_final: 0.7755 (mmpt) REVERT: F 576 LEU cc_start: 0.8912 (mt) cc_final: 0.8248 (tt) REVERT: F 584 GLU cc_start: 0.8545 (tp30) cc_final: 0.8219 (tm-30) REVERT: F 647 GLU cc_start: 0.8232 (pt0) cc_final: 0.7884 (pt0) REVERT: F 652 GLN cc_start: 0.8132 (tp40) cc_final: 0.7764 (tp-100) REVERT: B 530 MET cc_start: 0.8944 (mtp) cc_final: 0.8404 (ppp) REVERT: B 538 THR cc_start: 0.9333 (t) cc_final: 0.9130 (t) REVERT: B 584 GLU cc_start: 0.9023 (tt0) cc_final: 0.8409 (tp30) REVERT: B 591 GLN cc_start: 0.9083 (tp40) cc_final: 0.8436 (tp40) REVERT: L 91 TYR cc_start: 0.7482 (t80) cc_final: 0.7105 (t80) REVERT: H 16 ARG cc_start: 0.9314 (mpt180) cc_final: 0.9079 (mtp180) REVERT: H 66 ARG cc_start: 0.7992 (mtp-110) cc_final: 0.7558 (ptm160) REVERT: H 68 THR cc_start: 0.9076 (m) cc_final: 0.8740 (p) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.2671 time to fit residues: 91.4962 Evaluate side-chains 150 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 1.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 151 optimal weight: 0.9980 chunk 103 optimal weight: 8.9990 chunk 2 optimal weight: 8.9990 chunk 135 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 125 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 92 optimal weight: 0.7980 chunk 163 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 630 GLN D 656 ASN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 ASN ** B 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 HIS ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.4587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 16905 Z= 0.228 Angle : 0.660 10.829 22962 Z= 0.330 Chirality : 0.049 0.473 2879 Planarity : 0.005 0.112 2788 Dihedral : 8.810 60.400 4217 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.54 % Favored : 95.41 % Rotamer: Outliers : 0.12 % Allowed : 1.77 % Favored : 98.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.19), residues: 1894 helix: 0.32 (0.28), residues: 366 sheet: -0.14 (0.22), residues: 513 loop : -0.49 (0.20), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP H 36 HIS 0.007 0.001 HIS A 249 PHE 0.030 0.001 PHE E 233 TYR 0.015 0.001 TYR L 49 ARG 0.010 0.000 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 208 time to evaluate : 1.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.8467 (m-10) cc_final: 0.8230 (m-10) REVERT: A 104 MET cc_start: 0.9490 (ttt) cc_final: 0.9218 (ttt) REVERT: A 374 HIS cc_start: 0.7724 (t70) cc_final: 0.6905 (t70) REVERT: A 434 MET cc_start: 0.8901 (ptt) cc_final: 0.8613 (ptt) REVERT: A 475 MET cc_start: 0.8730 (mpp) cc_final: 0.8525 (mmm) REVERT: C 69 TRP cc_start: 0.8769 (m-90) cc_final: 0.7862 (m-10) REVERT: C 111 LEU cc_start: 0.9358 (mm) cc_final: 0.8927 (mt) REVERT: C 116 LEU cc_start: 0.9500 (tt) cc_final: 0.9165 (mt) REVERT: C 136 ASN cc_start: 0.6781 (t0) cc_final: 0.6336 (m110) REVERT: C 260 LEU cc_start: 0.8951 (mt) cc_final: 0.8673 (mt) REVERT: D 584 GLU cc_start: 0.8965 (tp30) cc_final: 0.8301 (tm-30) REVERT: D 607 ASN cc_start: 0.8152 (m-40) cc_final: 0.7827 (p0) REVERT: D 653 GLN cc_start: 0.8580 (mp10) cc_final: 0.7916 (mp10) REVERT: D 657 GLU cc_start: 0.9038 (mt-10) cc_final: 0.8601 (mp0) REVERT: E 45 TRP cc_start: 0.7874 (m-10) cc_final: 0.7619 (m-10) REVERT: E 180 ASP cc_start: 0.8678 (m-30) cc_final: 0.8087 (m-30) REVERT: F 574 LYS cc_start: 0.7931 (ptpp) cc_final: 0.7702 (mmpt) REVERT: F 576 LEU cc_start: 0.8816 (mt) cc_final: 0.8180 (tt) REVERT: F 584 GLU cc_start: 0.8381 (tp30) cc_final: 0.8121 (tm-30) REVERT: F 647 GLU cc_start: 0.8025 (pt0) cc_final: 0.7741 (pt0) REVERT: F 652 GLN cc_start: 0.8056 (tp40) cc_final: 0.7661 (tp-100) REVERT: B 530 MET cc_start: 0.8733 (mtp) cc_final: 0.8377 (ppp) REVERT: B 584 GLU cc_start: 0.8964 (tt0) cc_final: 0.8209 (tp30) REVERT: B 601 LYS cc_start: 0.9115 (mmtp) cc_final: 0.8890 (mmmm) REVERT: L 47 MET cc_start: 0.8477 (mmp) cc_final: 0.8256 (mmm) REVERT: L 53 ASN cc_start: 0.7975 (t0) cc_final: 0.7716 (t0) REVERT: L 91 TYR cc_start: 0.7375 (t80) cc_final: 0.7109 (t80) REVERT: H 67 PHE cc_start: 0.8530 (m-10) cc_final: 0.7676 (m-10) REVERT: H 80 LEU cc_start: 0.9402 (tp) cc_final: 0.9089 (tp) outliers start: 2 outliers final: 0 residues processed: 210 average time/residue: 0.2657 time to fit residues: 87.0780 Evaluate side-chains 162 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 1.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 61 optimal weight: 1.9990 chunk 163 optimal weight: 0.4980 chunk 35 optimal weight: 10.0000 chunk 106 optimal weight: 3.9990 chunk 44 optimal weight: 7.9990 chunk 181 optimal weight: 6.9990 chunk 150 optimal weight: 3.9990 chunk 84 optimal weight: 20.0000 chunk 15 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 95 optimal weight: 9.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 630 GLN E 85 HIS E 348 GLN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 HIS ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.4876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 16905 Z= 0.239 Angle : 0.646 9.261 22962 Z= 0.323 Chirality : 0.047 0.464 2879 Planarity : 0.004 0.079 2788 Dihedral : 8.289 60.261 4217 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.96 % Favored : 94.98 % Rotamer: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.20), residues: 1894 helix: 0.25 (0.28), residues: 366 sheet: -0.20 (0.22), residues: 521 loop : -0.49 (0.20), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP H 36 HIS 0.008 0.001 HIS E 85 PHE 0.021 0.001 PHE E 233 TYR 0.012 0.001 TYR E 484 ARG 0.007 0.000 ARG B 617 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 1.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 374 HIS cc_start: 0.7887 (t70) cc_final: 0.7236 (t-90) REVERT: A 434 MET cc_start: 0.9021 (ptt) cc_final: 0.8716 (ptt) REVERT: A 475 MET cc_start: 0.8723 (mpp) cc_final: 0.8482 (mmm) REVERT: C 69 TRP cc_start: 0.8777 (m-90) cc_final: 0.7877 (m-10) REVERT: C 111 LEU cc_start: 0.9340 (mm) cc_final: 0.8916 (mt) REVERT: C 116 LEU cc_start: 0.9493 (tt) cc_final: 0.9218 (mt) REVERT: C 136 ASN cc_start: 0.6804 (t0) cc_final: 0.6384 (m110) REVERT: C 207 LYS cc_start: 0.8580 (pttt) cc_final: 0.8295 (tptt) REVERT: C 260 LEU cc_start: 0.8907 (mt) cc_final: 0.8652 (mt) REVERT: C 477 ASP cc_start: 0.8490 (p0) cc_final: 0.8287 (p0) REVERT: D 584 GLU cc_start: 0.8996 (tp30) cc_final: 0.8360 (tm-30) REVERT: D 607 ASN cc_start: 0.8143 (m-40) cc_final: 0.7281 (t0) REVERT: D 653 GLN cc_start: 0.8598 (mp10) cc_final: 0.7883 (mp10) REVERT: D 657 GLU cc_start: 0.8997 (mt-10) cc_final: 0.8612 (mp0) REVERT: E 45 TRP cc_start: 0.7914 (m-10) cc_final: 0.7639 (m-10) REVERT: E 95 MET cc_start: 0.8513 (mmp) cc_final: 0.8225 (mmm) REVERT: E 180 ASP cc_start: 0.8687 (m-30) cc_final: 0.7911 (m-30) REVERT: F 574 LYS cc_start: 0.7928 (ptpp) cc_final: 0.7679 (mmpt) REVERT: F 576 LEU cc_start: 0.8834 (mt) cc_final: 0.8228 (tt) REVERT: F 584 GLU cc_start: 0.8379 (tp30) cc_final: 0.8176 (tm-30) REVERT: F 647 GLU cc_start: 0.7990 (pt0) cc_final: 0.7669 (pt0) REVERT: F 652 GLN cc_start: 0.8098 (tp40) cc_final: 0.7666 (tp-100) REVERT: B 530 MET cc_start: 0.8823 (mtp) cc_final: 0.8443 (ppp) REVERT: B 634 GLU cc_start: 0.8401 (mt-10) cc_final: 0.7666 (mp0) REVERT: L 91 TYR cc_start: 0.7330 (t80) cc_final: 0.7109 (t80) REVERT: H 80 LEU cc_start: 0.9406 (tp) cc_final: 0.9038 (tp) outliers start: 0 outliers final: 0 residues processed: 203 average time/residue: 0.2566 time to fit residues: 81.0116 Evaluate side-chains 151 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 1.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 175 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 132 optimal weight: 0.9980 chunk 102 optimal weight: 8.9990 chunk 153 optimal weight: 0.0670 chunk 101 optimal weight: 2.9990 chunk 181 optimal weight: 4.9990 chunk 113 optimal weight: 6.9990 chunk 110 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 overall best weight: 2.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 630 GLN ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 ASN ** B 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.5156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16905 Z= 0.250 Angle : 0.649 9.234 22962 Z= 0.324 Chirality : 0.047 0.454 2879 Planarity : 0.004 0.073 2788 Dihedral : 8.039 61.436 4217 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.33 % Favored : 94.61 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.20), residues: 1894 helix: 0.33 (0.28), residues: 366 sheet: -0.15 (0.22), residues: 548 loop : -0.63 (0.21), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP H 36 HIS 0.005 0.001 HIS E 85 PHE 0.016 0.001 PHE H 67 TYR 0.012 0.001 TYR L 49 ARG 0.014 0.001 ARG H 83 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 197 time to evaluate : 1.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.8718 (m-40) cc_final: 0.8197 (t0) REVERT: A 374 HIS cc_start: 0.7925 (t70) cc_final: 0.7325 (t70) REVERT: A 434 MET cc_start: 0.9071 (ptt) cc_final: 0.8761 (ptt) REVERT: A 475 MET cc_start: 0.8787 (mpp) cc_final: 0.8534 (mmm) REVERT: C 111 LEU cc_start: 0.9382 (mm) cc_final: 0.8957 (mt) REVERT: C 136 ASN cc_start: 0.6746 (t0) cc_final: 0.6490 (m110) REVERT: C 207 LYS cc_start: 0.8573 (pttt) cc_final: 0.8251 (tptt) REVERT: C 260 LEU cc_start: 0.8875 (mt) cc_final: 0.8661 (mt) REVERT: D 574 LYS cc_start: 0.8779 (tmmt) cc_final: 0.8362 (pttp) REVERT: D 584 GLU cc_start: 0.8996 (tp30) cc_final: 0.8366 (tm-30) REVERT: D 653 GLN cc_start: 0.8554 (mp10) cc_final: 0.7878 (mp10) REVERT: D 657 GLU cc_start: 0.9009 (mt-10) cc_final: 0.8611 (mp0) REVERT: E 45 TRP cc_start: 0.8050 (m-10) cc_final: 0.7811 (m-10) REVERT: E 95 MET cc_start: 0.8550 (mmp) cc_final: 0.8248 (mmm) REVERT: E 180 ASP cc_start: 0.8698 (m-30) cc_final: 0.7977 (m-30) REVERT: F 574 LYS cc_start: 0.7948 (ptpp) cc_final: 0.7676 (mmpt) REVERT: F 576 LEU cc_start: 0.8856 (mt) cc_final: 0.8239 (tt) REVERT: F 584 GLU cc_start: 0.8453 (tp30) cc_final: 0.8113 (tm-30) REVERT: F 625 ASN cc_start: 0.8311 (t0) cc_final: 0.8043 (t0) REVERT: F 647 GLU cc_start: 0.7982 (pt0) cc_final: 0.7683 (pt0) REVERT: B 530 MET cc_start: 0.8799 (mtp) cc_final: 0.8350 (ppp) REVERT: L 91 TYR cc_start: 0.7297 (t80) cc_final: 0.7047 (t80) REVERT: H 68 THR cc_start: 0.9132 (m) cc_final: 0.8877 (t) REVERT: H 80 LEU cc_start: 0.9307 (tp) cc_final: 0.8544 (tp) REVERT: H 100 ASP cc_start: 0.9028 (t0) cc_final: 0.8825 (t0) outliers start: 0 outliers final: 0 residues processed: 197 average time/residue: 0.2692 time to fit residues: 81.9142 Evaluate side-chains 147 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 1.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 112 optimal weight: 0.3980 chunk 72 optimal weight: 8.9990 chunk 108 optimal weight: 8.9990 chunk 54 optimal weight: 0.6980 chunk 35 optimal weight: 10.0000 chunk 115 optimal weight: 0.4980 chunk 123 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 16 optimal weight: 0.0000 chunk 142 optimal weight: 1.9990 chunk 164 optimal weight: 2.9990 overall best weight: 0.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 630 GLN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.5277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 16905 Z= 0.151 Angle : 0.604 9.341 22962 Z= 0.300 Chirality : 0.047 0.448 2879 Planarity : 0.004 0.075 2788 Dihedral : 7.585 64.546 4217 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.59 % Favored : 95.35 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.20), residues: 1894 helix: 0.31 (0.29), residues: 369 sheet: -0.11 (0.22), residues: 549 loop : -0.52 (0.21), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP H 36 HIS 0.008 0.001 HIS E 85 PHE 0.013 0.001 PHE E 233 TYR 0.011 0.001 TYR E 484 ARG 0.006 0.000 ARG H 66 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 1.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.8643 (m-40) cc_final: 0.8194 (t0) REVERT: A 374 HIS cc_start: 0.7655 (t70) cc_final: 0.7383 (t70) REVERT: A 434 MET cc_start: 0.8922 (ptt) cc_final: 0.8569 (ptt) REVERT: A 475 MET cc_start: 0.8657 (mpp) cc_final: 0.8362 (mmm) REVERT: C 104 MET cc_start: 0.8825 (tmm) cc_final: 0.8584 (tmm) REVERT: C 111 LEU cc_start: 0.9305 (mm) cc_final: 0.8963 (mt) REVERT: C 116 LEU cc_start: 0.9436 (tt) cc_final: 0.9213 (mt) REVERT: C 207 LYS cc_start: 0.8602 (pttt) cc_final: 0.8266 (tptt) REVERT: C 210 PHE cc_start: 0.8964 (m-80) cc_final: 0.8549 (m-10) REVERT: D 574 LYS cc_start: 0.8729 (tmmt) cc_final: 0.8473 (pttp) REVERT: D 584 GLU cc_start: 0.8973 (tp30) cc_final: 0.8331 (tm-30) REVERT: D 653 GLN cc_start: 0.8562 (mp10) cc_final: 0.7929 (mp10) REVERT: D 657 GLU cc_start: 0.8948 (mt-10) cc_final: 0.8629 (mp0) REVERT: E 45 TRP cc_start: 0.7855 (m-10) cc_final: 0.7517 (m-10) REVERT: E 95 MET cc_start: 0.8357 (mmp) cc_final: 0.7921 (mmm) REVERT: E 180 ASP cc_start: 0.8666 (m-30) cc_final: 0.7749 (m-30) REVERT: F 574 LYS cc_start: 0.7876 (ptpp) cc_final: 0.7543 (mmpt) REVERT: F 576 LEU cc_start: 0.8803 (mt) cc_final: 0.8216 (tt) REVERT: F 584 GLU cc_start: 0.8457 (tp30) cc_final: 0.8137 (tm-30) REVERT: F 592 LEU cc_start: 0.9038 (tt) cc_final: 0.8522 (mm) REVERT: F 647 GLU cc_start: 0.7743 (pt0) cc_final: 0.7468 (pt0) REVERT: B 530 MET cc_start: 0.8817 (mtp) cc_final: 0.8386 (ppp) REVERT: B 634 GLU cc_start: 0.8464 (mt-10) cc_final: 0.7732 (mp0) REVERT: H 80 LEU cc_start: 0.9264 (tp) cc_final: 0.8591 (tp) REVERT: H 100 ASP cc_start: 0.9027 (t0) cc_final: 0.8802 (t0) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.2593 time to fit residues: 83.0913 Evaluate side-chains 159 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 1.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 173 optimal weight: 4.9990 chunk 158 optimal weight: 6.9990 chunk 168 optimal weight: 7.9990 chunk 101 optimal weight: 1.9990 chunk 73 optimal weight: 7.9990 chunk 132 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 159 optimal weight: 0.7980 chunk 110 optimal weight: 8.9990 chunk 178 optimal weight: 6.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 630 GLN E 85 HIS ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.5457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16905 Z= 0.217 Angle : 0.615 9.292 22962 Z= 0.306 Chirality : 0.046 0.449 2879 Planarity : 0.004 0.065 2788 Dihedral : 7.484 64.255 4217 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.39 % Favored : 94.56 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.20), residues: 1894 helix: 0.50 (0.30), residues: 348 sheet: -0.16 (0.22), residues: 546 loop : -0.49 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.002 TRP H 36 HIS 0.011 0.001 HIS E 85 PHE 0.011 0.001 PHE E 233 TYR 0.018 0.001 TYR L 91 ARG 0.010 0.000 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 1.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.8709 (m-40) cc_final: 0.8220 (t0) REVERT: A 434 MET cc_start: 0.8970 (ptt) cc_final: 0.8625 (ptt) REVERT: A 475 MET cc_start: 0.8660 (mpp) cc_final: 0.8420 (mmm) REVERT: C 104 MET cc_start: 0.9053 (tmm) cc_final: 0.8649 (tmm) REVERT: C 111 LEU cc_start: 0.9337 (mm) cc_final: 0.8967 (mt) REVERT: C 116 LEU cc_start: 0.9458 (tt) cc_final: 0.9251 (mt) REVERT: C 207 LYS cc_start: 0.8614 (pttt) cc_final: 0.8251 (tptt) REVERT: C 260 LEU cc_start: 0.8479 (mt) cc_final: 0.8139 (mt) REVERT: C 477 ASP cc_start: 0.8563 (p0) cc_final: 0.8329 (p0) REVERT: D 574 LYS cc_start: 0.8766 (tmmt) cc_final: 0.8324 (tptp) REVERT: D 584 GLU cc_start: 0.8963 (tp30) cc_final: 0.8347 (tm-30) REVERT: D 653 GLN cc_start: 0.8578 (mp10) cc_final: 0.7874 (mp10) REVERT: D 657 GLU cc_start: 0.8951 (mt-10) cc_final: 0.8648 (mp0) REVERT: E 45 TRP cc_start: 0.7993 (m-10) cc_final: 0.7711 (m-10) REVERT: E 95 MET cc_start: 0.8463 (mmp) cc_final: 0.8165 (mmm) REVERT: E 150 MET cc_start: 0.8953 (mmm) cc_final: 0.8736 (mmt) REVERT: E 180 ASP cc_start: 0.8690 (m-30) cc_final: 0.7909 (m-30) REVERT: F 530 MET cc_start: 0.9283 (pmm) cc_final: 0.9066 (pmm) REVERT: F 574 LYS cc_start: 0.7904 (ptpp) cc_final: 0.7555 (mmpt) REVERT: F 576 LEU cc_start: 0.8842 (mt) cc_final: 0.8244 (tt) REVERT: F 584 GLU cc_start: 0.8461 (tp30) cc_final: 0.8170 (tm-30) REVERT: F 592 LEU cc_start: 0.9082 (tt) cc_final: 0.8539 (mm) REVERT: F 647 GLU cc_start: 0.7892 (pt0) cc_final: 0.7638 (pt0) REVERT: B 530 MET cc_start: 0.8830 (mtp) cc_final: 0.8400 (ppp) REVERT: B 601 LYS cc_start: 0.9056 (mmtp) cc_final: 0.8838 (mmmm) REVERT: B 634 GLU cc_start: 0.8479 (mt-10) cc_final: 0.7732 (mp0) REVERT: L 91 TYR cc_start: 0.6656 (t80) cc_final: 0.6255 (t80) REVERT: H 34 MET cc_start: 0.9034 (mmp) cc_final: 0.8823 (mmm) REVERT: H 80 LEU cc_start: 0.9159 (tp) cc_final: 0.7961 (tp) REVERT: H 100 ASP cc_start: 0.9037 (t0) cc_final: 0.8809 (t0) outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.2538 time to fit residues: 76.2675 Evaluate side-chains 145 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 1.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 108 optimal weight: 8.9990 chunk 84 optimal weight: 10.0000 chunk 124 optimal weight: 7.9990 chunk 187 optimal weight: 0.9990 chunk 172 optimal weight: 8.9990 chunk 149 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 118 optimal weight: 9.9990 chunk 158 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 478 ASN D 630 GLN ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.5657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16905 Z= 0.264 Angle : 0.648 9.957 22962 Z= 0.324 Chirality : 0.047 0.445 2879 Planarity : 0.004 0.070 2788 Dihedral : 7.551 63.828 4217 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.97 % Favored : 93.98 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.20), residues: 1894 helix: 0.35 (0.29), residues: 369 sheet: -0.29 (0.22), residues: 548 loop : -0.60 (0.21), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP H 36 HIS 0.006 0.001 HIS A 249 PHE 0.011 0.001 PHE E 53 TYR 0.018 0.002 TYR L 91 ARG 0.007 0.001 ARG H 66 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 1.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.8858 (m-40) cc_final: 0.8309 (t0) REVERT: A 374 HIS cc_start: 0.7570 (t70) cc_final: 0.7165 (t70) REVERT: A 475 MET cc_start: 0.8529 (mpp) cc_final: 0.8266 (mmm) REVERT: C 104 MET cc_start: 0.9180 (tmm) cc_final: 0.8811 (tmm) REVERT: C 111 LEU cc_start: 0.9412 (mm) cc_final: 0.9019 (mt) REVERT: C 207 LYS cc_start: 0.8734 (pttt) cc_final: 0.8335 (tptt) REVERT: C 260 LEU cc_start: 0.8506 (mt) cc_final: 0.8186 (mt) REVERT: D 584 GLU cc_start: 0.8983 (tp30) cc_final: 0.8359 (tm-30) REVERT: D 653 GLN cc_start: 0.8584 (mp10) cc_final: 0.7883 (mp10) REVERT: D 657 GLU cc_start: 0.8986 (mt-10) cc_final: 0.8672 (mp0) REVERT: E 45 TRP cc_start: 0.8035 (m-10) cc_final: 0.7804 (m-10) REVERT: E 95 MET cc_start: 0.8508 (mmp) cc_final: 0.8243 (mmm) REVERT: E 150 MET cc_start: 0.8881 (mmm) cc_final: 0.8520 (mmt) REVERT: E 180 ASP cc_start: 0.8710 (m-30) cc_final: 0.8005 (m-30) REVERT: F 530 MET cc_start: 0.9223 (pmm) cc_final: 0.8990 (pmm) REVERT: F 576 LEU cc_start: 0.8845 (mt) cc_final: 0.8227 (tt) REVERT: F 584 GLU cc_start: 0.8495 (tp30) cc_final: 0.8198 (tm-30) REVERT: F 647 GLU cc_start: 0.7941 (pt0) cc_final: 0.7692 (pt0) REVERT: B 530 MET cc_start: 0.8850 (mtp) cc_final: 0.8427 (ppp) REVERT: B 634 GLU cc_start: 0.8527 (mt-10) cc_final: 0.7842 (mp0) REVERT: L 95 SER cc_start: 0.9413 (m) cc_final: 0.8985 (t) REVERT: H 80 LEU cc_start: 0.9210 (tp) cc_final: 0.8492 (tp) REVERT: H 100 ASP cc_start: 0.9023 (t0) cc_final: 0.8790 (t0) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.2599 time to fit residues: 76.4991 Evaluate side-chains 141 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 1.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 45 optimal weight: 0.9990 chunk 137 optimal weight: 0.2980 chunk 22 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 149 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 153 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 131 optimal weight: 0.8980 chunk 8 optimal weight: 0.0020 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 478 ASN D 630 GLN E 85 HIS ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 GLN ** B 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** 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 = 0.3269 r_free = 0.3269 target = 0.066629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.050297 restraints weight = 71756.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.052149 restraints weight = 41647.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.053459 restraints weight = 29179.195| |-----------------------------------------------------------------------------| r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.5739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 16905 Z= 0.155 Angle : 0.588 9.309 22962 Z= 0.292 Chirality : 0.046 0.438 2879 Planarity : 0.004 0.052 2788 Dihedral : 7.233 65.827 4217 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.70 % Favored : 95.25 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.20), residues: 1894 helix: 0.43 (0.29), residues: 345 sheet: -0.20 (0.22), residues: 546 loop : -0.48 (0.21), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP H 36 HIS 0.013 0.001 HIS E 85 PHE 0.010 0.001 PHE A 383 TYR 0.020 0.001 TYR H 100R ARG 0.006 0.000 ARG H 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2946.55 seconds wall clock time: 54 minutes 42.65 seconds (3282.65 seconds total)