Starting phenix.real_space_refine on Tue Feb 20 14:49:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ru3_24695/02_2024/7ru3_24695.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ru3_24695/02_2024/7ru3_24695.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ru3_24695/02_2024/7ru3_24695.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ru3_24695/02_2024/7ru3_24695.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ru3_24695/02_2024/7ru3_24695.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ru3_24695/02_2024/7ru3_24695.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.024 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 130 5.16 5 C 17906 2.51 5 N 4644 2.21 5 O 5477 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 583": "OE1" <-> "OE2" Residue "C PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 309": "OE1" <-> "OE2" Residue "B TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 28157 Number of models: 1 Model: "" Number of chains: 16 Chain: "H" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 882 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain: "L" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 817 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} Chain: "A" Number of atoms: 8304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1062, 8304 Classifications: {'peptide': 1062} Link IDs: {'PTRANS': 56, 'TRANS': 1005} Chain breaks: 7 Chain: "C" Number of atoms: 7737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 989, 7737 Classifications: {'peptide': 989} Link IDs: {'PTRANS': 53, 'TRANS': 935} Chain breaks: 16 Chain: "B" Number of atoms: 8134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8134 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 8 Chain: "E" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 882 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain: "F" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 817 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} 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: "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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: "A" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 14.62, per 1000 atoms: 0.52 Number of scatterers: 28157 At special positions: 0 Unit cell: (150.38, 141.11, 194.67, 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 130 16.00 O 5477 8.00 N 4644 7.00 C 17906 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=47, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.05 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.10 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.09 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.10 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 705 " - pdb=" SG CYS C 883 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.06 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A 883 " - pdb=" SG CYS B 705 " distance=2.73 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.12 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.07 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.05 Simple disulfide: pdb=" SG CYS C 705 " - pdb=" SG CYS B 883 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=1.78 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.09 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.05 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.20 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.05 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=1.75 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.02 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " 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 " BETA1-6 " NAG I 1 " - " FUC I 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A1301 " - " ASN A 17 " " NAG A1302 " - " ASN A 61 " " NAG A1303 " - " ASN A 122 " " NAG A1304 " - " ASN A 165 " " NAG A1305 " - " ASN A 234 " " NAG A1306 " - " ASN A 282 " " NAG A1307 " - " ASN A 331 " " NAG A1308 " - " ASN A 616 " " NAG A1309 " - " ASN A 657 " " NAG A1310 " - " ASN A 709 " " NAG A1311 " - " ASN A 801 " " NAG A1312 " - " ASN A1074 " " NAG A1313 " - " ASN A1098 " " NAG A1314 " - " ASN A1134 " " NAG B1301 " - " ASN B 331 " " NAG B1302 " - " ASN B 616 " " NAG B1303 " - " ASN B 709 " " NAG B1304 " - " ASN B1074 " " NAG B1305 " - " ASN B1134 " " NAG C1301 " - " ASN C 17 " " NAG C1302 " - " ASN C 234 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C 717 " " NAG C1307 " - " ASN C 801 " " NAG C1308 " - " ASN C1074 " " NAG C1309 " - " ASN C1098 " " NAG C1310 " - " ASN C1134 " " NAG D 1 " - " ASN A 343 " " NAG G 1 " - " ASN A 717 " " NAG I 1 " - " ASN B 343 " " NAG J 1 " - " ASN B 717 " " NAG K 1 " - " ASN B 801 " " NAG M 1 " - " ASN B1098 " Time building additional restraints: 10.87 Conformation dependent library (CDL) restraints added in 4.9 seconds 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6616 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 60 sheets defined 24.1% alpha, 31.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.84 Creating SS restraints... Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 29 through 31 No H-bonds generated for 'chain 'L' and resid 29 through 31' Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 383 through 388 removed outlier: 3.925A pdb=" N ASN A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.453A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 744 removed outlier: 3.516A pdb=" N GLY A 744 " --> pdb=" O MET A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.535A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 849 through 855 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.265A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.108A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1034 removed outlier: 4.169A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 Processing helix chain 'C' and resid 254 through 258 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 364 through 371 removed outlier: 3.510A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 Processing helix chain 'C' and resid 418 through 422 Processing helix chain 'C' and resid 439 through 441 No H-bonds generated for 'chain 'C' and resid 439 through 441' Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 849 through 855 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.505A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 3.926A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.649A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 405 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 753 Processing helix chain 'B' and resid 754 through 756 No H-bonds generated for 'chain 'B' and resid 754 through 756' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.679A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 802 through 806 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 852 through 856 removed outlier: 3.526A pdb=" N ASN B 856 " --> pdb=" O ALA B 852 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 852 through 856' Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.115A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'E' and resid 61 through 64 Processing helix chain 'E' and resid 73 through 75 No H-bonds generated for 'chain 'E' and resid 73 through 75' Processing helix chain 'E' and resid 83 through 87 Processing helix chain 'F' and resid 29 through 31 No H-bonds generated for 'chain 'F' and resid 29 through 31' Processing helix chain 'F' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.338A pdb=" N GLU H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.338A pdb=" N GLU H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 12 Processing sheet with id=AA6, first strand: chain 'L' and resid 52 through 54 removed outlier: 4.641A pdb=" N ARG L 54 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N LEU L 47 " --> pdb=" O ARG L 54 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.884A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N ASN A 188 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ILE A 210 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N ARG A 190 " --> pdb=" O THR A 208 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N THR A 208 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N PHE A 192 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N LYS A 206 " --> pdb=" O PHE A 192 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N PHE A 194 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N TYR A 204 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N ASN A 196 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N LYS A 202 " --> pdb=" O ASN A 196 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 10.035A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 27 through 30 Processing sheet with id=AA9, first strand: chain 'A' and resid 42 through 43 removed outlier: 4.095A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 48 through 55 removed outlier: 7.413A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.138A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.637A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 9.310A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 311 through 315 removed outlier: 3.752A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.971A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.971A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB8, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB9, first strand: chain 'A' and resid 538 through 540 removed outlier: 5.681A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 654 through 660 removed outlier: 5.363A pdb=" N THR A 696 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASN A 658 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.589A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'A' and resid 711 through 715 removed outlier: 4.827A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.419A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AC6, first strand: chain 'A' and resid 787 through 789 Processing sheet with id=AC7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.842A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.110A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 10.615A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 47 through 55 removed outlier: 7.405A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.691A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 84 through 85 removed outlier: 7.008A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 133 through 135 removed outlier: 6.471A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 311 through 317 removed outlier: 5.656A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 324 through 328 removed outlier: 3.564A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N PHE C 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.133A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 376 through 379 Processing sheet with id=AD8, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.284A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.577A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 701 through 703 removed outlier: 6.399A pdb=" N ALA C 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'C' and resid 711 through 715 removed outlier: 4.595A pdb=" N GLN C1106 " --> pdb=" O GLU C1111 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N GLU C1111 " --> pdb=" O GLN C1106 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 719 through 728 removed outlier: 6.302A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE4, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.777A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.186A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 48 through 55 removed outlier: 7.368A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 84 through 85 removed outlier: 5.908A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N SER B 112 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 8.581A pdb=" N PHE B 135 " --> pdb=" O SER B 112 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N THR B 114 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N PHE B 133 " --> pdb=" O THR B 114 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 141 through 143 removed outlier: 5.775A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N SER B 112 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 8.581A pdb=" N PHE B 135 " --> pdb=" O SER B 112 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N THR B 114 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N PHE B 133 " --> pdb=" O THR B 114 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 311 through 314 Processing sheet with id=AF1, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.135A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.135A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AF4, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AF5, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.450A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.749A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AF7, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.011A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AF9, first strand: chain 'B' and resid 1081 through 1082 removed outlier: 4.821A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 5 through 6 Processing sheet with id=AG2, first strand: chain 'E' and resid 10 through 11 removed outlier: 6.227A pdb=" N GLU E 10 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 10 through 11 removed outlier: 6.227A pdb=" N GLU E 10 " --> pdb=" O THR E 110 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 4 through 7 removed outlier: 5.437A pdb=" N THR F 69 " --> pdb=" O ALA F 25 " (cutoff:3.500A) removed outlier: 9.666A pdb=" N GLN F 27 " --> pdb=" O SER F 67 " (cutoff:3.500A) removed outlier: 9.872A pdb=" N SER F 67 " --> pdb=" O GLN F 27 " (cutoff:3.500A) removed outlier: 11.403A pdb=" N VAL F 28 " --> pdb=" O SER F 65 " (cutoff:3.500A) removed outlier: 11.744A pdb=" N SER F 65 " --> pdb=" O VAL F 28 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.602A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'F' and resid 10 through 12 1238 hydrogen bonds defined for protein. 3303 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: 15.35 Time building geometry restraints manager: 11.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.32: 6867 1.32 - 1.47: 10119 1.47 - 1.62: 11617 1.62 - 1.78: 53 1.78 - 1.93: 122 Bond restraints: 28778 Sorted by residual: bond pdb=" CB LEU B 828 " pdb=" CG LEU B 828 " ideal model delta sigma weight residual 1.530 1.680 -0.150 2.00e-02 2.50e+03 5.60e+01 bond pdb=" NE ARG C 466 " pdb=" CZ ARG C 466 " ideal model delta sigma weight residual 1.326 1.401 -0.075 1.10e-02 8.26e+03 4.69e+01 bond pdb=" CZ2 TRP A 152 " pdb=" CH2 TRP A 152 " ideal model delta sigma weight residual 1.368 1.495 -0.127 1.90e-02 2.77e+03 4.46e+01 bond pdb=" CB TYR C1067 " pdb=" CG TYR C1067 " ideal model delta sigma weight residual 1.512 1.365 0.147 2.20e-02 2.07e+03 4.45e+01 bond pdb=" CB TYR F 49 " pdb=" CG TYR F 49 " ideal model delta sigma weight residual 1.512 1.371 0.141 2.20e-02 2.07e+03 4.12e+01 ... (remaining 28773 not shown) Histogram of bond angle deviations from ideal: 85.60 - 103.04: 386 103.04 - 120.47: 28448 120.47 - 137.91: 10305 137.91 - 155.34: 1 155.34 - 172.78: 4 Bond angle restraints: 39144 Sorted by residual: angle pdb=" N SER F 52 " pdb=" CA SER F 52 " pdb=" C SER F 52 " ideal model delta sigma weight residual 112.72 146.50 -33.78 1.28e+00 6.10e-01 6.96e+02 angle pdb=" N2 NAG A1304 " pdb=" C7 NAG A1304 " pdb=" O7 NAG A1304 " ideal model delta sigma weight residual 123.46 172.78 -49.32 3.00e+00 1.11e-01 2.70e+02 angle pdb=" C8 NAG A1304 " pdb=" C7 NAG A1304 " pdb=" O7 NAG A1304 " ideal model delta sigma weight residual 121.48 85.60 35.88 3.00e+00 1.11e-01 1.43e+02 angle pdb=" C2 NAG A1304 " pdb=" N2 NAG A1304 " pdb=" C7 NAG A1304 " ideal model delta sigma weight residual 124.56 159.58 -35.02 3.00e+00 1.11e-01 1.36e+02 angle pdb=" C2 NAG A1308 " pdb=" N2 NAG A1308 " pdb=" C7 NAG A1308 " ideal model delta sigma weight residual 124.56 159.41 -34.85 3.00e+00 1.11e-01 1.35e+02 ... (remaining 39139 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 17050 17.95 - 35.90: 434 35.90 - 53.85: 145 53.85 - 71.81: 67 71.81 - 89.76: 23 Dihedral angle restraints: 17719 sinusoidal: 7453 harmonic: 10266 Sorted by residual: dihedral pdb=" CB CYS A 883 " pdb=" SG CYS A 883 " pdb=" SG CYS B 705 " pdb=" CB CYS B 705 " ideal model delta sinusoidal sigma weight residual 93.00 -177.62 -89.38 1 1.00e+01 1.00e-02 9.50e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -162.18 76.18 1 1.00e+01 1.00e-02 7.31e+01 dihedral pdb=" CB CYS C 538 " pdb=" SG CYS C 538 " pdb=" SG CYS C 590 " pdb=" CB CYS C 590 " ideal model delta sinusoidal sigma weight residual -86.00 -141.84 55.84 1 1.00e+01 1.00e-02 4.21e+01 ... (remaining 17716 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.222: 4314 0.222 - 0.444: 240 0.444 - 0.666: 14 0.666 - 0.887: 0 0.887 - 1.109: 1 Chirality restraints: 4569 Sorted by residual: chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.44e+02 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 9.94e+01 chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 8.92e+01 ... (remaining 4566 not shown) Planarity restraints: 5032 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C1074 " -0.101 2.00e-02 2.50e+03 1.05e-01 1.37e+02 pdb=" CG ASN C1074 " 0.048 2.00e-02 2.50e+03 pdb=" OD1 ASN C1074 " 0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN C1074 " 0.161 2.00e-02 2.50e+03 pdb=" C1 NAG C1308 " -0.126 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 616 " 0.073 2.00e-02 2.50e+03 7.75e-02 7.51e+01 pdb=" CG ASN C 616 " -0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN C 616 " -0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN C 616 " -0.122 2.00e-02 2.50e+03 pdb=" C1 NAG C1304 " 0.094 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A1074 " 0.066 2.00e-02 2.50e+03 6.99e-02 6.10e+01 pdb=" CG ASN A1074 " -0.029 2.00e-02 2.50e+03 pdb=" OD1 ASN A1074 " -0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN A1074 " -0.109 2.00e-02 2.50e+03 pdb=" C1 NAG A1312 " 0.084 2.00e-02 2.50e+03 ... (remaining 5029 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.62: 351 2.62 - 3.19: 25255 3.19 - 3.76: 44048 3.76 - 4.33: 62512 4.33 - 4.90: 100128 Nonbonded interactions: 232294 Sorted by model distance: nonbonded pdb=" NZ LYS B 529 " pdb=" O ILE E 53 " model vdw 2.056 2.520 nonbonded pdb=" O ILE A 235 " pdb=" CG2 ILE A 235 " model vdw 2.263 3.460 nonbonded pdb=" N HIS A 519 " pdb=" O HIS A 519 " model vdw 2.330 2.496 nonbonded pdb=" C SER F 52 " pdb=" OG SER F 52 " model vdw 2.350 2.616 nonbonded pdb=" NZ LYS A 557 " pdb=" OD2 ASP A 574 " model vdw 2.380 2.520 ... (remaining 232289 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 17 through 66 or resid 79 through 143 or resid 153 through \ 175 or resid 185 through 255 or resid 257 through 260 or resid 263 through 337 \ or resid 341 through 396 or resid 400 through 415 or resid 418 through 426 or re \ sid 429 through 441 or resid 450 through 454 or resid 462 through 466 or resid 4 \ 92 through 515 or resid 522 through 618 or resid 641 through 827 or resid 851 th \ rough 1147 or resid 1301 through 1305)) selection = (chain 'B' and (resid 17 through 66 or resid 79 through 143 or resid 153 through \ 175 or resid 185 through 260 or resid 263 through 337 or resid 341 through 396 \ or resid 400 through 415 or resid 418 through 426 or resid 429 through 441 or re \ sid 450 through 454 or resid 462 through 466 or resid 492 through 515 or resid 5 \ 22 through 827 or resid 851 through 1147 or resid 1301 through 1305)) selection = (chain 'C' and (resid 17 through 255 or resid 257 through 441 or resid 450 throu \ gh 618 or resid 641 through 827 or resid 851 through 1147 or resid 1301 through \ 1305)) } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'J' selection = chain 'K' selection = chain 'M' } ncs_group { reference = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'F' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.840 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: 0.030 Extract box with map and model: 19.930 Check model and map are aligned: 0.460 Set scattering table: 0.280 Process input model: 77.810 Find NCS groups from input model: 2.420 Set up NCS constraints: 0.210 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 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 0.153 28778 Z= 1.409 Angle : 1.849 49.321 39144 Z= 1.215 Chirality : 0.116 1.109 4569 Planarity : 0.008 0.089 4997 Dihedral : 10.457 89.756 10962 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 1.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.32 % Allowed : 0.68 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % 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: 0.61 (0.13), residues: 3461 helix: 0.67 (0.18), residues: 677 sheet: 1.02 (0.18), residues: 814 loop : 0.13 (0.13), residues: 1970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.010 TRP B 258 HIS 0.007 0.002 HIS A 66 PHE 0.036 0.006 PHE B 58 TYR 0.077 0.008 TYR C 37 ARG 0.011 0.001 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 3090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 386 time to evaluate : 3.090 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: H 18 VAL cc_start: 0.9100 (p) cc_final: 0.8853 (m) REVERT: H 48 MET cc_start: 0.8429 (mtp) cc_final: 0.7413 (mtm) REVERT: H 75 THR cc_start: 0.8258 (p) cc_final: 0.8004 (p) REVERT: H 82 LEU cc_start: 0.7411 (tp) cc_final: 0.7015 (tp) REVERT: H 86 ASP cc_start: 0.7823 (m-30) cc_final: 0.7434 (m-30) REVERT: H 99 ASP cc_start: 0.6598 (t0) cc_final: 0.6240 (p0) REVERT: L 5 THR cc_start: 0.9193 (m) cc_final: 0.8986 (p) REVERT: L 24 ARG cc_start: 0.9218 (ttm170) cc_final: 0.9008 (tmm160) REVERT: L 35 TRP cc_start: 0.7041 (m100) cc_final: 0.5978 (m100) REVERT: L 42 GLN cc_start: 0.8595 (mm-40) cc_final: 0.8299 (mp10) REVERT: L 58 ILE cc_start: 0.8083 (tt) cc_final: 0.7146 (tt) REVERT: L 95 LEU cc_start: 0.7817 (tp) cc_final: 0.7595 (tp) REVERT: L 102 THR cc_start: 0.7465 (p) cc_final: 0.7187 (p) REVERT: C 33 THR cc_start: 0.7788 (p) cc_final: 0.7438 (t) REVERT: C 153 MET cc_start: 0.4619 (ptt) cc_final: 0.2890 (pmm) REVERT: C 988 GLU cc_start: 0.8592 (tp30) cc_final: 0.8186 (tp30) REVERT: C 1005 GLN cc_start: 0.8507 (tp40) cc_final: 0.7961 (tm-30) REVERT: B 79 PHE cc_start: 0.4446 (m-10) cc_final: 0.4224 (m-80) REVERT: E 39 GLN cc_start: 0.5577 (tt0) cc_final: 0.5273 (tt0) REVERT: E 75 THR cc_start: 0.8642 (p) cc_final: 0.8332 (m) REVERT: E 79 PHE cc_start: 0.8138 (m-80) cc_final: 0.7612 (m-10) REVERT: E 94 LEU cc_start: 0.6860 (mt) cc_final: 0.6643 (mp) REVERT: E 99 ASP cc_start: 0.6558 (t0) cc_final: 0.6274 (t0) REVERT: F 47 LEU cc_start: 0.9159 (mt) cc_final: 0.8909 (mp) outliers start: 10 outliers final: 3 residues processed: 395 average time/residue: 0.4692 time to fit residues: 279.4970 Evaluate side-chains 219 residues out of total 3090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 216 time to evaluate : 3.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain F residue 46 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 295 optimal weight: 6.9990 chunk 265 optimal weight: 3.9990 chunk 147 optimal weight: 5.9990 chunk 90 optimal weight: 0.5980 chunk 178 optimal weight: 1.9990 chunk 141 optimal weight: 5.9990 chunk 274 optimal weight: 0.9980 chunk 106 optimal weight: 5.9990 chunk 166 optimal weight: 7.9990 chunk 204 optimal weight: 0.7980 chunk 317 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 61 GLN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN L 90 HIS A 134 GLN A 188 ASN A1002 GLN C 49 HIS B 239 GLN B 370 ASN B 655 HIS ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 90 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 28778 Z= 0.244 Angle : 0.771 38.361 39144 Z= 0.387 Chirality : 0.048 0.289 4569 Planarity : 0.005 0.050 4997 Dihedral : 6.095 56.021 4660 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.28 % Favored : 97.69 % Rotamer: Outliers : 1.10 % Allowed : 4.43 % Favored : 94.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % 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: 0.72 (0.14), residues: 3461 helix: 2.47 (0.20), residues: 651 sheet: 0.74 (0.17), residues: 873 loop : -0.32 (0.13), residues: 1937 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP E 98 HIS 0.009 0.001 HIS L 90 PHE 0.036 0.002 PHE F 83 TYR 0.027 0.002 TYR L 91 ARG 0.007 0.001 ARG E 95 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 3090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 271 time to evaluate : 4.105 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: H 66 ARG cc_start: 0.7348 (mtm110) cc_final: 0.7073 (mtm-85) REVERT: H 72 ASP cc_start: 0.8148 (t0) cc_final: 0.7697 (t0) REVERT: H 75 THR cc_start: 0.8422 (p) cc_final: 0.8018 (p) REVERT: H 80 MET cc_start: 0.7756 (tmm) cc_final: 0.7477 (tmm) REVERT: H 82 LEU cc_start: 0.8772 (mt) cc_final: 0.8179 (mp) REVERT: L 35 TRP cc_start: 0.6854 (m100) cc_final: 0.6109 (m100) REVERT: L 37 GLN cc_start: 0.8101 (tm-30) cc_final: 0.7807 (tp40) REVERT: L 42 GLN cc_start: 0.8619 (mm-40) cc_final: 0.8267 (mp10) REVERT: A 544 ASN cc_start: 0.8314 (t0) cc_final: 0.7689 (t0) REVERT: C 88 ASP cc_start: 0.8654 (m-30) cc_final: 0.8347 (p0) REVERT: C 153 MET cc_start: 0.4985 (ptt) cc_final: 0.3198 (pmm) REVERT: C 869 MET cc_start: 0.8760 (mtt) cc_final: 0.8536 (mtt) REVERT: B 79 PHE cc_start: 0.4426 (m-80) cc_final: 0.4154 (m-80) REVERT: B 376 THR cc_start: 0.8752 (m) cc_final: 0.8258 (p) REVERT: B 1005 GLN cc_start: 0.7906 (tm-30) cc_final: 0.7472 (tm-30) REVERT: E 12 LYS cc_start: 0.7609 (mmtt) cc_final: 0.7364 (mmtt) REVERT: E 23 LYS cc_start: 0.7101 (tptp) cc_final: 0.6900 (tptp) REVERT: E 46 GLU cc_start: 0.7873 (tp30) cc_final: 0.7626 (tp30) REVERT: F 75 ILE cc_start: 0.7701 (OUTLIER) cc_final: 0.7480 (mm) REVERT: F 79 GLU cc_start: 0.7142 (mm-30) cc_final: 0.6919 (mp0) outliers start: 34 outliers final: 19 residues processed: 291 average time/residue: 0.4550 time to fit residues: 204.7161 Evaluate side-chains 227 residues out of total 3090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 207 time to evaluate : 2.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 87 TYR Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 104 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 176 optimal weight: 4.9990 chunk 98 optimal weight: 0.0670 chunk 264 optimal weight: 20.0000 chunk 216 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 chunk 318 optimal weight: 4.9990 chunk 343 optimal weight: 5.9990 chunk 283 optimal weight: 1.9990 chunk 315 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 255 optimal weight: 8.9990 overall best weight: 1.1924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN H 39 GLN ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN A 125 ASN C 965 GLN C1005 GLN B 370 ASN B 690 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 28778 Z= 0.218 Angle : 0.617 11.788 39144 Z= 0.323 Chirality : 0.045 0.285 4569 Planarity : 0.004 0.051 4997 Dihedral : 5.655 58.387 4660 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.89 % Favored : 97.02 % Rotamer: Outliers : 1.33 % Allowed : 5.73 % Favored : 92.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % 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: 0.68 (0.14), residues: 3461 helix: 2.77 (0.20), residues: 656 sheet: 0.54 (0.17), residues: 903 loop : -0.41 (0.13), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 98 HIS 0.003 0.001 HIS C1058 PHE 0.024 0.002 PHE A 888 TYR 0.022 0.001 TYR E 102 ARG 0.008 0.001 ARG E 66 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 3090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 225 time to evaluate : 3.042 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: H 3 GLN cc_start: 0.7512 (mp-120) cc_final: 0.7265 (mp-120) REVERT: H 80 MET cc_start: 0.7984 (tmm) cc_final: 0.7427 (tmm) REVERT: H 91 TYR cc_start: 0.8074 (m-80) cc_final: 0.7308 (m-80) REVERT: L 35 TRP cc_start: 0.6889 (m100) cc_final: 0.5857 (m100) REVERT: A 519 HIS cc_start: 0.7072 (t-90) cc_final: 0.6716 (t-90) REVERT: A 544 ASN cc_start: 0.8401 (t0) cc_final: 0.7956 (t0) REVERT: C 88 ASP cc_start: 0.8681 (m-30) cc_final: 0.8437 (p0) REVERT: C 153 MET cc_start: 0.4828 (ptt) cc_final: 0.2978 (pmm) REVERT: C 869 MET cc_start: 0.8775 (mtt) cc_final: 0.8543 (mtt) REVERT: C 988 GLU cc_start: 0.8194 (mp0) cc_final: 0.7956 (mp0) REVERT: B 79 PHE cc_start: 0.4581 (m-80) cc_final: 0.4331 (m-80) REVERT: B 173 GLN cc_start: 0.8842 (mm-40) cc_final: 0.8626 (tp40) REVERT: B 376 THR cc_start: 0.8721 (m) cc_final: 0.8296 (p) REVERT: B 740 MET cc_start: 0.8399 (tpt) cc_final: 0.8126 (tpp) REVERT: B 1005 GLN cc_start: 0.7980 (tm-30) cc_final: 0.7498 (tm-30) REVERT: E 12 LYS cc_start: 0.7636 (mmtt) cc_final: 0.7429 (mmtt) REVERT: F 47 LEU cc_start: 0.9282 (mt) cc_final: 0.8980 (mp) REVERT: F 54 ARG cc_start: 0.7486 (ptp90) cc_final: 0.7061 (ptp-110) REVERT: F 79 GLU cc_start: 0.7069 (mm-30) cc_final: 0.6755 (mp0) outliers start: 41 outliers final: 26 residues processed: 250 average time/residue: 0.4436 time to fit residues: 173.0590 Evaluate side-chains 223 residues out of total 3090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 197 time to evaluate : 3.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 99 ASP Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 87 TYR Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 104 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 314 optimal weight: 4.9990 chunk 239 optimal weight: 3.9990 chunk 165 optimal weight: 30.0000 chunk 35 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 213 optimal weight: 3.9990 chunk 319 optimal weight: 0.8980 chunk 338 optimal weight: 9.9990 chunk 166 optimal weight: 3.9990 chunk 302 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 GLN A1048 HIS C 218 GLN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 64 GLN ** E 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 28778 Z= 0.309 Angle : 0.633 12.980 39144 Z= 0.329 Chirality : 0.046 0.289 4569 Planarity : 0.004 0.078 4997 Dihedral : 5.517 54.734 4660 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.18 % Favored : 96.74 % Rotamer: Outliers : 1.65 % Allowed : 6.21 % Favored : 92.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % 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: 0.46 (0.14), residues: 3461 helix: 2.74 (0.20), residues: 656 sheet: 0.45 (0.17), residues: 917 loop : -0.67 (0.14), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 96 HIS 0.006 0.001 HIS C1058 PHE 0.023 0.002 PHE A 888 TYR 0.026 0.002 TYR E 102 ARG 0.009 0.001 ARG E 66 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 3090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 215 time to evaluate : 3.420 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: H 12 LYS cc_start: 0.8137 (mmtt) cc_final: 0.7804 (mptt) REVERT: H 80 MET cc_start: 0.8198 (tmm) cc_final: 0.7826 (tmm) REVERT: H 95 ARG cc_start: 0.8108 (ttp80) cc_final: 0.7609 (ptm-80) REVERT: L 35 TRP cc_start: 0.6844 (m100) cc_final: 0.6620 (m100) REVERT: A 519 HIS cc_start: 0.7321 (t-90) cc_final: 0.6863 (t-90) REVERT: C 88 ASP cc_start: 0.8737 (m-30) cc_final: 0.8412 (p0) REVERT: C 153 MET cc_start: 0.5166 (ptt) cc_final: 0.3089 (pmm) REVERT: B 79 PHE cc_start: 0.4720 (m-80) cc_final: 0.4497 (m-80) REVERT: B 118 LEU cc_start: 0.8883 (tt) cc_final: 0.8398 (mm) REVERT: B 376 THR cc_start: 0.8802 (m) cc_final: 0.8389 (p) REVERT: B 380 TYR cc_start: 0.8715 (m-80) cc_final: 0.8387 (m-10) REVERT: B 740 MET cc_start: 0.8450 (tpt) cc_final: 0.8197 (tpp) REVERT: B 1005 GLN cc_start: 0.8103 (tm-30) cc_final: 0.7609 (tm-30) REVERT: E 12 LYS cc_start: 0.7658 (mmtt) cc_final: 0.7364 (mmtt) REVERT: E 80 MET cc_start: 0.8157 (tpt) cc_final: 0.7704 (tpt) REVERT: E 83 ARG cc_start: 0.7903 (ptp90) cc_final: 0.7680 (ptp-170) REVERT: F 45 ARG cc_start: 0.7451 (mtt90) cc_final: 0.7201 (mtt90) REVERT: F 47 LEU cc_start: 0.9215 (mt) cc_final: 0.8949 (mp) REVERT: F 54 ARG cc_start: 0.7643 (ptp90) cc_final: 0.7221 (ptp-110) REVERT: F 62 PHE cc_start: 0.8472 (m-80) cc_final: 0.8041 (m-80) outliers start: 51 outliers final: 33 residues processed: 252 average time/residue: 0.4190 time to fit residues: 167.4026 Evaluate side-chains 223 residues out of total 3090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 190 time to evaluate : 3.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 99 ASP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 95 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 281 optimal weight: 4.9990 chunk 192 optimal weight: 0.2980 chunk 4 optimal weight: 6.9990 chunk 251 optimal weight: 2.9990 chunk 139 optimal weight: 0.9990 chunk 288 optimal weight: 3.9990 chunk 233 optimal weight: 0.0970 chunk 0 optimal weight: 20.0000 chunk 172 optimal weight: 9.9990 chunk 303 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 ASN C1005 GLN ** E 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 28778 Z= 0.221 Angle : 0.581 12.891 39144 Z= 0.302 Chirality : 0.044 0.290 4569 Planarity : 0.004 0.045 4997 Dihedral : 5.261 55.444 4658 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.29 % Favored : 96.62 % Rotamer: Outliers : 1.52 % Allowed : 7.02 % Favored : 91.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % 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: 0.49 (0.14), residues: 3461 helix: 2.91 (0.20), residues: 649 sheet: 0.53 (0.17), residues: 889 loop : -0.71 (0.14), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 96 HIS 0.004 0.001 HIS C1058 PHE 0.022 0.002 PHE H 29 TYR 0.017 0.001 TYR B1067 ARG 0.007 0.000 ARG F 18 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 3090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 206 time to evaluate : 3.473 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: H 12 LYS cc_start: 0.8142 (mmtt) cc_final: 0.7850 (mptt) REVERT: H 80 MET cc_start: 0.8180 (tmm) cc_final: 0.7930 (tmm) REVERT: H 91 TYR cc_start: 0.8238 (m-80) cc_final: 0.7676 (m-80) REVERT: H 95 ARG cc_start: 0.7951 (ttp80) cc_final: 0.7617 (ptm-80) REVERT: L 91 TYR cc_start: 0.5439 (t80) cc_final: 0.4692 (t80) REVERT: A 519 HIS cc_start: 0.7392 (t-90) cc_final: 0.7044 (t-90) REVERT: C 153 MET cc_start: 0.5200 (ptt) cc_final: 0.3045 (pmm) REVERT: B 118 LEU cc_start: 0.8993 (tt) cc_final: 0.8500 (mm) REVERT: B 376 THR cc_start: 0.8805 (m) cc_final: 0.8413 (p) REVERT: B 380 TYR cc_start: 0.8696 (m-80) cc_final: 0.8373 (m-80) REVERT: B 740 MET cc_start: 0.8527 (tpt) cc_final: 0.8316 (tpp) REVERT: B 1005 GLN cc_start: 0.8075 (tm-30) cc_final: 0.7553 (tm-30) REVERT: E 12 LYS cc_start: 0.7742 (mmtt) cc_final: 0.7483 (mmtt) REVERT: E 52 ILE cc_start: 0.7927 (mt) cc_final: 0.7638 (tp) REVERT: F 47 LEU cc_start: 0.9229 (mt) cc_final: 0.8905 (mp) outliers start: 47 outliers final: 28 residues processed: 239 average time/residue: 0.4386 time to fit residues: 165.1063 Evaluate side-chains 220 residues out of total 3090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 192 time to evaluate : 3.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 87 TYR Chi-restraints excluded: chain F residue 95 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 113 optimal weight: 0.5980 chunk 304 optimal weight: 0.5980 chunk 66 optimal weight: 8.9990 chunk 198 optimal weight: 0.5980 chunk 83 optimal weight: 4.9990 chunk 338 optimal weight: 9.9990 chunk 281 optimal weight: 6.9990 chunk 156 optimal weight: 0.9990 chunk 28 optimal weight: 7.9990 chunk 112 optimal weight: 2.9990 chunk 177 optimal weight: 5.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 ASN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN A 658 ASN A 926 GLN C1005 GLN B 955 ASN ** E 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.3780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28778 Z= 0.192 Angle : 0.561 14.434 39144 Z= 0.291 Chirality : 0.044 0.292 4569 Planarity : 0.004 0.047 4997 Dihedral : 5.105 55.311 4658 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.58 % Favored : 96.33 % Rotamer: Outliers : 1.29 % Allowed : 7.48 % Favored : 91.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % 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: 0.49 (0.14), residues: 3461 helix: 2.99 (0.20), residues: 647 sheet: 0.58 (0.17), residues: 898 loop : -0.77 (0.14), residues: 1916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 96 HIS 0.003 0.001 HIS C1058 PHE 0.030 0.001 PHE H 29 TYR 0.017 0.001 TYR B1067 ARG 0.006 0.000 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 3090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 215 time to evaluate : 3.380 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: H 12 LYS cc_start: 0.8158 (mmtt) cc_final: 0.7865 (mptt) REVERT: H 39 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.8099 (tp40) REVERT: H 80 MET cc_start: 0.8121 (tmm) cc_final: 0.7749 (tmm) REVERT: H 83 ARG cc_start: 0.7509 (mtm110) cc_final: 0.7210 (mtm180) REVERT: H 95 ARG cc_start: 0.8055 (ttp80) cc_final: 0.7658 (ptm-80) REVERT: L 91 TYR cc_start: 0.5642 (t80) cc_final: 0.5375 (t80) REVERT: L 100 GLN cc_start: 0.7645 (mp10) cc_final: 0.7413 (mp10) REVERT: A 519 HIS cc_start: 0.7481 (t-90) cc_final: 0.7119 (t-90) REVERT: C 153 MET cc_start: 0.5198 (ptt) cc_final: 0.3292 (pmm) REVERT: C 985 ASP cc_start: 0.7831 (p0) cc_final: 0.6476 (p0) REVERT: B 18 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.7855 (mp) REVERT: B 220 PHE cc_start: 0.6120 (t80) cc_final: 0.5817 (t80) REVERT: B 376 THR cc_start: 0.8771 (m) cc_final: 0.8399 (p) REVERT: B 740 MET cc_start: 0.8613 (tpt) cc_final: 0.8399 (tpp) REVERT: B 902 MET cc_start: 0.8696 (tpp) cc_final: 0.8470 (tpp) REVERT: B 1005 GLN cc_start: 0.8068 (tm-30) cc_final: 0.7512 (tm-30) REVERT: E 12 LYS cc_start: 0.7777 (mmtt) cc_final: 0.7505 (mmtt) REVERT: E 48 MET cc_start: 0.8580 (ttm) cc_final: 0.8273 (ttm) REVERT: E 52 ILE cc_start: 0.8108 (mt) cc_final: 0.7889 (tp) REVERT: E 80 MET cc_start: 0.7833 (tpt) cc_final: 0.7589 (tpt) REVERT: E 98 TRP cc_start: 0.7031 (m100) cc_final: 0.6782 (m100) REVERT: F 36 TYR cc_start: 0.8328 (m-80) cc_final: 0.8070 (m-80) REVERT: F 47 LEU cc_start: 0.9184 (mt) cc_final: 0.8956 (mp) outliers start: 40 outliers final: 30 residues processed: 239 average time/residue: 0.4264 time to fit residues: 162.2812 Evaluate side-chains 226 residues out of total 3090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 194 time to evaluate : 3.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 64 GLN Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 103 LYS Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 87 TYR Chi-restraints excluded: chain F residue 95 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 326 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 192 optimal weight: 0.9980 chunk 247 optimal weight: 7.9990 chunk 191 optimal weight: 3.9990 chunk 285 optimal weight: 1.9990 chunk 189 optimal weight: 5.9990 chunk 337 optimal weight: 4.9990 chunk 211 optimal weight: 1.9990 chunk 205 optimal weight: 0.9980 chunk 155 optimal weight: 20.0000 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 28778 Z= 0.285 Angle : 0.595 14.739 39144 Z= 0.307 Chirality : 0.045 0.283 4569 Planarity : 0.004 0.045 4997 Dihedral : 5.161 56.913 4658 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.84 % Favored : 96.04 % Rotamer: Outliers : 1.20 % Allowed : 8.19 % Favored : 90.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % 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 (0.14), residues: 3461 helix: 2.92 (0.20), residues: 647 sheet: 0.45 (0.17), residues: 919 loop : -0.84 (0.14), residues: 1895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 353 HIS 0.005 0.001 HIS C1058 PHE 0.033 0.002 PHE H 29 TYR 0.017 0.001 TYR A1067 ARG 0.007 0.000 ARG E 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 3090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 196 time to evaluate : 3.434 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: H 12 LYS cc_start: 0.8178 (mmtt) cc_final: 0.7895 (mptt) REVERT: H 39 GLN cc_start: 0.8334 (OUTLIER) cc_final: 0.8048 (tp40) REVERT: H 80 MET cc_start: 0.8142 (tmm) cc_final: 0.7787 (tmm) REVERT: H 83 ARG cc_start: 0.7534 (mtm110) cc_final: 0.7228 (mtm180) REVERT: H 95 ARG cc_start: 0.8057 (ttp80) cc_final: 0.7375 (ptm-80) REVERT: L 91 TYR cc_start: 0.5654 (t80) cc_final: 0.4824 (t80) REVERT: A 519 HIS cc_start: 0.7558 (t-90) cc_final: 0.7204 (t-90) REVERT: C 153 MET cc_start: 0.5073 (ptt) cc_final: 0.3236 (pmm) REVERT: B 376 THR cc_start: 0.8681 (m) cc_final: 0.8354 (p) REVERT: B 740 MET cc_start: 0.8594 (tpt) cc_final: 0.8388 (tpp) REVERT: B 902 MET cc_start: 0.8722 (tpp) cc_final: 0.8508 (tpp) REVERT: B 1005 GLN cc_start: 0.8122 (tm-30) cc_final: 0.7573 (tm-30) REVERT: E 12 LYS cc_start: 0.7923 (mmtt) cc_final: 0.7604 (mmtt) REVERT: E 52 ILE cc_start: 0.8121 (mt) cc_final: 0.7902 (tp) REVERT: E 66 ARG cc_start: 0.8035 (tmm-80) cc_final: 0.7816 (ttp80) REVERT: E 82 LEU cc_start: 0.6807 (mt) cc_final: 0.6485 (mt) REVERT: F 47 LEU cc_start: 0.9308 (mt) cc_final: 0.9058 (mp) outliers start: 37 outliers final: 30 residues processed: 220 average time/residue: 0.4399 time to fit residues: 153.2029 Evaluate side-chains 218 residues out of total 3090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 187 time to evaluate : 3.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 103 LYS Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 152 TRP Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 87 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 208 optimal weight: 3.9990 chunk 134 optimal weight: 9.9990 chunk 201 optimal weight: 0.5980 chunk 101 optimal weight: 0.9980 chunk 66 optimal weight: 0.4980 chunk 65 optimal weight: 10.0000 chunk 214 optimal weight: 3.9990 chunk 229 optimal weight: 5.9990 chunk 166 optimal weight: 30.0000 chunk 31 optimal weight: 3.9990 chunk 265 optimal weight: 0.0870 overall best weight: 1.2360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 ASN B 913 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.4106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 28778 Z= 0.199 Angle : 0.566 14.648 39144 Z= 0.291 Chirality : 0.044 0.290 4569 Planarity : 0.004 0.045 4997 Dihedral : 5.036 56.293 4658 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.67 % Favored : 96.21 % Rotamer: Outliers : 1.33 % Allowed : 8.19 % Favored : 90.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.14), residues: 3461 helix: 3.00 (0.20), residues: 648 sheet: 0.53 (0.17), residues: 897 loop : -0.88 (0.14), residues: 1916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 96 HIS 0.003 0.001 HIS A1064 PHE 0.031 0.001 PHE H 29 TYR 0.018 0.001 TYR B 674 ARG 0.007 0.000 ARG A1019 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 3090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 191 time to evaluate : 3.207 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: H 12 LYS cc_start: 0.8192 (mmtt) cc_final: 0.7900 (mptt) REVERT: H 39 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.8028 (tp-100) REVERT: H 80 MET cc_start: 0.8226 (tmm) cc_final: 0.7821 (tmm) REVERT: H 83 ARG cc_start: 0.7523 (mtm110) cc_final: 0.7219 (mtm180) REVERT: H 95 ARG cc_start: 0.8102 (ttp80) cc_final: 0.7743 (ttp80) REVERT: L 91 TYR cc_start: 0.5721 (t80) cc_final: 0.5276 (t80) REVERT: A 516 GLU cc_start: 0.6174 (tm-30) cc_final: 0.5774 (tm-30) REVERT: A 519 HIS cc_start: 0.7580 (t-90) cc_final: 0.6982 (t-90) REVERT: C 153 MET cc_start: 0.5051 (ptt) cc_final: 0.3258 (pmm) REVERT: B 900 MET cc_start: 0.8742 (mtp) cc_final: 0.8535 (mtp) REVERT: B 1005 GLN cc_start: 0.8099 (tm-30) cc_final: 0.7552 (tm-30) REVERT: E 12 LYS cc_start: 0.7951 (mmtt) cc_final: 0.7632 (mmtt) REVERT: E 82 LEU cc_start: 0.6930 (mt) cc_final: 0.6241 (mt) REVERT: E 83 ARG cc_start: 0.8380 (mtm110) cc_final: 0.8081 (ptm-80) REVERT: F 47 LEU cc_start: 0.9352 (mt) cc_final: 0.9071 (mp) REVERT: F 54 ARG cc_start: 0.7491 (ptp90) cc_final: 0.7045 (ptp-110) REVERT: F 62 PHE cc_start: 0.8307 (m-80) cc_final: 0.7894 (m-80) outliers start: 41 outliers final: 32 residues processed: 214 average time/residue: 0.4403 time to fit residues: 148.2069 Evaluate side-chains 217 residues out of total 3090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 184 time to evaluate : 2.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 64 GLN Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 103 LYS Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain F residue 49 TYR Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 87 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 306 optimal weight: 0.9980 chunk 323 optimal weight: 1.9990 chunk 294 optimal weight: 0.8980 chunk 314 optimal weight: 3.9990 chunk 189 optimal weight: 2.9990 chunk 136 optimal weight: 10.0000 chunk 246 optimal weight: 8.9990 chunk 96 optimal weight: 0.6980 chunk 284 optimal weight: 3.9990 chunk 297 optimal weight: 0.9990 chunk 313 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.4242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 28778 Z= 0.167 Angle : 0.552 15.524 39144 Z= 0.283 Chirality : 0.044 0.293 4569 Planarity : 0.004 0.042 4997 Dihedral : 4.887 55.369 4658 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.73 % Favored : 96.16 % Rotamer: Outliers : 1.26 % Allowed : 8.28 % Favored : 90.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % 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: 0.43 (0.14), residues: 3461 helix: 3.06 (0.20), residues: 655 sheet: 0.53 (0.17), residues: 897 loop : -0.87 (0.14), residues: 1909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 353 HIS 0.003 0.001 HIS F 90 PHE 0.033 0.001 PHE H 29 TYR 0.016 0.001 TYR B1067 ARG 0.006 0.000 ARG E 83 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 3090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 198 time to evaluate : 3.199 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: H 12 LYS cc_start: 0.8234 (mmtt) cc_final: 0.7955 (mptt) REVERT: H 39 GLN cc_start: 0.8283 (OUTLIER) cc_final: 0.8013 (tp-100) REVERT: H 83 ARG cc_start: 0.7581 (mtm110) cc_final: 0.7264 (mtm180) REVERT: H 95 ARG cc_start: 0.8116 (ttp80) cc_final: 0.7764 (ttp80) REVERT: L 91 TYR cc_start: 0.5676 (t80) cc_final: 0.5367 (t80) REVERT: A 516 GLU cc_start: 0.6145 (tm-30) cc_final: 0.5763 (tm-30) REVERT: A 519 HIS cc_start: 0.7644 (t-90) cc_final: 0.7026 (t-90) REVERT: C 153 MET cc_start: 0.4877 (ptt) cc_final: 0.3178 (pmm) REVERT: B 900 MET cc_start: 0.8696 (mtp) cc_final: 0.8474 (mtp) REVERT: B 1005 GLN cc_start: 0.8073 (tm-30) cc_final: 0.7515 (tm-30) REVERT: E 12 LYS cc_start: 0.7951 (mmtt) cc_final: 0.7626 (mmtt) REVERT: E 82 LEU cc_start: 0.7259 (mt) cc_final: 0.7005 (mt) REVERT: F 95 LEU cc_start: 0.9035 (mt) cc_final: 0.8367 (pp) outliers start: 39 outliers final: 34 residues processed: 222 average time/residue: 0.4431 time to fit residues: 154.3439 Evaluate side-chains 227 residues out of total 3090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 192 time to evaluate : 3.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 64 GLN Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 103 LYS Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 87 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 206 optimal weight: 2.9990 chunk 332 optimal weight: 8.9990 chunk 202 optimal weight: 0.0770 chunk 157 optimal weight: 30.0000 chunk 231 optimal weight: 9.9990 chunk 348 optimal weight: 10.0000 chunk 320 optimal weight: 0.7980 chunk 277 optimal weight: 0.9980 chunk 28 optimal weight: 8.9990 chunk 214 optimal weight: 3.9990 chunk 170 optimal weight: 0.9990 overall best weight: 1.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 690 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.4328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 28778 Z= 0.194 Angle : 0.572 16.028 39144 Z= 0.291 Chirality : 0.044 0.291 4569 Planarity : 0.004 0.043 4997 Dihedral : 4.869 55.541 4658 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.73 % Favored : 96.16 % Rotamer: Outliers : 1.13 % Allowed : 8.74 % Favored : 90.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % 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 (0.14), residues: 3461 helix: 3.06 (0.20), residues: 655 sheet: 0.51 (0.17), residues: 903 loop : -0.88 (0.14), residues: 1903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 96 HIS 0.003 0.001 HIS A1064 PHE 0.035 0.001 PHE H 29 TYR 0.016 0.001 TYR B1067 ARG 0.012 0.000 ARG C 995 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 3090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 191 time to evaluate : 3.725 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: H 12 LYS cc_start: 0.8227 (mmtt) cc_final: 0.7948 (mptt) REVERT: H 80 MET cc_start: 0.8268 (tmm) cc_final: 0.7701 (tmm) REVERT: H 83 ARG cc_start: 0.7605 (mtm110) cc_final: 0.7283 (mtm180) REVERT: H 91 TYR cc_start: 0.8161 (m-80) cc_final: 0.7534 (m-80) REVERT: H 95 ARG cc_start: 0.8086 (ttp80) cc_final: 0.7759 (ttp80) REVERT: L 91 TYR cc_start: 0.5672 (t80) cc_final: 0.5385 (t80) REVERT: A 516 GLU cc_start: 0.6168 (tm-30) cc_final: 0.5791 (tm-30) REVERT: A 519 HIS cc_start: 0.7685 (t-90) cc_final: 0.7049 (t-90) REVERT: C 153 MET cc_start: 0.4837 (ptt) cc_final: 0.3131 (pmm) REVERT: B 900 MET cc_start: 0.8730 (mtp) cc_final: 0.8498 (mtp) REVERT: B 1005 GLN cc_start: 0.8086 (tm-30) cc_final: 0.7528 (tm-30) REVERT: E 12 LYS cc_start: 0.7903 (mmtt) cc_final: 0.7559 (mmtt) REVERT: E 66 ARG cc_start: 0.7334 (ttp80) cc_final: 0.7075 (tmm160) REVERT: E 82 LEU cc_start: 0.7037 (mt) cc_final: 0.6760 (mt) REVERT: E 98 TRP cc_start: 0.7216 (m100) cc_final: 0.6982 (m100) REVERT: F 54 ARG cc_start: 0.7369 (ptp90) cc_final: 0.7038 (ptp-110) REVERT: F 95 LEU cc_start: 0.9064 (mt) cc_final: 0.8424 (pp) outliers start: 35 outliers final: 33 residues processed: 215 average time/residue: 0.4451 time to fit residues: 149.7647 Evaluate side-chains 217 residues out of total 3090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 184 time to evaluate : 3.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 64 GLN Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 103 LYS Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain F residue 73 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 220 optimal weight: 0.6980 chunk 295 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 256 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 278 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 285 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 51 optimal weight: 0.0970 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 ASN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN B1135 ASN E 39 GLN ** F 37 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 = 0.3838 r_free = 0.3838 target = 0.082459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.056313 restraints weight = 97733.610| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 3.52 r_work: 0.3130 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.4408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 28778 Z= 0.272 Angle : 0.603 16.738 39144 Z= 0.307 Chirality : 0.044 0.283 4569 Planarity : 0.004 0.048 4997 Dihedral : 5.008 57.297 4658 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.13 % Favored : 95.75 % Rotamer: Outliers : 1.13 % Allowed : 8.80 % Favored : 90.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.14), residues: 3461 helix: 2.91 (0.20), residues: 658 sheet: 0.40 (0.17), residues: 926 loop : -0.97 (0.14), residues: 1877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 96 HIS 0.005 0.001 HIS C1058 PHE 0.035 0.002 PHE H 29 TYR 0.034 0.001 TYR C 421 ARG 0.010 0.000 ARG E 95 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5738.29 seconds wall clock time: 105 minutes 52.14 seconds (6352.14 seconds total)