Starting phenix.real_space_refine on Fri Aug 9 13:46:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x5r_38073/08_2024/8x5r_38073.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x5r_38073/08_2024/8x5r_38073.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x5r_38073/08_2024/8x5r_38073.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x5r_38073/08_2024/8x5r_38073.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x5r_38073/08_2024/8x5r_38073.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x5r_38073/08_2024/8x5r_38073.cif" } resolution = 3.72 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= 0.002 sd= 0.052 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 111 5.16 5 C 16689 2.51 5 N 4278 2.21 5 O 5130 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ASP 40": "OD1" <-> "OD2" Residue "C PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 138": "OD1" <-> "OD2" Residue "C PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 294": "OD1" <-> "OD2" Residue "C TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 554": "OE1" <-> "OE2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 661": "OE1" <-> "OE2" Residue "C TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 775": "OD1" <-> "OD2" Residue "C ASP 867": "OD1" <-> "OD2" Residue "C PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 927": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 950": "OD1" <-> "OD2" Residue "C GLU 988": "OE1" <-> "OE2" Residue "C ASP 1041": "OD1" <-> "OD2" Residue "C ASP 1118": "OD1" <-> "OD2" Residue "C GLU 1144": "OE1" <-> "OE2" Residue "A TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 40": "OD1" <-> "OD2" Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 420": "OD1" <-> "OD2" Residue "A TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 465": "OE1" <-> "OE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 654": "OE1" <-> "OE2" Residue "A TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 661": "OE1" <-> "OE2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 780": "OE1" <-> "OE2" Residue "A TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 985": "OD1" <-> "OD2" Residue "A GLU 988": "OE1" <-> "OE2" Residue "A GLU 1017": "OE1" <-> "OE2" Residue "A ASP 1118": "OD1" <-> "OD2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 88": "OD1" <-> "OD2" Residue "B ASP 138": "OD1" <-> "OD2" Residue "B PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 294": "OD1" <-> "OD2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 406": "OE1" <-> "OE2" Residue "B TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 571": "OD1" <-> "OD2" Residue "B TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 773": "OE1" <-> "OE2" Residue "B ASP 775": "OD1" <-> "OD2" Residue "B TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 927": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 950": "OD1" <-> "OD2" Residue "B GLU 988": "OE1" <-> "OE2" Residue "B GLU 990": "OE1" <-> "OE2" Residue "B PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1092": "OE1" <-> "OE2" Residue "B PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 26208 Number of models: 1 Model: "" Number of chains: 27 Chain: "C" Number of atoms: 8442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1086, 8442 Classifications: {'peptide': 1086} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 7} Link IDs: {'PTRANS': 58, 'TRANS': 1027} Chain breaks: 3 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 3, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "A" Number of atoms: 8442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1086, 8442 Classifications: {'peptide': 1086} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 7} Link IDs: {'PTRANS': 58, 'TRANS': 1027} Chain breaks: 3 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 3, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "B" Number of atoms: 8442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1086, 8442 Classifications: {'peptide': 1086} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 7} Link IDs: {'PTRANS': 58, 'TRANS': 1027} Chain breaks: 3 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 3, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 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: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 13.28, per 1000 atoms: 0.51 Number of scatterers: 26208 At special positions: 0 Unit cell: (151, 141, 192, 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 111 16.00 O 5130 8.00 N 4278 7.00 C 16689 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 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=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " 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=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 603 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A 616 " " NAG B1301 " - " ASN B 616 " " NAG B1302 " - " ASN B 61 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 603 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 657 " " NAG B1307 " - " ASN B 709 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 603 " " NAG C1304 " - " ASN C 657 " " NAG C1305 " - " ASN C 331 " " NAG C1306 " - " ASN C 709 " " NAG C1307 " - " ASN C 616 " " NAG D 1 " - " ASN C 122 " " NAG E 1 " - " ASN C 165 " " NAG F 1 " - " ASN C 234 " " NAG G 1 " - " ASN C1098 " " NAG H 1 " - " ASN C1134 " " NAG I 1 " - " ASN C 343 " " NAG J 1 " - " ASN C 354 " " NAG K 1 " - " ASN A 122 " " NAG L 1 " - " ASN A 165 " " NAG M 1 " - " ASN A 234 " " NAG N 1 " - " ASN A 343 " " NAG O 1 " - " ASN A 354 " " NAG P 1 " - " ASN A1098 " " NAG Q 1 " - " ASN A1134 " " NAG R 1 " - " ASN B 122 " " NAG S 1 " - " ASN B 165 " " NAG T 1 " - " ASN B 234 " " NAG U 1 " - " ASN B 343 " " NAG V 1 " - " ASN B 354 " " NAG W 1 " - " ASN B1098 " " NAG X 1 " - " ASN B1134 " Time building additional restraints: 12.18 Conformation dependent library (CDL) restraints added in 4.8 seconds 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6096 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 50 sheets defined 21.7% alpha, 18.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.21 Creating SS restraints... Processing helix chain 'C' and resid 69 through 73 removed outlier: 4.010A pdb=" N THR C 73 " --> pdb=" O VAL C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 367 through 371 removed outlier: 4.030A pdb=" N ASN C 370 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 388 removed outlier: 4.457A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 407 Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 543 through 546 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.796A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 760 through 783 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 850 through 854 removed outlier: 3.683A pdb=" N LYS C 854 " --> pdb=" O ILE C 850 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 850 through 854' Processing helix chain 'C' and resid 869 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.580A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 911 through 941 removed outlier: 4.575A pdb=" N VAL C 915 " --> pdb=" O VAL C 911 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.582A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.297A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 247 removed outlier: 3.999A pdb=" N SER A 247 " --> pdb=" O LEU A 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 244 through 247' Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 367 through 371 removed outlier: 4.051A pdb=" N ASN A 370 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.826A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 783 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 869 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 911 through 941 removed outlier: 4.479A pdb=" N VAL A 915 " --> pdb=" O VAL A 911 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.604A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 983 Processing helix chain 'A' and resid 985 through 1031 removed outlier: 4.434A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE A1013 " --> pdb=" O THR A1009 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 74 removed outlier: 4.505A pdb=" N THR B 73 " --> pdb=" O VAL B 70 " (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 366 through 371 removed outlier: 3.777A pdb=" N TYR B 369 " --> pdb=" O SER B 366 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASN B 370 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 543 through 546 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.818A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 783 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 869 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 911 through 941 removed outlier: 4.513A pdb=" N VAL B 915 " --> pdb=" O VAL B 911 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.502A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.653A pdb=" N LEU B 984 " --> pdb=" O ILE B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.468A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 26 through 30 removed outlier: 7.641A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 36 through 37 removed outlier: 6.858A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 50 through 55 removed outlier: 7.492A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 166 through 172 removed outlier: 6.539A pdb=" N VAL C 130 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLU C 169 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ILE C 128 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N VAL C 171 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL C 126 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL C 120 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 311 through 318 removed outlier: 7.125A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 325 through 326 Processing sheet with id=AA7, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.184A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AA9, first strand: chain 'C' and resid 452 through 454 removed outlier: 4.308A pdb=" N TYR C 453 " --> pdb=" O GLN C 493 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLN C 493 " --> pdb=" O TYR C 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 654 through 656 removed outlier: 3.687A pdb=" N GLU C 654 " --> pdb=" O ILE C 692 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL C 656 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N THR C 696 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 701 through 702 removed outlier: 6.772A pdb=" N ALA C 701 " --> pdb=" O ILE A 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AB4, first strand: chain 'C' and resid 719 through 722 removed outlier: 3.504A pdb=" N GLU C 725 " --> pdb=" O PHE C1062 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 719 through 722 removed outlier: 7.190A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AB7, first strand: chain 'C' and resid 787 through 790 removed outlier: 5.678A pdb=" N ILE C 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 1081 through 1082 Processing sheet with id=AB9, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'A' and resid 26 through 30 removed outlier: 7.968A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER A 94 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 50 through 55 removed outlier: 3.501A pdb=" N PHE A 55 " --> pdb=" O GLN A 271 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.659A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 120 through 122 removed outlier: 3.524A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 311 through 318 removed outlier: 7.044A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 325 through 326 removed outlier: 7.466A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.943A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TRP A 436 " --> pdb=" O ARG A 509 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N THR A 430 " --> pdb=" O PHE A 515 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.432A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 452 through 454 removed outlier: 4.294A pdb=" N TYR A 453 " --> pdb=" O GLN A 493 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLN A 493 " --> pdb=" O TYR A 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'A' and resid 551 through 554 removed outlier: 5.468A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.681A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.508A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AD5, first strand: chain 'A' and resid 719 through 727 removed outlier: 3.565A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AD7, first strand: chain 'A' and resid 1081 through 1082 Processing sheet with id=AD8, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AD9, first strand: chain 'B' and resid 28 through 30 removed outlier: 7.454A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR B 204 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.931A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 169 through 170 removed outlier: 3.575A pdb=" N VAL B 120 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 311 through 317 removed outlier: 7.219A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 325 through 326 Processing sheet with id=AE5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.587A pdb=" N ALA B 397 " --> pdb=" O THR B 356 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TRP B 436 " --> pdb=" O ARG B 509 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N THR B 430 " --> pdb=" O PHE B 515 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.244A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'B' and resid 452 through 454 removed outlier: 4.319A pdb=" N TYR B 453 " --> pdb=" O GLN B 493 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLN B 493 " --> pdb=" O TYR B 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'B' and resid 551 through 554 removed outlier: 5.489A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 654 through 656 removed outlier: 3.694A pdb=" N GLU B 654 " --> pdb=" O ILE B 692 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N THR B 696 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR B 695 " --> pdb=" O CYS B 671 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AF2, first strand: chain 'B' and resid 719 through 727 removed outlier: 7.372A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AF4, first strand: chain 'B' and resid 1081 through 1082 Processing sheet with id=AF5, first strand: chain 'B' and resid 1094 through 1097 809 hydrogen bonds defined for protein. 2202 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: 10.32 Time building geometry restraints manager: 13.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8240 1.34 - 1.46: 6414 1.46 - 1.59: 12022 1.59 - 1.71: 0 1.71 - 1.83: 138 Bond restraints: 26814 Sorted by residual: bond pdb=" C1 NAG V 1 " pdb=" O5 NAG V 1 " ideal model delta sigma weight residual 1.406 1.500 -0.094 2.00e-02 2.50e+03 2.19e+01 bond pdb=" C1 NAG J 1 " pdb=" O5 NAG J 1 " ideal model delta sigma weight residual 1.406 1.498 -0.092 2.00e-02 2.50e+03 2.09e+01 bond pdb=" C1 NAG O 1 " pdb=" O5 NAG O 1 " ideal model delta sigma weight residual 1.406 1.493 -0.087 2.00e-02 2.50e+03 1.91e+01 bond pdb=" N ILE C 714 " pdb=" CA ILE C 714 " ideal model delta sigma weight residual 1.457 1.494 -0.037 9.00e-03 1.23e+04 1.70e+01 bond pdb=" N VAL C 159 " pdb=" CA VAL C 159 " ideal model delta sigma weight residual 1.457 1.494 -0.037 9.30e-03 1.16e+04 1.58e+01 ... (remaining 26809 not shown) Histogram of bond angle deviations from ideal: 93.54 - 101.72: 33 101.72 - 109.90: 4130 109.90 - 118.08: 16612 118.08 - 126.26: 15461 126.26 - 134.44: 289 Bond angle restraints: 36525 Sorted by residual: angle pdb=" N THR B 604 " pdb=" CA THR B 604 " pdb=" C THR B 604 " ideal model delta sigma weight residual 114.62 107.40 7.22 1.14e+00 7.69e-01 4.01e+01 angle pdb=" N VAL C 159 " pdb=" CA VAL C 159 " pdb=" C VAL C 159 " ideal model delta sigma weight residual 113.20 107.29 5.91 9.60e-01 1.09e+00 3.79e+01 angle pdb=" N THR A 604 " pdb=" CA THR A 604 " pdb=" C THR A 604 " ideal model delta sigma weight residual 114.62 107.96 6.66 1.14e+00 7.69e-01 3.42e+01 angle pdb=" N PHE C 855 " pdb=" CA PHE C 855 " pdb=" C PHE C 855 " ideal model delta sigma weight residual 112.25 104.47 7.78 1.36e+00 5.41e-01 3.27e+01 angle pdb=" C SER A 708 " pdb=" N ASN A 709 " pdb=" CA ASN A 709 " ideal model delta sigma weight residual 122.65 113.81 8.84 1.66e+00 3.63e-01 2.83e+01 ... (remaining 36520 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.25: 14936 23.25 - 46.50: 1383 46.50 - 69.75: 251 69.75 - 92.99: 98 92.99 - 116.24: 105 Dihedral angle restraints: 16773 sinusoidal: 7287 harmonic: 9486 Sorted by residual: dihedral pdb=" CB CYS A 617 " pdb=" SG CYS A 617 " pdb=" SG CYS A 649 " pdb=" CB CYS A 649 " ideal model delta sinusoidal sigma weight residual 93.00 171.21 -78.21 1 1.00e+01 1.00e-02 7.64e+01 dihedral pdb=" CB CYS B 662 " pdb=" SG CYS B 662 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual -86.00 -14.10 -71.90 1 1.00e+01 1.00e-02 6.62e+01 dihedral pdb=" CB CYS C 336 " pdb=" SG CYS C 336 " pdb=" SG CYS C 361 " pdb=" CB CYS C 361 " ideal model delta sinusoidal sigma weight residual 93.00 35.05 57.95 1 1.00e+01 1.00e-02 4.51e+01 ... (remaining 16770 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 4072 0.106 - 0.212: 243 0.212 - 0.318: 7 0.318 - 0.423: 7 0.423 - 0.529: 3 Chirality restraints: 4332 Sorted by residual: chirality pdb=" C1 NAG S 2 " pdb=" O4 NAG S 1 " pdb=" C2 NAG S 2 " pdb=" O5 NAG S 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-02 2.50e+03 1.60e+02 chirality pdb=" C1 NAG R 2 " pdb=" O4 NAG R 1 " pdb=" C2 NAG R 2 " pdb=" O5 NAG R 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-02 2.50e+03 5.25e+01 chirality pdb=" C1 NAG W 2 " pdb=" O4 NAG W 1 " pdb=" C2 NAG W 2 " pdb=" O5 NAG W 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.33 -0.07 2.00e-02 2.50e+03 1.12e+01 ... (remaining 4329 not shown) Planarity restraints: 4692 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1307 " 0.327 2.00e-02 2.50e+03 2.85e-01 1.02e+03 pdb=" C7 NAG B1307 " -0.075 2.00e-02 2.50e+03 pdb=" C8 NAG B1307 " 0.089 2.00e-02 2.50e+03 pdb=" N2 NAG B1307 " -0.508 2.00e-02 2.50e+03 pdb=" O7 NAG B1307 " 0.166 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1306 " -0.321 2.00e-02 2.50e+03 2.78e-01 9.63e+02 pdb=" C7 NAG C1306 " 0.077 2.00e-02 2.50e+03 pdb=" C8 NAG C1306 " -0.149 2.00e-02 2.50e+03 pdb=" N2 NAG C1306 " 0.494 2.00e-02 2.50e+03 pdb=" O7 NAG C1306 " -0.101 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG R 1 " 0.134 2.00e-02 2.50e+03 1.14e-01 1.61e+02 pdb=" C7 NAG R 1 " -0.024 2.00e-02 2.50e+03 pdb=" C8 NAG R 1 " -0.030 2.00e-02 2.50e+03 pdb=" N2 NAG R 1 " -0.185 2.00e-02 2.50e+03 pdb=" O7 NAG R 1 " 0.105 2.00e-02 2.50e+03 ... (remaining 4689 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2476 2.74 - 3.28: 27807 3.28 - 3.82: 44560 3.82 - 4.36: 51294 4.36 - 4.90: 87493 Nonbonded interactions: 213630 Sorted by model distance: nonbonded pdb=" O GLN B 580 " pdb=" O3 NAG B1305 " model vdw 2.203 3.040 nonbonded pdb=" O VAL B 608 " pdb=" OH TYR B 636 " model vdw 2.205 3.040 nonbonded pdb=" OG1 THR C 323 " pdb=" OE1 GLU C 324 " model vdw 2.208 3.040 nonbonded pdb=" NZ LYS A 386 " pdb=" O LEU B 984 " model vdw 2.213 3.120 nonbonded pdb=" O ILE B 805 " pdb=" OG SER B 816 " model vdw 2.225 3.040 ... (remaining 213625 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.350 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: 0.890 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 70.730 Find NCS groups from input model: 1.370 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 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 : 0.006 0.094 26814 Z= 0.382 Angle : 0.845 9.774 36525 Z= 0.497 Chirality : 0.056 0.529 4332 Planarity : 0.009 0.285 4650 Dihedral : 20.776 116.242 10569 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.21 % Favored : 90.26 % Rotamer: Outliers : 1.06 % Allowed : 23.58 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.14), residues: 3234 helix: 0.71 (0.21), residues: 641 sheet: -0.68 (0.20), residues: 622 loop : -2.20 (0.13), residues: 1971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 633 HIS 0.004 0.001 HIS A 207 PHE 0.042 0.002 PHE A 201 TYR 0.024 0.002 TYR C 423 ARG 0.007 0.001 ARG A1107 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 136 time to evaluate : 3.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 139 PRO cc_start: 0.8037 (OUTLIER) cc_final: 0.7055 (Cg_endo) REVERT: C 140 PHE cc_start: 0.7020 (t80) cc_final: 0.6706 (t80) REVERT: C 902 MET cc_start: 0.8824 (tpp) cc_final: 0.8616 (tpt) REVERT: A 835 LYS cc_start: 0.3154 (OUTLIER) cc_final: 0.2328 (pttm) REVERT: A 1030 SER cc_start: 0.8973 (m) cc_final: 0.8152 (m) REVERT: B 1079 PRO cc_start: 0.9141 (Cg_exo) cc_final: 0.8828 (Cg_endo) outliers start: 30 outliers final: 7 residues processed: 160 average time/residue: 0.3555 time to fit residues: 94.2915 Evaluate side-chains 115 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 106 time to evaluate : 2.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 139 PRO Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 835 LYS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 456 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 273 optimal weight: 5.9990 chunk 245 optimal weight: 7.9990 chunk 136 optimal weight: 8.9990 chunk 83 optimal weight: 2.9990 chunk 165 optimal weight: 4.9990 chunk 131 optimal weight: 9.9990 chunk 253 optimal weight: 0.0370 chunk 98 optimal weight: 0.0570 chunk 154 optimal weight: 0.0770 chunk 189 optimal weight: 0.8980 chunk 294 optimal weight: 6.9990 overall best weight: 0.8136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 321 GLN C 644 GLN C1088 HIS ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 GLN A 901 GLN B 49 HIS B 164 ASN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 409 GLN B 644 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN B1054 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 26814 Z= 0.211 Angle : 0.716 11.073 36525 Z= 0.348 Chirality : 0.049 0.335 4332 Planarity : 0.005 0.061 4650 Dihedral : 16.354 101.455 4831 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.34 % Allowed : 8.35 % Favored : 91.31 % Rotamer: Outliers : 2.77 % Allowed : 21.74 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.14), residues: 3234 helix: 1.01 (0.21), residues: 641 sheet: -0.43 (0.20), residues: 613 loop : -2.16 (0.13), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 64 HIS 0.004 0.001 HIS A1088 PHE 0.023 0.001 PHE C 238 TYR 0.019 0.002 TYR A1067 ARG 0.004 0.001 ARG B 995 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 135 time to evaluate : 2.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 115 GLN cc_start: 0.7781 (mp10) cc_final: 0.7539 (mt0) REVERT: C 140 PHE cc_start: 0.6833 (t80) cc_final: 0.6468 (t80) REVERT: C 995 ARG cc_start: 0.8821 (OUTLIER) cc_final: 0.8582 (ttm170) REVERT: C 1041 ASP cc_start: 0.8091 (t0) cc_final: 0.7391 (t0) REVERT: A 54 LEU cc_start: 0.8259 (mm) cc_final: 0.7604 (tp) REVERT: A 317 ASN cc_start: 0.7708 (m-40) cc_final: 0.7462 (m-40) REVERT: A 423 TYR cc_start: 0.5010 (t80) cc_final: 0.4659 (t80) REVERT: A 434 ILE cc_start: -0.0294 (OUTLIER) cc_final: -0.0581 (mt) REVERT: A 835 LYS cc_start: 0.3150 (OUTLIER) cc_final: 0.2337 (pttm) REVERT: A 1030 SER cc_start: 0.9190 (m) cc_final: 0.8738 (m) REVERT: A 1107 ARG cc_start: 0.7717 (mmp-170) cc_final: 0.7271 (tpt90) REVERT: B 409 GLN cc_start: 0.8349 (OUTLIER) cc_final: 0.7511 (tt0) REVERT: B 468 ILE cc_start: 0.8671 (OUTLIER) cc_final: 0.8392 (tt) REVERT: B 674 TYR cc_start: 0.8768 (OUTLIER) cc_final: 0.8429 (t80) outliers start: 78 outliers final: 28 residues processed: 204 average time/residue: 0.3477 time to fit residues: 117.6220 Evaluate side-chains 146 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 112 time to evaluate : 3.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 835 LYS Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 409 GLN Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 674 TYR Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 954 HIS Chi-restraints excluded: chain B residue 1045 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 163 optimal weight: 0.3980 chunk 91 optimal weight: 6.9990 chunk 244 optimal weight: 1.9990 chunk 200 optimal weight: 9.9990 chunk 81 optimal weight: 1.9990 chunk 294 optimal weight: 10.0000 chunk 318 optimal weight: 9.9990 chunk 262 optimal weight: 2.9990 chunk 292 optimal weight: 10.0000 chunk 100 optimal weight: 4.9990 chunk 236 optimal weight: 10.0000 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 506 GLN C 751 ASN ** C 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 81 ASN ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN B 409 GLN B 895 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1011 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 26814 Z= 0.321 Angle : 0.724 11.761 36525 Z= 0.352 Chirality : 0.049 0.304 4332 Planarity : 0.004 0.049 4650 Dihedral : 13.399 94.912 4822 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.53 % Favored : 91.16 % Rotamer: Outliers : 3.83 % Allowed : 22.16 % Favored : 74.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.14), residues: 3234 helix: 0.94 (0.21), residues: 641 sheet: -0.70 (0.21), residues: 543 loop : -2.03 (0.13), residues: 2050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 633 HIS 0.006 0.001 HIS B 245 PHE 0.021 0.002 PHE A 106 TYR 0.019 0.002 TYR B1067 ARG 0.005 0.001 ARG C 102 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 122 time to evaluate : 3.141 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: C 115 GLN cc_start: 0.7922 (mp10) cc_final: 0.7703 (mp10) REVERT: C 633 TRP cc_start: 0.4966 (p-90) cc_final: 0.4399 (p-90) REVERT: C 974 SER cc_start: 0.9261 (OUTLIER) cc_final: 0.8867 (t) REVERT: C 995 ARG cc_start: 0.8858 (OUTLIER) cc_final: 0.8549 (ttm170) REVERT: A 54 LEU cc_start: 0.8259 (mm) cc_final: 0.7233 (tp) REVERT: A 317 ASN cc_start: 0.7641 (m-40) cc_final: 0.7375 (m-40) REVERT: A 423 TYR cc_start: 0.5275 (t80) cc_final: 0.5027 (t80) REVERT: A 456 PHE cc_start: 0.8233 (m-80) cc_final: 0.7968 (m-80) REVERT: A 835 LYS cc_start: 0.3250 (OUTLIER) cc_final: 0.2427 (pttm) REVERT: B 200 TYR cc_start: 0.7840 (m-80) cc_final: 0.7487 (m-80) REVERT: B 388 ASN cc_start: 0.8250 (OUTLIER) cc_final: 0.7665 (m110) REVERT: B 409 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.7906 (tm-30) REVERT: B 916 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8592 (tt) REVERT: B 1041 ASP cc_start: 0.8520 (t70) cc_final: 0.8261 (t70) outliers start: 108 outliers final: 54 residues processed: 221 average time/residue: 0.3619 time to fit residues: 133.1561 Evaluate side-chains 169 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 109 time to evaluate : 2.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 835 LYS Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 409 GLN Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1122 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 291 optimal weight: 3.9990 chunk 221 optimal weight: 0.0870 chunk 152 optimal weight: 9.9990 chunk 32 optimal weight: 5.9990 chunk 140 optimal weight: 2.9990 chunk 197 optimal weight: 4.9990 chunk 295 optimal weight: 9.9990 chunk 313 optimal weight: 2.9990 chunk 154 optimal weight: 4.9990 chunk 280 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 overall best weight: 1.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 26814 Z= 0.266 Angle : 0.685 11.524 36525 Z= 0.331 Chirality : 0.048 0.276 4332 Planarity : 0.004 0.051 4650 Dihedral : 11.597 88.657 4822 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.53 % Favored : 91.22 % Rotamer: Outliers : 3.48 % Allowed : 22.70 % Favored : 73.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.14), residues: 3234 helix: 0.96 (0.21), residues: 651 sheet: -0.69 (0.22), residues: 527 loop : -1.99 (0.13), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 353 HIS 0.003 0.001 HIS B 519 PHE 0.023 0.001 PHE A 106 TYR 0.017 0.001 TYR A1067 ARG 0.009 0.001 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 126 time to evaluate : 3.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 115 GLN cc_start: 0.8002 (mp10) cc_final: 0.7760 (mp10) REVERT: C 974 SER cc_start: 0.9282 (OUTLIER) cc_final: 0.8850 (t) REVERT: C 995 ARG cc_start: 0.8852 (OUTLIER) cc_final: 0.8512 (ttm170) REVERT: A 317 ASN cc_start: 0.7524 (m-40) cc_final: 0.7315 (m-40) REVERT: A 464 PHE cc_start: 0.8361 (OUTLIER) cc_final: 0.7864 (m-80) REVERT: A 835 LYS cc_start: 0.3354 (OUTLIER) cc_final: 0.2456 (pttm) REVERT: A 1107 ARG cc_start: 0.7815 (mmp-170) cc_final: 0.7392 (tpt90) REVERT: B 755 GLN cc_start: 0.8845 (pp30) cc_final: 0.8579 (pp30) REVERT: B 902 MET cc_start: 0.9570 (tpt) cc_final: 0.9329 (tpt) outliers start: 98 outliers final: 57 residues processed: 216 average time/residue: 0.3421 time to fit residues: 123.0891 Evaluate side-chains 167 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 106 time to evaluate : 2.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 943 SER Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 835 LYS Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 969 LYS Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1122 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 260 optimal weight: 8.9990 chunk 177 optimal weight: 3.9990 chunk 4 optimal weight: 9.9990 chunk 233 optimal weight: 0.9990 chunk 129 optimal weight: 0.6980 chunk 267 optimal weight: 9.9990 chunk 216 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 159 optimal weight: 5.9990 chunk 281 optimal weight: 9.9990 chunk 79 optimal weight: 10.0000 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 245 HIS C 836 GLN A 52 GLN ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1054 GLN ** A1058 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.125 26814 Z= 0.482 Angle : 0.778 14.623 36525 Z= 0.383 Chirality : 0.050 0.294 4332 Planarity : 0.005 0.053 4650 Dihedral : 10.838 86.838 4822 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.52 % Favored : 90.26 % Rotamer: Outliers : 4.43 % Allowed : 23.05 % Favored : 72.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.14), residues: 3234 helix: 0.62 (0.20), residues: 664 sheet: -0.79 (0.21), residues: 527 loop : -2.09 (0.13), residues: 2043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 633 HIS 0.005 0.001 HIS C1064 PHE 0.021 0.002 PHE A 168 TYR 0.026 0.002 TYR B 636 ARG 0.005 0.001 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 113 time to evaluate : 2.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 115 GLN cc_start: 0.8038 (mp10) cc_final: 0.7807 (mp10) REVERT: C 138 ASP cc_start: 0.7721 (OUTLIER) cc_final: 0.7145 (t0) REVERT: C 241 LEU cc_start: 0.7807 (mp) cc_final: 0.7300 (mp) REVERT: C 974 SER cc_start: 0.9324 (OUTLIER) cc_final: 0.8978 (t) REVERT: A 423 TYR cc_start: 0.5276 (t80) cc_final: 0.5069 (t80) REVERT: A 464 PHE cc_start: 0.8411 (OUTLIER) cc_final: 0.8194 (m-10) REVERT: A 835 LYS cc_start: 0.3636 (OUTLIER) cc_final: 0.2663 (pttm) REVERT: A 976 VAL cc_start: 0.9228 (OUTLIER) cc_final: 0.9027 (m) REVERT: A 1001 LEU cc_start: 0.9220 (tp) cc_final: 0.8949 (tt) REVERT: A 1107 ARG cc_start: 0.7912 (mmp-170) cc_final: 0.7546 (mmm160) REVERT: B 564 GLN cc_start: 0.6943 (OUTLIER) cc_final: 0.5860 (tp40) REVERT: B 763 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8677 (tt) REVERT: B 985 ASP cc_start: 0.8243 (OUTLIER) cc_final: 0.7863 (m-30) outliers start: 125 outliers final: 82 residues processed: 227 average time/residue: 0.3370 time to fit residues: 129.3661 Evaluate side-chains 192 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 102 time to evaluate : 2.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 835 LYS Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 969 LYS Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1122 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 105 optimal weight: 0.9990 chunk 282 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 183 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 313 optimal weight: 0.9990 chunk 260 optimal weight: 5.9990 chunk 145 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 164 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 317 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 GLN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1058 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 26814 Z= 0.199 Angle : 0.660 12.574 36525 Z= 0.320 Chirality : 0.047 0.284 4332 Planarity : 0.004 0.052 4650 Dihedral : 9.980 82.544 4817 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.95 % Favored : 91.87 % Rotamer: Outliers : 2.98 % Allowed : 24.79 % Favored : 72.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.14), residues: 3234 helix: 0.90 (0.21), residues: 659 sheet: -0.70 (0.21), residues: 532 loop : -2.00 (0.13), residues: 2043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 104 HIS 0.004 0.001 HIS B1088 PHE 0.030 0.001 PHE A 106 TYR 0.017 0.001 TYR B 265 ARG 0.015 0.001 ARG A 498 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 125 time to evaluate : 2.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 115 GLN cc_start: 0.8067 (mp10) cc_final: 0.7840 (mp10) REVERT: C 995 ARG cc_start: 0.8912 (OUTLIER) cc_final: 0.8642 (ttm170) REVERT: A 423 TYR cc_start: 0.5116 (t80) cc_final: 0.4834 (t80) REVERT: A 456 PHE cc_start: 0.8356 (m-10) cc_final: 0.8084 (m-80) REVERT: A 464 PHE cc_start: 0.8356 (OUTLIER) cc_final: 0.8006 (m-10) REVERT: A 835 LYS cc_start: 0.3541 (OUTLIER) cc_final: 0.2280 (pttm) REVERT: A 1107 ARG cc_start: 0.7875 (mmp-170) cc_final: 0.7489 (mmm160) REVERT: B 763 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8622 (tt) outliers start: 84 outliers final: 57 residues processed: 201 average time/residue: 0.3313 time to fit residues: 111.9308 Evaluate side-chains 165 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 104 time to evaluate : 2.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 943 SER Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 835 LYS Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 969 LYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1122 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 302 optimal weight: 0.8980 chunk 35 optimal weight: 7.9990 chunk 178 optimal weight: 3.9990 chunk 228 optimal weight: 6.9990 chunk 177 optimal weight: 0.6980 chunk 263 optimal weight: 0.8980 chunk 175 optimal weight: 6.9990 chunk 312 optimal weight: 4.9990 chunk 195 optimal weight: 0.9980 chunk 190 optimal weight: 0.8980 chunk 144 optimal weight: 9.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 853 GLN C 907 ASN ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1058 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26814 Z= 0.194 Angle : 0.643 13.346 36525 Z= 0.312 Chirality : 0.047 0.281 4332 Planarity : 0.004 0.053 4650 Dihedral : 9.310 80.574 4816 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.26 % Favored : 91.62 % Rotamer: Outliers : 3.19 % Allowed : 24.75 % Favored : 72.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.14), residues: 3234 helix: 1.00 (0.21), residues: 660 sheet: -0.54 (0.22), residues: 512 loop : -1.99 (0.13), residues: 2062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 633 HIS 0.003 0.001 HIS B1048 PHE 0.019 0.001 PHE A 106 TYR 0.027 0.001 TYR A 501 ARG 0.006 0.000 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 118 time to evaluate : 3.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 115 GLN cc_start: 0.8128 (mp10) cc_final: 0.7915 (mp10) REVERT: C 498 ARG cc_start: 0.8265 (mmt-90) cc_final: 0.7712 (mmp80) REVERT: C 995 ARG cc_start: 0.8893 (OUTLIER) cc_final: 0.8644 (ttm170) REVERT: A 423 TYR cc_start: 0.5318 (t80) cc_final: 0.5109 (t80) REVERT: A 456 PHE cc_start: 0.8557 (m-10) cc_final: 0.8271 (m-80) REVERT: A 464 PHE cc_start: 0.8258 (OUTLIER) cc_final: 0.7811 (m-80) REVERT: A 835 LYS cc_start: 0.3528 (OUTLIER) cc_final: 0.2265 (pttm) REVERT: A 1107 ARG cc_start: 0.7919 (mmp-170) cc_final: 0.7502 (mmm160) REVERT: B 388 ASN cc_start: 0.8276 (OUTLIER) cc_final: 0.7706 (m110) REVERT: B 763 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8586 (tt) REVERT: B 985 ASP cc_start: 0.8274 (OUTLIER) cc_final: 0.7869 (m-30) outliers start: 90 outliers final: 61 residues processed: 198 average time/residue: 0.3375 time to fit residues: 111.9196 Evaluate side-chains 172 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 105 time to evaluate : 2.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 853 GLN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 835 LYS Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1122 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 193 optimal weight: 4.9990 chunk 124 optimal weight: 6.9990 chunk 186 optimal weight: 9.9990 chunk 94 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 60 optimal weight: 7.9990 chunk 198 optimal weight: 3.9990 chunk 212 optimal weight: 0.0470 chunk 154 optimal weight: 7.9990 chunk 29 optimal weight: 6.9990 chunk 245 optimal weight: 0.0970 overall best weight: 1.8280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 853 GLN ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 HIS ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 GLN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 787 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 GLN ** A1058 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 26814 Z= 0.255 Angle : 0.652 13.918 36525 Z= 0.318 Chirality : 0.047 0.285 4332 Planarity : 0.004 0.053 4650 Dihedral : 8.910 79.158 4816 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.44 % Favored : 91.47 % Rotamer: Outliers : 3.37 % Allowed : 24.57 % Favored : 72.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.14), residues: 3234 helix: 1.00 (0.21), residues: 659 sheet: -0.47 (0.22), residues: 523 loop : -2.03 (0.13), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 633 HIS 0.003 0.001 HIS B1048 PHE 0.030 0.001 PHE A 201 TYR 0.017 0.001 TYR B 265 ARG 0.004 0.000 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 113 time to evaluate : 2.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 115 GLN cc_start: 0.8202 (mp10) cc_final: 0.7979 (mp10) REVERT: C 176 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.7202 (pt) REVERT: C 498 ARG cc_start: 0.8230 (mmt-90) cc_final: 0.7635 (mmp80) REVERT: C 995 ARG cc_start: 0.8899 (OUTLIER) cc_final: 0.8635 (ttm170) REVERT: A 423 TYR cc_start: 0.5385 (t80) cc_final: 0.5178 (t80) REVERT: A 456 PHE cc_start: 0.8604 (m-10) cc_final: 0.8295 (m-80) REVERT: A 464 PHE cc_start: 0.8280 (OUTLIER) cc_final: 0.7800 (m-80) REVERT: A 1107 ARG cc_start: 0.7953 (mmp-170) cc_final: 0.7530 (mmm160) REVERT: B 388 ASN cc_start: 0.8310 (OUTLIER) cc_final: 0.7784 (m110) REVERT: B 756 TYR cc_start: 0.8993 (OUTLIER) cc_final: 0.8067 (t80) REVERT: B 763 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8604 (tt) REVERT: B 967 SER cc_start: 0.8597 (m) cc_final: 0.8104 (p) REVERT: B 985 ASP cc_start: 0.8328 (OUTLIER) cc_final: 0.7903 (m-30) outliers start: 95 outliers final: 75 residues processed: 196 average time/residue: 0.3267 time to fit residues: 108.4339 Evaluate side-chains 189 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 107 time to evaluate : 2.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 835 LYS Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1122 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 284 optimal weight: 0.0770 chunk 299 optimal weight: 0.5980 chunk 272 optimal weight: 4.9990 chunk 291 optimal weight: 0.5980 chunk 175 optimal weight: 5.9990 chunk 126 optimal weight: 3.9990 chunk 228 optimal weight: 9.9990 chunk 89 optimal weight: 0.0670 chunk 262 optimal weight: 5.9990 chunk 275 optimal weight: 2.9990 chunk 289 optimal weight: 0.8980 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 895 GLN C 960 ASN ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 GLN ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1058 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 26814 Z= 0.168 Angle : 0.631 15.456 36525 Z= 0.307 Chirality : 0.046 0.278 4332 Planarity : 0.004 0.054 4650 Dihedral : 8.334 76.608 4816 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.95 % Favored : 91.96 % Rotamer: Outliers : 2.66 % Allowed : 25.35 % Favored : 71.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.14), residues: 3234 helix: 1.19 (0.21), residues: 637 sheet: -0.55 (0.20), residues: 606 loop : -2.00 (0.13), residues: 1991 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 633 HIS 0.003 0.001 HIS B1048 PHE 0.028 0.001 PHE A 201 TYR 0.018 0.001 TYR C 707 ARG 0.003 0.000 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 116 time to evaluate : 2.945 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 115 GLN cc_start: 0.8150 (mp10) cc_final: 0.7923 (mp10) REVERT: C 176 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7230 (pt) REVERT: C 498 ARG cc_start: 0.8248 (mmt-90) cc_final: 0.7793 (mmp80) REVERT: C 960 ASN cc_start: 0.8607 (OUTLIER) cc_final: 0.8140 (t0) REVERT: C 995 ARG cc_start: 0.8827 (OUTLIER) cc_final: 0.8609 (ttm170) REVERT: C 1031 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.6807 (mt-10) REVERT: A 464 PHE cc_start: 0.8212 (OUTLIER) cc_final: 0.7548 (m-80) REVERT: A 835 LYS cc_start: 0.3480 (OUTLIER) cc_final: 0.2322 (pttm) REVERT: A 1107 ARG cc_start: 0.7909 (mmp-170) cc_final: 0.7513 (mmm160) REVERT: B 168 PHE cc_start: 0.8031 (t80) cc_final: 0.7712 (t80) REVERT: B 388 ASN cc_start: 0.8221 (OUTLIER) cc_final: 0.7689 (m110) REVERT: B 763 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8576 (tt) REVERT: B 967 SER cc_start: 0.8601 (m) cc_final: 0.8055 (p) REVERT: B 985 ASP cc_start: 0.8308 (OUTLIER) cc_final: 0.7913 (m-30) outliers start: 75 outliers final: 58 residues processed: 182 average time/residue: 0.3293 time to fit residues: 101.9094 Evaluate side-chains 176 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 109 time to evaluate : 2.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 960 ASN Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 835 LYS Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1122 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 191 optimal weight: 2.9990 chunk 307 optimal weight: 2.9990 chunk 187 optimal weight: 3.9990 chunk 145 optimal weight: 0.7980 chunk 213 optimal weight: 1.9990 chunk 322 optimal weight: 3.9990 chunk 297 optimal weight: 1.9990 chunk 257 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 198 optimal weight: 6.9990 chunk 157 optimal weight: 0.7980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1058 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 HIS ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.369 26814 Z= 0.295 Angle : 0.753 59.200 36525 Z= 0.400 Chirality : 0.047 0.420 4332 Planarity : 0.004 0.054 4650 Dihedral : 8.316 75.675 4816 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.95 % Favored : 91.96 % Rotamer: Outliers : 2.59 % Allowed : 25.53 % Favored : 71.88 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.14), residues: 3234 helix: 1.14 (0.21), residues: 637 sheet: -0.54 (0.20), residues: 606 loop : -2.00 (0.13), residues: 1991 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 633 HIS 0.003 0.001 HIS B1048 PHE 0.050 0.001 PHE A 175 TYR 0.017 0.001 TYR C 707 ARG 0.003 0.000 ARG B 403 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 109 time to evaluate : 2.898 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 115 GLN cc_start: 0.8158 (mp10) cc_final: 0.7928 (mp10) REVERT: C 176 LEU cc_start: 0.7651 (OUTLIER) cc_final: 0.7233 (pt) REVERT: C 498 ARG cc_start: 0.8248 (mmt-90) cc_final: 0.7809 (mmp80) REVERT: C 995 ARG cc_start: 0.8834 (OUTLIER) cc_final: 0.8615 (ttm170) REVERT: C 1031 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.6822 (mt-10) REVERT: A 211 ASN cc_start: 0.4479 (OUTLIER) cc_final: 0.3112 (t0) REVERT: A 464 PHE cc_start: 0.7980 (OUTLIER) cc_final: 0.7550 (m-80) REVERT: A 835 LYS cc_start: 0.3479 (OUTLIER) cc_final: 0.2330 (pttm) REVERT: A 1107 ARG cc_start: 0.7916 (mmp-170) cc_final: 0.7520 (mmm160) REVERT: B 168 PHE cc_start: 0.8033 (t80) cc_final: 0.7716 (t80) REVERT: B 388 ASN cc_start: 0.8224 (OUTLIER) cc_final: 0.7691 (m110) REVERT: B 967 SER cc_start: 0.8607 (m) cc_final: 0.8062 (p) REVERT: B 985 ASP cc_start: 0.8317 (OUTLIER) cc_final: 0.7920 (m-30) outliers start: 73 outliers final: 61 residues processed: 172 average time/residue: 0.3275 time to fit residues: 95.9728 Evaluate side-chains 177 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 108 time to evaluate : 2.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 835 LYS Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1122 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 204 optimal weight: 2.9990 chunk 273 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 237 optimal weight: 20.0000 chunk 37 optimal weight: 9.9990 chunk 71 optimal weight: 0.9980 chunk 257 optimal weight: 10.0000 chunk 107 optimal weight: 8.9990 chunk 264 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1058 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.106139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.073304 restraints weight = 83728.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.075577 restraints weight = 47738.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.076485 restraints weight = 28129.815| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.369 26814 Z= 0.295 Angle : 0.753 59.200 36525 Z= 0.400 Chirality : 0.047 0.420 4332 Planarity : 0.004 0.054 4650 Dihedral : 8.316 75.675 4816 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.95 % Favored : 91.96 % Rotamer: Outliers : 2.45 % Allowed : 25.64 % Favored : 71.91 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.14), residues: 3234 helix: 1.14 (0.21), residues: 637 sheet: -0.54 (0.20), residues: 606 loop : -2.00 (0.13), residues: 1991 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 633 HIS 0.003 0.001 HIS B1048 PHE 0.050 0.001 PHE A 175 TYR 0.017 0.001 TYR C 707 ARG 0.003 0.000 ARG B 403 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4069.48 seconds wall clock time: 75 minutes 34.18 seconds (4534.18 seconds total)