Starting phenix.real_space_refine on Fri Aug 9 10:45:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x56_38064/08_2024/8x56_38064.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x56_38064/08_2024/8x56_38064.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x56_38064/08_2024/8x56_38064.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x56_38064/08_2024/8x56_38064.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x56_38064/08_2024/8x56_38064.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x56_38064/08_2024/8x56_38064.cif" } resolution = 3.93 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= 0.053 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 114 5.16 5 C 16422 2.51 5 N 4197 2.21 5 O 5016 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 40": "OD1" <-> "OD2" Residue "A ASP 53": "OD1" <-> "OD2" Residue "A PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 132": "OE1" <-> "OE2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 264": "OD1" <-> "OD2" Residue "A TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A GLU 340": "OE1" <-> "OE2" Residue "A ASP 364": "OD1" <-> "OD2" Residue "A TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 389": "OD1" <-> "OD2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 571": "OD1" <-> "OD2" Residue "A ASP 627": "OD1" <-> "OD2" Residue "A TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 737": "OD1" <-> "OD2" Residue "A ASP 745": "OD1" <-> "OD2" Residue "A TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 780": "OE1" <-> "OE2" Residue "A PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 830": "OD1" <-> "OD2" Residue "A TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 939": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1139": "OD1" <-> "OD2" Residue "B PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 224": "OE1" <-> "OE2" Residue "B TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 571": "OD1" <-> "OD2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 654": "OE1" <-> "OE2" Residue "B GLU 661": "OE1" <-> "OE2" Residue "B TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 773": "OE1" <-> "OE2" Residue "B PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 830": "OD1" <-> "OD2" Residue "B TYR 837": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 867": "OD1" <-> "OD2" Residue "B PHE 939": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 988": "OE1" <-> "OE2" Residue "B GLU 1031": "OE1" <-> "OE2" Residue "B GLU 1111": "OE1" <-> "OE2" Residue "B ASP 1127": "OD1" <-> "OD2" Residue "B ASP 1139": "OD1" <-> "OD2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 583": "OE1" <-> "OE2" Residue "C GLU 619": "OE1" <-> "OE2" Residue "C GLU 661": "OE1" <-> "OE2" Residue "C PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 745": "OD1" <-> "OD2" Residue "C PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 833": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 936": "OD1" <-> "OD2" Residue "C ASP 994": "OD1" <-> "OD2" Residue "C GLU 1017": "OE1" <-> "OE2" Residue "C GLU 1031": "OE1" <-> "OE2" Residue "C PHE 1042": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1139": "OD1" <-> "OD2" 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: 25749 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 8318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8318 Classifications: {'peptide': 1063} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 55, 'TRANS': 1007} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 8318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8318 Classifications: {'peptide': 1063} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 55, 'TRANS': 1007} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 8318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8318 Classifications: {'peptide': 1063} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 55, 'TRANS': 1007} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 14.49, per 1000 atoms: 0.56 Number of scatterers: 25749 At special positions: 0 Unit cell: (143.52, 142.48, 189.28, 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 114 16.00 O 5016 8.00 N 4197 7.00 C 16422 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 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=2.03 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=2.02 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " 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=2.02 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=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.05 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 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 B 840 " - pdb=" SG CYS B 851 " 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 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=2.03 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=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " 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=1, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " BMA D 2 " " NAG E 1 " - " BMA E 2 " " NAG F 1 " - " BMA F 2 " " NAG G 1 " - " BMA G 2 " " NAG H 1 " - " BMA H 2 " " NAG I 1 " - " BMA I 2 " " NAG J 1 " - " BMA J 2 " " NAG K 1 " - " BMA K 2 " " NAG L 1 " - " BMA L 2 " " NAG M 1 " - " BMA M 2 " " NAG N 1 " - " BMA N 2 " " NAG O 1 " - " BMA O 2 " " NAG P 1 " - " BMA P 2 " " NAG Q 1 " - " BMA Q 2 " " NAG R 1 " - " BMA R 2 " NAG-ASN " NAG A1301 " - " ASN A 122 " " NAG A1302 " - " ASN A 343 " " NAG A1303 " - " ASN A 331 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A1074 " " NAG A1308 " - " ASN A 61 " " NAG A1309 " - " ASN A 165 " " NAG A1310 " - " ASN A 234 " " NAG B1301 " - " ASN B 122 " " NAG B1302 " - " ASN B 61 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 709 " " NAG B1309 " - " ASN B1074 " " NAG B1310 " - " ASN B 343 " " NAG C1301 " - " ASN C 122 " " NAG C1302 " - " ASN C 61 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 657 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C1074 " " NAG C1309 " - " ASN C 343 " " NAG C1310 " - " ASN C 331 " " NAG E 1 " - " ASN A1134 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A 717 " " NAG H 1 " - " ASN A1098 " " NAG I 1 " - " ASN B 282 " " NAG J 1 " - " ASN B1134 " " NAG K 1 " - " ASN B 801 " " NAG L 1 " - " ASN B 717 " " NAG M 1 " - " ASN B1098 " " NAG N 1 " - " ASN C 282 " " NAG O 1 " - " ASN C1134 " " NAG P 1 " - " ASN C 801 " " NAG Q 1 " - " ASN C 717 " " NAG R 1 " - " ASN C1098 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.33 Conformation dependent library (CDL) restraints added in 4.5 seconds 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5958 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 53 sheets defined 25.3% alpha, 20.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.57 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.647A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.968A pdb=" N SER A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.858A pdb=" N TYR A 421 " --> pdb=" O ASN A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 506 removed outlier: 3.703A pdb=" N GLN A 506 " --> pdb=" O VAL A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 627 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.790A 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 825 Processing helix chain 'A' and resid 848 through 856 removed outlier: 3.594A pdb=" N ASN A 856 " --> pdb=" O ALA A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 884 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.175A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.855A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.991A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 365 through 372 removed outlier: 3.550A pdb=" N PHE B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA B 372 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.876A pdb=" N SER B 408 " --> pdb=" O GLY B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.598A pdb=" N TYR B 421 " --> pdb=" O ASN B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 543 through 546 Processing helix chain 'B' and resid 616 through 627 removed outlier: 3.829A pdb=" N VAL B 620 " --> pdb=" O ASN B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 Processing helix chain 'B' and resid 760 through 783 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 840 through 844 removed outlier: 4.361A pdb=" N ILE B 844 " --> pdb=" O LEU B 841 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 856 Processing helix chain 'B' and resid 866 through 884 removed outlier: 3.623A pdb=" N ALA B 871 " --> pdb=" O ASP B 867 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.661A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 4.510A pdb=" N SER B 982 " --> pdb=" O ASN B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 6.050A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.620A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.649A pdb=" N VAL C 407 " --> pdb=" O LYS C 403 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N SER C 408 " --> pdb=" O GLY C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 506 Processing helix chain 'C' and resid 618 through 627 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 Processing helix chain 'C' and resid 760 through 783 Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 840 through 844 removed outlier: 4.408A pdb=" N ILE C 844 " --> pdb=" O LEU C 841 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 855 Processing helix chain 'C' and resid 866 through 884 removed outlier: 3.581A pdb=" N ALA C 871 " --> pdb=" O ASP C 867 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.436A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.742A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.502A pdb=" N GLN C 965 " --> pdb=" O THR C 961 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.470A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.277A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.229A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 50 through 55 removed outlier: 3.514A pdb=" N ARG A 273 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.601A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 116 through 118 removed outlier: 3.621A pdb=" N LYS A 129 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 316 removed outlier: 7.172A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER A 596 " --> pdb=" O LEU A 611 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 326 removed outlier: 6.764A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.753A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N PHE A 543 " --> pdb=" O LEU A 546 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.038A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ALA A 435 " --> pdb=" O PHE A 375 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.932A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.914A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 565 through 566 removed outlier: 6.863A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 575 through 577 Processing sheet with id=AB5, first strand: chain 'A' and resid 654 through 660 removed outlier: 3.629A pdb=" N GLU A 654 " --> pdb=" O ILE A 692 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N THR A 696 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ASN A 658 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR A 695 " --> pdb=" O CYS A 671 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.811A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 713 through 715 removed outlier: 3.844A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.207A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 733 through 734 removed outlier: 4.198A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.586A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'A' and resid 1120 through 1122 removed outlier: 3.577A pdb=" N CYS A1082 " --> pdb=" O VAL A1133 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC4, first strand: chain 'B' and resid 26 through 30 removed outlier: 6.999A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ASP B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N THR B 95 " --> pdb=" O ASP B 264 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE B 194 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR B 208 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.906A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.698A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.703A pdb=" N LEU B 117 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL B 130 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 316 removed outlier: 7.311A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 324 through 326 removed outlier: 4.239A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.847A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.821A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD3, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.951A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 575 through 577 Processing sheet with id=AD5, first strand: chain 'B' and resid 654 through 660 removed outlier: 5.964A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.805A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 713 through 715 removed outlier: 3.590A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'B' and resid 718 through 722 removed outlier: 3.548A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 718 through 722 removed outlier: 5.601A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 733 through 734 removed outlier: 4.378A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 787 through 788 Processing sheet with id=AE2, first strand: chain 'B' and resid 1077 through 1078 removed outlier: 3.527A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL B1094 " --> pdb=" O THR B1105 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR B1105 " --> pdb=" O VAL B1094 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE4, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.520A pdb=" N VAL C 62 " --> pdb=" O THR C 29 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N PHE C 65 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 8.857A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.775A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.081A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N TRP C 104 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N VAL C 120 " --> pdb=" O PHE C 127 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 311 through 316 removed outlier: 3.507A pdb=" N THR C 315 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 325 through 326 removed outlier: 3.542A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.589A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF2, first strand: chain 'C' and resid 473 through 474 removed outlier: 4.104A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 654 through 660 removed outlier: 6.542A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.786A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 9.072A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 713 through 715 removed outlier: 3.638A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 718 through 728 removed outlier: 3.608A pdb=" N GLU C 725 " --> pdb=" O PHE C1062 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 733 through 734 removed outlier: 4.335A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 1120 through 1122 removed outlier: 3.814A pdb=" N CYS C1082 " --> pdb=" O VAL C1133 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 1094 through 1097 891 hydrogen bonds defined for protein. 2466 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: 10.81 Time building geometry restraints manager: 12.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8118 1.34 - 1.47: 6745 1.47 - 1.60: 11345 1.60 - 1.72: 0 1.72 - 1.85: 141 Bond restraints: 26349 Sorted by residual: bond pdb=" N PHE C 329 " pdb=" CA PHE C 329 " ideal model delta sigma weight residual 1.453 1.483 -0.030 8.30e-03 1.45e+04 1.30e+01 bond pdb=" N ILE C 212 " pdb=" CA ILE C 212 " ideal model delta sigma weight residual 1.459 1.502 -0.043 1.25e-02 6.40e+03 1.19e+01 bond pdb=" N ILE C 210 " pdb=" CA ILE C 210 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.15e+00 bond pdb=" N LYS C 529 " pdb=" CA LYS C 529 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.18e-02 7.18e+03 8.91e+00 bond pdb=" N THR C 208 " pdb=" CA THR C 208 " ideal model delta sigma weight residual 1.462 1.489 -0.028 9.30e-03 1.16e+04 8.79e+00 ... (remaining 26344 not shown) Histogram of bond angle deviations from ideal: 97.28 - 104.64: 420 104.64 - 112.01: 12966 112.01 - 119.37: 8631 119.37 - 126.74: 13569 126.74 - 134.10: 270 Bond angle restraints: 35856 Sorted by residual: angle pdb=" C ASN C1074 " pdb=" N PHE C1075 " pdb=" CA PHE C1075 " ideal model delta sigma weight residual 121.90 115.46 6.44 1.26e+00 6.30e-01 2.61e+01 angle pdb=" N LEU B 387 " pdb=" CA LEU B 387 " pdb=" C LEU B 387 " ideal model delta sigma weight residual 114.62 108.81 5.81 1.14e+00 7.69e-01 2.60e+01 angle pdb=" C ASN A1074 " pdb=" N PHE A1075 " pdb=" CA PHE A1075 " ideal model delta sigma weight residual 121.90 115.59 6.31 1.26e+00 6.30e-01 2.50e+01 angle pdb=" N ILE C 834 " pdb=" CA ILE C 834 " pdb=" C ILE C 834 " ideal model delta sigma weight residual 112.96 108.46 4.50 1.00e+00 1.00e+00 2.03e+01 angle pdb=" C PHE B 32 " pdb=" CA PHE B 32 " pdb=" CB PHE B 32 " ideal model delta sigma weight residual 115.89 110.37 5.52 1.32e+00 5.74e-01 1.75e+01 ... (remaining 35851 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.08: 14604 23.08 - 46.16: 1421 46.16 - 69.24: 162 69.24 - 92.32: 143 92.32 - 115.40: 113 Dihedral angle restraints: 16443 sinusoidal: 7167 harmonic: 9276 Sorted by residual: dihedral pdb=" CB CYS B 738 " pdb=" SG CYS B 738 " pdb=" SG CYS B 760 " pdb=" CB CYS B 760 " ideal model delta sinusoidal sigma weight residual 93.00 9.82 83.18 1 1.00e+01 1.00e-02 8.46e+01 dihedral pdb=" CB CYS B 617 " pdb=" SG CYS B 617 " pdb=" SG CYS B 649 " pdb=" CB CYS B 649 " ideal model delta sinusoidal sigma weight residual 93.00 26.01 66.99 1 1.00e+01 1.00e-02 5.85e+01 dihedral pdb=" CB CYS C 131 " pdb=" SG CYS C 131 " pdb=" SG CYS C 166 " pdb=" CB CYS C 166 " ideal model delta sinusoidal sigma weight residual 93.00 33.06 59.94 1 1.00e+01 1.00e-02 4.79e+01 ... (remaining 16440 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.180: 4185 0.180 - 0.360: 32 0.360 - 0.540: 0 0.540 - 0.721: 0 0.721 - 0.901: 3 Chirality restraints: 4220 Sorted by residual: chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN A1098 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.50 -0.90 2.00e-01 2.50e+01 2.03e+01 chirality pdb=" C1 NAG R 1 " pdb=" ND2 ASN C1098 " pdb=" C2 NAG R 1 " pdb=" O5 NAG R 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.51 -0.89 2.00e-01 2.50e+01 1.96e+01 chirality pdb=" C1 NAG M 1 " pdb=" ND2 ASN B1098 " pdb=" C2 NAG M 1 " pdb=" O5 NAG M 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.52 -0.88 2.00e-01 2.50e+01 1.92e+01 ... (remaining 4217 not shown) Planarity restraints: 4598 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 81 " 0.057 5.00e-02 4.00e+02 8.57e-02 1.18e+01 pdb=" N PRO A 82 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO A 82 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 82 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 216 " -0.053 5.00e-02 4.00e+02 8.03e-02 1.03e+01 pdb=" N PRO B 217 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO B 217 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO B 217 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 237 " 0.288 9.50e-02 1.11e+02 1.29e-01 1.02e+01 pdb=" NE ARG C 237 " -0.018 2.00e-02 2.50e+03 pdb=" CZ ARG C 237 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG C 237 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG C 237 " 0.009 2.00e-02 2.50e+03 ... (remaining 4595 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 449 2.63 - 3.20: 23986 3.20 - 3.77: 40142 3.77 - 4.33: 53976 4.33 - 4.90: 87247 Nonbonded interactions: 205800 Sorted by model distance: nonbonded pdb=" OD1 ASN B 532 " pdb=" N LEU B 533 " model vdw 2.064 3.120 nonbonded pdb=" O CYS A 590 " pdb=" OH TYR C 837 " model vdw 2.115 3.040 nonbonded pdb=" OG1 THR C 124 " pdb=" O7 NAG C1301 " model vdw 2.138 3.040 nonbonded pdb=" NE2 GLN C 173 " pdb=" O PRO C 174 " model vdw 2.138 3.120 nonbonded pdb=" O ASN B 978 " pdb=" OG1 THR C 547 " model vdw 2.148 3.040 ... (remaining 205795 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' } 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: 1.580 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: 1.080 Check model and map are aligned: 0.200 Set scattering table: 0.230 Process input model: 71.890 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 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 : 0.004 0.049 26349 Z= 0.281 Angle : 0.809 9.871 35856 Z= 0.426 Chirality : 0.056 0.901 4220 Planarity : 0.006 0.129 4554 Dihedral : 21.396 115.405 10371 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.96 % Favored : 92.85 % Rotamer: Outliers : 0.58 % Allowed : 27.32 % Favored : 72.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.65 (0.15), residues: 3159 helix: 0.91 (0.20), residues: 699 sheet: -0.93 (0.21), residues: 584 loop : -2.04 (0.14), residues: 1876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP B 633 HIS 0.010 0.001 HIS C 339 PHE 0.034 0.001 PHE C 342 TYR 0.023 0.001 TYR A 365 ARG 0.006 0.001 ARG C1107 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 172 time to evaluate : 2.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 697 MET cc_start: 0.8885 (mmm) cc_final: 0.8585 (mmp) REVERT: A 896 ILE cc_start: 0.8637 (tp) cc_final: 0.8075 (tt) REVERT: A 1050 MET cc_start: 0.7898 (ptp) cc_final: 0.7559 (ptp) REVERT: A 1107 ARG cc_start: 0.7615 (mmt-90) cc_final: 0.7343 (mmt-90) REVERT: B 377 PHE cc_start: 0.7024 (t80) cc_final: 0.6746 (t80) REVERT: B 985 ASP cc_start: 0.7608 (p0) cc_final: 0.7390 (p0) REVERT: C 699 LEU cc_start: 0.8592 (mt) cc_final: 0.8363 (mp) outliers start: 16 outliers final: 8 residues processed: 184 average time/residue: 0.3401 time to fit residues: 104.1089 Evaluate side-chains 160 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 152 time to evaluate : 2.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 620 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 268 optimal weight: 4.9990 chunk 241 optimal weight: 7.9990 chunk 133 optimal weight: 20.0000 chunk 82 optimal weight: 0.6980 chunk 162 optimal weight: 6.9990 chunk 128 optimal weight: 2.9990 chunk 249 optimal weight: 0.0770 chunk 96 optimal weight: 8.9990 chunk 151 optimal weight: 8.9990 chunk 185 optimal weight: 2.9990 chunk 288 optimal weight: 30.0000 overall best weight: 2.3544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 26349 Z= 0.268 Angle : 0.725 10.499 35856 Z= 0.360 Chirality : 0.051 0.655 4220 Planarity : 0.005 0.071 4554 Dihedral : 14.947 107.852 4663 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.47 % Favored : 92.43 % Rotamer: Outliers : 3.14 % Allowed : 24.25 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.52 (0.15), residues: 3159 helix: 1.00 (0.20), residues: 716 sheet: -0.99 (0.20), residues: 624 loop : -1.94 (0.14), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 633 HIS 0.005 0.001 HIS A 625 PHE 0.014 0.001 PHE C1042 TYR 0.026 0.002 TYR B 204 ARG 0.005 0.001 ARG C 34 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 156 time to evaluate : 2.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8279 (tm-30) cc_final: 0.8013 (tm-30) REVERT: A 127 PHE cc_start: 0.8248 (t80) cc_final: 0.7873 (t80) REVERT: A 177 MET cc_start: 0.5804 (mmt) cc_final: 0.3458 (tmm) REVERT: A 220 PHE cc_start: 0.6485 (OUTLIER) cc_final: 0.6251 (t80) REVERT: A 896 ILE cc_start: 0.8793 (tp) cc_final: 0.8274 (tt) REVERT: B 102 ARG cc_start: 0.3813 (ptt180) cc_final: 0.3485 (ptt-90) REVERT: B 164 ASN cc_start: 0.6053 (OUTLIER) cc_final: 0.5540 (p0) REVERT: B 200 TYR cc_start: 0.7006 (OUTLIER) cc_final: 0.6760 (t80) REVERT: B 204 TYR cc_start: 0.7511 (m-10) cc_final: 0.6979 (m-10) REVERT: B 697 MET cc_start: 0.8353 (mmt) cc_final: 0.8141 (tpt) REVERT: B 869 MET cc_start: 0.8827 (pmm) cc_final: 0.8587 (pmm) REVERT: B 904 TYR cc_start: 0.7459 (OUTLIER) cc_final: 0.7238 (m-10) REVERT: C 173 GLN cc_start: 0.6968 (tp-100) cc_final: 0.6763 (tp-100) REVERT: C 378 LYS cc_start: 0.9505 (mmmt) cc_final: 0.9279 (mmmt) REVERT: C 726 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.8528 (mm) REVERT: C 756 TYR cc_start: 0.7983 (OUTLIER) cc_final: 0.7363 (t80) REVERT: C 816 SER cc_start: 0.7481 (OUTLIER) cc_final: 0.7221 (m) REVERT: C 1029 MET cc_start: 0.8789 (tpp) cc_final: 0.8555 (tpp) outliers start: 87 outliers final: 42 residues processed: 227 average time/residue: 0.3260 time to fit residues: 123.9543 Evaluate side-chains 185 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 136 time to evaluate : 2.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 978 ASN Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 160 optimal weight: 5.9990 chunk 89 optimal weight: 10.0000 chunk 240 optimal weight: 9.9990 chunk 196 optimal weight: 0.8980 chunk 79 optimal weight: 5.9990 chunk 289 optimal weight: 1.9990 chunk 312 optimal weight: 0.9980 chunk 257 optimal weight: 3.9990 chunk 286 optimal weight: 0.8980 chunk 98 optimal weight: 0.6980 chunk 232 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 926 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 26349 Z= 0.175 Angle : 0.647 9.504 35856 Z= 0.321 Chirality : 0.050 0.613 4220 Planarity : 0.005 0.067 4554 Dihedral : 9.562 107.851 4656 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.77 % Favored : 93.13 % Rotamer: Outliers : 4.00 % Allowed : 23.21 % Favored : 72.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.49 (0.15), residues: 3159 helix: 1.10 (0.20), residues: 721 sheet: -1.17 (0.20), residues: 609 loop : -1.87 (0.14), residues: 1829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 436 HIS 0.006 0.001 HIS C 339 PHE 0.029 0.001 PHE A 562 TYR 0.019 0.001 TYR A 837 ARG 0.004 0.000 ARG C1107 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 171 time to evaluate : 3.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 PHE cc_start: 0.8306 (t80) cc_final: 0.7894 (t80) REVERT: A 177 MET cc_start: 0.5594 (mmt) cc_final: 0.4186 (tmm) REVERT: A 188 ASN cc_start: 0.7214 (OUTLIER) cc_final: 0.6704 (p0) REVERT: A 392 PHE cc_start: 0.8744 (OUTLIER) cc_final: 0.8098 (m-80) REVERT: B 102 ARG cc_start: 0.4217 (ptt180) cc_final: 0.3866 (mtt180) REVERT: B 164 ASN cc_start: 0.6107 (OUTLIER) cc_final: 0.5609 (p0) REVERT: B 200 TYR cc_start: 0.6988 (OUTLIER) cc_final: 0.6781 (t80) REVERT: B 869 MET cc_start: 0.8898 (OUTLIER) cc_final: 0.7881 (pmm) REVERT: B 904 TYR cc_start: 0.7467 (OUTLIER) cc_final: 0.7211 (m-10) REVERT: C 173 GLN cc_start: 0.6855 (tp-100) cc_final: 0.6601 (tp-100) REVERT: C 378 LYS cc_start: 0.9508 (mmmt) cc_final: 0.9262 (mmmt) REVERT: C 393 THR cc_start: 0.8243 (OUTLIER) cc_final: 0.7883 (t) REVERT: C 756 TYR cc_start: 0.7807 (OUTLIER) cc_final: 0.7227 (t80) outliers start: 111 outliers final: 54 residues processed: 266 average time/residue: 0.3302 time to fit residues: 146.3720 Evaluate side-chains 198 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 136 time to evaluate : 2.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 346 ARG Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1137 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 285 optimal weight: 1.9990 chunk 217 optimal weight: 4.9990 chunk 150 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 138 optimal weight: 3.9990 chunk 194 optimal weight: 6.9990 chunk 290 optimal weight: 0.4980 chunk 307 optimal weight: 10.0000 chunk 151 optimal weight: 6.9990 chunk 275 optimal weight: 0.1980 chunk 82 optimal weight: 0.7980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 321 GLN A 777 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN B 762 GLN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 ASN C 437 ASN C 955 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26349 Z= 0.202 Angle : 0.631 14.606 35856 Z= 0.314 Chirality : 0.049 0.606 4220 Planarity : 0.005 0.062 4554 Dihedral : 8.269 100.794 4654 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.84 % Favored : 93.07 % Rotamer: Outliers : 3.82 % Allowed : 23.82 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.38 (0.15), residues: 3159 helix: 1.28 (0.20), residues: 707 sheet: -1.00 (0.20), residues: 643 loop : -1.87 (0.14), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.005 0.001 HIS C 339 PHE 0.025 0.001 PHE B 592 TYR 0.021 0.001 TYR A 380 ARG 0.008 0.000 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 136 time to evaluate : 2.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 PHE cc_start: 0.8316 (t80) cc_final: 0.7887 (t80) REVERT: A 177 MET cc_start: 0.5804 (mmt) cc_final: 0.4095 (tmm) REVERT: A 392 PHE cc_start: 0.8737 (OUTLIER) cc_final: 0.8073 (m-80) REVERT: A 630 THR cc_start: 0.8301 (m) cc_final: 0.8083 (m) REVERT: A 1050 MET cc_start: 0.8144 (OUTLIER) cc_final: 0.7697 (ptp) REVERT: B 102 ARG cc_start: 0.4295 (ptt180) cc_final: 0.3970 (mtt180) REVERT: B 164 ASN cc_start: 0.5993 (OUTLIER) cc_final: 0.5508 (p0) REVERT: B 869 MET cc_start: 0.8922 (OUTLIER) cc_final: 0.7893 (pmm) REVERT: B 904 TYR cc_start: 0.7554 (OUTLIER) cc_final: 0.7327 (m-10) REVERT: B 996 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.9169 (mm) REVERT: B 1029 MET cc_start: 0.9090 (tpp) cc_final: 0.8159 (tpp) REVERT: C 328 ARG cc_start: 0.6096 (OUTLIER) cc_final: 0.4646 (ttm-80) REVERT: C 378 LYS cc_start: 0.9504 (mmmt) cc_final: 0.9247 (mmmt) REVERT: C 532 ASN cc_start: 0.9003 (t0) cc_final: 0.8788 (t0) REVERT: C 756 TYR cc_start: 0.7910 (OUTLIER) cc_final: 0.7336 (t80) REVERT: C 973 ILE cc_start: 0.8223 (OUTLIER) cc_final: 0.7916 (tp) outliers start: 106 outliers final: 67 residues processed: 229 average time/residue: 0.3448 time to fit residues: 129.9118 Evaluate side-chains 206 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 130 time to evaluate : 2.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 346 ARG Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1137 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 255 optimal weight: 9.9990 chunk 174 optimal weight: 5.9990 chunk 4 optimal weight: 20.0000 chunk 228 optimal weight: 7.9990 chunk 126 optimal weight: 10.0000 chunk 262 optimal weight: 9.9990 chunk 212 optimal weight: 20.0000 chunk 0 optimal weight: 9.9990 chunk 156 optimal weight: 4.9990 chunk 275 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN A1108 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 26349 Z= 0.480 Angle : 0.808 11.535 35856 Z= 0.414 Chirality : 0.053 0.659 4220 Planarity : 0.006 0.051 4554 Dihedral : 8.288 106.890 4654 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.31 % Favored : 90.60 % Rotamer: Outliers : 5.98 % Allowed : 23.06 % Favored : 70.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.15), residues: 3159 helix: 0.68 (0.19), residues: 718 sheet: -1.03 (0.21), residues: 593 loop : -2.10 (0.14), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 633 HIS 0.013 0.002 HIS B 49 PHE 0.029 0.002 PHE B 927 TYR 0.024 0.002 TYR B1067 ARG 0.005 0.001 ARG B1107 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 133 time to evaluate : 3.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ILE cc_start: 0.9303 (OUTLIER) cc_final: 0.8826 (mm) REVERT: A 177 MET cc_start: 0.6246 (mmt) cc_final: 0.4129 (tmm) REVERT: A 191 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8315 (mp0) REVERT: A 220 PHE cc_start: 0.6927 (OUTLIER) cc_final: 0.6585 (t80) REVERT: A 495 TYR cc_start: 0.3983 (OUTLIER) cc_final: 0.3749 (m-80) REVERT: A 630 THR cc_start: 0.8354 (m) cc_final: 0.8072 (m) REVERT: A 1031 GLU cc_start: 0.7533 (mt-10) cc_final: 0.7225 (tt0) REVERT: A 1107 ARG cc_start: 0.7800 (mmt-90) cc_final: 0.7457 (mmt-90) REVERT: B 55 PHE cc_start: 0.7655 (m-80) cc_final: 0.7379 (m-10) REVERT: B 164 ASN cc_start: 0.6167 (OUTLIER) cc_final: 0.5750 (p0) REVERT: B 200 TYR cc_start: 0.8022 (OUTLIER) cc_final: 0.7407 (t80) REVERT: B 204 TYR cc_start: 0.7434 (m-10) cc_final: 0.6853 (m-10) REVERT: B 495 TYR cc_start: 0.1072 (OUTLIER) cc_final: 0.0787 (t80) REVERT: B 869 MET cc_start: 0.9016 (OUTLIER) cc_final: 0.8069 (pmm) REVERT: B 996 LEU cc_start: 0.9486 (OUTLIER) cc_final: 0.9279 (mm) REVERT: C 173 GLN cc_start: 0.7199 (tp40) cc_final: 0.6854 (tp-100) REVERT: C 328 ARG cc_start: 0.6394 (OUTLIER) cc_final: 0.5190 (ttm-80) REVERT: C 374 PHE cc_start: 0.7220 (m-80) cc_final: 0.6741 (m-10) REVERT: C 378 LYS cc_start: 0.9537 (mmmt) cc_final: 0.9308 (mmmt) REVERT: C 532 ASN cc_start: 0.9003 (t0) cc_final: 0.8704 (t0) REVERT: C 586 ASP cc_start: 0.7745 (t0) cc_final: 0.7506 (t0) REVERT: C 756 TYR cc_start: 0.8154 (OUTLIER) cc_final: 0.7655 (t80) REVERT: C 816 SER cc_start: 0.7870 (OUTLIER) cc_final: 0.7633 (m) REVERT: C 1005 GLN cc_start: 0.8452 (tp40) cc_final: 0.8190 (tp40) REVERT: C 1029 MET cc_start: 0.8613 (tpp) cc_final: 0.8403 (tpp) outliers start: 166 outliers final: 100 residues processed: 280 average time/residue: 0.3361 time to fit residues: 155.8577 Evaluate side-chains 229 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 117 time to evaluate : 2.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 978 ASN Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 707 TYR Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1137 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 103 optimal weight: 10.0000 chunk 276 optimal weight: 1.9990 chunk 60 optimal weight: 0.3980 chunk 180 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 307 optimal weight: 5.9990 chunk 255 optimal weight: 8.9990 chunk 142 optimal weight: 20.0000 chunk 25 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 161 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 628 GLN A 960 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN C 919 ASN C1083 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 26349 Z= 0.186 Angle : 0.654 10.177 35856 Z= 0.326 Chirality : 0.049 0.615 4220 Planarity : 0.005 0.053 4554 Dihedral : 7.742 102.333 4653 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.87 % Favored : 93.04 % Rotamer: Outliers : 4.00 % Allowed : 25.23 % Favored : 70.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.52 (0.15), residues: 3159 helix: 1.19 (0.20), residues: 706 sheet: -1.02 (0.20), residues: 641 loop : -2.00 (0.14), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 104 HIS 0.006 0.001 HIS C 339 PHE 0.030 0.001 PHE A 562 TYR 0.023 0.001 TYR C 636 ARG 0.005 0.000 ARG B 102 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 144 time to evaluate : 2.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 PHE cc_start: 0.8709 (t80) cc_final: 0.8185 (t80) REVERT: A 177 MET cc_start: 0.6262 (mmt) cc_final: 0.4499 (tmm) REVERT: A 191 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.7896 (mp0) REVERT: A 495 TYR cc_start: 0.3890 (OUTLIER) cc_final: 0.3615 (m-80) REVERT: A 563 GLN cc_start: 0.7758 (mm-40) cc_final: 0.7442 (mm-40) REVERT: A 630 THR cc_start: 0.8293 (m) cc_final: 0.8060 (p) REVERT: A 697 MET cc_start: 0.8721 (mmm) cc_final: 0.8173 (mmm) REVERT: A 900 MET cc_start: 0.8989 (OUTLIER) cc_final: 0.8471 (pmm) REVERT: A 1029 MET cc_start: 0.7713 (tpp) cc_final: 0.7474 (tpp) REVERT: B 54 LEU cc_start: 0.8829 (mm) cc_final: 0.8542 (mt) REVERT: B 102 ARG cc_start: 0.3758 (ptt180) cc_final: 0.2915 (mtt90) REVERT: B 164 ASN cc_start: 0.6174 (OUTLIER) cc_final: 0.5755 (p0) REVERT: B 200 TYR cc_start: 0.7887 (OUTLIER) cc_final: 0.7297 (t80) REVERT: B 204 TYR cc_start: 0.7147 (m-10) cc_final: 0.6631 (m-10) REVERT: B 869 MET cc_start: 0.8865 (OUTLIER) cc_final: 0.7934 (pmm) REVERT: B 996 LEU cc_start: 0.9404 (OUTLIER) cc_final: 0.9201 (mm) REVERT: B 1029 MET cc_start: 0.9195 (tpp) cc_final: 0.8986 (tpp) REVERT: C 173 GLN cc_start: 0.6959 (tp40) cc_final: 0.6591 (tp-100) REVERT: C 328 ARG cc_start: 0.6387 (OUTLIER) cc_final: 0.5047 (ttm-80) REVERT: C 374 PHE cc_start: 0.7060 (m-80) cc_final: 0.6749 (m-10) REVERT: C 378 LYS cc_start: 0.9537 (mmmt) cc_final: 0.9307 (mmmt) REVERT: C 532 ASN cc_start: 0.8988 (t0) cc_final: 0.8539 (p0) REVERT: C 592 PHE cc_start: 0.6487 (t80) cc_final: 0.6256 (t80) REVERT: C 756 TYR cc_start: 0.7894 (OUTLIER) cc_final: 0.7377 (t80) REVERT: C 759 PHE cc_start: 0.7220 (OUTLIER) cc_final: 0.7017 (m-80) REVERT: C 816 SER cc_start: 0.7940 (OUTLIER) cc_final: 0.7694 (m) outliers start: 111 outliers final: 69 residues processed: 242 average time/residue: 0.3189 time to fit residues: 129.8928 Evaluate side-chains 216 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 136 time to evaluate : 3.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1137 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 296 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 175 optimal weight: 1.9990 chunk 224 optimal weight: 10.0000 chunk 174 optimal weight: 0.8980 chunk 259 optimal weight: 0.8980 chunk 171 optimal weight: 0.9980 chunk 306 optimal weight: 9.9990 chunk 191 optimal weight: 1.9990 chunk 186 optimal weight: 8.9990 chunk 141 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 784 GLN A 960 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 919 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 26349 Z= 0.198 Angle : 0.639 12.400 35856 Z= 0.317 Chirality : 0.048 0.607 4220 Planarity : 0.004 0.052 4554 Dihedral : 7.421 99.836 4653 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.41 % Favored : 92.50 % Rotamer: Outliers : 4.11 % Allowed : 24.68 % Favored : 71.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.44 (0.15), residues: 3159 helix: 1.20 (0.20), residues: 714 sheet: -0.94 (0.20), residues: 663 loop : -1.95 (0.14), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 104 HIS 0.007 0.001 HIS C 339 PHE 0.016 0.001 PHE B 592 TYR 0.014 0.001 TYR B1067 ARG 0.007 0.000 ARG C1107 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 144 time to evaluate : 2.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.6123 (mmt) cc_final: 0.4372 (tmm) REVERT: A 191 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.7998 (mp0) REVERT: A 495 TYR cc_start: 0.3964 (OUTLIER) cc_final: 0.3656 (m-80) REVERT: A 630 THR cc_start: 0.8203 (m) cc_final: 0.7922 (m) REVERT: A 697 MET cc_start: 0.8575 (mmm) cc_final: 0.8266 (mmm) REVERT: A 731 MET cc_start: 0.8818 (ptp) cc_final: 0.8370 (ptp) REVERT: A 900 MET cc_start: 0.8999 (OUTLIER) cc_final: 0.8530 (pmm) REVERT: A 1050 MET cc_start: 0.8387 (ptp) cc_final: 0.8122 (ptp) REVERT: B 54 LEU cc_start: 0.8965 (mm) cc_final: 0.8674 (mt) REVERT: B 102 ARG cc_start: 0.3597 (ptt180) cc_final: 0.2837 (mtt90) REVERT: B 164 ASN cc_start: 0.6185 (OUTLIER) cc_final: 0.5682 (p0) REVERT: B 200 TYR cc_start: 0.7973 (OUTLIER) cc_final: 0.7382 (t80) REVERT: B 204 TYR cc_start: 0.7256 (m-10) cc_final: 0.6698 (m-10) REVERT: B 495 TYR cc_start: 0.1465 (OUTLIER) cc_final: 0.1233 (t80) REVERT: B 869 MET cc_start: 0.8893 (OUTLIER) cc_final: 0.7992 (pmm) REVERT: B 996 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.9188 (mm) REVERT: C 102 ARG cc_start: 0.5104 (mtt180) cc_final: 0.4835 (mtt180) REVERT: C 173 GLN cc_start: 0.7013 (tp40) cc_final: 0.6621 (tp-100) REVERT: C 242 LEU cc_start: 0.8963 (mp) cc_final: 0.8707 (mp) REVERT: C 328 ARG cc_start: 0.6461 (OUTLIER) cc_final: 0.5293 (ttp80) REVERT: C 374 PHE cc_start: 0.6939 (m-80) cc_final: 0.6618 (m-10) REVERT: C 378 LYS cc_start: 0.9541 (mmmt) cc_final: 0.9306 (mmmt) REVERT: C 532 ASN cc_start: 0.8979 (t0) cc_final: 0.8466 (p0) REVERT: C 756 TYR cc_start: 0.7861 (OUTLIER) cc_final: 0.7421 (t80) REVERT: C 816 SER cc_start: 0.7930 (OUTLIER) cc_final: 0.7695 (m) REVERT: C 900 MET cc_start: 0.9034 (mmm) cc_final: 0.8191 (mmp) REVERT: C 973 ILE cc_start: 0.8346 (OUTLIER) cc_final: 0.8077 (tp) outliers start: 114 outliers final: 80 residues processed: 244 average time/residue: 0.3240 time to fit residues: 132.3001 Evaluate side-chains 226 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 134 time to evaluate : 3.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 919 ASN Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1137 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 189 optimal weight: 0.1980 chunk 122 optimal weight: 0.7980 chunk 183 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 59 optimal weight: 0.8980 chunk 194 optimal weight: 6.9990 chunk 208 optimal weight: 0.3980 chunk 151 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 chunk 240 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 774 GLN B 957 GLN B1083 HIS ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26349 Z= 0.166 Angle : 0.634 11.581 35856 Z= 0.313 Chirality : 0.048 0.611 4220 Planarity : 0.004 0.051 4554 Dihedral : 7.227 98.222 4653 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.81 % Favored : 93.10 % Rotamer: Outliers : 3.42 % Allowed : 25.69 % Favored : 70.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.30 (0.15), residues: 3159 helix: 1.31 (0.20), residues: 713 sheet: -0.79 (0.20), residues: 656 loop : -1.88 (0.14), residues: 1790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 104 HIS 0.007 0.001 HIS C 339 PHE 0.027 0.001 PHE B 92 TYR 0.026 0.001 TYR C 636 ARG 0.006 0.000 ARG C1107 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 141 time to evaluate : 2.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 PHE cc_start: 0.8657 (t80) cc_final: 0.8173 (t80) REVERT: A 177 MET cc_start: 0.6060 (mmt) cc_final: 0.4376 (tmm) REVERT: A 191 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.7873 (mp0) REVERT: A 495 TYR cc_start: 0.3828 (OUTLIER) cc_final: 0.3502 (m-80) REVERT: A 630 THR cc_start: 0.8188 (m) cc_final: 0.7907 (m) REVERT: A 856 ASN cc_start: 0.8294 (p0) cc_final: 0.8029 (p0) REVERT: A 900 MET cc_start: 0.8921 (OUTLIER) cc_final: 0.8499 (pmm) REVERT: A 1050 MET cc_start: 0.8317 (ptp) cc_final: 0.8106 (ptp) REVERT: B 54 LEU cc_start: 0.8936 (mm) cc_final: 0.8663 (mt) REVERT: B 102 ARG cc_start: 0.3788 (ptt180) cc_final: 0.3171 (mtt180) REVERT: B 164 ASN cc_start: 0.6379 (OUTLIER) cc_final: 0.5926 (p0) REVERT: B 200 TYR cc_start: 0.7926 (OUTLIER) cc_final: 0.7328 (t80) REVERT: B 204 TYR cc_start: 0.7156 (m-10) cc_final: 0.6580 (m-10) REVERT: B 996 LEU cc_start: 0.9382 (OUTLIER) cc_final: 0.9181 (mm) REVERT: C 102 ARG cc_start: 0.5076 (mtt180) cc_final: 0.4868 (mtt180) REVERT: C 242 LEU cc_start: 0.8944 (mp) cc_final: 0.8609 (mp) REVERT: C 328 ARG cc_start: 0.6350 (OUTLIER) cc_final: 0.5020 (ttm-80) REVERT: C 374 PHE cc_start: 0.7011 (m-80) cc_final: 0.6705 (m-10) REVERT: C 378 LYS cc_start: 0.9540 (mmmt) cc_final: 0.9290 (mmmt) REVERT: C 532 ASN cc_start: 0.9001 (t0) cc_final: 0.8569 (p0) REVERT: C 756 TYR cc_start: 0.7795 (OUTLIER) cc_final: 0.7340 (t80) REVERT: C 816 SER cc_start: 0.7901 (OUTLIER) cc_final: 0.7678 (m) REVERT: C 900 MET cc_start: 0.8906 (mmm) cc_final: 0.8116 (mmp) REVERT: C 973 ILE cc_start: 0.8220 (OUTLIER) cc_final: 0.7947 (tp) outliers start: 95 outliers final: 66 residues processed: 224 average time/residue: 0.3269 time to fit residues: 122.2025 Evaluate side-chains 210 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 134 time to evaluate : 3.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 919 ASN Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1137 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 278 optimal weight: 5.9990 chunk 293 optimal weight: 0.0980 chunk 267 optimal weight: 7.9990 chunk 285 optimal weight: 0.3980 chunk 171 optimal weight: 5.9990 chunk 124 optimal weight: 8.9990 chunk 224 optimal weight: 9.9990 chunk 87 optimal weight: 10.0000 chunk 258 optimal weight: 10.0000 chunk 270 optimal weight: 0.9990 chunk 284 optimal weight: 0.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 853 GLN A 960 ASN B 774 GLN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 919 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 26349 Z= 0.217 Angle : 0.648 10.972 35856 Z= 0.319 Chirality : 0.048 0.611 4220 Planarity : 0.004 0.050 4554 Dihedral : 7.122 99.228 4651 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.19 % Favored : 92.72 % Rotamer: Outliers : 3.14 % Allowed : 25.84 % Favored : 71.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.28 (0.15), residues: 3159 helix: 1.28 (0.20), residues: 716 sheet: -0.83 (0.20), residues: 667 loop : -1.84 (0.14), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 104 HIS 0.007 0.001 HIS C 339 PHE 0.025 0.001 PHE B 92 TYR 0.015 0.001 TYR A 170 ARG 0.003 0.000 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 142 time to evaluate : 2.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 PHE cc_start: 0.8710 (t80) cc_final: 0.8205 (t80) REVERT: A 177 MET cc_start: 0.5934 (mmt) cc_final: 0.4235 (tmm) REVERT: A 191 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8143 (mm-30) REVERT: A 495 TYR cc_start: 0.3894 (OUTLIER) cc_final: 0.3639 (m-80) REVERT: A 856 ASN cc_start: 0.8343 (p0) cc_final: 0.8075 (m110) REVERT: A 900 MET cc_start: 0.8984 (OUTLIER) cc_final: 0.8525 (pmm) REVERT: A 1050 MET cc_start: 0.8379 (ptp) cc_final: 0.8125 (ptp) REVERT: B 54 LEU cc_start: 0.8974 (mm) cc_final: 0.8698 (mt) REVERT: B 102 ARG cc_start: 0.3929 (ptt180) cc_final: 0.3357 (mtt180) REVERT: B 164 ASN cc_start: 0.6362 (OUTLIER) cc_final: 0.5919 (p0) REVERT: B 200 TYR cc_start: 0.7952 (OUTLIER) cc_final: 0.7413 (t80) REVERT: B 204 TYR cc_start: 0.7237 (m-10) cc_final: 0.6623 (m-10) REVERT: B 869 MET cc_start: 0.8886 (OUTLIER) cc_final: 0.7957 (pmm) REVERT: B 974 SER cc_start: 0.8894 (t) cc_final: 0.8365 (m) REVERT: C 102 ARG cc_start: 0.5255 (mtt180) cc_final: 0.5010 (mtt180) REVERT: C 242 LEU cc_start: 0.8976 (mp) cc_final: 0.8622 (mp) REVERT: C 328 ARG cc_start: 0.6480 (OUTLIER) cc_final: 0.5128 (ttm-80) REVERT: C 374 PHE cc_start: 0.6980 (m-80) cc_final: 0.6719 (m-10) REVERT: C 378 LYS cc_start: 0.9543 (mmmt) cc_final: 0.9293 (mmmt) REVERT: C 532 ASN cc_start: 0.9027 (t0) cc_final: 0.8620 (p0) REVERT: C 756 TYR cc_start: 0.7845 (OUTLIER) cc_final: 0.7421 (t80) REVERT: C 816 SER cc_start: 0.7954 (OUTLIER) cc_final: 0.7708 (m) REVERT: C 900 MET cc_start: 0.9010 (mmm) cc_final: 0.8259 (mmp) REVERT: C 973 ILE cc_start: 0.8302 (OUTLIER) cc_final: 0.8045 (tp) outliers start: 87 outliers final: 69 residues processed: 218 average time/residue: 0.3312 time to fit residues: 120.0108 Evaluate side-chains 220 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 141 time to evaluate : 2.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 919 ASN Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1137 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 187 optimal weight: 4.9990 chunk 302 optimal weight: 1.9990 chunk 184 optimal weight: 0.1980 chunk 143 optimal weight: 40.0000 chunk 209 optimal weight: 4.9990 chunk 316 optimal weight: 20.0000 chunk 291 optimal weight: 3.9990 chunk 252 optimal weight: 20.0000 chunk 26 optimal weight: 0.2980 chunk 194 optimal weight: 6.9990 chunk 154 optimal weight: 5.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 GLN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 26349 Z= 0.255 Angle : 0.666 11.477 35856 Z= 0.331 Chirality : 0.049 0.613 4220 Planarity : 0.005 0.051 4554 Dihedral : 7.155 101.087 4651 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.50 % Favored : 92.40 % Rotamer: Outliers : 3.03 % Allowed : 26.20 % Favored : 70.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.29 (0.15), residues: 3159 helix: 1.28 (0.20), residues: 717 sheet: -0.81 (0.20), residues: 664 loop : -1.86 (0.14), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 104 HIS 0.007 0.001 HIS C 339 PHE 0.029 0.001 PHE A 592 TYR 0.028 0.001 TYR C 170 ARG 0.007 0.000 ARG A 319 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 145 time to evaluate : 2.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ILE cc_start: 0.9296 (OUTLIER) cc_final: 0.8827 (mm) REVERT: A 127 PHE cc_start: 0.8721 (t80) cc_final: 0.8224 (t80) REVERT: A 495 TYR cc_start: 0.3940 (OUTLIER) cc_final: 0.3650 (m-80) REVERT: A 731 MET cc_start: 0.8861 (ptp) cc_final: 0.8418 (ptt) REVERT: A 1050 MET cc_start: 0.8424 (ptp) cc_final: 0.8191 (ptp) REVERT: B 54 LEU cc_start: 0.8985 (mm) cc_final: 0.8699 (mt) REVERT: B 102 ARG cc_start: 0.3853 (ptt180) cc_final: 0.3269 (mtt180) REVERT: B 164 ASN cc_start: 0.6210 (OUTLIER) cc_final: 0.5805 (p0) REVERT: B 200 TYR cc_start: 0.8020 (OUTLIER) cc_final: 0.7584 (t80) REVERT: B 204 TYR cc_start: 0.7275 (m-10) cc_final: 0.6626 (m-10) REVERT: B 869 MET cc_start: 0.8892 (OUTLIER) cc_final: 0.7958 (pmm) REVERT: B 974 SER cc_start: 0.8915 (t) cc_final: 0.8430 (m) REVERT: C 102 ARG cc_start: 0.5394 (mtt180) cc_final: 0.5151 (mtt180) REVERT: C 242 LEU cc_start: 0.8987 (mp) cc_final: 0.8657 (mp) REVERT: C 328 ARG cc_start: 0.6537 (OUTLIER) cc_final: 0.5145 (ttm-80) REVERT: C 374 PHE cc_start: 0.6983 (m-80) cc_final: 0.6757 (m-10) REVERT: C 378 LYS cc_start: 0.9546 (mmmt) cc_final: 0.9304 (mmmt) REVERT: C 532 ASN cc_start: 0.9032 (t0) cc_final: 0.8669 (p0) REVERT: C 756 TYR cc_start: 0.7949 (OUTLIER) cc_final: 0.7474 (t80) REVERT: C 816 SER cc_start: 0.8028 (OUTLIER) cc_final: 0.7795 (m) REVERT: C 973 ILE cc_start: 0.8298 (OUTLIER) cc_final: 0.8068 (tp) outliers start: 84 outliers final: 72 residues processed: 218 average time/residue: 0.3365 time to fit residues: 122.1108 Evaluate side-chains 221 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 140 time to evaluate : 2.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 919 ASN Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1137 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 200 optimal weight: 0.7980 chunk 268 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 232 optimal weight: 1.9990 chunk 37 optimal weight: 20.0000 chunk 70 optimal weight: 1.9990 chunk 252 optimal weight: 8.9990 chunk 105 optimal weight: 2.9990 chunk 259 optimal weight: 0.7980 chunk 31 optimal weight: 8.9990 chunk 46 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 GLN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 919 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.089972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.062556 restraints weight = 96178.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.065128 restraints weight = 58074.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.065927 restraints weight = 34180.581| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 26349 Z= 0.192 Angle : 0.650 9.925 35856 Z= 0.319 Chirality : 0.049 0.618 4220 Planarity : 0.004 0.051 4554 Dihedral : 7.047 100.514 4651 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.28 % Favored : 92.62 % Rotamer: Outliers : 3.14 % Allowed : 25.98 % Favored : 70.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.26 (0.15), residues: 3159 helix: 1.31 (0.20), residues: 717 sheet: -0.84 (0.20), residues: 650 loop : -1.82 (0.14), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 104 HIS 0.007 0.001 HIS C 339 PHE 0.027 0.001 PHE A 592 TYR 0.022 0.001 TYR A 170 ARG 0.004 0.000 ARG A 190 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4230.09 seconds wall clock time: 78 minutes 5.81 seconds (4685.81 seconds total)