Starting phenix.real_space_refine on Fri Aug 9 10:50:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x4h_38049/08_2024/8x4h_38049.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x4h_38049/08_2024/8x4h_38049.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x4h_38049/08_2024/8x4h_38049.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x4h_38049/08_2024/8x4h_38049.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x4h_38049/08_2024/8x4h_38049.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x4h_38049/08_2024/8x4h_38049.cif" } resolution = 3.65 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= 0.001 sd= 0.057 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 16458 2.51 5 N 4200 2.21 5 O 5052 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 PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 53": "OD1" <-> "OD2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 169": "OE1" <-> "OE2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A GLU 281": "OE1" <-> "OE2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A GLU 340": "OE1" <-> "OE2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 364": "OD1" <-> "OD2" Residue "A ASP 389": "OD1" <-> "OD2" Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 745": "OD1" <-> "OD2" Residue "A GLU 780": "OE1" <-> "OE2" Residue "A ASP 950": "OD1" <-> "OD2" Residue "A GLU 1092": "OE1" <-> "OE2" Residue "A GLU 1111": "OE1" <-> "OE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 132": "OE1" <-> "OE2" Residue "B TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 198": "OD1" <-> "OD2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 215": "OD1" <-> "OD2" Residue "B ASP 287": "OD1" <-> "OD2" Residue "B GLU 309": "OE1" <-> "OE2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 619": "OE1" <-> "OE2" Residue "B TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 661": "OE1" <-> "OE2" Residue "B GLU 773": "OE1" <-> "OE2" Residue "B TYR 837": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 868": "OE1" <-> "OE2" Residue "B GLU 988": "OE1" <-> "OE2" Residue "B GLU 990": "OE1" <-> "OE2" Residue "B TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1092": "OE1" <-> "OE2" Residue "B GLU 1111": "OE1" <-> "OE2" Residue "B ASP 1118": "OD1" <-> "OD2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 281": "OE1" <-> "OE2" Residue "C TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 389": "OD1" <-> "OD2" Residue "C PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 833": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 985": "OD1" <-> "OD2" Residue "C GLU 988": "OE1" <-> "OE2" Residue "C GLU 1031": "OE1" <-> "OE2" Residue "C GLU 1092": "OE1" <-> "OE2" 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: 25824 Number of models: 1 Model: "" Number of chains: 24 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': 1} Link IDs: {'PTRANS': 55, 'TRANS': 1007} Chain breaks: 4 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 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': 1} Link IDs: {'PTRANS': 55, 'TRANS': 1007} Chain breaks: 4 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 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': 1} Link IDs: {'PTRANS': 55, 'TRANS': 1007} Chain breaks: 4 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 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: "S" 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: "T" 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: "U" 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: 14.28, per 1000 atoms: 0.55 Number of scatterers: 25824 At special positions: 0 Unit cell: (134, 148, 171, 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 5052 8.00 N 4200 7.00 C 16458 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, 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=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 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 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 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=0, 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 S 1 " - " BMA S 2 " " NAG T 1 " - " BMA T 2 " " NAG U 1 " - " BMA U 2 " NAG-ASN " NAG A1301 " - " ASN A 122 " " NAG A1302 " - " ASN A 343 " " NAG A1303 " - " ASN A 61 " " NAG A1304 " - " ASN A 165 " " NAG A1305 " - " ASN A 234 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A1074 " " NAG B1301 " - " ASN B 122 " " NAG B1302 " - " ASN B 343 " " NAG B1303 " - " ASN B 61 " " NAG B1304 " - " ASN B 165 " " NAG B1305 " - " ASN B 234 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B1074 " " NAG C1301 " - " ASN C 122 " " NAG C1302 " - " ASN C 343 " " NAG C1303 " - " ASN C 61 " " NAG C1304 " - " ASN C 165 " " NAG C1305 " - " ASN C 234 " " NAG C1306 " - " ASN C 331 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 657 " " NAG C1309 " - " ASN C 709 " " NAG C1310 " - " ASN C1074 " " NAG D 1 " - " ASN A 354 " " NAG E 1 " - " ASN A 282 " " NAG F 1 " - " ASN A1134 " " NAG G 1 " - " ASN A 801 " " NAG H 1 " - " ASN A 717 " " NAG I 1 " - " ASN A1098 " " NAG J 1 " - " ASN B 354 " " NAG K 1 " - " ASN B 282 " " NAG L 1 " - " ASN B1134 " " NAG M 1 " - " ASN B 801 " " NAG N 1 " - " ASN B 717 " " NAG O 1 " - " ASN B1098 " " NAG P 1 " - " ASN C 354 " " NAG Q 1 " - " ASN C 282 " " NAG R 1 " - " ASN C1134 " " NAG S 1 " - " ASN C 801 " " NAG T 1 " - " ASN C 717 " " NAG U 1 " - " ASN C1098 " Time building additional restraints: 10.73 Conformation dependent library (CDL) restraints added in 5.0 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: 69 helices and 52 sheets defined 25.2% alpha, 19.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.48 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: 3.667A 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 403 through 409 removed outlier: 4.218A pdb=" N SER A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 506 removed outlier: 3.567A pdb=" N GLN A 506 " --> pdb=" O VAL A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 626 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 760 through 783 Processing helix chain 'A' and resid 816 through 825 removed outlier: 3.504A pdb=" N LEU A 821 " --> pdb=" O PRO A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 840 through 844 removed outlier: 4.161A pdb=" N ILE A 844 " --> pdb=" O LEU A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 856 removed outlier: 3.521A pdb=" N ASN A 856 " --> pdb=" O ALA A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.599A pdb=" N GLN A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.294A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.753A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU A 938 " --> pdb=" O ILE A 934 " (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: 3.855A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN A1002 " --> pdb=" O THR A 998 " (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 349 through 353 Processing helix chain 'B' and resid 365 through 371 removed outlier: 3.843A pdb=" N PHE B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.822A pdb=" N SER B 408 " --> pdb=" O GLY B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 616 through 626 removed outlier: 3.632A 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 removed outlier: 3.594A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 783 Processing helix chain 'B' and resid 816 through 825 removed outlier: 3.610A pdb=" N LEU B 821 " --> pdb=" O PRO B 817 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU B 822 " --> pdb=" O ILE B 818 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 856 Processing helix chain 'B' and resid 869 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.234A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 removed outlier: 3.557A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU B 938 " --> pdb=" O ILE B 934 " (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 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 5.332A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLN B1002 " --> pdb=" O THR B 998 " (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: 3.791A 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: 3.826A pdb=" N SER C 408 " --> pdb=" O GLY C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.504A pdb=" N TYR C 421 " --> pdb=" O ASN C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 506 Processing helix chain 'C' and resid 616 through 626 removed outlier: 3.608A pdb=" N VAL C 620 " --> pdb=" O ASN C 616 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.775A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 removed outlier: 3.624A pdb=" N LEU C 821 " --> pdb=" O PRO C 817 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU C 822 " --> pdb=" O ILE C 818 " (cutoff:3.500A) Processing helix chain 'C' and resid 840 through 844 removed outlier: 4.068A 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 868 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.237A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.590A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.986A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN C1002 " --> pdb=" O THR C 998 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 30 removed outlier: 6.955A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N ASP A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N THR A 95 " --> pdb=" O ASP A 264 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (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: 3.726A 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: 3.865A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE A 106 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU A 117 " --> pdb=" O PHE A 106 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 316 removed outlier: 7.122A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 326 Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.625A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.846A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 453 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.999A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 552 through 553 removed outlier: 3.874A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP A 586 " --> pdb=" O THR A 553 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 565 through 566 removed outlier: 6.810A 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 654 through 655 removed outlier: 5.990A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 713 through 715 removed outlier: 3.840A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.219A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 734 removed outlier: 4.106A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB9, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'B' and resid 26 through 30 removed outlier: 7.187A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ASP B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N THR B 95 " --> pdb=" O ASP B 264 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 42 through 43 Processing sheet with id=AC3, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.808A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.900A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N TRP B 104 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE B 106 " --> pdb=" O LEU B 117 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU B 117 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 316 removed outlier: 7.007A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY B 648 " --> pdb=" O THR B 645 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 324 through 326 Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.543A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.924A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 575 through 577 Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.015A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 713 through 715 removed outlier: 3.694A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.566A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 733 through 734 removed outlier: 4.182A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 788 through 790 removed outlier: 5.584A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD8, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD9, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.761A pdb=" N VAL C 62 " --> pdb=" O THR C 29 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N PHE C 65 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 50 through 55 Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.122A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 116 through 118 removed outlier: 4.833A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 311 through 316 removed outlier: 7.022A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 325 through 326 Processing sheet with id=AE6, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.837A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 361 through 362 removed outlier: 7.017A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE9, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.879A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 575 through 577 Processing sheet with id=AF2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.107A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 713 through 715 removed outlier: 3.840A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.243A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 733 through 734 removed outlier: 4.109A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF7, first strand: chain 'C' and resid 1094 through 1097 906 hydrogen bonds defined for protein. 2475 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: 10.70 Time building geometry restraints manager: 11.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 7768 1.34 - 1.46: 6688 1.46 - 1.59: 11826 1.59 - 1.71: 1 1.71 - 1.84: 141 Bond restraints: 26424 Sorted by residual: bond pdb=" N VAL C 308 " pdb=" CA VAL C 308 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.10e-02 8.26e+03 9.75e+00 bond pdb=" N VAL B 193 " pdb=" CA VAL B 193 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.19e-02 7.06e+03 9.53e+00 bond pdb=" N ILE A 410 " pdb=" CA ILE A 410 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.19e-02 7.06e+03 9.23e+00 bond pdb=" N VAL C 159 " pdb=" CA VAL C 159 " ideal model delta sigma weight residual 1.462 1.494 -0.031 1.06e-02 8.90e+03 8.69e+00 bond pdb=" N GLN A 414 " pdb=" CA GLN A 414 " ideal model delta sigma weight residual 1.453 1.489 -0.035 1.22e-02 6.72e+03 8.37e+00 ... (remaining 26419 not shown) Histogram of bond angle deviations from ideal: 95.33 - 103.11: 176 103.11 - 110.90: 9801 110.90 - 118.68: 11431 118.68 - 126.47: 14253 126.47 - 134.25: 297 Bond angle restraints: 35958 Sorted by residual: angle pdb=" C ASN A1074 " pdb=" N PHE A1075 " pdb=" CA PHE A1075 " ideal model delta sigma weight residual 121.90 114.32 7.58 1.26e+00 6.30e-01 3.62e+01 angle pdb=" N CYS C 136 " pdb=" CA CYS C 136 " pdb=" C CYS C 136 " ideal model delta sigma weight residual 114.62 108.48 6.14 1.14e+00 7.69e-01 2.90e+01 angle pdb=" N CYS A 136 " pdb=" CA CYS A 136 " pdb=" C CYS A 136 " ideal model delta sigma weight residual 114.75 108.33 6.42 1.26e+00 6.30e-01 2.60e+01 angle pdb=" CA ASP B 198 " pdb=" CB ASP B 198 " pdb=" CG ASP B 198 " ideal model delta sigma weight residual 112.60 117.33 -4.73 1.00e+00 1.00e+00 2.23e+01 angle pdb=" CA GLY B 89 " pdb=" C GLY B 89 " pdb=" O GLY B 89 " ideal model delta sigma weight residual 122.24 118.18 4.06 8.70e-01 1.32e+00 2.18e+01 ... (remaining 35953 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.97: 14775 22.97 - 45.95: 1372 45.95 - 68.92: 165 68.92 - 91.90: 133 91.90 - 114.87: 121 Dihedral angle restraints: 16566 sinusoidal: 7290 harmonic: 9276 Sorted by residual: dihedral pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " pdb=" SG CYS C 760 " pdb=" CB CYS C 760 " ideal model delta sinusoidal sigma weight residual 93.00 145.16 -52.16 1 1.00e+01 1.00e-02 3.71e+01 dihedral pdb=" CB CYS A 617 " pdb=" SG CYS A 617 " pdb=" SG CYS A 649 " pdb=" CB CYS A 649 " ideal model delta sinusoidal sigma weight residual 93.00 42.68 50.32 1 1.00e+01 1.00e-02 3.47e+01 dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual 93.00 142.14 -49.14 1 1.00e+01 1.00e-02 3.32e+01 ... (remaining 16563 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.182: 4200 0.182 - 0.364: 48 0.364 - 0.546: 0 0.546 - 0.728: 0 0.728 - 0.909: 3 Chirality restraints: 4251 Sorted by residual: chirality pdb=" C1 NAG O 1 " pdb=" ND2 ASN B1098 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.49 -0.91 2.00e-01 2.50e+01 2.07e+01 chirality pdb=" C1 NAG U 1 " pdb=" ND2 ASN C1098 " pdb=" C2 NAG U 1 " pdb=" O5 NAG U 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.52 -0.88 2.00e-01 2.50e+01 1.93e+01 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN A1098 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.56 -0.84 2.00e-01 2.50e+01 1.75e+01 ... (remaining 4248 not shown) Planarity restraints: 4605 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1303 " 0.069 2.00e-02 2.50e+03 5.71e-02 4.07e+01 pdb=" C7 NAG C1303 " -0.021 2.00e-02 2.50e+03 pdb=" C8 NAG C1303 " 0.053 2.00e-02 2.50e+03 pdb=" N2 NAG C1303 " -0.090 2.00e-02 2.50e+03 pdb=" O7 NAG C1303 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 592 " 0.028 2.00e-02 2.50e+03 3.18e-02 1.77e+01 pdb=" CG PHE B 592 " -0.068 2.00e-02 2.50e+03 pdb=" CD1 PHE B 592 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 PHE B 592 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE B 592 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE B 592 " 0.025 2.00e-02 2.50e+03 pdb=" CZ PHE B 592 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 371 " -0.034 2.00e-02 2.50e+03 3.11e-02 1.70e+01 pdb=" CG PHE C 371 " 0.060 2.00e-02 2.50e+03 pdb=" CD1 PHE C 371 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE C 371 " 0.020 2.00e-02 2.50e+03 pdb=" CE1 PHE C 371 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 PHE C 371 " -0.033 2.00e-02 2.50e+03 pdb=" CZ PHE C 371 " 0.000 2.00e-02 2.50e+03 ... (remaining 4602 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 554 2.64 - 3.21: 24741 3.21 - 3.77: 40149 3.77 - 4.34: 55575 4.34 - 4.90: 90859 Nonbonded interactions: 211878 Sorted by model distance: nonbonded pdb=" O CYS A 590 " pdb=" OH TYR C 837 " model vdw 2.078 3.040 nonbonded pdb=" OH TYR B 837 " pdb=" O CYS C 590 " model vdw 2.111 3.040 nonbonded pdb=" OG1 THR B 912 " pdb=" OD1 ASN B 914 " model vdw 2.132 3.040 nonbonded pdb=" OH TYR A 837 " pdb=" O PRO B 589 " model vdw 2.142 3.040 nonbonded pdb=" NE2 GLN A 804 " pdb=" OE1 GLN A 935 " model vdw 2.147 3.120 ... (remaining 211873 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } 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: 2.590 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: 1.110 Check model and map are aligned: 0.200 Set scattering table: 0.280 Process input model: 70.070 Find NCS groups from input model: 1.190 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 26424 Z= 0.396 Angle : 0.851 12.668 35958 Z= 0.470 Chirality : 0.060 0.909 4251 Planarity : 0.005 0.072 4557 Dihedral : 20.987 114.871 10491 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.67 % Favored : 91.23 % Rotamer: Outliers : 0.68 % Allowed : 23.87 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.15), residues: 3159 helix: 0.56 (0.21), residues: 690 sheet: -1.27 (0.21), residues: 582 loop : -2.01 (0.13), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP C 633 HIS 0.005 0.001 HIS B 66 PHE 0.068 0.002 PHE B 592 TYR 0.024 0.002 TYR C 873 ARG 0.014 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 167 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 148 time to evaluate : 3.067 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: B 201 PHE cc_start: 0.8199 (t80) cc_final: 0.7977 (t80) REVERT: C 214 ARG cc_start: -0.0039 (OUTLIER) cc_final: -0.1926 (ptt-90) outliers start: 19 outliers final: 11 residues processed: 160 average time/residue: 0.3485 time to fit residues: 93.1545 Evaluate side-chains 134 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 122 time to evaluate : 2.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 973 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 268 optimal weight: 7.9990 chunk 241 optimal weight: 8.9990 chunk 133 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 162 optimal weight: 1.9990 chunk 128 optimal weight: 7.9990 chunk 249 optimal weight: 8.9990 chunk 96 optimal weight: 0.0000 chunk 151 optimal weight: 2.9990 chunk 185 optimal weight: 3.9990 chunk 288 optimal weight: 20.0000 overall best weight: 1.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 GLN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN B 804 GLN B1106 GLN C 30 ASN ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 26424 Z= 0.223 Angle : 0.687 9.574 35958 Z= 0.342 Chirality : 0.051 0.624 4251 Planarity : 0.004 0.042 4557 Dihedral : 14.754 111.475 4796 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 3.42 % Allowed : 21.20 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.15), residues: 3159 helix: 0.95 (0.20), residues: 699 sheet: -1.37 (0.19), residues: 684 loop : -1.91 (0.14), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 633 HIS 0.004 0.001 HIS A 339 PHE 0.034 0.001 PHE C 592 TYR 0.020 0.001 TYR C1067 ARG 0.007 0.000 ARG A 214 *********************** 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: 95 poor density : 148 time to evaluate : 2.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 759 PHE cc_start: 0.8638 (t80) cc_final: 0.8280 (t80) REVERT: A 869 MET cc_start: 0.9075 (ptp) cc_final: 0.8814 (ptp) REVERT: B 421 TYR cc_start: 0.7482 (m-10) cc_final: 0.7066 (m-10) REVERT: B 591 SER cc_start: 0.7505 (OUTLIER) cc_final: 0.7102 (m) REVERT: B 740 MET cc_start: 0.8436 (ttm) cc_final: 0.8226 (ttm) REVERT: C 133 PHE cc_start: 0.6830 (OUTLIER) cc_final: 0.5802 (m-80) REVERT: C 214 ARG cc_start: 0.0833 (OUTLIER) cc_final: -0.1611 (ptt-90) REVERT: C 495 TYR cc_start: 0.4277 (OUTLIER) cc_final: 0.4055 (m-10) REVERT: C 592 PHE cc_start: 0.6813 (t80) cc_final: 0.6491 (t80) REVERT: C 882 ILE cc_start: 0.9338 (pt) cc_final: 0.8902 (mt) outliers start: 95 outliers final: 35 residues processed: 236 average time/residue: 0.3388 time to fit residues: 136.4023 Evaluate side-chains 159 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 120 time to evaluate : 2.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 160 optimal weight: 1.9990 chunk 89 optimal weight: 7.9990 chunk 240 optimal weight: 9.9990 chunk 196 optimal weight: 8.9990 chunk 79 optimal weight: 0.9990 chunk 289 optimal weight: 9.9990 chunk 312 optimal weight: 3.9990 chunk 257 optimal weight: 3.9990 chunk 286 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 chunk 232 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS A1011 GLN B 185 ASN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN C1036 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 26424 Z= 0.288 Angle : 0.681 10.581 35958 Z= 0.341 Chirality : 0.052 0.721 4251 Planarity : 0.004 0.048 4557 Dihedral : 10.465 108.114 4783 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 4.10 % Allowed : 21.71 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.15), residues: 3159 helix: 0.93 (0.20), residues: 711 sheet: -1.62 (0.20), residues: 648 loop : -1.95 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 104 HIS 0.003 0.001 HIS C1064 PHE 0.024 0.001 PHE C 592 TYR 0.019 0.002 TYR B 369 ARG 0.004 0.000 ARG A 214 *********************** 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 238 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 124 time to evaluate : 2.656 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 740 MET cc_start: 0.7656 (ttt) cc_final: 0.6666 (ttt) REVERT: A 759 PHE cc_start: 0.8692 (OUTLIER) cc_final: 0.8372 (t80) REVERT: B 421 TYR cc_start: 0.7468 (m-10) cc_final: 0.7055 (m-10) REVERT: B 902 MET cc_start: 0.9329 (mmm) cc_final: 0.9021 (mmm) REVERT: C 46 SER cc_start: 0.8410 (m) cc_final: 0.7927 (p) REVERT: C 129 LYS cc_start: 0.7770 (OUTLIER) cc_final: 0.7476 (tttt) REVERT: C 133 PHE cc_start: 0.6715 (OUTLIER) cc_final: 0.6033 (m-80) REVERT: C 176 LEU cc_start: 0.5401 (OUTLIER) cc_final: 0.5080 (mp) REVERT: C 214 ARG cc_start: 0.0944 (OUTLIER) cc_final: 0.0566 (mmm160) REVERT: C 882 ILE cc_start: 0.9333 (pt) cc_final: 0.8954 (mt) REVERT: C 1039 ARG cc_start: 0.8812 (OUTLIER) cc_final: 0.8413 (ptm160) outliers start: 114 outliers final: 48 residues processed: 228 average time/residue: 0.3071 time to fit residues: 119.7358 Evaluate side-chains 171 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 117 time to evaluate : 2.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 830 ASP Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1039 ARG Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 285 optimal weight: 10.0000 chunk 217 optimal weight: 7.9990 chunk 150 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 chunk 138 optimal weight: 6.9990 chunk 194 optimal weight: 1.9990 chunk 290 optimal weight: 0.9980 chunk 307 optimal weight: 0.9990 chunk 151 optimal weight: 4.9990 chunk 275 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN B 487 ASN B1005 GLN ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 26424 Z= 0.240 Angle : 0.630 9.496 35958 Z= 0.319 Chirality : 0.049 0.619 4251 Planarity : 0.004 0.051 4557 Dihedral : 8.341 101.275 4779 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.44 % Favored : 92.53 % Rotamer: Outliers : 3.56 % Allowed : 22.35 % Favored : 74.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.15), residues: 3159 helix: 1.10 (0.20), residues: 687 sheet: -1.35 (0.20), residues: 657 loop : -1.88 (0.14), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 104 HIS 0.005 0.001 HIS C 505 PHE 0.025 0.001 PHE C 592 TYR 0.017 0.001 TYR C1067 ARG 0.008 0.000 ARG A1039 *********************** 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 234 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 135 time to evaluate : 2.740 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 492 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7420 (pp) REVERT: A 759 PHE cc_start: 0.8647 (OUTLIER) cc_final: 0.8388 (t80) REVERT: A 981 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8298 (mm) REVERT: B 421 TYR cc_start: 0.7570 (m-10) cc_final: 0.7173 (m-10) REVERT: B 588 THR cc_start: 0.9361 (OUTLIER) cc_final: 0.9090 (p) REVERT: B 591 SER cc_start: 0.7445 (OUTLIER) cc_final: 0.7110 (m) REVERT: B 869 MET cc_start: 0.8659 (pmm) cc_final: 0.8398 (pmm) REVERT: C 46 SER cc_start: 0.8390 (m) cc_final: 0.7949 (p) REVERT: C 129 LYS cc_start: 0.7767 (OUTLIER) cc_final: 0.7500 (tttt) REVERT: C 133 PHE cc_start: 0.6985 (OUTLIER) cc_final: 0.6261 (m-80) REVERT: C 176 LEU cc_start: 0.5398 (OUTLIER) cc_final: 0.4900 (mp) REVERT: C 214 ARG cc_start: 0.1045 (OUTLIER) cc_final: 0.0711 (mmm160) REVERT: C 1039 ARG cc_start: 0.8733 (OUTLIER) cc_final: 0.8431 (ptm160) outliers start: 99 outliers final: 51 residues processed: 222 average time/residue: 0.3118 time to fit residues: 117.5419 Evaluate side-chains 179 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 118 time to evaluate : 2.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 830 ASP Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1039 ARG 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: 6.9990 chunk 4 optimal weight: 10.0000 chunk 228 optimal weight: 4.9990 chunk 126 optimal weight: 0.9990 chunk 262 optimal weight: 9.9990 chunk 212 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 156 optimal weight: 3.9990 chunk 275 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 914 ASN ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 26424 Z= 0.406 Angle : 0.707 11.417 35958 Z= 0.359 Chirality : 0.050 0.620 4251 Planarity : 0.005 0.069 4557 Dihedral : 8.240 98.714 4779 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.45 % Favored : 91.52 % Rotamer: Outliers : 4.68 % Allowed : 22.14 % Favored : 73.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.15), residues: 3159 helix: 0.90 (0.20), residues: 699 sheet: -1.50 (0.20), residues: 666 loop : -1.91 (0.14), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP B 104 HIS 0.004 0.001 HIS C1064 PHE 0.034 0.002 PHE C 592 TYR 0.018 0.002 TYR A 741 ARG 0.005 0.001 ARG A1039 *********************** 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 247 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 117 time to evaluate : 2.882 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 492 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7582 (pp) REVERT: A 759 PHE cc_start: 0.8761 (OUTLIER) cc_final: 0.8519 (t80) REVERT: A 981 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8514 (mm) REVERT: B 421 TYR cc_start: 0.7677 (m-10) cc_final: 0.7063 (m-10) REVERT: B 588 THR cc_start: 0.9383 (OUTLIER) cc_final: 0.9079 (p) REVERT: B 592 PHE cc_start: 0.6324 (t80) cc_final: 0.6013 (t80) REVERT: B 699 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8823 (mt) REVERT: B 869 MET cc_start: 0.8664 (pmm) cc_final: 0.8289 (pmm) REVERT: C 46 SER cc_start: 0.8599 (m) cc_final: 0.8199 (p) REVERT: C 129 LYS cc_start: 0.7718 (OUTLIER) cc_final: 0.7447 (tttt) REVERT: C 133 PHE cc_start: 0.7372 (OUTLIER) cc_final: 0.6595 (m-80) REVERT: C 176 LEU cc_start: 0.5343 (OUTLIER) cc_final: 0.4672 (mp) REVERT: C 214 ARG cc_start: 0.0991 (OUTLIER) cc_final: 0.0568 (mmm160) REVERT: C 873 TYR cc_start: 0.9177 (OUTLIER) cc_final: 0.8828 (m-80) outliers start: 130 outliers final: 78 residues processed: 231 average time/residue: 0.3172 time to fit residues: 125.3677 Evaluate side-chains 198 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 110 time to evaluate : 2.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 245 ASN Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1039 ARG Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 103 optimal weight: 1.9990 chunk 276 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 180 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 307 optimal weight: 3.9990 chunk 255 optimal weight: 1.9990 chunk 142 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 101 optimal weight: 0.7980 chunk 161 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN C 317 ASN C 448 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 26424 Z= 0.199 Angle : 0.623 9.123 35958 Z= 0.315 Chirality : 0.048 0.622 4251 Planarity : 0.004 0.056 4557 Dihedral : 7.701 97.055 4779 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.38 % Favored : 92.59 % Rotamer: Outliers : 3.46 % Allowed : 23.15 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.15), residues: 3159 helix: 0.99 (0.20), residues: 702 sheet: -1.48 (0.20), residues: 630 loop : -1.83 (0.14), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP B 104 HIS 0.002 0.000 HIS C1048 PHE 0.021 0.001 PHE C 592 TYR 0.016 0.001 TYR C1067 ARG 0.005 0.000 ARG C1107 *********************** 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 230 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 134 time to evaluate : 2.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 492 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7501 (pt) REVERT: A 759 PHE cc_start: 0.8659 (OUTLIER) cc_final: 0.8440 (t80) REVERT: A 981 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8401 (mm) REVERT: A 1029 MET cc_start: 0.9114 (tpp) cc_final: 0.8885 (tpp) REVERT: B 421 TYR cc_start: 0.7609 (m-10) cc_final: 0.7171 (m-10) REVERT: B 588 THR cc_start: 0.9307 (OUTLIER) cc_final: 0.9051 (p) REVERT: B 699 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8783 (mt) REVERT: B 869 MET cc_start: 0.8565 (pmm) cc_final: 0.8276 (pmm) REVERT: C 46 SER cc_start: 0.8549 (m) cc_final: 0.8151 (p) REVERT: C 129 LYS cc_start: 0.7697 (OUTLIER) cc_final: 0.7396 (tttt) REVERT: C 133 PHE cc_start: 0.7219 (OUTLIER) cc_final: 0.6484 (m-80) REVERT: C 176 LEU cc_start: 0.5262 (OUTLIER) cc_final: 0.4665 (mp) REVERT: C 214 ARG cc_start: 0.0954 (OUTLIER) cc_final: 0.0709 (mmm160) REVERT: C 873 TYR cc_start: 0.9100 (OUTLIER) cc_final: 0.8804 (m-80) REVERT: C 1039 ARG cc_start: 0.8755 (OUTLIER) cc_final: 0.8425 (ptm160) outliers start: 96 outliers final: 54 residues processed: 221 average time/residue: 0.3100 time to fit residues: 117.0650 Evaluate side-chains 182 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 117 time to evaluate : 2.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1039 ARG Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 296 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 175 optimal weight: 4.9990 chunk 224 optimal weight: 8.9990 chunk 174 optimal weight: 1.9990 chunk 259 optimal weight: 6.9990 chunk 171 optimal weight: 2.9990 chunk 306 optimal weight: 4.9990 chunk 191 optimal weight: 2.9990 chunk 186 optimal weight: 2.9990 chunk 141 optimal weight: 20.0000 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 26424 Z= 0.255 Angle : 0.643 10.771 35958 Z= 0.323 Chirality : 0.049 0.618 4251 Planarity : 0.004 0.058 4557 Dihedral : 7.512 94.515 4779 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.44 % Favored : 92.53 % Rotamer: Outliers : 3.31 % Allowed : 23.11 % Favored : 73.58 % 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: -1.61 (0.15), residues: 3159 helix: 0.95 (0.20), residues: 705 sheet: -1.47 (0.20), residues: 630 loop : -1.80 (0.14), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP B 104 HIS 0.003 0.001 HIS B 207 PHE 0.019 0.001 PHE C 592 TYR 0.015 0.001 TYR C 265 ARG 0.004 0.000 ARG B 319 *********************** 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 212 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 120 time to evaluate : 3.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 492 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7551 (pt) REVERT: A 759 PHE cc_start: 0.8722 (OUTLIER) cc_final: 0.8514 (t80) REVERT: A 981 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8414 (mm) REVERT: B 421 TYR cc_start: 0.7682 (m-10) cc_final: 0.7070 (m-10) REVERT: B 588 THR cc_start: 0.9328 (OUTLIER) cc_final: 0.9119 (p) REVERT: B 699 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8794 (mt) REVERT: B 869 MET cc_start: 0.8604 (pmm) cc_final: 0.8342 (pmm) REVERT: B 873 TYR cc_start: 0.9438 (OUTLIER) cc_final: 0.9131 (m-10) REVERT: C 46 SER cc_start: 0.8600 (m) cc_final: 0.8234 (p) REVERT: C 129 LYS cc_start: 0.7695 (OUTLIER) cc_final: 0.7432 (tttt) REVERT: C 133 PHE cc_start: 0.7319 (OUTLIER) cc_final: 0.6496 (m-80) REVERT: C 176 LEU cc_start: 0.5221 (OUTLIER) cc_final: 0.4419 (mp) REVERT: C 214 ARG cc_start: 0.0839 (OUTLIER) cc_final: 0.0584 (mmm160) REVERT: C 873 TYR cc_start: 0.9127 (OUTLIER) cc_final: 0.8837 (m-80) outliers start: 92 outliers final: 63 residues processed: 205 average time/residue: 0.3254 time to fit residues: 112.1008 Evaluate side-chains 190 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 116 time to evaluate : 2.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 189 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 183 optimal weight: 10.0000 chunk 92 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 194 optimal weight: 5.9990 chunk 208 optimal weight: 0.9990 chunk 151 optimal weight: 0.2980 chunk 28 optimal weight: 10.0000 chunk 240 optimal weight: 0.6980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 26424 Z= 0.223 Angle : 0.623 9.401 35958 Z= 0.314 Chirality : 0.048 0.617 4251 Planarity : 0.004 0.065 4557 Dihedral : 7.348 92.308 4779 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 3.49 % Allowed : 23.00 % Favored : 73.51 % 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: -1.57 (0.15), residues: 3159 helix: 0.98 (0.20), residues: 699 sheet: -1.44 (0.20), residues: 630 loop : -1.77 (0.14), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP B 104 HIS 0.002 0.000 HIS C1048 PHE 0.026 0.001 PHE B 592 TYR 0.017 0.001 TYR A 380 ARG 0.006 0.000 ARG B 319 *********************** 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 221 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 124 time to evaluate : 2.757 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 492 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7556 (pt) REVERT: A 759 PHE cc_start: 0.8750 (OUTLIER) cc_final: 0.8533 (t80) REVERT: A 981 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8385 (mm) REVERT: B 421 TYR cc_start: 0.7648 (m-10) cc_final: 0.7134 (m-10) REVERT: B 699 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8854 (mt) REVERT: B 869 MET cc_start: 0.8632 (pmm) cc_final: 0.8336 (pmm) REVERT: B 873 TYR cc_start: 0.9425 (OUTLIER) cc_final: 0.9128 (m-10) REVERT: C 129 LYS cc_start: 0.7679 (OUTLIER) cc_final: 0.7417 (tttt) REVERT: C 133 PHE cc_start: 0.7243 (OUTLIER) cc_final: 0.6356 (m-80) REVERT: C 176 LEU cc_start: 0.5309 (OUTLIER) cc_final: 0.4504 (mp) REVERT: C 873 TYR cc_start: 0.9092 (OUTLIER) cc_final: 0.8772 (m-80) REVERT: C 973 ILE cc_start: 0.9211 (OUTLIER) cc_final: 0.8973 (pt) outliers start: 97 outliers final: 63 residues processed: 212 average time/residue: 0.3210 time to fit residues: 115.0353 Evaluate side-chains 189 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 116 time to evaluate : 2.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 278 optimal weight: 0.9990 chunk 293 optimal weight: 1.9990 chunk 267 optimal weight: 0.9980 chunk 285 optimal weight: 7.9990 chunk 171 optimal weight: 4.9990 chunk 124 optimal weight: 9.9990 chunk 224 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 258 optimal weight: 7.9990 chunk 270 optimal weight: 1.9990 chunk 284 optimal weight: 0.7980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 26424 Z= 0.208 Angle : 0.622 9.713 35958 Z= 0.310 Chirality : 0.048 0.621 4251 Planarity : 0.004 0.057 4557 Dihedral : 7.169 90.214 4775 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 2.88 % Allowed : 23.83 % Favored : 73.29 % 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: -1.53 (0.15), residues: 3159 helix: 1.05 (0.20), residues: 699 sheet: -1.39 (0.20), residues: 624 loop : -1.76 (0.14), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP B 104 HIS 0.002 0.000 HIS C1048 PHE 0.030 0.001 PHE B 592 TYR 0.015 0.001 TYR B 501 ARG 0.005 0.000 ARG B 319 *********************** 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 203 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 123 time to evaluate : 2.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 492 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7608 (pt) REVERT: A 981 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8364 (mm) REVERT: B 421 TYR cc_start: 0.7676 (m-10) cc_final: 0.6993 (m-10) REVERT: B 699 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8847 (mt) REVERT: B 869 MET cc_start: 0.8615 (pmm) cc_final: 0.8339 (pmm) REVERT: B 873 TYR cc_start: 0.9422 (OUTLIER) cc_final: 0.9132 (m-10) REVERT: B 1050 MET cc_start: 0.7682 (mtm) cc_final: 0.7322 (mtm) REVERT: C 129 LYS cc_start: 0.7709 (OUTLIER) cc_final: 0.7471 (tttt) REVERT: C 133 PHE cc_start: 0.7146 (OUTLIER) cc_final: 0.6278 (m-80) REVERT: C 176 LEU cc_start: 0.5322 (OUTLIER) cc_final: 0.4519 (mp) REVERT: C 873 TYR cc_start: 0.9059 (OUTLIER) cc_final: 0.8767 (m-80) REVERT: C 973 ILE cc_start: 0.9208 (OUTLIER) cc_final: 0.8984 (pt) outliers start: 80 outliers final: 60 residues processed: 195 average time/residue: 0.3207 time to fit residues: 106.6647 Evaluate side-chains 184 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 115 time to evaluate : 2.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 187 optimal weight: 0.2980 chunk 302 optimal weight: 1.9990 chunk 184 optimal weight: 0.5980 chunk 143 optimal weight: 30.0000 chunk 209 optimal weight: 4.9990 chunk 316 optimal weight: 5.9990 chunk 291 optimal weight: 3.9990 chunk 252 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 194 optimal weight: 0.9990 chunk 154 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN B 188 ASN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 26424 Z= 0.221 Angle : 0.627 9.426 35958 Z= 0.314 Chirality : 0.048 0.617 4251 Planarity : 0.004 0.061 4557 Dihedral : 7.101 88.825 4775 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 2.95 % Allowed : 23.87 % Favored : 73.18 % 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: -1.50 (0.15), residues: 3159 helix: 1.05 (0.20), residues: 705 sheet: -1.40 (0.20), residues: 624 loop : -1.73 (0.14), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP B 104 HIS 0.002 0.001 HIS C1048 PHE 0.031 0.001 PHE B 201 TYR 0.015 0.001 TYR A 741 ARG 0.007 0.000 ARG B 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 201 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 119 time to evaluate : 2.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 492 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7644 (pt) REVERT: B 104 TRP cc_start: 0.6008 (m-10) cc_final: 0.5773 (m-10) REVERT: B 421 TYR cc_start: 0.7676 (m-10) cc_final: 0.6982 (m-10) REVERT: B 699 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8806 (mt) REVERT: B 869 MET cc_start: 0.8637 (pmm) cc_final: 0.8339 (pmm) REVERT: B 873 TYR cc_start: 0.9429 (OUTLIER) cc_final: 0.9128 (m-10) REVERT: B 902 MET cc_start: 0.9022 (tpp) cc_final: 0.8660 (tpt) REVERT: C 129 LYS cc_start: 0.7723 (OUTLIER) cc_final: 0.7489 (tttt) REVERT: C 133 PHE cc_start: 0.7164 (OUTLIER) cc_final: 0.6311 (m-80) REVERT: C 176 LEU cc_start: 0.5232 (OUTLIER) cc_final: 0.4405 (mp) REVERT: C 873 TYR cc_start: 0.9064 (OUTLIER) cc_final: 0.8749 (m-80) REVERT: C 973 ILE cc_start: 0.9209 (OUTLIER) cc_final: 0.8988 (pt) outliers start: 82 outliers final: 61 residues processed: 194 average time/residue: 0.3325 time to fit residues: 108.9708 Evaluate side-chains 179 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 110 time to evaluate : 2.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 328 ARG Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 200 optimal weight: 0.6980 chunk 268 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 232 optimal weight: 0.9980 chunk 37 optimal weight: 0.0980 chunk 70 optimal weight: 0.5980 chunk 252 optimal weight: 6.9990 chunk 105 optimal weight: 8.9990 chunk 259 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 46 optimal weight: 9.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.089692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.069635 restraints weight = 88505.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.072024 restraints weight = 43334.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.073578 restraints weight = 27439.452| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.3372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 26424 Z= 0.177 Angle : 0.623 12.165 35958 Z= 0.311 Chirality : 0.048 0.623 4251 Planarity : 0.004 0.057 4557 Dihedral : 6.948 86.329 4775 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 2.52 % Allowed : 24.37 % Favored : 73.11 % 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: -1.36 (0.15), residues: 3159 helix: 1.28 (0.20), residues: 687 sheet: -1.14 (0.19), residues: 669 loop : -1.74 (0.14), residues: 1803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP B 104 HIS 0.002 0.000 HIS C1048 PHE 0.018 0.001 PHE C 238 TYR 0.025 0.001 TYR B 369 ARG 0.011 0.000 ARG B 319 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3886.40 seconds wall clock time: 72 minutes 22.05 seconds (4342.05 seconds total)