Starting phenix.real_space_refine on Fri Aug 9 13:00:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x5q_38072/08_2024/8x5q_38072.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x5q_38072/08_2024/8x5q_38072.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x5q_38072/08_2024/8x5q_38072.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x5q_38072/08_2024/8x5q_38072.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x5q_38072/08_2024/8x5q_38072.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x5q_38072/08_2024/8x5q_38072.cif" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.066 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 111 5.16 5 C 16689 2.51 5 N 4278 2.21 5 O 5130 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 53": "OD1" <-> "OD2" Residue "C PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 138": "OD1" <-> "OD2" Residue "C PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 568": "OD1" <-> "OD2" Residue "C GLU 773": "OE1" <-> "OE2" Residue "C TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 979": "OD1" <-> "OD2" Residue "C ASP 985": "OD1" <-> "OD2" Residue "C GLU 988": "OE1" <-> "OE2" Residue "C ASP 994": "OD1" <-> "OD2" Residue "C GLU 1031": "OE1" <-> "OE2" Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 53": "OD1" <-> "OD2" Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 138": "OD1" <-> "OD2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A ARG 355": "NH1" <-> "NH2" Residue "A PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 927": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 985": "OD1" <-> "OD2" Residue "A ASP 994": "OD1" <-> "OD2" Residue "A PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 138": "OD1" <-> "OD2" Residue "B PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 471": "OE1" <-> "OE2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 927": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 979": "OD1" <-> "OD2" Residue "B ASP 985": "OD1" <-> "OD2" Residue "B GLU 990": "OE1" <-> "OE2" Residue "B ASP 994": "OD1" <-> "OD2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 26208 Number of models: 1 Model: "" Number of chains: 27 Chain: "C" Number of atoms: 8442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1086, 8442 Classifications: {'peptide': 1086} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 7} Link IDs: {'PTRANS': 58, 'TRANS': 1027} Chain breaks: 3 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 3, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "A" Number of atoms: 8442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1086, 8442 Classifications: {'peptide': 1086} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 7} Link IDs: {'PTRANS': 58, 'TRANS': 1027} Chain breaks: 3 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 3, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "B" Number of atoms: 8442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1086, 8442 Classifications: {'peptide': 1086} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 7} Link IDs: {'PTRANS': 58, 'TRANS': 1027} Chain breaks: 3 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 3, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 13.91, per 1000 atoms: 0.53 Number of scatterers: 26208 At special positions: 0 Unit cell: (150, 140, 167, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 111 16.00 O 5130 8.00 N 4278 7.00 C 16689 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.02 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.02 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.02 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.02 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 603 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A 616 " " NAG B1301 " - " ASN B 616 " " NAG B1302 " - " ASN B 61 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 603 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 657 " " NAG B1307 " - " ASN B 709 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 603 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C 709 " " NAG C1307 " - " ASN C 616 " " NAG D 1 " - " ASN C 122 " " NAG E 1 " - " ASN C 165 " " NAG F 1 " - " ASN C 234 " " NAG G 1 " - " ASN C 343 " " NAG H 1 " - " ASN C 354 " " NAG I 1 " - " ASN C1098 " " NAG J 1 " - " ASN C1134 " " NAG K 1 " - " ASN A 122 " " NAG L 1 " - " ASN A 165 " " NAG M 1 " - " ASN A 234 " " NAG N 1 " - " ASN A 343 " " NAG O 1 " - " ASN A 354 " " NAG P 1 " - " ASN A1098 " " NAG Q 1 " - " ASN A1134 " " NAG R 1 " - " ASN B 122 " " NAG S 1 " - " ASN B 165 " " NAG T 1 " - " ASN B 234 " " NAG U 1 " - " ASN B 343 " " NAG V 1 " - " ASN B 354 " " NAG W 1 " - " ASN B1098 " " NAG X 1 " - " ASN B1134 " Time building additional restraints: 10.91 Conformation dependent library (CDL) restraints added in 4.8 seconds 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6096 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 51 sheets defined 21.3% alpha, 17.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.18 Creating SS restraints... Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 386 through 389 Processing helix chain 'C' and resid 403 through 407 Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.712A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 760 through 783 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 850 through 854 removed outlier: 3.660A pdb=" N LYS C 854 " --> pdb=" O ILE C 850 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 850 through 854' Processing helix chain 'C' and resid 869 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 941 removed outlier: 4.299A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.605A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.782A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 386 through 389 Processing helix chain 'A' and resid 403 through 407 Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.694A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 783 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 850 through 854 removed outlier: 3.646A pdb=" N LYS A 854 " --> pdb=" O ILE A 850 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 850 through 854' Processing helix chain 'A' and resid 869 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.586A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 941 removed outlier: 4.460A pdb=" N VAL A 915 " --> pdb=" O VAL A 911 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.584A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.016A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 247 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 403 through 407 Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.722A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 783 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 850 through 854 removed outlier: 3.579A pdb=" N LYS B 854 " --> pdb=" O ILE B 850 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 850 through 854' Processing helix chain 'B' and resid 869 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.535A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 911 through 941 removed outlier: 4.466A pdb=" N VAL B 915 " --> pdb=" O VAL B 911 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.593A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.339A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 26 through 30 removed outlier: 3.643A pdb=" N SER C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 42 through 43 removed outlier: 5.603A pdb=" N PHE C 43 " --> pdb=" O ARG B 567 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43 removed outlier: 5.603A pdb=" N PHE C 43 " --> pdb=" O ARG B 567 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.571A pdb=" N GLN C 271 " --> pdb=" O PHE C 55 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.259A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 120 through 122 Processing sheet with id=AA7, first strand: chain 'C' and resid 311 through 317 removed outlier: 7.200A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 325 through 326 removed outlier: 7.666A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 325 through 326 removed outlier: 7.666A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.240A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N THR C 430 " --> pdb=" O PHE C 515 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.302A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 452 through 454 removed outlier: 4.430A pdb=" N TYR C 453 " --> pdb=" O GLN C 493 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLN C 493 " --> pdb=" O TYR C 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 654 through 656 removed outlier: 5.572A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 701 through 702 removed outlier: 6.545A pdb=" N ALA C 701 " --> pdb=" O ILE A 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AB7, first strand: chain 'C' and resid 719 through 727 removed outlier: 7.606A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 734 through 735 Processing sheet with id=AB9, first strand: chain 'C' and resid 787 through 788 Processing sheet with id=AC1, first strand: chain 'C' and resid 1081 through 1082 Processing sheet with id=AC2, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AC3, first strand: chain 'A' and resid 26 through 30 removed outlier: 3.676A pdb=" N SER A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER A 94 " --> pdb=" O ARG A 190 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 50 through 55 removed outlier: 4.070A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.250A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 120 through 122 Processing sheet with id=AC7, first strand: chain 'A' and resid 311 through 317 removed outlier: 7.221A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 325 through 326 removed outlier: 7.621A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 325 through 326 removed outlier: 7.621A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 356 through 358 removed outlier: 4.166A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N THR A 430 " --> pdb=" O PHE A 515 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.384A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 452 through 454 removed outlier: 4.334A pdb=" N TYR A 453 " --> pdb=" O GLN A 493 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLN A 493 " --> pdb=" O TYR A 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'A' and resid 654 through 656 removed outlier: 5.574A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.566A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AD7, first strand: chain 'A' and resid 719 through 727 removed outlier: 7.573A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 734 through 735 Processing sheet with id=AD9, first strand: chain 'A' and resid 1081 through 1082 Processing sheet with id=AE1, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AE2, first strand: chain 'B' and resid 26 through 30 removed outlier: 3.660A pdb=" N SER B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 50 through 55 removed outlier: 4.083A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.114A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 120 through 122 removed outlier: 3.526A pdb=" N VAL B 120 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 311 through 317 removed outlier: 7.143A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.052A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N THR B 430 " --> pdb=" O PHE B 515 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AE9, first strand: chain 'B' and resid 452 through 454 removed outlier: 4.336A pdb=" N TYR B 453 " --> pdb=" O GLN B 493 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLN B 493 " --> pdb=" O TYR B 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.437A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AF3, first strand: chain 'B' and resid 719 through 727 removed outlier: 7.332A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 734 through 735 Processing sheet with id=AF5, first strand: chain 'B' and resid 1081 through 1082 Processing sheet with id=AF6, first strand: chain 'B' and resid 1094 through 1097 826 hydrogen bonds defined for protein. 2238 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: 12.09 Time building geometry restraints manager: 11.86 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: 8085 1.34 - 1.46: 6456 1.46 - 1.59: 12135 1.59 - 1.71: 0 1.71 - 1.84: 138 Bond restraints: 26814 Sorted by residual: bond pdb=" N VAL C 70 " pdb=" CA VAL C 70 " ideal model delta sigma weight residual 1.456 1.494 -0.037 9.50e-03 1.11e+04 1.53e+01 bond pdb=" N VAL A 70 " pdb=" CA VAL A 70 " ideal model delta sigma weight residual 1.456 1.493 -0.037 9.50e-03 1.11e+04 1.52e+01 bond pdb=" N VAL C 159 " pdb=" CA VAL C 159 " ideal model delta sigma weight residual 1.455 1.494 -0.039 1.04e-02 9.25e+03 1.41e+01 bond pdb=" N GLY B 566 " pdb=" CA GLY B 566 " ideal model delta sigma weight residual 1.444 1.479 -0.035 1.02e-02 9.61e+03 1.21e+01 bond pdb=" N PHE C 140 " pdb=" CA PHE C 140 " ideal model delta sigma weight residual 1.458 1.488 -0.030 9.00e-03 1.23e+04 1.14e+01 ... (remaining 26809 not shown) Histogram of bond angle deviations from ideal: 96.61 - 104.17: 408 104.17 - 111.73: 12746 111.73 - 119.29: 9429 119.29 - 126.85: 13681 126.85 - 134.41: 261 Bond angle restraints: 36525 Sorted by residual: angle pdb=" N THR C 604 " pdb=" CA THR C 604 " pdb=" C THR C 604 " ideal model delta sigma weight residual 114.62 108.61 6.01 1.14e+00 7.69e-01 2.77e+01 angle pdb=" N THR B 604 " pdb=" CA THR B 604 " pdb=" C THR B 604 " ideal model delta sigma weight residual 114.62 108.62 6.00 1.14e+00 7.69e-01 2.77e+01 angle pdb=" N GLN A 628 " pdb=" CA GLN A 628 " pdb=" C GLN A 628 " ideal model delta sigma weight residual 114.56 107.96 6.60 1.27e+00 6.20e-01 2.70e+01 angle pdb=" N THR A 604 " pdb=" CA THR A 604 " pdb=" C THR A 604 " ideal model delta sigma weight residual 114.62 108.72 5.90 1.14e+00 7.69e-01 2.68e+01 angle pdb=" C PHE C 32 " pdb=" CA PHE C 32 " pdb=" CB PHE C 32 " ideal model delta sigma weight residual 116.54 111.06 5.48 1.15e+00 7.56e-01 2.27e+01 ... (remaining 36520 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.60: 14934 22.60 - 45.20: 1395 45.20 - 67.80: 233 67.80 - 90.40: 89 90.40 - 113.00: 122 Dihedral angle restraints: 16773 sinusoidal: 7287 harmonic: 9486 Sorted by residual: dihedral pdb=" CB CYS C 336 " pdb=" SG CYS C 336 " pdb=" SG CYS C 361 " pdb=" CB CYS C 361 " ideal model delta sinusoidal sigma weight residual 93.00 31.10 61.90 1 1.00e+01 1.00e-02 5.08e+01 dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual 93.00 31.10 61.90 1 1.00e+01 1.00e-02 5.08e+01 dihedral pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual 93.00 32.10 60.90 1 1.00e+01 1.00e-02 4.93e+01 ... (remaining 16770 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 3886 0.092 - 0.184: 413 0.184 - 0.276: 27 0.276 - 0.368: 4 0.368 - 0.460: 2 Chirality restraints: 4332 Sorted by residual: chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-02 2.50e+03 1.16e+02 chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.33 -0.07 2.00e-02 2.50e+03 1.36e+01 chirality pdb=" C1 NAG O 1 " pdb=" ND2 ASN A 354 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.30e+00 ... (remaining 4329 not shown) Planarity restraints: 4692 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1307 " -0.254 2.00e-02 2.50e+03 2.12e-01 5.62e+02 pdb=" C7 NAG B1307 " 0.070 2.00e-02 2.50e+03 pdb=" C8 NAG B1307 " -0.173 2.00e-02 2.50e+03 pdb=" N2 NAG B1307 " 0.355 2.00e-02 2.50e+03 pdb=" O7 NAG B1307 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1306 " 0.101 2.00e-02 2.50e+03 8.38e-02 8.77e+01 pdb=" C7 NAG A1306 " -0.029 2.00e-02 2.50e+03 pdb=" C8 NAG A1306 " 0.077 2.00e-02 2.50e+03 pdb=" N2 NAG A1306 " -0.134 2.00e-02 2.50e+03 pdb=" O7 NAG A1306 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 190 " 0.741 9.50e-02 1.11e+02 3.32e-01 6.71e+01 pdb=" NE ARG A 190 " -0.044 2.00e-02 2.50e+03 pdb=" CZ ARG A 190 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 190 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 190 " 0.022 2.00e-02 2.50e+03 ... (remaining 4689 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2155 2.74 - 3.28: 27214 3.28 - 3.82: 44072 3.82 - 4.36: 51547 4.36 - 4.90: 88873 Nonbonded interactions: 213861 Sorted by model distance: nonbonded pdb=" NH2 ARG B 34 " pdb=" O PRO B 217 " model vdw 2.198 3.120 nonbonded pdb=" O VAL C 608 " pdb=" OH TYR C 636 " model vdw 2.201 3.040 nonbonded pdb=" O VAL B 608 " pdb=" OH TYR B 636 " model vdw 2.205 3.040 nonbonded pdb=" NE2 GLN B 804 " pdb=" OE1 GLN B 935 " model vdw 2.207 3.120 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.207 3.040 ... (remaining 213856 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.910 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 71.920 Find NCS groups from input model: 1.620 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 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 0.078 26814 Z= 0.365 Angle : 0.801 8.200 36525 Z= 0.489 Chirality : 0.054 0.460 4332 Planarity : 0.009 0.332 4650 Dihedral : 20.555 112.997 10569 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.43 % Allowed : 9.15 % Favored : 90.41 % Rotamer: Outliers : 1.21 % Allowed : 22.41 % Favored : 76.38 % 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: -1.75 (0.14), residues: 3234 helix: 1.01 (0.21), residues: 624 sheet: -0.77 (0.20), residues: 636 loop : -2.14 (0.13), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 633 HIS 0.004 0.001 HIS C 519 PHE 0.047 0.001 PHE C 643 TYR 0.035 0.002 TYR A 655 ARG 0.008 0.001 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 268 time to evaluate : 2.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 137 ASN cc_start: 0.7038 (t0) cc_final: 0.6274 (p0) REVERT: C 141 LEU cc_start: 0.5370 (OUTLIER) cc_final: 0.4314 (tt) REVERT: C 298 GLU cc_start: 0.8718 (tp30) cc_final: 0.8517 (tp30) REVERT: C 457 ARG cc_start: 0.6180 (mtp-110) cc_final: 0.5694 (mtp-110) REVERT: A 141 LEU cc_start: 0.6414 (OUTLIER) cc_final: 0.6188 (mt) REVERT: A 655 TYR cc_start: 0.8361 (t80) cc_final: 0.8026 (t80) REVERT: B 582 LEU cc_start: 0.8435 (mp) cc_final: 0.8207 (pp) outliers start: 34 outliers final: 14 residues processed: 291 average time/residue: 0.3437 time to fit residues: 163.1197 Evaluate side-chains 227 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 211 time to evaluate : 2.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 663 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 273 optimal weight: 2.9990 chunk 245 optimal weight: 5.9990 chunk 136 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 165 optimal weight: 4.9990 chunk 131 optimal weight: 5.9990 chunk 253 optimal weight: 2.9990 chunk 98 optimal weight: 0.3980 chunk 154 optimal weight: 7.9990 chunk 189 optimal weight: 0.8980 chunk 294 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 239 GLN C 580 GLN C 613 GLN C 804 GLN C 895 GLN C 955 ASN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1088 HIS C1125 ASN A 69 HIS A 321 GLN A 580 GLN A 613 GLN A 804 GLN ** A 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN B 804 GLN B 955 ASN B1005 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 26814 Z= 0.230 Angle : 0.700 11.186 36525 Z= 0.344 Chirality : 0.050 0.414 4332 Planarity : 0.004 0.072 4650 Dihedral : 15.511 98.483 4839 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.04 % Favored : 91.68 % Rotamer: Outliers : 3.30 % Allowed : 21.06 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.14), residues: 3234 helix: 1.22 (0.21), residues: 609 sheet: -0.64 (0.19), residues: 648 loop : -2.01 (0.13), residues: 1977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 353 HIS 0.004 0.001 HIS B 519 PHE 0.022 0.001 PHE C 168 TYR 0.024 0.002 TYR B 796 ARG 0.007 0.001 ARG C 102 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 241 time to evaluate : 3.256 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 137 ASN cc_start: 0.7363 (t0) cc_final: 0.6827 (m-40) REVERT: C 170 TYR cc_start: 0.7701 (t80) cc_final: 0.7293 (t80) REVERT: C 290 ASP cc_start: 0.8479 (t0) cc_final: 0.8096 (m-30) REVERT: C 298 GLU cc_start: 0.8665 (tp30) cc_final: 0.8462 (tp30) REVERT: C 655 TYR cc_start: 0.8403 (t80) cc_final: 0.8009 (t80) REVERT: C 988 GLU cc_start: 0.8085 (tt0) cc_final: 0.7746 (mt-10) REVERT: A 136 CYS cc_start: 0.6541 (t) cc_final: 0.6177 (p) REVERT: A 140 PHE cc_start: 0.6861 (p90) cc_final: 0.6507 (p90) REVERT: A 141 LEU cc_start: 0.6386 (mm) cc_final: 0.6077 (mt) REVERT: A 176 LEU cc_start: 0.4446 (OUTLIER) cc_final: 0.4127 (pt) REVERT: A 338 PHE cc_start: 0.8450 (OUTLIER) cc_final: 0.7757 (t80) REVERT: A 655 TYR cc_start: 0.8324 (t80) cc_final: 0.8007 (t80) REVERT: A 1125 ASN cc_start: 0.7275 (t0) cc_final: 0.6993 (t0) REVERT: B 1031 GLU cc_start: 0.8468 (mt-10) cc_final: 0.8067 (mt-10) outliers start: 93 outliers final: 47 residues processed: 313 average time/residue: 0.3293 time to fit residues: 172.3275 Evaluate side-chains 252 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 203 time to evaluate : 2.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1130 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 163 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 244 optimal weight: 0.9980 chunk 200 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 294 optimal weight: 7.9990 chunk 318 optimal weight: 7.9990 chunk 262 optimal weight: 0.0570 chunk 292 optimal weight: 10.0000 chunk 100 optimal weight: 1.9990 chunk 236 optimal weight: 0.0470 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 HIS C 81 ASN C 245 HIS ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN ** A 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN B 580 GLN B 895 GLN B1002 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26814 Z= 0.187 Angle : 0.635 8.630 36525 Z= 0.310 Chirality : 0.049 0.572 4332 Planarity : 0.004 0.062 4650 Dihedral : 12.600 93.664 4820 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.70 % Favored : 92.18 % Rotamer: Outliers : 3.79 % Allowed : 21.74 % Favored : 74.47 % 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: -1.42 (0.14), residues: 3234 helix: 1.37 (0.21), residues: 618 sheet: -0.57 (0.19), residues: 648 loop : -1.95 (0.13), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 633 HIS 0.005 0.001 HIS B 245 PHE 0.014 0.001 PHE C 643 TYR 0.019 0.001 TYR B 170 ARG 0.005 0.000 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 234 time to evaluate : 3.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 52 GLN cc_start: 0.8285 (tm-30) cc_final: 0.7840 (tt0) REVERT: C 118 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.8116 (tt) REVERT: C 137 ASN cc_start: 0.7236 (t0) cc_final: 0.6765 (m-40) REVERT: C 298 GLU cc_start: 0.8652 (tp30) cc_final: 0.8443 (tp30) REVERT: C 362 VAL cc_start: 0.8757 (p) cc_final: 0.8379 (m) REVERT: C 655 TYR cc_start: 0.8511 (t80) cc_final: 0.8054 (t80) REVERT: C 988 GLU cc_start: 0.8132 (tt0) cc_final: 0.7855 (mt-10) REVERT: A 136 CYS cc_start: 0.6320 (t) cc_final: 0.6082 (p) REVERT: A 176 LEU cc_start: 0.4310 (OUTLIER) cc_final: 0.3934 (pt) REVERT: A 338 PHE cc_start: 0.8424 (OUTLIER) cc_final: 0.7792 (t80) REVERT: A 655 TYR cc_start: 0.8426 (t80) cc_final: 0.8109 (t80) REVERT: A 1125 ASN cc_start: 0.7087 (t0) cc_final: 0.6706 (t0) REVERT: B 197 ILE cc_start: 0.7494 (tp) cc_final: 0.7286 (tt) REVERT: B 633 TRP cc_start: 0.7670 (p-90) cc_final: 0.7375 (p-90) REVERT: B 1031 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8163 (mt-10) outliers start: 107 outliers final: 60 residues processed: 314 average time/residue: 0.3179 time to fit residues: 169.4883 Evaluate side-chains 263 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 200 time to evaluate : 2.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1130 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 291 optimal weight: 3.9990 chunk 221 optimal weight: 5.9990 chunk 152 optimal weight: 10.0000 chunk 32 optimal weight: 0.8980 chunk 140 optimal weight: 1.9990 chunk 197 optimal weight: 5.9990 chunk 295 optimal weight: 5.9990 chunk 313 optimal weight: 0.9990 chunk 154 optimal weight: 5.9990 chunk 280 optimal weight: 5.9990 chunk 84 optimal weight: 0.8980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 409 GLN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 GLN B 239 GLN B 321 GLN B 493 GLN B 613 GLN B1005 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 26814 Z= 0.323 Angle : 0.681 7.966 36525 Z= 0.335 Chirality : 0.050 0.450 4332 Planarity : 0.004 0.072 4650 Dihedral : 10.864 88.311 4818 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.84 % Favored : 91.13 % Rotamer: Outliers : 5.32 % Allowed : 20.85 % Favored : 73.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.14), residues: 3234 helix: 1.09 (0.21), residues: 618 sheet: -0.52 (0.20), residues: 612 loop : -1.95 (0.13), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 633 HIS 0.005 0.001 HIS B 519 PHE 0.019 0.002 PHE A 823 TYR 0.026 0.002 TYR C 380 ARG 0.008 0.001 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 195 time to evaluate : 2.928 Fit side-chains revert: symmetry clash REVERT: C 118 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8327 (tt) REVERT: C 229 LEU cc_start: 0.6705 (OUTLIER) cc_final: 0.6437 (pp) REVERT: C 265 TYR cc_start: 0.5924 (OUTLIER) cc_final: 0.4865 (t80) REVERT: C 266 TYR cc_start: 0.8292 (m-80) cc_final: 0.8018 (m-80) REVERT: C 298 GLU cc_start: 0.8692 (tp30) cc_final: 0.8394 (tp30) REVERT: C 655 TYR cc_start: 0.8663 (t80) cc_final: 0.7983 (t80) REVERT: C 988 GLU cc_start: 0.8180 (tt0) cc_final: 0.7827 (mt-10) REVERT: C 1050 MET cc_start: 0.9124 (ptt) cc_final: 0.8832 (ptp) REVERT: C 1125 ASN cc_start: 0.7134 (t0) cc_final: 0.6450 (t0) REVERT: A 136 CYS cc_start: 0.6644 (t) cc_final: 0.6293 (p) REVERT: A 176 LEU cc_start: 0.4484 (OUTLIER) cc_final: 0.4079 (pt) REVERT: A 265 TYR cc_start: 0.6477 (OUTLIER) cc_final: 0.6001 (t80) REVERT: A 655 TYR cc_start: 0.8608 (t80) cc_final: 0.8128 (t80) REVERT: A 764 LYS cc_start: 0.7476 (OUTLIER) cc_final: 0.7048 (ttpp) REVERT: A 1125 ASN cc_start: 0.7377 (t0) cc_final: 0.6838 (t0) REVERT: B 229 LEU cc_start: 0.6490 (OUTLIER) cc_final: 0.6269 (pp) REVERT: B 265 TYR cc_start: 0.6167 (OUTLIER) cc_final: 0.4501 (t80) REVERT: B 266 TYR cc_start: 0.8325 (m-80) cc_final: 0.8110 (m-80) REVERT: B 633 TRP cc_start: 0.7915 (p-90) cc_final: 0.7609 (p-90) REVERT: B 1031 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8293 (mt-10) REVERT: B 1125 ASN cc_start: 0.7206 (t0) cc_final: 0.6584 (t0) outliers start: 150 outliers final: 89 residues processed: 319 average time/residue: 0.3269 time to fit residues: 177.5160 Evaluate side-chains 262 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 164 time to evaluate : 2.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1028 LYS Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1141 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 260 optimal weight: 30.0000 chunk 177 optimal weight: 0.8980 chunk 4 optimal weight: 6.9990 chunk 233 optimal weight: 8.9990 chunk 129 optimal weight: 9.9990 chunk 267 optimal weight: 0.9990 chunk 216 optimal weight: 10.0000 chunk 0 optimal weight: 4.9990 chunk 159 optimal weight: 7.9990 chunk 281 optimal weight: 7.9990 chunk 79 optimal weight: 5.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 188 ASN C 321 GLN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.136 26814 Z= 0.597 Angle : 0.827 12.657 36525 Z= 0.413 Chirality : 0.054 0.424 4332 Planarity : 0.005 0.071 4650 Dihedral : 10.572 88.680 4818 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.05 % Favored : 89.92 % Rotamer: Outliers : 6.49 % Allowed : 20.85 % Favored : 72.66 % 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: -2.01 (0.14), residues: 3234 helix: 0.49 (0.20), residues: 618 sheet: -0.74 (0.20), residues: 594 loop : -2.25 (0.12), residues: 2022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 633 HIS 0.009 0.002 HIS A 519 PHE 0.024 0.002 PHE B 592 TYR 0.036 0.003 TYR C 380 ARG 0.008 0.001 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 162 time to evaluate : 2.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 34 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7908 (tpp-160) REVERT: C 118 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8456 (tt) REVERT: C 202 LYS cc_start: 0.6843 (mptt) cc_final: 0.6614 (mptt) REVERT: C 265 TYR cc_start: 0.7079 (OUTLIER) cc_final: 0.6062 (t80) REVERT: C 394 ASN cc_start: 0.7787 (OUTLIER) cc_final: 0.7111 (t0) REVERT: C 655 TYR cc_start: 0.8800 (t80) cc_final: 0.8024 (t80) REVERT: C 988 GLU cc_start: 0.8329 (tt0) cc_final: 0.8120 (mt-10) REVERT: C 1050 MET cc_start: 0.9249 (ptt) cc_final: 0.9009 (ptp) REVERT: C 1125 ASN cc_start: 0.7909 (t0) cc_final: 0.7224 (t0) REVERT: A 176 LEU cc_start: 0.5077 (OUTLIER) cc_final: 0.4580 (pt) REVERT: A 265 TYR cc_start: 0.6850 (OUTLIER) cc_final: 0.6041 (t80) REVERT: A 338 PHE cc_start: 0.8957 (OUTLIER) cc_final: 0.8424 (t80) REVERT: A 346 ARG cc_start: 0.6967 (mmm160) cc_final: 0.6629 (ttm-80) REVERT: A 365 TYR cc_start: 0.8782 (m-80) cc_final: 0.8339 (m-80) REVERT: A 655 TYR cc_start: 0.8688 (t80) cc_final: 0.8325 (t80) REVERT: A 754 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8372 (mp) REVERT: A 878 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8276 (mp) REVERT: A 994 ASP cc_start: 0.8532 (t0) cc_final: 0.8193 (t0) REVERT: A 1014 ARG cc_start: 0.8623 (OUTLIER) cc_final: 0.8109 (mtt90) REVERT: A 1125 ASN cc_start: 0.7912 (t0) cc_final: 0.7203 (t0) REVERT: B 229 LEU cc_start: 0.7151 (OUTLIER) cc_final: 0.6915 (pp) REVERT: B 265 TYR cc_start: 0.7290 (OUTLIER) cc_final: 0.5908 (t80) REVERT: B 346 ARG cc_start: 0.7047 (mmm160) cc_final: 0.6707 (ttm-80) REVERT: B 633 TRP cc_start: 0.8147 (p-90) cc_final: 0.7775 (p-90) REVERT: B 752 LEU cc_start: 0.9196 (tt) cc_final: 0.8934 (tt) REVERT: B 1017 GLU cc_start: 0.8509 (tm-30) cc_final: 0.8256 (tt0) REVERT: B 1125 ASN cc_start: 0.7754 (t0) cc_final: 0.7363 (t0) outliers start: 183 outliers final: 113 residues processed: 320 average time/residue: 0.3267 time to fit residues: 175.9948 Evaluate side-chains 265 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 140 time to evaluate : 2.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1028 LYS Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1014 ARG Chi-restraints excluded: chain A residue 1028 LYS Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1028 LYS Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1130 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 105 optimal weight: 0.9980 chunk 282 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 183 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 313 optimal weight: 0.6980 chunk 260 optimal weight: 50.0000 chunk 145 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 103 optimal weight: 4.9990 chunk 164 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 317 ASN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 317 ASN A 394 ASN A 409 GLN ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 ASN B 388 ASN B 409 GLN ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.3500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 26814 Z= 0.232 Angle : 0.662 8.362 36525 Z= 0.332 Chirality : 0.049 0.446 4332 Planarity : 0.004 0.079 4650 Dihedral : 9.915 86.863 4817 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer: Outliers : 4.72 % Allowed : 22.52 % Favored : 72.77 % 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: -1.77 (0.14), residues: 3234 helix: 0.85 (0.21), residues: 627 sheet: -0.71 (0.21), residues: 579 loop : -2.11 (0.13), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 633 HIS 0.004 0.001 HIS B 519 PHE 0.022 0.001 PHE B 643 TYR 0.022 0.002 TYR C 380 ARG 0.004 0.001 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 176 time to evaluate : 2.760 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 118 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8446 (tt) REVERT: C 265 TYR cc_start: 0.6328 (OUTLIER) cc_final: 0.5172 (t80) REVERT: C 298 GLU cc_start: 0.8667 (tp30) cc_final: 0.8322 (tp30) REVERT: C 365 TYR cc_start: 0.8665 (m-80) cc_final: 0.8361 (m-80) REVERT: C 655 TYR cc_start: 0.8735 (t80) cc_final: 0.8219 (t80) REVERT: C 895 GLN cc_start: 0.8655 (OUTLIER) cc_final: 0.8117 (pt0) REVERT: C 1125 ASN cc_start: 0.7708 (t0) cc_final: 0.6960 (t0) REVERT: A 176 LEU cc_start: 0.5026 (OUTLIER) cc_final: 0.4535 (pt) REVERT: A 265 TYR cc_start: 0.6380 (OUTLIER) cc_final: 0.5756 (t80) REVERT: A 346 ARG cc_start: 0.6895 (mmm160) cc_final: 0.6542 (ttm-80) REVERT: A 365 TYR cc_start: 0.8727 (m-80) cc_final: 0.8316 (m-80) REVERT: A 655 TYR cc_start: 0.8633 (t80) cc_final: 0.8332 (t80) REVERT: A 754 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8334 (mp) REVERT: A 878 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.7886 (mp) REVERT: A 1028 LYS cc_start: 0.9385 (OUTLIER) cc_final: 0.9155 (mttm) REVERT: A 1125 ASN cc_start: 0.7776 (t0) cc_final: 0.7061 (t0) REVERT: B 52 GLN cc_start: 0.8624 (tm-30) cc_final: 0.8410 (tm-30) REVERT: B 69 HIS cc_start: 0.5835 (OUTLIER) cc_final: 0.3901 (t70) REVERT: B 201 PHE cc_start: 0.6035 (OUTLIER) cc_final: 0.5812 (m-80) REVERT: B 229 LEU cc_start: 0.7043 (OUTLIER) cc_final: 0.6737 (pp) REVERT: B 265 TYR cc_start: 0.6625 (OUTLIER) cc_final: 0.5544 (t80) REVERT: B 294 ASP cc_start: 0.7613 (m-30) cc_final: 0.7391 (m-30) REVERT: B 633 TRP cc_start: 0.8034 (p-90) cc_final: 0.7782 (p-90) REVERT: B 752 LEU cc_start: 0.9144 (tt) cc_final: 0.8898 (tt) REVERT: B 1017 GLU cc_start: 0.8479 (tm-30) cc_final: 0.8236 (tt0) REVERT: B 1125 ASN cc_start: 0.7635 (t0) cc_final: 0.7128 (t0) outliers start: 133 outliers final: 85 residues processed: 285 average time/residue: 0.3209 time to fit residues: 154.3677 Evaluate side-chains 241 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 144 time to evaluate : 2.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 1028 LYS Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 1028 LYS Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1141 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 302 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 178 optimal weight: 1.9990 chunk 228 optimal weight: 9.9990 chunk 177 optimal weight: 0.7980 chunk 263 optimal weight: 0.8980 chunk 175 optimal weight: 3.9990 chunk 312 optimal weight: 0.9980 chunk 195 optimal weight: 0.8980 chunk 190 optimal weight: 4.9990 chunk 144 optimal weight: 4.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN A 394 ASN B 317 ASN B 493 GLN B 751 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 26814 Z= 0.258 Angle : 0.651 11.648 36525 Z= 0.324 Chirality : 0.048 0.426 4332 Planarity : 0.004 0.080 4650 Dihedral : 9.405 85.278 4817 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.37 % Favored : 90.63 % Rotamer: Outliers : 4.50 % Allowed : 22.87 % Favored : 72.62 % 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: -1.70 (0.14), residues: 3234 helix: 0.86 (0.21), residues: 636 sheet: -0.62 (0.21), residues: 555 loop : -2.06 (0.13), residues: 2043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 633 HIS 0.004 0.001 HIS B 519 PHE 0.018 0.001 PHE B 592 TYR 0.021 0.002 TYR C 380 ARG 0.007 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 166 time to evaluate : 3.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 118 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8402 (tt) REVERT: C 265 TYR cc_start: 0.6296 (OUTLIER) cc_final: 0.5159 (t80) REVERT: C 298 GLU cc_start: 0.8670 (tp30) cc_final: 0.8328 (tp30) REVERT: C 365 TYR cc_start: 0.8674 (m-80) cc_final: 0.8311 (m-80) REVERT: C 655 TYR cc_start: 0.8735 (t80) cc_final: 0.8222 (t80) REVERT: C 1125 ASN cc_start: 0.7739 (t0) cc_final: 0.6947 (t0) REVERT: A 176 LEU cc_start: 0.5014 (OUTLIER) cc_final: 0.4515 (pt) REVERT: A 265 TYR cc_start: 0.6398 (OUTLIER) cc_final: 0.5779 (t80) REVERT: A 346 ARG cc_start: 0.6922 (mmm160) cc_final: 0.6573 (ttm-80) REVERT: A 365 TYR cc_start: 0.8734 (m-80) cc_final: 0.8301 (m-80) REVERT: A 655 TYR cc_start: 0.8634 (t80) cc_final: 0.8342 (t80) REVERT: A 754 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8562 (tt) REVERT: A 1028 LYS cc_start: 0.9382 (OUTLIER) cc_final: 0.9151 (mttm) REVERT: A 1125 ASN cc_start: 0.7766 (t0) cc_final: 0.7046 (t0) REVERT: B 52 GLN cc_start: 0.8611 (tm-30) cc_final: 0.8408 (tm-30) REVERT: B 69 HIS cc_start: 0.5925 (OUTLIER) cc_final: 0.3932 (t70) REVERT: B 229 LEU cc_start: 0.7106 (OUTLIER) cc_final: 0.6845 (pp) REVERT: B 265 TYR cc_start: 0.6588 (OUTLIER) cc_final: 0.5405 (t80) REVERT: B 266 TYR cc_start: 0.8419 (m-80) cc_final: 0.8207 (m-80) REVERT: B 294 ASP cc_start: 0.7627 (m-30) cc_final: 0.7406 (m-30) REVERT: B 633 TRP cc_start: 0.8035 (p-90) cc_final: 0.7795 (p-90) REVERT: B 752 LEU cc_start: 0.9147 (tt) cc_final: 0.8881 (tt) REVERT: B 1125 ASN cc_start: 0.7668 (t0) cc_final: 0.7213 (t0) outliers start: 127 outliers final: 90 residues processed: 271 average time/residue: 0.3175 time to fit residues: 146.0000 Evaluate side-chains 243 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 144 time to evaluate : 2.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 1028 LYS Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 1028 LYS Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 1130 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 193 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 186 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 198 optimal weight: 0.6980 chunk 212 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 245 optimal weight: 0.1980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1088 HIS A 394 ASN B 493 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 26814 Z= 0.234 Angle : 0.637 12.343 36525 Z= 0.317 Chirality : 0.047 0.414 4332 Planarity : 0.004 0.085 4650 Dihedral : 8.845 83.448 4817 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.28 % Favored : 90.72 % Rotamer: Outliers : 4.26 % Allowed : 23.44 % Favored : 72.30 % 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: -1.61 (0.14), residues: 3234 helix: 0.97 (0.21), residues: 630 sheet: -0.57 (0.21), residues: 573 loop : -2.02 (0.13), residues: 2031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 633 HIS 0.003 0.001 HIS B 519 PHE 0.014 0.001 PHE B 592 TYR 0.019 0.001 TYR C 380 ARG 0.006 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 169 time to evaluate : 2.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 118 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8392 (tt) REVERT: C 265 TYR cc_start: 0.6205 (OUTLIER) cc_final: 0.5145 (t80) REVERT: C 266 TYR cc_start: 0.8254 (m-80) cc_final: 0.7956 (m-80) REVERT: C 298 GLU cc_start: 0.8641 (tp30) cc_final: 0.8329 (tp30) REVERT: C 365 TYR cc_start: 0.8674 (m-80) cc_final: 0.8360 (m-80) REVERT: C 655 TYR cc_start: 0.8697 (t80) cc_final: 0.8218 (t80) REVERT: C 1050 MET cc_start: 0.9032 (ptt) cc_final: 0.8775 (ptp) REVERT: C 1125 ASN cc_start: 0.7732 (t0) cc_final: 0.6929 (t0) REVERT: A 176 LEU cc_start: 0.5154 (OUTLIER) cc_final: 0.4644 (pt) REVERT: A 265 TYR cc_start: 0.6412 (OUTLIER) cc_final: 0.5707 (t80) REVERT: A 346 ARG cc_start: 0.6922 (mmm160) cc_final: 0.6571 (ttm-80) REVERT: A 365 TYR cc_start: 0.8782 (m-80) cc_final: 0.8399 (m-80) REVERT: A 462 LYS cc_start: 0.8905 (mmtm) cc_final: 0.8575 (mtmm) REVERT: A 655 TYR cc_start: 0.8622 (t80) cc_final: 0.8346 (t80) REVERT: A 754 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8575 (tt) REVERT: A 1125 ASN cc_start: 0.7651 (t0) cc_final: 0.6973 (t0) REVERT: B 69 HIS cc_start: 0.5923 (OUTLIER) cc_final: 0.3941 (t70) REVERT: B 201 PHE cc_start: 0.6502 (OUTLIER) cc_final: 0.6229 (m-80) REVERT: B 229 LEU cc_start: 0.7099 (OUTLIER) cc_final: 0.6801 (pp) REVERT: B 265 TYR cc_start: 0.6435 (OUTLIER) cc_final: 0.5179 (t80) REVERT: B 294 ASP cc_start: 0.7621 (m-30) cc_final: 0.7401 (m-30) REVERT: B 633 TRP cc_start: 0.8066 (p-90) cc_final: 0.7840 (p-90) REVERT: B 752 LEU cc_start: 0.9146 (tt) cc_final: 0.8907 (tt) REVERT: B 754 LEU cc_start: 0.8988 (tt) cc_final: 0.8753 (tt) REVERT: B 1125 ASN cc_start: 0.7621 (t0) cc_final: 0.7167 (t0) outliers start: 120 outliers final: 89 residues processed: 269 average time/residue: 0.3093 time to fit residues: 142.8594 Evaluate side-chains 252 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 154 time to evaluate : 2.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 1028 LYS Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 1028 LYS Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 1130 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 284 optimal weight: 2.9990 chunk 299 optimal weight: 1.9990 chunk 272 optimal weight: 0.9990 chunk 291 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 chunk 126 optimal weight: 10.0000 chunk 228 optimal weight: 5.9990 chunk 89 optimal weight: 0.9980 chunk 262 optimal weight: 3.9990 chunk 275 optimal weight: 7.9990 chunk 289 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1088 HIS A 394 ASN B 493 GLN ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.3890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 26814 Z= 0.280 Angle : 0.649 12.357 36525 Z= 0.321 Chirality : 0.048 0.396 4332 Planarity : 0.004 0.083 4650 Dihedral : 8.357 81.387 4815 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.25 % Favored : 90.75 % Rotamer: Outliers : 3.94 % Allowed : 23.83 % Favored : 72.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.14), residues: 3234 helix: 0.94 (0.21), residues: 627 sheet: -0.57 (0.21), residues: 573 loop : -2.00 (0.13), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 633 HIS 0.003 0.001 HIS B 519 PHE 0.015 0.001 PHE B 515 TYR 0.021 0.001 TYR C 380 ARG 0.006 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 156 time to evaluate : 2.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 118 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8427 (tt) REVERT: C 265 TYR cc_start: 0.6179 (OUTLIER) cc_final: 0.5093 (t80) REVERT: C 266 TYR cc_start: 0.8274 (m-80) cc_final: 0.8009 (m-80) REVERT: C 298 GLU cc_start: 0.8649 (tp30) cc_final: 0.8331 (tp30) REVERT: C 365 TYR cc_start: 0.8649 (m-80) cc_final: 0.8274 (m-80) REVERT: C 655 TYR cc_start: 0.8705 (t80) cc_final: 0.8224 (t80) REVERT: C 878 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8714 (tt) REVERT: C 1050 MET cc_start: 0.9051 (ptt) cc_final: 0.8776 (ptp) REVERT: C 1125 ASN cc_start: 0.7819 (t0) cc_final: 0.7072 (t0) REVERT: A 176 LEU cc_start: 0.5227 (OUTLIER) cc_final: 0.4718 (pt) REVERT: A 265 TYR cc_start: 0.6425 (OUTLIER) cc_final: 0.5816 (t80) REVERT: A 346 ARG cc_start: 0.6970 (mmm160) cc_final: 0.6621 (ttm-80) REVERT: A 365 TYR cc_start: 0.8757 (m-80) cc_final: 0.8363 (m-80) REVERT: A 754 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8601 (tt) REVERT: A 902 MET cc_start: 0.9061 (tpp) cc_final: 0.8809 (mmt) REVERT: A 1125 ASN cc_start: 0.7861 (t0) cc_final: 0.7141 (t0) REVERT: B 69 HIS cc_start: 0.5930 (OUTLIER) cc_final: 0.3927 (t70) REVERT: B 201 PHE cc_start: 0.6589 (OUTLIER) cc_final: 0.6296 (m-80) REVERT: B 229 LEU cc_start: 0.7180 (OUTLIER) cc_final: 0.6977 (pp) REVERT: B 265 TYR cc_start: 0.6671 (OUTLIER) cc_final: 0.5343 (t80) REVERT: B 266 TYR cc_start: 0.8425 (m-80) cc_final: 0.8052 (m-80) REVERT: B 294 ASP cc_start: 0.7604 (m-30) cc_final: 0.7397 (m-30) REVERT: B 378 LYS cc_start: 0.7744 (pttp) cc_final: 0.7544 (ptmt) REVERT: B 633 TRP cc_start: 0.8101 (p-90) cc_final: 0.7890 (p-90) REVERT: B 752 LEU cc_start: 0.9150 (tt) cc_final: 0.8943 (tp) REVERT: B 1125 ASN cc_start: 0.7669 (t0) cc_final: 0.7291 (t0) outliers start: 111 outliers final: 93 residues processed: 251 average time/residue: 0.3478 time to fit residues: 147.9468 Evaluate side-chains 255 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 152 time to evaluate : 3.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1028 LYS Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 1028 LYS Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1130 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 191 optimal weight: 0.8980 chunk 307 optimal weight: 0.5980 chunk 187 optimal weight: 0.0040 chunk 145 optimal weight: 2.9990 chunk 213 optimal weight: 1.9990 chunk 322 optimal weight: 0.0010 chunk 297 optimal weight: 0.9980 chunk 257 optimal weight: 8.9990 chunk 26 optimal weight: 0.5980 chunk 198 optimal weight: 0.5980 chunk 157 optimal weight: 5.9990 overall best weight: 0.3598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 394 ASN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1088 HIS ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.3934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 26814 Z= 0.178 Angle : 0.619 13.049 36525 Z= 0.307 Chirality : 0.046 0.399 4332 Planarity : 0.004 0.086 4650 Dihedral : 7.677 73.134 4815 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 3.37 % Allowed : 24.36 % Favored : 72.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.14), residues: 3234 helix: 1.05 (0.21), residues: 630 sheet: -0.45 (0.21), residues: 573 loop : -1.95 (0.13), residues: 2031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 633 HIS 0.003 0.001 HIS B 519 PHE 0.016 0.001 PHE A 392 TYR 0.019 0.001 TYR B 265 ARG 0.007 0.000 ARG A 357 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 174 time to evaluate : 2.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 118 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8330 (tt) REVERT: C 265 TYR cc_start: 0.6015 (OUTLIER) cc_final: 0.5077 (t80) REVERT: C 298 GLU cc_start: 0.8615 (tp30) cc_final: 0.8315 (tp30) REVERT: C 365 TYR cc_start: 0.8631 (m-80) cc_final: 0.8251 (m-80) REVERT: C 655 TYR cc_start: 0.8670 (t80) cc_final: 0.8249 (t80) REVERT: C 1125 ASN cc_start: 0.7677 (t0) cc_final: 0.6906 (t0) REVERT: A 176 LEU cc_start: 0.5123 (OUTLIER) cc_final: 0.4616 (pt) REVERT: A 196 ASN cc_start: 0.7355 (p0) cc_final: 0.6928 (t0) REVERT: A 265 TYR cc_start: 0.6167 (OUTLIER) cc_final: 0.5531 (t80) REVERT: A 365 TYR cc_start: 0.8732 (m-80) cc_final: 0.8391 (m-80) REVERT: A 878 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8161 (mt) REVERT: A 902 MET cc_start: 0.9054 (tpp) cc_final: 0.8773 (mmt) REVERT: A 1125 ASN cc_start: 0.7690 (t0) cc_final: 0.7010 (t0) REVERT: B 69 HIS cc_start: 0.6091 (OUTLIER) cc_final: 0.4166 (t70) REVERT: B 196 ASN cc_start: 0.7421 (p0) cc_final: 0.7040 (t0) REVERT: B 265 TYR cc_start: 0.6465 (OUTLIER) cc_final: 0.5442 (t80) REVERT: B 266 TYR cc_start: 0.8320 (m-80) cc_final: 0.8074 (m-80) REVERT: B 752 LEU cc_start: 0.9111 (tt) cc_final: 0.8776 (tt) REVERT: B 754 LEU cc_start: 0.8998 (tt) cc_final: 0.8753 (tt) REVERT: B 1125 ASN cc_start: 0.7546 (t0) cc_final: 0.7095 (t0) outliers start: 95 outliers final: 78 residues processed: 248 average time/residue: 0.3183 time to fit residues: 134.9284 Evaluate side-chains 243 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 158 time to evaluate : 2.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 1028 LYS Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1028 LYS Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1130 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 204 optimal weight: 0.9980 chunk 273 optimal weight: 3.9990 chunk 78 optimal weight: 0.5980 chunk 237 optimal weight: 0.0470 chunk 37 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 257 optimal weight: 8.9990 chunk 107 optimal weight: 3.9990 chunk 264 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1088 HIS ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.122814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.093471 restraints weight = 50053.164| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 3.00 r_work: 0.3166 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.3954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.182 26814 Z= 0.218 Angle : 0.740 59.180 36525 Z= 0.397 Chirality : 0.051 1.350 4332 Planarity : 0.005 0.092 4650 Dihedral : 7.680 73.074 4815 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.75 % Favored : 91.22 % Rotamer: Outliers : 3.19 % Allowed : 24.72 % Favored : 72.09 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.14), residues: 3234 helix: 1.05 (0.21), residues: 630 sheet: -0.44 (0.21), residues: 573 loop : -1.94 (0.13), residues: 2031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 633 HIS 0.003 0.001 HIS B 519 PHE 0.015 0.001 PHE A 392 TYR 0.019 0.001 TYR B 265 ARG 0.007 0.000 ARG A 357 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4902.31 seconds wall clock time: 89 minutes 52.19 seconds (5392.19 seconds total)