Starting phenix.real_space_refine on Fri Apr 12 15:16:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8z_22736/04_2024/7k8z_22736_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8z_22736/04_2024/7k8z_22736.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8z_22736/04_2024/7k8z_22736.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8z_22736/04_2024/7k8z_22736.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8z_22736/04_2024/7k8z_22736_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8z_22736/04_2024/7k8z_22736_neut.pdb" } resolution = 3.5 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= 0.016 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 110 5.16 5 C 16542 2.51 5 N 4278 2.21 5 O 5085 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 88": "OD1" <-> "OD2" Residue "A TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 428": "OD1" <-> "OD2" Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 454": "NH1" <-> "NH2" Residue "A PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 467": "OD1" <-> "OD2" Residue "A TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 725": "OE1" <-> "OE2" Residue "A PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 868": "OE1" <-> "OE2" Residue "A TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 979": "OD1" <-> "OD2" Residue "A ASP 985": "OD1" <-> "OD2" Residue "A GLU 988": "OE1" <-> "OE2" Residue "A TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1107": "NH1" <-> "NH2" Residue "A PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1111": "OE1" <-> "OE2" Residue "B PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 571": "OD1" <-> "OD2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 867": "OD1" <-> "OD2" Residue "B TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1017": "OE1" <-> "OE2" Residue "B TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 298": "OE1" <-> "OE2" Residue "C GLU 309": "OE1" <-> "OE2" Residue "C PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 428": "OD1" <-> "OD2" Residue "C TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 467": "OD1" <-> "OD2" Residue "C TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1017": "OE1" <-> "OE2" Residue "C ARG 1019": "NH1" <-> "NH2" Residue "C PHE 1042": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1111": "OE1" <-> "OE2" Residue "C ASP 1127": "OD1" <-> "OD2" Residue "C TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 55": "NH1" <-> "NH2" Residue "H TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 50": "OE1" <-> "OE2" Residue "L TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 55": "NH1" <-> "NH2" Residue "M ASP 61": "OD1" <-> "OD2" Residue "M TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 50": "OE1" <-> "OE2" Residue "N TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 26015 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 7401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 967, 7401 Classifications: {'peptide': 967} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 47, 'TRANS': 919} Chain breaks: 12 Unresolved non-hydrogen bonds: 173 Unresolved non-hydrogen angles: 216 Unresolved non-hydrogen dihedrals: 139 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 5, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 10, 'ASP:plan': 12} Unresolved non-hydrogen planarities: 120 Chain: "B" Number of atoms: 6865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 949, 6865 Classifications: {'peptide': 949} Incomplete info: {'truncation_to_alanine': 150} Link IDs: {'PTRANS': 46, 'TRANS': 902} Chain breaks: 13 Unresolved non-hydrogen bonds: 576 Unresolved non-hydrogen angles: 742 Unresolved non-hydrogen dihedrals: 481 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'GLN:plan1': 9, 'TYR:plan': 13, 'ASN:plan1': 17, 'TRP:plan': 2, 'ASP:plan': 13, 'PHE:plan': 9, 'GLU:plan': 12, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 382 Chain: "C" Number of atoms: 7341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 7341 Classifications: {'peptide': 972} Incomplete info: {'truncation_to_alanine': 80} Link IDs: {'PTRANS': 47, 'TRANS': 924} Chain breaks: 10 Unresolved non-hydrogen bonds: 276 Unresolved non-hydrogen angles: 345 Unresolved non-hydrogen dihedrals: 222 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 3, 'ASN:plan1': 9, 'ASP:plan': 13, 'PHE:plan': 3, 'GLU:plan': 13, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 179 Chain: "H" Number of atoms: 916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 916 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "L" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 818 Classifications: {'peptide': 106} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 99} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 910 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain: "N" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 818 Classifications: {'peptide': 106} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 99} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 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: "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: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 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: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 13.23, per 1000 atoms: 0.51 Number of scatterers: 26015 At special positions: 0 Unit cell: (131.252, 127.072, 196.46, 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 110 16.00 O 5085 8.00 N 4278 7.00 C 16542 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " 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=2.06 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.02 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.06 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 H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " 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 ALPHA1-3 " BMA K 3 " - " MAN K 4 " ALPHA1-6 " BMA K 3 " - " MAN K 5 " 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 I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " 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 V 2 " - " BMA V 3 " BETA1-6 " NAG K 1 " - " FUC K 6 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG V 1 " - " FUC V 4 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 603 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 657 " " NAG A1308 " - " ASN A 709 " " NAG A1309 " - " ASN A1074 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 234 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 343 " " NAG B1307 " - " ASN B 603 " " NAG B1308 " - " ASN B 616 " " NAG B1309 " - " ASN B 657 " " NAG B1310 " - " ASN B 709 " " NAG B1311 " - " ASN B 717 " " NAG B1312 " - " ASN B1074 " " NAG B1313 " - " ASN B 165 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 234 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 603 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 657 " " NAG C1308 " - " ASN C 709 " " NAG C1309 " - " ASN C1074 " " NAG C1310 " - " ASN C 165 " " NAG C1311 " - " ASN C 331 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1098 " " NAG I 1 " - " ASN A1134 " " NAG J 1 " - " ASN A 165 " " NAG K 1 " - " ASN A 343 " " NAG O 1 " - " ASN B 801 " " NAG P 1 " - " ASN B1098 " " NAG Q 1 " - " ASN B1134 " " NAG R 1 " - " ASN C 717 " " NAG S 1 " - " ASN C 801 " " NAG T 1 " - " ASN C1098 " " NAG U 1 " - " ASN C1134 " " NAG V 1 " - " ASN C 343 " Time building additional restraints: 10.35 Conformation dependent library (CDL) restraints added in 4.6 seconds 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6244 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 52 sheets defined 25.1% alpha, 27.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.18 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.634A pdb=" N ASN A 343 " --> pdb=" O GLY A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.227A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 389 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.362A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.999A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.514A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.566A pdb=" N TYR A 873 " --> pdb=" O MET A 869 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.913A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 907 removed outlier: 3.900A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASN A 907 " --> pdb=" O ALA A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 910 No H-bonds generated for 'chain 'A' and resid 908 through 910' Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.833A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU A 918 " --> pdb=" O ASN A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.544A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.688A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.088A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 341 Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.761A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.819A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.689A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 removed outlier: 3.518A pdb=" N LEU B 821 " --> pdb=" O PHE B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 removed outlier: 3.516A pdb=" N LEU B 878 " --> pdb=" O THR B 874 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.973A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.923A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.920A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.527A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.980A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.034A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.758A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.282A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 389 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.592A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.512A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.813A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.828A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.503A pdb=" N MET C 902 " --> pdb=" O PHE C 898 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.699A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.542A pdb=" N GLN C 965 " --> pdb=" O THR C 961 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.610A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.385A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.117A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 100A through 103 removed outlier: 3.896A pdb=" N TRP H 103 " --> pdb=" O SER H 100B" (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.021A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 32 Processing helix chain 'M' and resid 61 through 64 Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'M' and resid 100A through 103 removed outlier: 3.716A pdb=" N TRP M 103 " --> pdb=" O SER M 100B" (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 83 removed outlier: 4.021A pdb=" N PHE N 83 " --> pdb=" O PRO N 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.927A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.555A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.585A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 118 through 121 Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.107A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.822A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.550A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 538 through 543 removed outlier: 5.680A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.137A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 703 through 704 removed outlier: 7.466A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 3.542A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 3.542A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 735 Processing sheet with id=AB6, first strand: chain 'A' and resid 789 through 790 removed outlier: 3.713A pdb=" N LYS A 790 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.090A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1094 through 1097 removed outlier: 3.643A pdb=" N VAL A1104 " --> pdb=" O GLN A1113 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 31 removed outlier: 4.206A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.489A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.723A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.651A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 83 through 85 Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 318 removed outlier: 3.686A pdb=" N GLY B 311 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC5, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.266A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AC7, first strand: chain 'B' and resid 538 through 542 Processing sheet with id=AC8, first strand: chain 'B' and resid 565 through 566 removed outlier: 6.616A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.111A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.203A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 734 through 735 Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.609A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 31 removed outlier: 4.068A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.523A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.434A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.993A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 83 through 85 Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.057A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 324 through 328 removed outlier: 4.373A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.473A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TRP C 436 " --> pdb=" O ARG C 509 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.506A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.487A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.395A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE C1052 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE7, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE8, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AE9, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AF1, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.597A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.544A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.539A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'M' and resid 3 through 7 Processing sheet with id=AF5, first strand: chain 'M' and resid 58 through 59 removed outlier: 6.547A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N VAL M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N MET M 34 " --> pdb=" O VAL M 50 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'N' and resid 4 through 7 removed outlier: 3.544A pdb=" N VAL N 19 " --> pdb=" O ILE N 75 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU N 70 " --> pdb=" O SER N 67 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.539A pdb=" N LEU N 11 " --> pdb=" O GLU N 105 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LEU N 33 " --> pdb=" O TYR N 49 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N TYR N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) 1063 hydrogen bonds defined for protein. 2841 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: 11.60 Time building geometry restraints manager: 11.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8233 1.34 - 1.46: 6768 1.46 - 1.59: 11416 1.59 - 1.71: 1 1.71 - 1.83: 140 Bond restraints: 26558 Sorted by residual: bond pdb=" C1 MAN K 4 " pdb=" O5 MAN K 4 " ideal model delta sigma weight residual 1.399 1.491 -0.092 2.00e-02 2.50e+03 2.11e+01 bond pdb=" C1 MAN K 4 " pdb=" C2 MAN K 4 " ideal model delta sigma weight residual 1.526 1.601 -0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" C VAL B 860 " pdb=" N LEU B 861 " ideal model delta sigma weight residual 1.331 1.259 0.072 2.07e-02 2.33e+03 1.21e+01 bond pdb=" C3 BMA K 3 " pdb=" O3 BMA K 3 " ideal model delta sigma weight residual 1.406 1.467 -0.061 2.00e-02 2.50e+03 9.40e+00 bond pdb=" C VAL A 860 " pdb=" N LEU A 861 " ideal model delta sigma weight residual 1.331 1.247 0.084 2.83e-02 1.25e+03 8.80e+00 ... (remaining 26553 not shown) Histogram of bond angle deviations from ideal: 97.20 - 104.63: 462 104.63 - 112.06: 13629 112.06 - 119.49: 8170 119.49 - 126.92: 13675 126.92 - 134.35: 260 Bond angle restraints: 36196 Sorted by residual: angle pdb=" CG ARG N 24 " pdb=" CD ARG N 24 " pdb=" NE ARG N 24 " ideal model delta sigma weight residual 112.00 127.91 -15.91 2.20e+00 2.07e-01 5.23e+01 angle pdb=" CG ARG L 24 " pdb=" CD ARG L 24 " pdb=" NE ARG L 24 " ideal model delta sigma weight residual 112.00 127.90 -15.90 2.20e+00 2.07e-01 5.22e+01 angle pdb=" CA GLU L 50 " pdb=" CB GLU L 50 " pdb=" CG GLU L 50 " ideal model delta sigma weight residual 114.10 127.38 -13.28 2.00e+00 2.50e-01 4.41e+01 angle pdb=" CA GLU N 50 " pdb=" CB GLU N 50 " pdb=" CG GLU N 50 " ideal model delta sigma weight residual 114.10 127.33 -13.23 2.00e+00 2.50e-01 4.38e+01 angle pdb=" CD ARG N 24 " pdb=" NE ARG N 24 " pdb=" CZ ARG N 24 " ideal model delta sigma weight residual 124.40 132.92 -8.52 1.40e+00 5.10e-01 3.70e+01 ... (remaining 36191 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.50: 15712 21.50 - 43.01: 683 43.01 - 64.51: 159 64.51 - 86.02: 43 86.02 - 107.52: 14 Dihedral angle restraints: 16611 sinusoidal: 6941 harmonic: 9670 Sorted by residual: dihedral pdb=" CB CYS B 738 " pdb=" SG CYS B 738 " pdb=" SG CYS B 760 " pdb=" CB CYS B 760 " ideal model delta sinusoidal sigma weight residual 93.00 4.69 88.31 1 1.00e+01 1.00e-02 9.32e+01 dihedral pdb=" CA ILE L 29 " pdb=" C ILE L 29 " pdb=" N SER L 30 " pdb=" CA SER L 30 " ideal model delta harmonic sigma weight residual -180.00 -132.00 -48.00 0 5.00e+00 4.00e-02 9.21e+01 dihedral pdb=" CA ILE N 29 " pdb=" C ILE N 29 " pdb=" N SER N 30 " pdb=" CA SER N 30 " ideal model delta harmonic sigma weight residual 180.00 -132.05 -47.95 0 5.00e+00 4.00e-02 9.20e+01 ... (remaining 16608 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.154: 4364 0.154 - 0.308: 36 0.308 - 0.462: 1 0.462 - 0.616: 0 0.616 - 0.770: 1 Chirality restraints: 4402 Sorted by residual: chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 61 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.63 -0.77 2.00e-01 2.50e+01 1.48e+01 chirality pdb=" C1 NAG C1311 " pdb=" ND2 ASN C 331 " pdb=" C2 NAG C1311 " pdb=" O5 NAG C1311 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" C3 BMA K 3 " pdb=" C2 BMA K 3 " pdb=" C4 BMA K 3 " pdb=" O3 BMA K 3 " both_signs ideal model delta sigma weight residual False 2.41 2.11 0.30 2.00e-01 2.50e+01 2.19e+00 ... (remaining 4399 not shown) Planarity restraints: 4621 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE M 100 " 0.036 2.00e-02 2.50e+03 2.77e-02 1.34e+01 pdb=" CG PHE M 100 " -0.060 2.00e-02 2.50e+03 pdb=" CD1 PHE M 100 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE M 100 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE M 100 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE M 100 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE M 100 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 61 " 0.029 2.00e-02 2.50e+03 2.82e-02 9.95e+00 pdb=" CG ASN A 61 " -0.032 2.00e-02 2.50e+03 pdb=" OD1 ASN A 61 " 0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN A 61 " -0.035 2.00e-02 2.50e+03 pdb=" C1 NAG A1301 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE C 329 " -0.050 5.00e-02 4.00e+02 7.66e-02 9.38e+00 pdb=" N PRO C 330 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO C 330 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 330 " -0.042 5.00e-02 4.00e+02 ... (remaining 4618 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 490 2.66 - 3.22: 25463 3.22 - 3.78: 39633 3.78 - 4.34: 53824 4.34 - 4.90: 87570 Nonbonded interactions: 206980 Sorted by model distance: nonbonded pdb=" OE1 GLU B 725 " pdb=" NE2 HIS B1064 " model vdw 2.103 2.520 nonbonded pdb=" OE1 GLU A 725 " pdb=" NE2 HIS A1064 " model vdw 2.135 2.520 nonbonded pdb=" NE2 GLN B 949 " pdb=" OD1 ASN B 953 " model vdw 2.146 2.520 nonbonded pdb=" OD1 ASN B 616 " pdb=" N CYS B 617 " model vdw 2.147 2.520 nonbonded pdb=" OE1 GLU C 725 " pdb=" NE2 HIS C1064 " model vdw 2.156 2.520 ... (remaining 206975 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 52 or (resid 53 and (name N or nam \ e CA or name C or name O or name CB )) or resid 54 through 66 or resid 82 throug \ h 87 or (resid 88 and (name N or name CA or name C or name O or name CB )) or re \ sid 89 through 95 or (resid 96 through 97 and (name N or name CA or name C or na \ me O or name CB )) or resid 98 through 109 or (resid 110 through 113 and (name N \ or name CA or name C or name O or name CB )) or resid 116 through 124 or (resid \ 125 and (name N or name CA or name C or name O or name CB )) or resid 126 throu \ gh 131 or (resid 132 and (name N or name CA or name C or name O or name CB )) or \ resid 133 or (resid 134 through 138 and (name N or name CA or name C or name O \ or name CB )) or resid 139 through 140 or resid 165 through 168 or (resid 169 an \ d (name N or name CA or name C or name O or name CB )) or resid 170 through 171 \ or (resid 172 and (name N or name CA or name C or name O or name CB )) or resid \ 186 through 190 or (resid 191 and (name N or name CA or name C or name O or name \ CB )) or resid 192 through 196 or resid 200 through 210 or (resid 211 and (name \ N or name CA or name C or name O or name CB )) or (resid 215 and (name N or nam \ e CA or name C or name O or name CB )) or resid 216 through 217 or (resid 218 an \ d (name N or name CA or name C or name O or name CB )) or resid 219 through 223 \ or (resid 224 and (name N or name CA or name C or name O or name CB )) or resid \ 225 through 238 or (resid 239 and (name N or name CA or name C or name O or name \ CB )) or resid 240 through 263 or resid 265 through 308 or (resid 309 and (name \ N or name CA or name C or name O or name CB )) or resid 310 through 323 or (res \ id 324 and (name N or name CA or name C or name O or name CB )) or resid 325 thr \ ough 332 or (resid 333 through 334 and (name N or name CA or name C or name O or \ name CB )) or resid 335 through 345 or (resid 346 through 360 and (name N or na \ me CA or name C or name O or name CB )) or resid 361 or (resid 362 through 378 a \ nd (name N or name CA or name C or name O or name CB )) or resid 379 or (resid 3 \ 80 and (name N or name CA or name C or name O or name CB )) or resid 381 or (res \ id 382 through 383 and (name N or name CA or name C or name O or name CB )) or r \ esid 384 or (resid 385 through 390 and (name N or name CA or name C or name O or \ name CB )) or resid 391 or (resid 392 through 403 and (name N or name CA or nam \ e C or name O or name CB )) or (resid 404 through 411 and (name N or name CA or \ name C or name O or name CB )) or resid 412 through 413 or (resid 414 through 41 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 416 or (resi \ d 417 through 425 and (name N or name CA or name C or name O or name CB )) or re \ sid 426 through 427 or (resid 428 through 430 and (name N or name CA or name C o \ r name O or name CB )) or resid 431 through 432 or (resid 433 through 454 and (n \ ame N or name CA or name C or name O or name CB )) or (resid 462 and (name N or \ name CA or name C or name O or name CB )) or resid 463 or (resid 464 through 466 \ and (name N or name CA or name C or name O or name CB )) or resid 491 or (resid \ 492 through 495 and (name N or name CA or name C or name O or name CB )) or res \ id 496 or (resid 497 through 498 and (name N or name CA or name C or name O or n \ ame CB )) or resid 499 or (resid 500 through 503 and (name N or name CA or name \ C or name O or name CB )) or (resid 504 through 506 and (name N or name CA or na \ me C or name O or name CB )) or resid 507 or (resid 508 through 515 and (name N \ or name CA or name C or name O or name CB )) or (resid 522 through 524 and (name \ N or name CA or name C or name O or name CB )) or resid 525 through 528 or (res \ id 529 and (name N or name CA or name C or name O or name CB )) or resid 530 thr \ ough 553 or (resid 554 and (name N or name CA or name C or name O or name CB )) \ or resid 555 through 793 or (resid 794 and (name N or name CA or name C or name \ O or name CB )) or resid 795 or (resid 796 and (name N or name CA or name C or n \ ame O or name CB )) or resid 797 through 810 or (resid 811 and (name N or name C \ A or name C or name O or name CB )) or resid 813 through 827 or resid 856 throug \ h 866 or (resid 867 through 868 and (name N or name CA or name C or name O or na \ me CB )) or resid 869 through 939 or (resid 940 and (name N or name CA or name C \ or name O or name CB )) or resid 941 through 984 or (resid 985 and (name N or n \ ame CA or name C or name O or name CB )) or resid 986 through 987 or (resid 988 \ through 989 and (name N or name CA or name C or name O or name CB )) or resid 99 \ 0 through 1141 or (resid 1142 and (name N or name CA or name C or name O or name \ CB )) or resid 1143 through 1144 or (resid 1145 through 1146 and (name N or nam \ e CA or name C or name O or name CB )) or resid 1147 or resid 1301 through 1309) \ ) selection = (chain 'B' and (resid 27 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 66 or resid 82 through 87 or (resi \ d 88 and (name N or name CA or name C or name O or name CB )) or resid 89 throug \ h 96 or (resid 97 and (name N or name CA or name C or name O or name CB )) or re \ sid 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or \ resid 100 through 109 or (resid 110 through 113 and (name N or name CA or name C \ or name O or name CB )) or resid 116 through 128 or (resid 129 and (name N or n \ ame CA or name C or name O or name CB )) or resid 130 through 134 or (resid 135 \ through 138 and (name N or name CA or name C or name O or name CB )) or resid 13 \ 9 through 140 or resid 165 through 168 or (resid 169 and (name N or name CA or n \ ame C or name O or name CB )) or resid 170 through 187 or (resid 188 and (name N \ or name CA or name C or name O or name CB )) or resid 189 through 190 or (resid \ 191 and (name N or name CA or name C or name O or name CB )) or resid 192 throu \ gh 195 or (resid 196 and (name N or name CA or name C or name O or name CB )) or \ resid 200 through 210 or (resid 211 through 215 and (name N or name CA or name \ C or name O or name CB )) or resid 216 through 241 or (resid 242 through 263 and \ (name N or name CA or name C or name O or name CB )) or resid 265 through 280 o \ r (resid 281 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 82 through 323 or (resid 324 and (name N or name CA or name C or name O or name \ CB )) or resid 325 through 442 or resid 448 through 501 or resid 503 through 567 \ or (resid 568 and (name N or name CA or name C or name O or name CB )) or resid \ 569 through 570 or (resid 571 and (name N or name CA or name C or name O or nam \ e CB )) or resid 572 through 581 or (resid 582 through 583 and (name N or name C \ A or name C or name O or name CB )) or resid 584 through 585 or (resid 586 and ( \ name N or name CA or name C or name O or name CB )) or resid 587 through 613 or \ (resid 614 and (name N or name CA or name C or name O or name CB )) or resid 615 \ through 618 or (resid 619 and (name N or name CA or name C or name O or name CB \ )) or resid 620 through 676 or resid 690 through 744 or (resid 745 and (name N \ or name CA or name C or name O or name CB )) or resid 746 through 810 or (resid \ 811 and (name N or name CA or name C or name O or name CB )) or resid 813 throug \ h 827 or resid 856 through 866 or (resid 867 through 868 and (name N or name CA \ or name C or name O or name CB )) or resid 869 through 920 or (resid 921 and (na \ me N or name CA or name C or name O or name CB )) or resid 922 through 939 or (r \ esid 940 and (name N or name CA or name C or name O or name CB )) or resid 941 t \ hrough 984 or (resid 985 and (name N or name CA or name C or name O or name CB ) \ ) or resid 986 through 987 or (resid 988 through 989 and (name N or name CA or n \ ame C or name O or name CB )) or resid 990 through 1072 or (resid 1073 and (name \ N or name CA or name C or name O or name CB )) or resid 1074 through 1117 or (r \ esid 1118 and (name N or name CA or name C or name O or name CB )) or resid 1119 \ through 1143 or (resid 1144 through 1146 and (name N or name CA or name C or na \ me O or name CB )) or resid 1147 or resid 1301 through 1309)) selection = (chain 'C' and (resid 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 66 or resid 82 through 95 or (resi \ d 96 through 97 and (name N or name CA or name C or name O or name CB )) or resi \ d 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or re \ sid 100 through 110 or (resid 111 through 113 and (name N or name CA or name C o \ r name O or name CB )) or resid 116 through 134 or (resid 135 through 138 and (n \ ame N or name CA or name C or name O or name CB )) or resid 139 through 140 or r \ esid 165 through 187 or (resid 188 and (name N or name CA or name C or name O or \ name CB )) or resid 189 through 195 or (resid 196 and (name N or name CA or nam \ e C or name O or name CB )) or resid 200 through 211 or resid 215 through 217 or \ (resid 218 and (name N or name CA or name C or name O or name CB )) or resid 21 \ 9 through 223 or (resid 224 and (name N or name CA or name C or name O or name C \ B )) or resid 225 through 238 or (resid 239 and (name N or name CA or name C or \ name O or name CB )) or resid 240 through 308 or (resid 309 and (name N or name \ CA or name C or name O or name CB )) or resid 310 through 332 or (resid 333 thro \ ugh 334 and (name N or name CA or name C or name O or name CB )) or resid 335 th \ rough 344 or (resid 345 through 360 and (name N or name CA or name C or name O o \ r name CB )) or resid 361 or (resid 362 through 378 and (name N or name CA or na \ me C or name O or name CB )) or resid 379 or (resid 380 and (name N or name CA o \ r name C or name O or name CB )) or resid 381 or (resid 382 through 383 and (nam \ e N or name CA or name C or name O or name CB )) or resid 384 or (resid 385 thro \ ugh 390 and (name N or name CA or name C or name O or name CB )) or resid 391 or \ (resid 392 through 403 and (name N or name CA or name C or name O or name CB )) \ or (resid 404 through 411 and (name N or name CA or name C or name O or name CB \ )) or resid 412 through 413 or (resid 414 through 415 and (name N or name CA or \ name C or name O or name CB )) or (resid 416 through 425 and (name N or name CA \ or name C or name O or name CB )) or resid 426 or (resid 427 through 430 and (n \ ame N or name CA or name C or name O or name CB )) or resid 431 through 432 or ( \ resid 433 through 442 and (name N or name CA or name C or name O or name CB )) o \ r (resid 448 through 454 and (name N or name CA or name C or name O or name CB ) \ ) or resid 462 through 463 or (resid 464 through 466 and (name N or name CA or n \ ame C or name O or name CB )) or resid 491 or (resid 492 through 495 and (name N \ or name CA or name C or name O or name CB )) or resid 496 or (resid 497 through \ 498 and (name N or name CA or name C or name O or name CB )) or resid 499 throu \ gh 500 or (resid 501 and (name N or name CA or name C or name O or name CB )) or \ (resid 503 and (name N or name CA or name C or name O or name CB )) or (resid 5 \ 04 through 506 and (name N or name CA or name C or name O or name CB )) or resid \ 507 or (resid 508 through 515 and (name N or name CA or name C or name O or nam \ e CB )) or (resid 522 through 524 and (name N or name CA or name C or name O or \ name CB )) or resid 525 through 527 or (resid 528 through 529 and (name N or nam \ e CA or name C or name O or name CB )) or resid 530 through 553 or (resid 554 an \ d (name N or name CA or name C or name O or name CB )) or resid 555 through 567 \ or (resid 568 and (name N or name CA or name C or name O or name CB )) or resid \ 569 through 570 or (resid 571 and (name N or name CA or name C or name O or name \ CB )) or resid 572 through 581 or (resid 582 through 583 and (name N or name CA \ or name C or name O or name CB )) or resid 584 through 585 or (resid 586 and (n \ ame N or name CA or name C or name O or name CB )) or resid 587 through 618 or ( \ resid 619 and (name N or name CA or name C or name O or name CB )) or resid 620 \ through 645 or (resid 646 through 647 and (name N or name CA or name C or name O \ or name CB )) or resid 648 through 793 or (resid 794 and (name N or name CA or \ name C or name O or name CB )) or resid 795 or (resid 796 and (name N or name CA \ or name C or name O or name CB )) or resid 797 through 920 or (resid 921 and (n \ ame N or name CA or name C or name O or name CB )) or resid 922 through 1072 or \ (resid 1073 and (name N or name CA or name C or name O or name CB )) or resid 10 \ 74 through 1117 or (resid 1118 and (name N or name CA or name C or name O or nam \ e CB )) or resid 1119 through 1141 or (resid 1142 and (name N or name CA or name \ C or name O or name CB )) or resid 1143 or (resid 1144 through 1146 and (name N \ or name CA or name C or name O or name CB )) or resid 1147 or resid 1301 throug \ h 1309)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } ncs_group { reference = (chain 'H' and resid 1 through 111) selection = chain 'M' } ncs_group { reference = chain 'L' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.790 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: 10.400 Check model and map are aligned: 0.400 Set scattering table: 0.210 Process input model: 69.020 Find NCS groups from input model: 2.170 Set up NCS constraints: 0.290 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 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 : 0.007 0.092 26558 Z= 0.478 Angle : 0.864 15.915 36196 Z= 0.465 Chirality : 0.053 0.770 4402 Planarity : 0.005 0.077 4573 Dihedral : 13.100 107.520 10250 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.52 % Favored : 95.42 % Rotamer: Outliers : 1.06 % Allowed : 0.49 % Favored : 98.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.14), residues: 3251 helix: -0.40 (0.19), residues: 675 sheet: -0.11 (0.17), residues: 841 loop : -0.62 (0.14), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP L 32 HIS 0.007 0.001 HIS H 35 PHE 0.060 0.003 PHE M 100 TYR 0.030 0.002 TYR L 49 ARG 0.035 0.001 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 309 time to evaluate : 3.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 950 ASP cc_start: 0.8511 (m-30) cc_final: 0.8285 (m-30) REVERT: B 110 LEU cc_start: 0.8005 (mp) cc_final: 0.6929 (tt) REVERT: B 274 THR cc_start: 0.8489 (m) cc_final: 0.8267 (m) REVERT: B 342 PHE cc_start: 0.7735 (m-10) cc_final: 0.7386 (m-80) REVERT: C 45 SER cc_start: 0.7367 (p) cc_final: 0.7137 (t) REVERT: C 140 PHE cc_start: 0.7570 (p90) cc_final: 0.7257 (p90) REVERT: C 902 MET cc_start: 0.8286 (mmm) cc_final: 0.7845 (mmt) REVERT: H 3 GLN cc_start: 0.7992 (mp10) cc_final: 0.7784 (mp10) REVERT: H 13 GLN cc_start: 0.7090 (mm-40) cc_final: 0.6801 (mm110) REVERT: H 29 PHE cc_start: 0.7586 (t80) cc_final: 0.7200 (t80) REVERT: H 82 MET cc_start: 0.9183 (mtm) cc_final: 0.8363 (mtm) REVERT: H 82 LEU cc_start: 0.7770 (mt) cc_final: 0.7272 (mp) REVERT: L 2 ILE cc_start: 0.7935 (tp) cc_final: 0.7681 (tp) REVERT: L 35 TRP cc_start: 0.6530 (m100) cc_final: 0.5352 (m100) REVERT: L 78 LEU cc_start: 0.7822 (OUTLIER) cc_final: 0.7160 (tp) REVERT: M 6 GLU cc_start: 0.3125 (mp0) cc_final: 0.2783 (mp0) REVERT: M 34 MET cc_start: 0.8081 (mmp) cc_final: 0.7259 (mmm) REVERT: M 35 HIS cc_start: 0.8105 (m90) cc_final: 0.7602 (m170) REVERT: N 3 GLN cc_start: 0.8591 (tp40) cc_final: 0.8351 (tp-100) REVERT: N 24 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.7410 (mmm160) REVERT: N 47 LEU cc_start: 0.8649 (mp) cc_final: 0.8412 (mp) REVERT: N 55 GLU cc_start: 0.8143 (tp30) cc_final: 0.7701 (tp30) REVERT: N 79 GLN cc_start: 0.8804 (OUTLIER) cc_final: 0.8470 (mm110) REVERT: N 97 THR cc_start: 0.8173 (p) cc_final: 0.7825 (p) outliers start: 28 outliers final: 6 residues processed: 320 average time/residue: 0.3788 time to fit residues: 193.9573 Evaluate side-chains 212 residues out of total 2913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 203 time to evaluate : 2.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 50 GLU Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 24 ARG Chi-restraints excluded: chain N residue 50 GLU Chi-restraints excluded: chain N residue 79 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 277 optimal weight: 0.7980 chunk 249 optimal weight: 2.9990 chunk 138 optimal weight: 6.9990 chunk 85 optimal weight: 0.6980 chunk 168 optimal weight: 0.9980 chunk 133 optimal weight: 50.0000 chunk 257 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 156 optimal weight: 0.9980 chunk 191 optimal weight: 3.9990 chunk 298 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 388 ASN ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 949 GLN A 953 ASN A1005 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 914 ASN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B1088 HIS ** C 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN C 926 GLN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 13 GLN L 79 GLN ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 76 ASN ** N 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26558 Z= 0.205 Angle : 0.628 9.522 36196 Z= 0.327 Chirality : 0.048 0.477 4402 Planarity : 0.004 0.060 4573 Dihedral : 8.299 87.654 4982 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.63 % Favored : 96.34 % Rotamer: Outliers : 1.48 % Allowed : 6.26 % Favored : 92.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.14), residues: 3251 helix: 0.98 (0.20), residues: 699 sheet: 0.06 (0.16), residues: 861 loop : -0.52 (0.15), residues: 1691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP L 32 HIS 0.008 0.001 HIS H 100A PHE 0.034 0.002 PHE M 100 TYR 0.023 0.002 TYR B 873 ARG 0.004 0.000 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 266 time to evaluate : 2.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 369 TYR cc_start: 0.8082 (t80) cc_final: 0.7858 (t80) REVERT: A 389 ASP cc_start: 0.8580 (m-30) cc_final: 0.8165 (t0) REVERT: A 698 SER cc_start: 0.8940 (t) cc_final: 0.8623 (m) REVERT: A 1050 MET cc_start: 0.7380 (ptt) cc_final: 0.6891 (ptt) REVERT: B 274 THR cc_start: 0.8535 (m) cc_final: 0.8230 (m) REVERT: B 869 MET cc_start: 0.8028 (mtp) cc_final: 0.7475 (mtp) REVERT: B 955 ASN cc_start: 0.8778 (m-40) cc_final: 0.8543 (m-40) REVERT: C 45 SER cc_start: 0.7162 (p) cc_final: 0.6937 (t) REVERT: C 697 MET cc_start: 0.8239 (OUTLIER) cc_final: 0.7729 (ptm) REVERT: H 34 MET cc_start: 0.8265 (tpp) cc_final: 0.7739 (tpp) REVERT: H 51 ILE cc_start: 0.8592 (tt) cc_final: 0.8307 (tp) REVERT: H 82 MET cc_start: 0.9265 (mtm) cc_final: 0.8660 (mpp) REVERT: H 86 ASP cc_start: 0.8086 (m-30) cc_final: 0.7515 (t70) REVERT: M 29 PHE cc_start: 0.6490 (t80) cc_final: 0.6230 (t80) REVERT: M 34 MET cc_start: 0.7815 (mmp) cc_final: 0.7482 (mmm) REVERT: M 35 HIS cc_start: 0.7806 (m90) cc_final: 0.7263 (m170) REVERT: M 36 TRP cc_start: 0.7410 (m100) cc_final: 0.6812 (m100) REVERT: M 79 TYR cc_start: 0.7299 (m-80) cc_final: 0.6770 (m-80) REVERT: N 3 GLN cc_start: 0.8615 (tp40) cc_final: 0.8411 (tp-100) REVERT: N 24 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.7860 (mmm-85) REVERT: N 70 GLU cc_start: 0.9020 (tp30) cc_final: 0.8606 (tp30) REVERT: N 79 GLN cc_start: 0.8944 (OUTLIER) cc_final: 0.8563 (mm110) outliers start: 39 outliers final: 17 residues processed: 282 average time/residue: 0.3408 time to fit residues: 159.2817 Evaluate side-chains 213 residues out of total 2913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 193 time to evaluate : 2.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain M residue 22 CYS Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 24 ARG Chi-restraints excluded: chain N residue 32 TRP Chi-restraints excluded: chain N residue 56 SER Chi-restraints excluded: chain N residue 79 GLN Chi-restraints excluded: chain N residue 106 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 166 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 248 optimal weight: 3.9990 chunk 203 optimal weight: 0.8980 chunk 82 optimal weight: 6.9990 chunk 299 optimal weight: 20.0000 chunk 323 optimal weight: 40.0000 chunk 266 optimal weight: 6.9990 chunk 296 optimal weight: 50.0000 chunk 102 optimal weight: 9.9990 chunk 240 optimal weight: 5.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 953 ASN A1106 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN C 935 GLN C 949 GLN C 955 ASN ** H 100AHIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 79 GLN N 38 GLN ** N 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 26558 Z= 0.337 Angle : 0.649 9.909 36196 Z= 0.334 Chirality : 0.048 0.531 4402 Planarity : 0.004 0.058 4573 Dihedral : 7.270 80.932 4971 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 1.75 % Allowed : 8.73 % Favored : 89.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.14), residues: 3251 helix: 1.18 (0.20), residues: 674 sheet: -0.07 (0.17), residues: 859 loop : -0.65 (0.15), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP H 36 HIS 0.007 0.001 HIS H 35 PHE 0.032 0.002 PHE B 133 TYR 0.028 0.002 TYR A 904 ARG 0.006 0.001 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 217 time to evaluate : 2.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 369 TYR cc_start: 0.8197 (t80) cc_final: 0.7979 (t80) REVERT: A 698 SER cc_start: 0.9004 (t) cc_final: 0.8627 (p) REVERT: A 990 GLU cc_start: 0.8812 (tt0) cc_final: 0.8266 (tm-30) REVERT: A 1050 MET cc_start: 0.7538 (ptt) cc_final: 0.6899 (ptt) REVERT: B 274 THR cc_start: 0.8514 (m) cc_final: 0.8191 (m) REVERT: B 315 THR cc_start: 0.8372 (p) cc_final: 0.8028 (t) REVERT: B 955 ASN cc_start: 0.8967 (m-40) cc_final: 0.8602 (m110) REVERT: B 1050 MET cc_start: 0.7582 (OUTLIER) cc_final: 0.7305 (ptp) REVERT: H 19 ARG cc_start: 0.9005 (tpp80) cc_final: 0.8793 (tpp80) REVERT: H 29 PHE cc_start: 0.7994 (t80) cc_final: 0.7755 (t80) REVERT: H 51 ILE cc_start: 0.8736 (tt) cc_final: 0.8459 (tp) REVERT: H 78 LEU cc_start: 0.7563 (OUTLIER) cc_final: 0.7193 (tp) REVERT: H 82 MET cc_start: 0.9305 (mtm) cc_final: 0.8189 (mpp) REVERT: L 35 TRP cc_start: 0.6563 (m100) cc_final: 0.5690 (m100) REVERT: L 55 GLU cc_start: 0.8503 (tp30) cc_final: 0.8135 (tp30) REVERT: M 34 MET cc_start: 0.8141 (mmp) cc_final: 0.7425 (mmm) REVERT: M 35 HIS cc_start: 0.7898 (m90) cc_final: 0.7367 (m170) REVERT: N 24 ARG cc_start: 0.8522 (mmm160) cc_final: 0.7851 (mmm-85) REVERT: N 37 GLN cc_start: 0.8778 (tt0) cc_final: 0.8201 (tt0) REVERT: N 70 GLU cc_start: 0.9093 (OUTLIER) cc_final: 0.8367 (tp30) outliers start: 46 outliers final: 25 residues processed: 243 average time/residue: 0.3635 time to fit residues: 145.8156 Evaluate side-chains 220 residues out of total 2913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 192 time to evaluate : 3.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 91 TYR Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain N residue 106 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 295 optimal weight: 20.0000 chunk 225 optimal weight: 8.9990 chunk 155 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 142 optimal weight: 7.9990 chunk 200 optimal weight: 30.0000 chunk 300 optimal weight: 20.0000 chunk 318 optimal weight: 9.9990 chunk 156 optimal weight: 2.9990 chunk 284 optimal weight: 0.7980 chunk 85 optimal weight: 0.5980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN ** C 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 949 GLN H 3 GLN ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 37 GLN N 79 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26558 Z= 0.179 Angle : 0.563 9.696 36196 Z= 0.289 Chirality : 0.046 0.543 4402 Planarity : 0.004 0.051 4573 Dihedral : 6.511 77.007 4962 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.52 % Allowed : 10.28 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.14), residues: 3251 helix: 1.63 (0.21), residues: 672 sheet: -0.01 (0.17), residues: 861 loop : -0.56 (0.15), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP M 36 HIS 0.007 0.001 HIS H 35 PHE 0.023 0.001 PHE C 140 TYR 0.018 0.001 TYR M 79 ARG 0.008 0.000 ARG N 61 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 225 time to evaluate : 2.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 312 ILE cc_start: 0.9302 (tt) cc_final: 0.9034 (pt) REVERT: A 389 ASP cc_start: 0.8591 (m-30) cc_final: 0.8235 (t0) REVERT: A 698 SER cc_start: 0.8979 (t) cc_final: 0.8610 (p) REVERT: A 1050 MET cc_start: 0.7347 (ptt) cc_final: 0.6577 (ptt) REVERT: B 274 THR cc_start: 0.8512 (m) cc_final: 0.8187 (m) REVERT: B 315 THR cc_start: 0.8392 (p) cc_final: 0.8085 (t) REVERT: B 955 ASN cc_start: 0.8843 (m-40) cc_final: 0.8543 (m-40) REVERT: C 508 TYR cc_start: 0.8263 (m-80) cc_final: 0.7317 (m-80) REVERT: C 697 MET cc_start: 0.8179 (OUTLIER) cc_final: 0.7672 (ptm) REVERT: H 34 MET cc_start: 0.8248 (tpp) cc_final: 0.7769 (tmm) REVERT: H 82 MET cc_start: 0.9318 (mtm) cc_final: 0.8023 (mpp) REVERT: H 86 ASP cc_start: 0.8081 (m-30) cc_final: 0.7546 (t70) REVERT: H 103 TRP cc_start: 0.7656 (m100) cc_final: 0.7413 (m-10) REVERT: L 55 GLU cc_start: 0.8526 (tp30) cc_final: 0.8184 (tp30) REVERT: L 78 LEU cc_start: 0.8428 (mm) cc_final: 0.7943 (tp) REVERT: M 34 MET cc_start: 0.8061 (mmp) cc_final: 0.7429 (mmm) REVERT: M 79 TYR cc_start: 0.7094 (m-80) cc_final: 0.6882 (m-80) REVERT: N 24 ARG cc_start: 0.8316 (mmm160) cc_final: 0.7896 (mmm-85) REVERT: N 37 GLN cc_start: 0.8843 (tt0) cc_final: 0.8499 (tt0) REVERT: N 47 LEU cc_start: 0.8805 (mp) cc_final: 0.8509 (pp) REVERT: N 50 GLU cc_start: 0.8232 (mp0) cc_final: 0.7977 (mp0) REVERT: N 70 GLU cc_start: 0.9125 (OUTLIER) cc_final: 0.8409 (mm-30) outliers start: 40 outliers final: 23 residues processed: 251 average time/residue: 0.3760 time to fit residues: 156.3113 Evaluate side-chains 228 residues out of total 2913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 203 time to evaluate : 2.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 91 TYR Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain N residue 81 ASP Chi-restraints excluded: chain N residue 106 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 264 optimal weight: 0.9980 chunk 180 optimal weight: 5.9990 chunk 4 optimal weight: 8.9990 chunk 236 optimal weight: 8.9990 chunk 131 optimal weight: 50.0000 chunk 271 optimal weight: 6.9990 chunk 219 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 162 optimal weight: 0.8980 chunk 285 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN ** C 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 949 GLN H 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26558 Z= 0.222 Angle : 0.570 9.518 36196 Z= 0.290 Chirality : 0.046 0.542 4402 Planarity : 0.004 0.056 4573 Dihedral : 6.223 72.152 4961 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.59 % Allowed : 11.12 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.15), residues: 3251 helix: 1.62 (0.21), residues: 673 sheet: 0.01 (0.17), residues: 844 loop : -0.61 (0.15), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP M 36 HIS 0.009 0.001 HIS M 35 PHE 0.026 0.001 PHE B 133 TYR 0.017 0.001 TYR A 904 ARG 0.006 0.000 ARG C1107 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 223 time to evaluate : 2.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 VAL cc_start: 0.8267 (m) cc_final: 0.8032 (p) REVERT: A 312 ILE cc_start: 0.9302 (tt) cc_final: 0.9026 (pt) REVERT: A 389 ASP cc_start: 0.8608 (m-30) cc_final: 0.8152 (t0) REVERT: A 698 SER cc_start: 0.9015 (t) cc_final: 0.8683 (p) REVERT: A 990 GLU cc_start: 0.8753 (tt0) cc_final: 0.8250 (tm-30) REVERT: A 1050 MET cc_start: 0.7391 (ptt) cc_final: 0.6642 (ptt) REVERT: B 274 THR cc_start: 0.8531 (m) cc_final: 0.8206 (m) REVERT: B 315 THR cc_start: 0.8577 (p) cc_final: 0.8325 (t) REVERT: B 955 ASN cc_start: 0.8892 (m-40) cc_final: 0.8530 (m110) REVERT: B 1050 MET cc_start: 0.7558 (ptp) cc_final: 0.7243 (ptp) REVERT: B 1107 ARG cc_start: 0.7962 (ptp-170) cc_final: 0.7651 (ptp90) REVERT: C 508 TYR cc_start: 0.8300 (m-80) cc_final: 0.7420 (m-80) REVERT: H 34 MET cc_start: 0.8123 (tpp) cc_final: 0.7765 (tmm) REVERT: H 39 GLN cc_start: 0.6631 (pp30) cc_final: 0.6338 (pp30) REVERT: H 82 MET cc_start: 0.9157 (mtm) cc_final: 0.7994 (mpp) REVERT: H 86 ASP cc_start: 0.8034 (m-30) cc_final: 0.7481 (t70) REVERT: L 55 GLU cc_start: 0.8577 (tp30) cc_final: 0.8201 (tp30) REVERT: M 34 MET cc_start: 0.7651 (mmp) cc_final: 0.7051 (mmm) REVERT: M 35 HIS cc_start: 0.7932 (m90) cc_final: 0.7589 (m170) REVERT: M 79 TYR cc_start: 0.7108 (m-80) cc_final: 0.6836 (m-80) REVERT: N 4 MET cc_start: 0.5252 (ptm) cc_final: 0.4400 (ttp) REVERT: N 24 ARG cc_start: 0.8333 (mmm160) cc_final: 0.7815 (mmm-85) REVERT: N 37 GLN cc_start: 0.8898 (tt0) cc_final: 0.8574 (tt0) REVERT: N 47 LEU cc_start: 0.8754 (mp) cc_final: 0.8468 (pp) REVERT: N 50 GLU cc_start: 0.8270 (mp0) cc_final: 0.7815 (mp0) REVERT: N 70 GLU cc_start: 0.9123 (OUTLIER) cc_final: 0.8463 (mm-30) outliers start: 42 outliers final: 27 residues processed: 251 average time/residue: 0.3908 time to fit residues: 157.4896 Evaluate side-chains 225 residues out of total 2913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 197 time to evaluate : 2.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 91 TYR Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain N residue 81 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 106 optimal weight: 50.0000 chunk 286 optimal weight: 5.9990 chunk 62 optimal weight: 0.6980 chunk 186 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 318 optimal weight: 10.0000 chunk 264 optimal weight: 5.9990 chunk 147 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 105 optimal weight: 8.9990 chunk 167 optimal weight: 0.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN ** C 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 81 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 26558 Z= 0.310 Angle : 0.613 11.819 36196 Z= 0.313 Chirality : 0.046 0.448 4402 Planarity : 0.004 0.054 4573 Dihedral : 6.118 59.844 4961 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.31 % Allowed : 11.61 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.14), residues: 3251 helix: 1.43 (0.20), residues: 674 sheet: -0.09 (0.17), residues: 880 loop : -0.74 (0.15), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP M 36 HIS 0.007 0.001 HIS H 35 PHE 0.023 0.002 PHE C1089 TYR 0.027 0.002 TYR A 904 ARG 0.007 0.000 ARG N 61 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 212 time to evaluate : 2.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ILE cc_start: 0.5226 (mt) cc_final: 0.5005 (mt) REVERT: A 389 ASP cc_start: 0.8596 (m-30) cc_final: 0.8161 (t0) REVERT: A 698 SER cc_start: 0.9054 (t) cc_final: 0.8665 (p) REVERT: A 790 LYS cc_start: 0.8408 (mmpt) cc_final: 0.7962 (mttm) REVERT: A 990 GLU cc_start: 0.8750 (tt0) cc_final: 0.8247 (tm-30) REVERT: A 1050 MET cc_start: 0.7480 (ptt) cc_final: 0.6910 (ptt) REVERT: B 101 ILE cc_start: 0.9003 (OUTLIER) cc_final: 0.8646 (tp) REVERT: B 274 THR cc_start: 0.8473 (m) cc_final: 0.8164 (m) REVERT: B 697 MET cc_start: 0.8392 (ppp) cc_final: 0.8089 (tmm) REVERT: B 1050 MET cc_start: 0.7513 (OUTLIER) cc_final: 0.7113 (ptt) REVERT: C 104 TRP cc_start: 0.7555 (m-90) cc_final: 0.7353 (m-90) REVERT: C 508 TYR cc_start: 0.8369 (m-80) cc_final: 0.7488 (m-80) REVERT: C 697 MET cc_start: 0.8173 (OUTLIER) cc_final: 0.7779 (ptm) REVERT: H 34 MET cc_start: 0.8215 (tpp) cc_final: 0.7852 (tmm) REVERT: H 82 MET cc_start: 0.9101 (mtm) cc_final: 0.7877 (mpp) REVERT: H 86 ASP cc_start: 0.8055 (m-30) cc_final: 0.7453 (t70) REVERT: L 55 GLU cc_start: 0.8604 (tp30) cc_final: 0.8118 (tp30) REVERT: L 78 LEU cc_start: 0.8388 (mm) cc_final: 0.7848 (tp) REVERT: M 29 PHE cc_start: 0.6110 (t80) cc_final: 0.5879 (t80) REVERT: M 34 MET cc_start: 0.7623 (mmp) cc_final: 0.6919 (mmm) REVERT: M 35 HIS cc_start: 0.8058 (m90) cc_final: 0.7787 (m170) REVERT: M 79 TYR cc_start: 0.7075 (m-80) cc_final: 0.6815 (m-80) REVERT: N 4 MET cc_start: 0.5606 (ptm) cc_final: 0.4447 (ttp) REVERT: N 24 ARG cc_start: 0.8263 (mmm160) cc_final: 0.7615 (mmm-85) REVERT: N 37 GLN cc_start: 0.8922 (tt0) cc_final: 0.8381 (tt0) REVERT: N 50 GLU cc_start: 0.8143 (mp0) cc_final: 0.7818 (mp0) REVERT: N 70 GLU cc_start: 0.9135 (OUTLIER) cc_final: 0.8671 (tp30) REVERT: N 79 GLN cc_start: 0.8677 (mm110) cc_final: 0.8223 (mp10) REVERT: N 105 GLU cc_start: 0.8809 (mp0) cc_final: 0.8606 (mp0) outliers start: 61 outliers final: 37 residues processed: 253 average time/residue: 0.3679 time to fit residues: 151.4696 Evaluate side-chains 234 residues out of total 2913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 193 time to evaluate : 2.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 777 ASN Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain N residue 81 ASP Chi-restraints excluded: chain N residue 106 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 306 optimal weight: 5.9990 chunk 35 optimal weight: 10.0000 chunk 181 optimal weight: 0.8980 chunk 232 optimal weight: 5.9990 chunk 180 optimal weight: 1.9990 chunk 267 optimal weight: 0.9980 chunk 177 optimal weight: 0.7980 chunk 317 optimal weight: 20.0000 chunk 198 optimal weight: 50.0000 chunk 193 optimal weight: 9.9990 chunk 146 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN B1119 ASN C 690 GLN H 3 GLN H 35 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26558 Z= 0.176 Angle : 0.550 9.489 36196 Z= 0.279 Chirality : 0.045 0.435 4402 Planarity : 0.004 0.059 4573 Dihedral : 5.469 57.758 4961 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.71 % Allowed : 12.29 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.15), residues: 3251 helix: 1.68 (0.21), residues: 675 sheet: -0.01 (0.17), residues: 880 loop : -0.66 (0.15), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP H 36 HIS 0.005 0.001 HIS M 35 PHE 0.019 0.001 PHE M 29 TYR 0.017 0.001 TYR A 369 ARG 0.008 0.000 ARG C1107 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 222 time to evaluate : 2.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ILE cc_start: 0.5315 (mt) cc_final: 0.5108 (mt) REVERT: A 312 ILE cc_start: 0.9361 (OUTLIER) cc_final: 0.9077 (pt) REVERT: A 389 ASP cc_start: 0.8566 (m-30) cc_final: 0.8218 (t0) REVERT: A 698 SER cc_start: 0.9018 (t) cc_final: 0.8642 (p) REVERT: A 790 LYS cc_start: 0.8384 (mmpt) cc_final: 0.7937 (mttm) REVERT: A 990 GLU cc_start: 0.8710 (tt0) cc_final: 0.8235 (tm-30) REVERT: A 1050 MET cc_start: 0.7459 (ptt) cc_final: 0.6949 (ptt) REVERT: B 110 LEU cc_start: 0.7000 (OUTLIER) cc_final: 0.6755 (mm) REVERT: B 274 THR cc_start: 0.8575 (m) cc_final: 0.8269 (m) REVERT: B 697 MET cc_start: 0.8421 (OUTLIER) cc_final: 0.8120 (tmm) REVERT: B 1050 MET cc_start: 0.7515 (OUTLIER) cc_final: 0.7173 (ptt) REVERT: C 508 TYR cc_start: 0.8357 (m-80) cc_final: 0.7500 (m-80) REVERT: C 697 MET cc_start: 0.8103 (OUTLIER) cc_final: 0.7727 (ptm) REVERT: C 740 MET cc_start: 0.8518 (tpp) cc_final: 0.8069 (tpp) REVERT: C 1005 GLN cc_start: 0.8328 (mp10) cc_final: 0.8052 (mp10) REVERT: H 18 LEU cc_start: 0.8155 (tp) cc_final: 0.7803 (tt) REVERT: H 34 MET cc_start: 0.8151 (tpp) cc_final: 0.7771 (tmm) REVERT: H 39 GLN cc_start: 0.6754 (pp30) cc_final: 0.6403 (pp30) REVERT: H 82 MET cc_start: 0.9143 (mtm) cc_final: 0.7879 (mpp) REVERT: H 86 ASP cc_start: 0.7993 (m-30) cc_final: 0.7410 (t70) REVERT: L 46 LEU cc_start: 0.7135 (tt) cc_final: 0.6846 (tp) REVERT: L 49 TYR cc_start: 0.7601 (OUTLIER) cc_final: 0.7381 (p90) REVERT: M 34 MET cc_start: 0.7608 (mmp) cc_final: 0.7176 (mmm) REVERT: M 79 TYR cc_start: 0.7127 (m-80) cc_final: 0.6709 (m-80) REVERT: N 4 MET cc_start: 0.5638 (ptm) cc_final: 0.4610 (ttp) REVERT: N 11 LEU cc_start: 0.5571 (mp) cc_final: 0.5264 (mp) REVERT: N 24 ARG cc_start: 0.8209 (mmm160) cc_final: 0.7766 (mmm-85) REVERT: N 37 GLN cc_start: 0.8922 (tt0) cc_final: 0.8532 (tt0) REVERT: N 47 LEU cc_start: 0.8808 (mp) cc_final: 0.8419 (pp) REVERT: N 50 GLU cc_start: 0.8163 (mp0) cc_final: 0.7840 (mp0) REVERT: N 70 GLU cc_start: 0.9139 (OUTLIER) cc_final: 0.8494 (mm-30) REVERT: N 79 GLN cc_start: 0.8668 (mm110) cc_final: 0.8217 (mp10) REVERT: N 105 GLU cc_start: 0.8802 (mp0) cc_final: 0.8591 (mp0) outliers start: 45 outliers final: 23 residues processed: 252 average time/residue: 0.3709 time to fit residues: 152.9187 Evaluate side-chains 230 residues out of total 2913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 200 time to evaluate : 2.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 70 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 196 optimal weight: 20.0000 chunk 126 optimal weight: 6.9990 chunk 189 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 201 optimal weight: 20.0000 chunk 216 optimal weight: 9.9990 chunk 156 optimal weight: 6.9990 chunk 29 optimal weight: 0.4980 chunk 249 optimal weight: 0.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN M 76 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 26558 Z= 0.178 Angle : 0.545 10.154 36196 Z= 0.277 Chirality : 0.045 0.393 4402 Planarity : 0.004 0.060 4573 Dihedral : 5.155 58.661 4961 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.63 % Allowed : 12.56 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.08 (0.15), residues: 3251 helix: 1.74 (0.21), residues: 677 sheet: 0.09 (0.17), residues: 870 loop : -0.63 (0.15), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP M 36 HIS 0.005 0.001 HIS M 35 PHE 0.026 0.001 PHE B 329 TYR 0.027 0.001 TYR A 423 ARG 0.007 0.000 ARG C1107 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 218 time to evaluate : 3.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ILE cc_start: 0.5386 (mt) cc_final: 0.5183 (mt) REVERT: A 312 ILE cc_start: 0.9354 (OUTLIER) cc_final: 0.9089 (pt) REVERT: A 389 ASP cc_start: 0.8526 (m-30) cc_final: 0.8203 (t0) REVERT: A 698 SER cc_start: 0.8984 (t) cc_final: 0.8611 (p) REVERT: A 790 LYS cc_start: 0.8404 (mmpt) cc_final: 0.7917 (mttm) REVERT: A 990 GLU cc_start: 0.8691 (tt0) cc_final: 0.8230 (tm-30) REVERT: A 1050 MET cc_start: 0.7440 (ptt) cc_final: 0.6803 (ptt) REVERT: B 110 LEU cc_start: 0.7069 (OUTLIER) cc_final: 0.6810 (mm) REVERT: B 274 THR cc_start: 0.8578 (m) cc_final: 0.8267 (m) REVERT: B 697 MET cc_start: 0.8398 (OUTLIER) cc_final: 0.8106 (tmm) REVERT: B 1050 MET cc_start: 0.7512 (OUTLIER) cc_final: 0.7179 (ptt) REVERT: B 1107 ARG cc_start: 0.7975 (ptp-170) cc_final: 0.7626 (ptp90) REVERT: C 508 TYR cc_start: 0.8376 (m-80) cc_final: 0.7545 (m-80) REVERT: C 697 MET cc_start: 0.8045 (OUTLIER) cc_final: 0.7756 (ptm) REVERT: C 740 MET cc_start: 0.8360 (tpp) cc_final: 0.8039 (tpp) REVERT: C 1005 GLN cc_start: 0.8332 (mp10) cc_final: 0.8050 (mp10) REVERT: C 1050 MET cc_start: 0.7240 (ptm) cc_final: 0.6896 (ptt) REVERT: H 34 MET cc_start: 0.8022 (tpp) cc_final: 0.7778 (tmm) REVERT: H 78 LEU cc_start: 0.7631 (tp) cc_final: 0.6694 (tp) REVERT: H 82 MET cc_start: 0.9193 (mtm) cc_final: 0.7937 (mpp) REVERT: H 86 ASP cc_start: 0.7942 (m-30) cc_final: 0.7354 (t70) REVERT: L 55 GLU cc_start: 0.8495 (mm-30) cc_final: 0.8218 (tt0) REVERT: L 78 LEU cc_start: 0.8388 (mm) cc_final: 0.7797 (tp) REVERT: M 19 ARG cc_start: 0.8060 (tpp80) cc_final: 0.7338 (tpp80) REVERT: M 34 MET cc_start: 0.7226 (mmp) cc_final: 0.6936 (mmm) REVERT: M 79 TYR cc_start: 0.7024 (m-80) cc_final: 0.6223 (m-80) REVERT: N 4 MET cc_start: 0.5586 (ptm) cc_final: 0.4633 (ttp) REVERT: N 11 LEU cc_start: 0.5565 (mp) cc_final: 0.5259 (mp) REVERT: N 24 ARG cc_start: 0.8201 (mmm160) cc_final: 0.7769 (mmm-85) REVERT: N 37 GLN cc_start: 0.8912 (tt0) cc_final: 0.8559 (tt0) REVERT: N 47 LEU cc_start: 0.8788 (mp) cc_final: 0.8399 (pp) REVERT: N 50 GLU cc_start: 0.8148 (mp0) cc_final: 0.7816 (mp0) REVERT: N 70 GLU cc_start: 0.9142 (OUTLIER) cc_final: 0.8475 (mm-30) REVERT: N 79 GLN cc_start: 0.8652 (mm110) cc_final: 0.8189 (mp10) REVERT: N 105 GLU cc_start: 0.8759 (mp0) cc_final: 0.8549 (mp0) outliers start: 43 outliers final: 32 residues processed: 246 average time/residue: 0.3686 time to fit residues: 148.8263 Evaluate side-chains 238 residues out of total 2913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 200 time to evaluate : 2.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 70 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 288 optimal weight: 1.9990 chunk 303 optimal weight: 10.0000 chunk 277 optimal weight: 0.9990 chunk 295 optimal weight: 5.9990 chunk 177 optimal weight: 0.8980 chunk 128 optimal weight: 0.0870 chunk 232 optimal weight: 5.9990 chunk 90 optimal weight: 0.9980 chunk 267 optimal weight: 0.8980 chunk 279 optimal weight: 0.0060 chunk 294 optimal weight: 9.9990 overall best weight: 0.5774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82AASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 26558 Z= 0.148 Angle : 0.546 9.861 36196 Z= 0.277 Chirality : 0.044 0.349 4402 Planarity : 0.004 0.061 4573 Dihedral : 4.892 59.201 4961 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.56 % Allowed : 13.13 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.16 (0.15), residues: 3251 helix: 1.71 (0.21), residues: 691 sheet: 0.19 (0.17), residues: 864 loop : -0.58 (0.15), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP M 36 HIS 0.008 0.001 HIS M 35 PHE 0.029 0.001 PHE B 823 TYR 0.025 0.001 TYR A 423 ARG 0.006 0.000 ARG C1107 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 218 time to evaluate : 3.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 312 ILE cc_start: 0.9341 (OUTLIER) cc_final: 0.9063 (pt) REVERT: A 389 ASP cc_start: 0.8501 (m-30) cc_final: 0.8160 (t0) REVERT: A 698 SER cc_start: 0.8961 (t) cc_final: 0.8580 (p) REVERT: A 790 LYS cc_start: 0.8420 (mmpt) cc_final: 0.7929 (mttm) REVERT: A 1050 MET cc_start: 0.7584 (ptt) cc_final: 0.7178 (ptt) REVERT: B 110 LEU cc_start: 0.7011 (OUTLIER) cc_final: 0.6605 (mm) REVERT: B 274 THR cc_start: 0.8569 (m) cc_final: 0.8263 (m) REVERT: B 697 MET cc_start: 0.8383 (OUTLIER) cc_final: 0.8093 (tmm) REVERT: B 1050 MET cc_start: 0.7461 (OUTLIER) cc_final: 0.7093 (ptt) REVERT: B 1107 ARG cc_start: 0.7957 (ptp-170) cc_final: 0.7617 (ptp90) REVERT: C 508 TYR cc_start: 0.8369 (m-80) cc_final: 0.7550 (m-80) REVERT: C 697 MET cc_start: 0.7899 (ptp) cc_final: 0.7698 (ptm) REVERT: C 1005 GLN cc_start: 0.8329 (mp10) cc_final: 0.8007 (mp10) REVERT: H 34 MET cc_start: 0.8009 (tpp) cc_final: 0.7662 (tmm) REVERT: H 39 GLN cc_start: 0.6569 (pp30) cc_final: 0.6263 (pp30) REVERT: H 78 LEU cc_start: 0.7511 (tp) cc_final: 0.6519 (tp) REVERT: H 82 MET cc_start: 0.9170 (mtm) cc_final: 0.7887 (mpp) REVERT: H 86 ASP cc_start: 0.7855 (m-30) cc_final: 0.7268 (t70) REVERT: M 16 ARG cc_start: 0.7765 (mmt180) cc_final: 0.7460 (mtm-85) REVERT: M 19 ARG cc_start: 0.8122 (tpp80) cc_final: 0.7513 (tpp80) REVERT: M 34 MET cc_start: 0.6976 (mmp) cc_final: 0.6330 (mmm) REVERT: M 73 ASN cc_start: 0.6726 (OUTLIER) cc_final: 0.6251 (m-40) REVERT: M 79 TYR cc_start: 0.6961 (m-80) cc_final: 0.6117 (m-80) REVERT: N 4 MET cc_start: 0.5476 (OUTLIER) cc_final: 0.4555 (ttp) REVERT: N 11 LEU cc_start: 0.5592 (mp) cc_final: 0.5291 (mp) REVERT: N 24 ARG cc_start: 0.8180 (mmm160) cc_final: 0.7770 (mmm-85) REVERT: N 37 GLN cc_start: 0.8914 (tt0) cc_final: 0.8549 (tt0) REVERT: N 47 LEU cc_start: 0.8830 (mp) cc_final: 0.8408 (pp) REVERT: N 50 GLU cc_start: 0.8218 (mp0) cc_final: 0.7886 (mp0) REVERT: N 70 GLU cc_start: 0.9156 (OUTLIER) cc_final: 0.8465 (mm-30) REVERT: N 79 GLN cc_start: 0.8650 (mm110) cc_final: 0.8175 (mp10) REVERT: N 105 GLU cc_start: 0.8751 (mp0) cc_final: 0.8543 (mp0) outliers start: 41 outliers final: 29 residues processed: 244 average time/residue: 0.3633 time to fit residues: 146.3120 Evaluate side-chains 233 residues out of total 2913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 197 time to evaluate : 2.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 91 TYR Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 73 ASN Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 4 MET Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 70 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 194 optimal weight: 20.0000 chunk 312 optimal weight: 1.9990 chunk 190 optimal weight: 10.0000 chunk 148 optimal weight: 4.9990 chunk 217 optimal weight: 6.9990 chunk 327 optimal weight: 0.9990 chunk 301 optimal weight: 8.9990 chunk 261 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 201 optimal weight: 20.0000 chunk 160 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN C 655 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 26558 Z= 0.233 Angle : 0.572 9.600 36196 Z= 0.290 Chirality : 0.045 0.356 4402 Planarity : 0.004 0.061 4573 Dihedral : 4.966 58.814 4961 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 1.59 % Allowed : 13.66 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.06 (0.15), residues: 3251 helix: 1.67 (0.20), residues: 686 sheet: 0.05 (0.17), residues: 889 loop : -0.62 (0.15), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP M 36 HIS 0.009 0.001 HIS M 35 PHE 0.025 0.001 PHE B 823 TYR 0.023 0.001 TYR A 423 ARG 0.007 0.000 ARG C1107 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 205 time to evaluate : 3.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 ASP cc_start: 0.8501 (m-30) cc_final: 0.8163 (t0) REVERT: A 698 SER cc_start: 0.8979 (t) cc_final: 0.8615 (p) REVERT: A 790 LYS cc_start: 0.8391 (mmpt) cc_final: 0.7919 (mttm) REVERT: A 808 ASP cc_start: 0.6970 (t0) cc_final: 0.6561 (p0) REVERT: A 990 GLU cc_start: 0.8696 (tt0) cc_final: 0.8236 (tm-30) REVERT: A 1050 MET cc_start: 0.7616 (ptt) cc_final: 0.7171 (ptt) REVERT: B 110 LEU cc_start: 0.6834 (OUTLIER) cc_final: 0.6569 (mm) REVERT: B 274 THR cc_start: 0.8545 (m) cc_final: 0.8246 (m) REVERT: B 697 MET cc_start: 0.8441 (OUTLIER) cc_final: 0.8136 (tmm) REVERT: B 1050 MET cc_start: 0.7564 (OUTLIER) cc_final: 0.7311 (ptt) REVERT: B 1107 ARG cc_start: 0.7950 (ptp-170) cc_final: 0.7553 (ptp90) REVERT: C 508 TYR cc_start: 0.8461 (m-80) cc_final: 0.7640 (m-80) REVERT: C 697 MET cc_start: 0.8074 (OUTLIER) cc_final: 0.7738 (ptm) REVERT: C 1005 GLN cc_start: 0.8381 (mp10) cc_final: 0.8129 (mp10) REVERT: H 34 MET cc_start: 0.7996 (tpp) cc_final: 0.7665 (tmm) REVERT: H 39 GLN cc_start: 0.6639 (pp30) cc_final: 0.6366 (pp30) REVERT: H 78 LEU cc_start: 0.7415 (tp) cc_final: 0.6456 (tp) REVERT: H 82 MET cc_start: 0.9188 (mtm) cc_final: 0.7873 (mpp) REVERT: H 86 ASP cc_start: 0.7867 (m-30) cc_final: 0.7266 (t70) REVERT: L 78 LEU cc_start: 0.8322 (mm) cc_final: 0.7697 (tp) REVERT: M 19 ARG cc_start: 0.8111 (tpp80) cc_final: 0.7642 (tpp80) REVERT: M 79 TYR cc_start: 0.7026 (m-80) cc_final: 0.6650 (m-80) REVERT: N 4 MET cc_start: 0.5575 (OUTLIER) cc_final: 0.4561 (ttp) REVERT: N 11 LEU cc_start: 0.5637 (mp) cc_final: 0.5332 (mp) REVERT: N 24 ARG cc_start: 0.8147 (mmm160) cc_final: 0.7709 (mmm-85) REVERT: N 37 GLN cc_start: 0.8870 (tt0) cc_final: 0.8511 (tt0) REVERT: N 47 LEU cc_start: 0.8859 (mp) cc_final: 0.8456 (pp) REVERT: N 50 GLU cc_start: 0.8154 (mp0) cc_final: 0.7808 (mp0) REVERT: N 70 GLU cc_start: 0.9153 (OUTLIER) cc_final: 0.8411 (mm-30) REVERT: N 79 GLN cc_start: 0.8654 (mm110) cc_final: 0.8165 (mp10) REVERT: N 105 GLU cc_start: 0.8764 (mp0) cc_final: 0.8551 (mp0) outliers start: 42 outliers final: 31 residues processed: 234 average time/residue: 0.3768 time to fit residues: 144.2106 Evaluate side-chains 231 residues out of total 2913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 194 time to evaluate : 3.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 4 MET Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain N residue 81 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 207 optimal weight: 0.9990 chunk 278 optimal weight: 0.9980 chunk 79 optimal weight: 7.9990 chunk 240 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 261 optimal weight: 0.1980 chunk 109 optimal weight: 0.0470 chunk 268 optimal weight: 3.9990 chunk 33 optimal weight: 8.9990 chunk 48 optimal weight: 0.9980 overall best weight: 0.6480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN L 79 GLN ** M 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 100 GLN ** 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 = 0.3907 r_free = 0.3907 target = 0.109786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.076406 restraints weight = 63195.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.079273 restraints weight = 30017.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.081166 restraints weight = 18658.823| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 26558 Z= 0.151 Angle : 0.553 13.698 36196 Z= 0.279 Chirality : 0.044 0.338 4402 Planarity : 0.004 0.065 4573 Dihedral : 4.745 59.034 4961 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.40 % Allowed : 14.19 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.15), residues: 3251 helix: 1.75 (0.21), residues: 690 sheet: 0.18 (0.17), residues: 867 loop : -0.59 (0.15), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP M 36 HIS 0.006 0.001 HIS M 35 PHE 0.024 0.001 PHE B 823 TYR 0.026 0.001 TYR A 423 ARG 0.006 0.000 ARG C1107 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4891.68 seconds wall clock time: 91 minutes 5.47 seconds (5465.47 seconds total)