Starting phenix.real_space_refine on Wed Feb 21 03:58:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8t_22730/02_2024/7k8t_22730_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8t_22730/02_2024/7k8t_22730.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8t_22730/02_2024/7k8t_22730.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8t_22730/02_2024/7k8t_22730.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8t_22730/02_2024/7k8t_22730_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8t_22730/02_2024/7k8t_22730_neut.pdb" } resolution = 3.4 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= 0.000 sd= 0.018 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 120 5.16 5 C 18783 2.51 5 N 4856 2.21 5 O 5817 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 138": "OD1" <-> "OD2" Residue "A GLU 169": "OE1" <-> "OE2" Residue "A PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 294": "OD1" <-> "OD2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 328": "NH1" <-> "NH2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 389": "OD1" <-> "OD2" Residue "A ASP 420": "OD1" <-> "OD2" Residue "A TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 428": "OD1" <-> "OD2" Residue "A ASP 442": "OD1" <-> "OD2" Residue "A TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 583": "OE1" <-> "OE2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 661": "OE1" <-> "OE2" Residue "A ASP 663": "OD1" <-> "OD2" Residue "A TYR 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 988": "OE1" <-> "OE2" Residue "A GLU 1017": "OE1" <-> "OE2" Residue "A TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 40": "OD1" <-> "OD2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 80": "OD1" <-> "OD2" Residue "B ASP 88": "OD1" <-> "OD2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 224": "OE1" <-> "OE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 281": "OE1" <-> "OE2" Residue "B ASP 294": "OD1" <-> "OD2" Residue "B TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 328": "NH1" <-> "NH2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 428": "OD1" <-> "OD2" Residue "B TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 554": "OE1" <-> "OE2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 614": "OD1" <-> "OD2" Residue "B GLU 661": "OE1" <-> "OE2" Residue "B ASP 663": "OD1" <-> "OD2" Residue "B ASP 737": "OD1" <-> "OD2" 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 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 994": "OD1" <-> "OD2" Residue "B PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1072": "OE1" <-> "OE2" Residue "B PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1146": "OD1" <-> "OD2" Residue "C PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 80": "OD1" <-> "OD2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "C PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 309": "OE1" <-> "OE2" Residue "C TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 328": "NH1" <-> "NH2" Residue "C PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 369": "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 ASP 398": "OD1" <-> "OD2" Residue "C ASP 420": "OD1" <-> "OD2" Residue "C ASP 428": "OD1" <-> "OD2" Residue "C ASP 442": "OD1" <-> "OD2" Residue "C TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 467": "OD1" <-> "OD2" Residue "C PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 568": "OD1" <-> "OD2" Residue "C PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 663": "OD1" <-> "OD2" Residue "C PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 988": "OE1" <-> "OE2" Residue "C GLU 1017": "OE1" <-> "OE2" Residue "C TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1062": "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 "H GLU 6": "OE1" <-> "OE2" Residue "H TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 61": "OD1" <-> "OD2" Residue "H ASP 72": "OD1" <-> "OD2" Residue "H ARG 83": "NH1" <-> "NH2" Residue "H ASP 100": "OD1" <-> "OD2" Residue "L TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 105": "OE1" <-> "OE2" Residue "M GLU 6": "OE1" <-> "OE2" Residue "M TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 72": "OD1" <-> "OD2" Residue "M ARG 83": "NH1" <-> "NH2" Residue "N TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 70": "OD1" <-> "OD2" Residue "N TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 6": "OE1" <-> "OE2" Residue "O TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 72": "OD1" <-> "OD2" Residue "O ARG 83": "NH1" <-> "NH2" Residue "P TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 105": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 29576 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 7810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7810 Classifications: {'peptide': 1001} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 49, 'TRANS': 951} Chain breaks: 9 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 7801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7801 Classifications: {'peptide': 1001} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 49, 'TRANS': 951} Chain breaks: 9 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 7809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7809 Classifications: {'peptide': 1001} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 49, 'TRANS': 951} Chain breaks: 9 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "H" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 959 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "L" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 813 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "M" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 959 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "N" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 813 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "O" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 959 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "P" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 813 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 13.98, per 1000 atoms: 0.47 Number of scatterers: 29576 At special positions: 0 Unit cell: (136.268, 157.168, 227.392, 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 120 16.00 O 5817 8.00 N 4856 7.00 C 18783 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.02 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 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=2.01 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=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.02 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " 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=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 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 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 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 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 Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 343 " " 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 A1310 " - " ASN A 165 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 282 " " NAG B1305 " - " ASN B 603 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 709 " " NAG B1309 " - " ASN B1074 " " NAG B1310 " - " ASN B 165 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " 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 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 B 234 " " NAG K 1 " - " ASN B 717 " " NAG Q 1 " - " ASN B 801 " " NAG R 1 " - " ASN B1098 " " NAG S 1 " - " ASN B1134 " " NAG T 1 " - " ASN C 234 " " NAG U 1 " - " ASN C 717 " " NAG V 1 " - " ASN C 801 " " NAG W 1 " - " ASN C1098 " " NAG X 1 " - " ASN C1134 " Time building additional restraints: 12.47 Conformation dependent library (CDL) restraints added in 5.2 seconds 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6904 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 53 sheets defined 23.4% alpha, 27.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.98 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.519A pdb=" N CYS A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.570A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.902A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 removed outlier: 3.970A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 388 removed outlier: 3.823A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.960A pdb=" N GLN A 409 " --> 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 743 removed outlier: 4.109A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 756 removed outlier: 3.596A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N TYR A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.503A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.539A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.648A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.593A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.588A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.743A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 5.138A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1125 through 1129 removed outlier: 3.868A pdb=" N VAL A1128 " --> pdb=" O ASN A1125 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.066A 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 343 Processing helix chain 'B' and resid 364 through 371 removed outlier: 3.544A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 removed outlier: 4.177A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ASP B 389 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 Processing helix chain 'B' and resid 416 through 421 Processing helix chain 'B' and resid 455 through 459 Processing helix chain 'B' and resid 501 through 501 No H-bonds generated for 'chain 'B' and resid 501 through 501' Processing helix chain 'B' and resid 503 through 506 Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.503A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 756 removed outlier: 3.744A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N TYR B 756 " --> pdb=" O LEU B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.566A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.573A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.593A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.541A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 968 removed outlier: 3.854A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N SER B 967 " --> pdb=" O VAL B 963 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER B 968 " --> pdb=" O LYS B 964 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.704A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 3.853A 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 337 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.579A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.925A 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 455 through 459 removed outlier: 3.831A pdb=" N LYS C 458 " --> pdb=" O LEU C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 501 No H-bonds generated for 'chain 'C' and resid 501 through 501' Processing helix chain 'C' and resid 503 through 505 No H-bonds generated for 'chain 'C' and resid 503 through 505' Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 756 removed outlier: 3.660A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.514A pdb=" N ARG C 765 " --> pdb=" O THR C 761 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.549A pdb=" N LEU C 822 " --> pdb=" O ILE C 818 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.626A pdb=" N GLN C 872 " --> pdb=" O GLU C 868 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N TYR C 873 " --> pdb=" O MET C 869 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.642A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.668A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASN C 960 " --> pdb=" O ALA C 956 " (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: 3.557A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.910A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 3.896A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.821A pdb=" N ILE H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 removed outlier: 3.699A pdb=" N LYS H 64 " --> pdb=" O ASP H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.606A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 32 removed outlier: 3.978A pdb=" N ILE M 31 " --> pdb=" O THR M 28 " (cutoff:3.500A) Processing helix chain 'M' and resid 61 through 64 Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.797A pdb=" N PHE N 83 " --> pdb=" O PRO N 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 28 through 32 removed outlier: 3.530A pdb=" N ILE O 31 " --> pdb=" O THR O 28 " (cutoff:3.500A) Processing helix chain 'O' and resid 61 through 64 Processing helix chain 'O' and resid 83 through 87 Processing helix chain 'P' and resid 79 through 83 removed outlier: 3.651A pdb=" N PHE P 83 " --> pdb=" O PRO P 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.160A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.594A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.554A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.884A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 7.095A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 132 through 134 removed outlier: 4.994A pdb=" N PHE A 133 " --> pdb=" O SER A 112 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 237 through 244 current: chain 'A' and resid 169 through 171 Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.302A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 326 Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.744A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ASN A 437 " --> pdb=" O PHE A 374 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N PHE A 374 " --> pdb=" O ASN A 437 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 565 through 566 removed outlier: 7.145A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.336A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 711 through 713 removed outlier: 3.572A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.807A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB4, first strand: chain 'A' and resid 1120 through 1123 removed outlier: 3.557A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N CYS A1082 " --> pdb=" O VAL A1133 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 28 through 31 removed outlier: 4.147A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N SER B 94 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR B 208 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL B 193 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.562A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.706A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 84 through 85 removed outlier: 7.033A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 311 through 317 removed outlier: 5.097A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 324 through 325 removed outlier: 6.386A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.746A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 361 through 362 removed outlier: 7.300A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.503A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.801A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 718 through 728 removed outlier: 7.128A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AC8, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AC9, first strand: chain 'C' and resid 28 through 30 removed outlier: 3.689A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU C 96 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.165A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.378A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.839A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.538A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.139A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU C 117 " --> pdb=" O PHE C 106 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.962A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 324 through 326 removed outlier: 4.141A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.706A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N THR C 430 " --> pdb=" O PHE C 515 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AD8, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.135A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 711 through 713 removed outlier: 3.638A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.894A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE3, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE4, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AE5, first strand: chain 'H' and resid 10 through 12 removed outlier: 5.900A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.915A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER L 67 " --> pdb=" O ASP L 70 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.499A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'M' and resid 3 through 7 Processing sheet with id=AE9, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.136A pdb=" N GLY M 10 " --> pdb=" O THR M 110 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N MET M 34 " --> pdb=" O VAL M 50 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N VAL M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'N' and resid 4 through 7 removed outlier: 3.601A pdb=" N ASP N 70 " --> pdb=" O SER N 67 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.299A pdb=" N LEU N 11 " --> pdb=" O GLU N 105 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N GLN N 37 " --> pdb=" O LEU N 46 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N LEU N 46 " --> pdb=" O GLN N 37 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.299A pdb=" N LEU N 11 " --> pdb=" O GLU N 105 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N THR N 97 " --> pdb=" O GLN N 90 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'O' and resid 3 through 7 removed outlier: 3.730A pdb=" N TYR O 79 " --> pdb=" O SER O 70 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER O 70 " --> pdb=" O TYR O 79 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'O' and resid 10 through 12 removed outlier: 6.002A pdb=" N ARG O 38 " --> pdb=" O TRP O 47 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N TRP O 47 " --> pdb=" O ARG O 38 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'P' and resid 4 through 7 removed outlier: 3.571A pdb=" N ASP P 70 " --> pdb=" O SER P 67 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THR P 72 " --> pdb=" O SER P 65 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER P 65 " --> pdb=" O THR P 72 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'P' and resid 10 through 13 removed outlier: 6.537A pdb=" N LEU P 11 " --> pdb=" O GLU P 105 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N GLN P 37 " --> pdb=" O LEU P 46 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N LEU P 46 " --> pdb=" O GLN P 37 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'P' and resid 10 through 13 removed outlier: 6.537A pdb=" N LEU P 11 " --> pdb=" O GLU P 105 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N THR P 97 " --> pdb=" O GLN P 90 " (cutoff:3.500A) 1147 hydrogen bonds defined for protein. 3099 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: 15.89 Time building geometry restraints manager: 13.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 1.25: 4784 1.25 - 1.40: 7548 1.40 - 1.54: 17692 1.54 - 1.69: 35 1.69 - 1.83: 151 Bond restraints: 30210 Sorted by residual: bond pdb=" N PRO A 85 " pdb=" CA PRO A 85 " ideal model delta sigma weight residual 1.469 1.701 -0.232 1.28e-02 6.10e+03 3.30e+02 bond pdb=" N PRO C 85 " pdb=" CA PRO C 85 " ideal model delta sigma weight residual 1.469 1.697 -0.229 1.28e-02 6.10e+03 3.19e+02 bond pdb=" CG PRO B 579 " pdb=" CD PRO B 579 " ideal model delta sigma weight residual 1.503 1.110 0.393 3.40e-02 8.65e+02 1.34e+02 bond pdb=" C LEU A 84 " pdb=" N PRO A 85 " ideal model delta sigma weight residual 1.334 1.454 -0.120 2.34e-02 1.83e+03 2.63e+01 bond pdb=" C LEU C 84 " pdb=" N PRO C 85 " ideal model delta sigma weight residual 1.334 1.451 -0.117 2.34e-02 1.83e+03 2.48e+01 ... (remaining 30205 not shown) Histogram of bond angle deviations from ideal: 81.68 - 93.19: 2 93.19 - 104.70: 497 104.70 - 116.22: 20012 116.22 - 127.73: 20339 127.73 - 139.24: 232 Bond angle restraints: 41082 Sorted by residual: angle pdb=" C LEU A 84 " pdb=" N PRO A 85 " pdb=" CA PRO A 85 " ideal model delta sigma weight residual 119.84 139.24 -19.40 1.25e+00 6.40e-01 2.41e+02 angle pdb=" C LEU C 84 " pdb=" N PRO C 85 " pdb=" CA PRO C 85 " ideal model delta sigma weight residual 119.84 139.19 -19.35 1.25e+00 6.40e-01 2.40e+02 angle pdb=" N PRO B 579 " pdb=" CD PRO B 579 " pdb=" CG PRO B 579 " ideal model delta sigma weight residual 103.20 81.68 21.52 1.50e+00 4.44e-01 2.06e+02 angle pdb=" CA PRO C 85 " pdb=" N PRO C 85 " pdb=" CD PRO C 85 " ideal model delta sigma weight residual 112.00 99.77 12.23 1.40e+00 5.10e-01 7.63e+01 angle pdb=" CA PRO A 85 " pdb=" N PRO A 85 " pdb=" CD PRO A 85 " ideal model delta sigma weight residual 112.00 100.20 11.80 1.40e+00 5.10e-01 7.11e+01 ... (remaining 41077 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 17141 17.93 - 35.85: 1265 35.85 - 53.78: 227 53.78 - 71.70: 62 71.70 - 89.63: 27 Dihedral angle restraints: 18722 sinusoidal: 7984 harmonic: 10738 Sorted by residual: dihedral pdb=" CA GLN A 474 " pdb=" C GLN A 474 " pdb=" N ALA A 475 " pdb=" CA ALA A 475 " ideal model delta harmonic sigma weight residual -180.00 -130.07 -49.93 0 5.00e+00 4.00e-02 9.97e+01 dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual 93.00 -177.37 -89.63 1 1.00e+01 1.00e-02 9.54e+01 dihedral pdb=" CA GLU B 471 " pdb=" C GLU B 471 " pdb=" N ILE B 472 " pdb=" CA ILE B 472 " ideal model delta harmonic sigma weight residual -180.00 -133.51 -46.49 0 5.00e+00 4.00e-02 8.65e+01 ... (remaining 18719 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.168: 4787 0.168 - 0.336: 43 0.336 - 0.505: 6 0.505 - 0.673: 2 0.673 - 0.841: 1 Chirality restraints: 4839 Sorted by residual: chirality pdb=" C1 NAG B1303 " pdb=" ND2 ASN B 282 " pdb=" C2 NAG B1303 " pdb=" O5 NAG B1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.56 -0.84 2.00e-01 2.50e+01 1.77e+01 chirality pdb=" CA PRO C 85 " pdb=" N PRO C 85 " pdb=" C PRO C 85 " pdb=" CB PRO C 85 " both_signs ideal model delta sigma weight residual False 2.72 3.27 -0.55 2.00e-01 2.50e+01 7.61e+00 chirality pdb=" C1 NAG B1305 " pdb=" ND2 ASN B 603 " pdb=" C2 NAG B1305 " pdb=" O5 NAG B1305 " both_signs ideal model delta sigma weight residual False -2.40 -1.87 -0.53 2.00e-01 2.50e+01 7.06e+00 ... (remaining 4836 not shown) Planarity restraints: 5268 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 84 " -0.026 2.00e-02 2.50e+03 4.90e-02 2.41e+01 pdb=" C LEU C 84 " 0.085 2.00e-02 2.50e+03 pdb=" O LEU C 84 " -0.032 2.00e-02 2.50e+03 pdb=" N PRO C 85 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL P 58 " -0.065 5.00e-02 4.00e+02 9.37e-02 1.40e+01 pdb=" N PRO P 59 " 0.162 5.00e-02 4.00e+02 pdb=" CA PRO P 59 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO P 59 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 578 " -0.060 5.00e-02 4.00e+02 8.39e-02 1.13e+01 pdb=" N PRO B 579 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO B 579 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 579 " -0.044 5.00e-02 4.00e+02 ... (remaining 5265 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.36: 99 2.36 - 3.00: 17659 3.00 - 3.63: 43274 3.63 - 4.27: 67555 4.27 - 4.90: 111624 Nonbonded interactions: 240211 Sorted by model distance: nonbonded pdb=" CG PRO M 98 " pdb=" CD1 ILE M 100A" model vdw 1.726 3.860 nonbonded pdb=" O PHE C 490 " pdb=" NH2 ARG H 97 " model vdw 1.813 2.520 nonbonded pdb=" CG PRO M 98 " pdb=" CG1 ILE M 100A" model vdw 1.903 3.840 nonbonded pdb=" CZ TYR A 489 " pdb=" O VAL O 100C" model vdw 1.960 3.260 nonbonded pdb=" OE1 GLN C 804 " pdb=" NE2 GLN C 935 " model vdw 2.042 2.520 ... (remaining 240206 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 329 or (resid 330 and (name N or name CA or nam \ e C or name O or name CB )) or resid 331 through 335 or (resid 336 and (name N o \ r name CA or name C or name O )) or resid 337 through 378 or (resid 379 and (nam \ e N or name CA or name C or name O or name CB )) or resid 380 through 524 or (re \ sid 525 and (name N or name CA or name C or name O or name CB )) or resid 526 th \ rough 527 or (resid 528 and (name N or name CA or name C or name O or name CB )) \ or resid 529 through 1147 or resid 1301 through 1310)) selection = (chain 'B' and (resid 27 through 335 or (resid 336 and (name N or name CA or nam \ e C or name O )) or resid 337 through 1147 or resid 1301 through 1310)) selection = (chain 'C' and (resid 27 through 329 or (resid 330 and (name N or name CA or nam \ e C or name O or name CB )) or resid 331 through 335 or (resid 336 and (name N o \ r name CA or name C or name O )) or resid 337 through 378 or (resid 379 and (nam \ e N or name CA or name C or name O or name CB )) or resid 380 through 524 or (re \ sid 525 and (name N or name CA or name C or name O or name CB )) or resid 526 th \ rough 527 or (resid 528 and (name N or name CA or name C or name O or name CB )) \ or resid 529 through 1147 or resid 1301 through 1310)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } ncs_group { reference = chain 'H' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'L' selection = chain 'N' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 25.180 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 78.200 Find NCS groups from input model: 2.150 Set up NCS constraints: 0.510 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 112.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 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 : 0.010 0.393 30210 Z= 0.657 Angle : 0.949 21.520 41082 Z= 0.546 Chirality : 0.059 0.841 4839 Planarity : 0.005 0.094 5225 Dihedral : 13.076 88.395 11713 Min Nonbonded Distance : 1.726 Molprobity Statistics. All-atom Clashscore : 17.04 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.37 % Favored : 93.41 % Rotamer: Outliers : 0.22 % Allowed : 0.63 % Favored : 99.15 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % 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: -0.76 (0.13), residues: 3627 helix: 0.24 (0.19), residues: 643 sheet: 0.28 (0.16), residues: 957 loop : -1.16 (0.13), residues: 2027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP C 64 HIS 0.005 0.001 HIS A 66 PHE 0.044 0.003 PHE B 464 TYR 0.038 0.003 TYR B 489 ARG 0.020 0.002 ARG B 346 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 306 time to evaluate : 3.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 GLU cc_start: 0.9120 (mm-30) cc_final: 0.8401 (tm-30) REVERT: A 370 ASN cc_start: 0.8537 (m110) cc_final: 0.8313 (m110) REVERT: A 405 ASP cc_start: 0.8409 (t0) cc_final: 0.8044 (t70) REVERT: A 408 ARG cc_start: 0.9133 (ptm-80) cc_final: 0.8926 (ppt170) REVERT: A 421 TYR cc_start: 0.8750 (m-80) cc_final: 0.8287 (m-80) REVERT: A 855 PHE cc_start: 0.6581 (m-80) cc_final: 0.6371 (m-80) REVERT: B 81 ASN cc_start: 0.8125 (p0) cc_final: 0.7775 (p0) REVERT: B 104 TRP cc_start: 0.8542 (m-90) cc_final: 0.8169 (m-90) REVERT: B 346 ARG cc_start: 0.9028 (mtp-110) cc_final: 0.8442 (tmm-80) REVERT: B 370 ASN cc_start: 0.9008 (m-40) cc_final: 0.8291 (p0) REVERT: B 386 LYS cc_start: 0.9391 (mmtt) cc_final: 0.9091 (ttpp) REVERT: C 104 TRP cc_start: 0.7886 (m-90) cc_final: 0.7556 (m-90) REVERT: C 378 LYS cc_start: 0.8530 (ttmm) cc_final: 0.8316 (ttmm) REVERT: C 406 GLU cc_start: 0.8735 (mp0) cc_final: 0.8209 (mp0) REVERT: C 855 PHE cc_start: 0.7245 (m-10) cc_final: 0.7043 (m-10) REVERT: H 4 LEU cc_start: 0.7634 (mt) cc_final: 0.7186 (mt) REVERT: H 19 ARG cc_start: 0.8620 (ttp-170) cc_final: 0.8359 (ttp80) REVERT: H 51 ILE cc_start: 0.9093 (tt) cc_final: 0.8765 (tt) REVERT: H 79 TYR cc_start: 0.8777 (m-80) cc_final: 0.8270 (m-80) REVERT: H 91 TYR cc_start: 0.7702 (m-80) cc_final: 0.7028 (m-80) REVERT: H 101 ASP cc_start: 0.4153 (p0) cc_final: 0.3945 (p0) REVERT: H 103 TRP cc_start: 0.8249 (m100) cc_final: 0.7667 (m-10) REVERT: L 18 ARG cc_start: 0.8497 (ttm-80) cc_final: 0.8252 (ttm-80) REVERT: L 21 ILE cc_start: 0.8669 (mp) cc_final: 0.8058 (mp) REVERT: L 34 ASN cc_start: 0.8662 (m-40) cc_final: 0.8019 (m-40) REVERT: L 35 TRP cc_start: 0.8604 (m100) cc_final: 0.8117 (m100) REVERT: L 37 GLN cc_start: 0.8315 (tt0) cc_final: 0.7604 (tt0) REVERT: M 95 GLU cc_start: 0.6206 (mt-10) cc_final: 0.5970 (mt-10) REVERT: N 32 TYR cc_start: 0.6078 (m-80) cc_final: 0.5769 (m-80) REVERT: N 105 GLU cc_start: 0.6768 (mt-10) cc_final: 0.6412 (tt0) REVERT: O 4 LEU cc_start: 0.7564 (mt) cc_final: 0.6944 (mt) REVERT: O 19 ARG cc_start: 0.7292 (ttp-170) cc_final: 0.6800 (tpp80) REVERT: O 34 MET cc_start: 0.7664 (mmp) cc_final: 0.6184 (mmm) REVERT: P 82 ASP cc_start: 0.3679 (m-30) cc_final: 0.2417 (m-30) REVERT: P 92 TYR cc_start: 0.7765 (t80) cc_final: 0.7537 (t80) outliers start: 7 outliers final: 1 residues processed: 311 average time/residue: 0.4637 time to fit residues: 220.6055 Evaluate side-chains 204 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 203 time to evaluate : 3.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 335 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 309 optimal weight: 20.0000 chunk 277 optimal weight: 0.5980 chunk 153 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 187 optimal weight: 0.9990 chunk 148 optimal weight: 1.9990 chunk 286 optimal weight: 0.8980 chunk 111 optimal weight: 10.0000 chunk 174 optimal weight: 0.4980 chunk 213 optimal weight: 2.9990 chunk 332 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 317 ASN A 321 GLN A 394 ASN ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 GLN A 751 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A1002 GLN B 49 HIS B 69 HIS ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN C 207 HIS ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN C 935 GLN C1010 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 30210 Z= 0.216 Angle : 0.685 10.177 41082 Z= 0.362 Chirality : 0.049 0.572 4839 Planarity : 0.005 0.048 5225 Dihedral : 7.086 59.167 5225 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.51 % Favored : 94.35 % Rotamer: Outliers : 0.66 % Allowed : 5.92 % Favored : 93.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % 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: -0.26 (0.14), residues: 3627 helix: 1.50 (0.20), residues: 678 sheet: 0.32 (0.16), residues: 951 loop : -1.03 (0.14), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 64 HIS 0.006 0.001 HIS C 66 PHE 0.029 0.002 PHE A 400 TYR 0.037 0.002 TYR C 489 ARG 0.011 0.001 ARG M 97 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 273 time to evaluate : 3.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 GLU cc_start: 0.9031 (mm-30) cc_final: 0.8305 (tm-30) REVERT: A 370 ASN cc_start: 0.8507 (m110) cc_final: 0.8208 (p0) REVERT: A 421 TYR cc_start: 0.8633 (m-80) cc_final: 0.8193 (m-80) REVERT: A 855 PHE cc_start: 0.6589 (m-80) cc_final: 0.6366 (m-80) REVERT: A 1017 GLU cc_start: 0.8406 (tm-30) cc_final: 0.8101 (tm-30) REVERT: B 81 ASN cc_start: 0.8262 (p0) cc_final: 0.7787 (p0) REVERT: B 346 ARG cc_start: 0.8977 (mtp-110) cc_final: 0.8519 (tmm-80) REVERT: B 386 LYS cc_start: 0.9360 (mmtt) cc_final: 0.9042 (ttpp) REVERT: B 483 VAL cc_start: 0.5509 (OUTLIER) cc_final: 0.5074 (p) REVERT: C 104 TRP cc_start: 0.8137 (m-90) cc_final: 0.7681 (m-90) REVERT: C 200 TYR cc_start: 0.7508 (m-80) cc_final: 0.7304 (t80) REVERT: C 406 GLU cc_start: 0.8596 (mp0) cc_final: 0.8085 (mp0) REVERT: C 739 THR cc_start: 0.9016 (m) cc_final: 0.8778 (p) REVERT: C 869 MET cc_start: 0.8874 (mmm) cc_final: 0.8418 (mmm) REVERT: H 59 TYR cc_start: 0.7177 (m-80) cc_final: 0.6743 (m-80) REVERT: H 64 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.8108 (tptp) REVERT: H 79 TYR cc_start: 0.8935 (m-80) cc_final: 0.8408 (m-10) REVERT: H 91 TYR cc_start: 0.7606 (m-80) cc_final: 0.6571 (m-80) REVERT: H 101 ASP cc_start: 0.4250 (p0) cc_final: 0.3915 (p0) REVERT: L 18 ARG cc_start: 0.8492 (ttm-80) cc_final: 0.8266 (ttm-80) REVERT: L 34 ASN cc_start: 0.8195 (m-40) cc_final: 0.7723 (m-40) REVERT: L 37 GLN cc_start: 0.8080 (tt0) cc_final: 0.7379 (tt0) REVERT: M 77 THR cc_start: 0.7246 (p) cc_final: 0.7032 (t) REVERT: N 35 TRP cc_start: 0.4230 (m100) cc_final: 0.3735 (m100) REVERT: N 89 GLN cc_start: 0.6713 (tm-30) cc_final: 0.6251 (tp-100) REVERT: N 105 GLU cc_start: 0.6612 (mt-10) cc_final: 0.6342 (tt0) REVERT: O 19 ARG cc_start: 0.7399 (ttp-170) cc_final: 0.6645 (tpt170) REVERT: O 79 TYR cc_start: 0.7066 (m-80) cc_final: 0.6857 (m-80) REVERT: P 3 GLN cc_start: 0.8071 (mm110) cc_final: 0.7708 (mm-40) REVERT: P 71 PHE cc_start: 0.5586 (m-80) cc_final: 0.5346 (m-80) outliers start: 21 outliers final: 7 residues processed: 286 average time/residue: 0.4407 time to fit residues: 196.6061 Evaluate side-chains 210 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 201 time to evaluate : 3.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain N residue 88 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 184 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 276 optimal weight: 1.9990 chunk 226 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 332 optimal weight: 2.9990 chunk 359 optimal weight: 10.0000 chunk 296 optimal weight: 4.9990 chunk 330 optimal weight: 10.0000 chunk 113 optimal weight: 9.9990 chunk 267 optimal weight: 0.2980 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 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 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 ASN C 196 ASN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 ASN ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 56 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 30210 Z= 0.265 Angle : 0.632 9.737 41082 Z= 0.332 Chirality : 0.047 0.527 4839 Planarity : 0.004 0.050 5225 Dihedral : 6.398 59.693 5225 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.29 % Favored : 93.58 % Rotamer: Outliers : 0.88 % Allowed : 9.67 % Favored : 89.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -0.21 (0.14), residues: 3627 helix: 1.82 (0.20), residues: 675 sheet: 0.21 (0.16), residues: 944 loop : -1.02 (0.14), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP M 36 HIS 0.004 0.001 HIS B 49 PHE 0.020 0.002 PHE A 201 TYR 0.036 0.002 TYR C 489 ARG 0.006 0.001 ARG P 24 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 220 time to evaluate : 3.291 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 421 TYR cc_start: 0.8623 (m-80) cc_final: 0.8256 (m-80) REVERT: A 855 PHE cc_start: 0.6692 (m-80) cc_final: 0.6472 (m-80) REVERT: A 900 MET cc_start: 0.8494 (mtt) cc_final: 0.8225 (mtt) REVERT: A 1017 GLU cc_start: 0.8479 (tm-30) cc_final: 0.8123 (tm-30) REVERT: B 81 ASN cc_start: 0.8358 (p0) cc_final: 0.7864 (p0) REVERT: B 346 ARG cc_start: 0.8973 (mtp-110) cc_final: 0.8548 (tmm-80) REVERT: B 386 LYS cc_start: 0.9348 (mmtt) cc_final: 0.9036 (ttpp) REVERT: B 474 GLN cc_start: 0.7366 (tm-30) cc_final: 0.6994 (tm-30) REVERT: B 483 VAL cc_start: 0.5458 (OUTLIER) cc_final: 0.5165 (p) REVERT: C 104 TRP cc_start: 0.8295 (m-90) cc_final: 0.7852 (m-90) REVERT: C 200 TYR cc_start: 0.7689 (m-80) cc_final: 0.7446 (t80) REVERT: C 406 GLU cc_start: 0.8653 (mp0) cc_final: 0.8096 (mp0) REVERT: C 453 TYR cc_start: 0.8090 (p90) cc_final: 0.7430 (p90) REVERT: H 64 LYS cc_start: 0.8455 (mttp) cc_final: 0.8114 (tptp) REVERT: H 75 LYS cc_start: 0.9045 (mtpp) cc_final: 0.8725 (mtmm) REVERT: H 79 TYR cc_start: 0.8889 (m-80) cc_final: 0.8448 (m-80) REVERT: H 101 ASP cc_start: 0.4101 (p0) cc_final: 0.3696 (p0) REVERT: L 34 ASN cc_start: 0.8278 (m-40) cc_final: 0.7830 (m110) REVERT: L 37 GLN cc_start: 0.8115 (tt0) cc_final: 0.7778 (tt0) REVERT: L 46 LEU cc_start: 0.8689 (tp) cc_final: 0.8472 (tt) REVERT: L 47 LEU cc_start: 0.8391 (mt) cc_final: 0.7960 (mt) REVERT: L 79 GLN cc_start: 0.7495 (mp-120) cc_final: 0.7042 (mp-120) REVERT: L 92 TYR cc_start: 0.8382 (t80) cc_final: 0.7989 (t80) REVERT: M 97 ARG cc_start: 0.6748 (mtm180) cc_final: 0.6502 (ttm110) REVERT: N 35 TRP cc_start: 0.4005 (m100) cc_final: 0.3360 (m100) REVERT: N 39 LYS cc_start: 0.6956 (mmpt) cc_final: 0.6089 (tmtt) REVERT: N 105 GLU cc_start: 0.6669 (mt-10) cc_final: 0.6435 (tt0) REVERT: O 19 ARG cc_start: 0.7440 (ttp-170) cc_final: 0.6723 (tpp-160) REVERT: O 32 TYR cc_start: 0.5584 (m-80) cc_final: 0.5196 (m-10) REVERT: O 34 MET cc_start: 0.7964 (mmp) cc_final: 0.7218 (mmm) REVERT: O 67 PHE cc_start: -0.0374 (m-80) cc_final: -0.0748 (m-80) REVERT: P 3 GLN cc_start: 0.8057 (mm110) cc_final: 0.7696 (mm-40) REVERT: P 71 PHE cc_start: 0.5485 (m-80) cc_final: 0.5267 (m-80) outliers start: 28 outliers final: 14 residues processed: 241 average time/residue: 0.4373 time to fit residues: 166.7147 Evaluate side-chains 214 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 199 time to evaluate : 3.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain M residue 100 ILE Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 88 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 328 optimal weight: 30.0000 chunk 250 optimal weight: 7.9990 chunk 172 optimal weight: 1.9990 chunk 36 optimal weight: 9.9990 chunk 158 optimal weight: 5.9990 chunk 223 optimal weight: 2.9990 chunk 334 optimal weight: 0.8980 chunk 353 optimal weight: 9.9990 chunk 174 optimal weight: 4.9990 chunk 316 optimal weight: 7.9990 chunk 95 optimal weight: 0.6980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 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 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 992 GLN C 69 HIS C 81 ASN ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 81 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 30210 Z= 0.300 Angle : 0.617 10.018 41082 Z= 0.324 Chirality : 0.046 0.529 4839 Planarity : 0.004 0.077 5225 Dihedral : 6.068 58.834 5225 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.34 % Favored : 93.55 % Rotamer: Outliers : 1.56 % Allowed : 10.95 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.22 (0.14), residues: 3627 helix: 1.87 (0.20), residues: 675 sheet: 0.25 (0.16), residues: 915 loop : -1.06 (0.14), residues: 2037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP H 47 HIS 0.004 0.001 HIS C 66 PHE 0.017 0.002 PHE A 400 TYR 0.030 0.002 TYR A 265 ARG 0.006 0.001 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 215 time to evaluate : 3.259 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 421 TYR cc_start: 0.8684 (m-80) cc_final: 0.8376 (m-80) REVERT: A 855 PHE cc_start: 0.6856 (m-80) cc_final: 0.6485 (m-80) REVERT: A 1017 GLU cc_start: 0.8495 (tm-30) cc_final: 0.8151 (tm-30) REVERT: B 81 ASN cc_start: 0.8353 (p0) cc_final: 0.7836 (p0) REVERT: B 346 ARG cc_start: 0.8963 (mtp-110) cc_final: 0.8646 (tmm-80) REVERT: B 386 LYS cc_start: 0.9342 (mmtt) cc_final: 0.9024 (ttpp) REVERT: B 473 TYR cc_start: 0.6196 (OUTLIER) cc_final: 0.5316 (m-10) REVERT: B 474 GLN cc_start: 0.7480 (tm-30) cc_final: 0.7161 (tm-30) REVERT: C 406 GLU cc_start: 0.8740 (mp0) cc_final: 0.8188 (mp0) REVERT: C 453 TYR cc_start: 0.8343 (p90) cc_final: 0.7397 (p90) REVERT: C 547 THR cc_start: 0.9032 (OUTLIER) cc_final: 0.8601 (p) REVERT: H 76 ASN cc_start: 0.9057 (OUTLIER) cc_final: 0.8777 (t0) REVERT: H 79 TYR cc_start: 0.8939 (m-80) cc_final: 0.8542 (m-80) REVERT: H 91 TYR cc_start: 0.7217 (m-10) cc_final: 0.6647 (m-10) REVERT: H 101 ASP cc_start: 0.4280 (p0) cc_final: 0.3760 (p0) REVERT: L 34 ASN cc_start: 0.8161 (m-40) cc_final: 0.7735 (m110) REVERT: L 37 GLN cc_start: 0.8093 (tt0) cc_final: 0.7417 (tt0) REVERT: L 46 LEU cc_start: 0.8662 (tp) cc_final: 0.8416 (tt) REVERT: L 61 ARG cc_start: 0.7864 (ptp90) cc_final: 0.7483 (ptp90) REVERT: L 79 GLN cc_start: 0.7627 (mp-120) cc_final: 0.7377 (mp10) REVERT: L 92 TYR cc_start: 0.8338 (t80) cc_final: 0.7884 (t80) REVERT: M 97 ARG cc_start: 0.6638 (mtm180) cc_final: 0.6325 (ttm110) REVERT: N 35 TRP cc_start: 0.3881 (m100) cc_final: 0.3433 (m100) REVERT: N 39 LYS cc_start: 0.7099 (mmpt) cc_final: 0.6261 (tmtt) REVERT: N 88 CYS cc_start: 0.4689 (OUTLIER) cc_final: 0.3790 (m) REVERT: N 105 GLU cc_start: 0.6927 (mt-10) cc_final: 0.6554 (tt0) REVERT: O 19 ARG cc_start: 0.7431 (ttp-170) cc_final: 0.6713 (tpp-160) REVERT: P 32 TYR cc_start: 0.5231 (m-80) cc_final: 0.4873 (m-80) outliers start: 50 outliers final: 22 residues processed: 256 average time/residue: 0.4174 time to fit residues: 170.9602 Evaluate side-chains 216 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 190 time to evaluate : 3.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain C residue 429 PHE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 88 CYS Chi-restraints excluded: chain P residue 47 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 294 optimal weight: 2.9990 chunk 200 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 263 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 301 optimal weight: 9.9990 chunk 244 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 180 optimal weight: 0.9990 chunk 317 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 GLN ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** 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 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 GLN ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 30210 Z= 0.302 Angle : 0.614 9.535 41082 Z= 0.321 Chirality : 0.046 0.528 4839 Planarity : 0.004 0.132 5225 Dihedral : 5.878 58.462 5223 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.87 % Favored : 93.05 % Rotamer: Outliers : 1.35 % Allowed : 12.46 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.27 (0.14), residues: 3627 helix: 1.93 (0.20), residues: 674 sheet: 0.19 (0.16), residues: 954 loop : -1.14 (0.14), residues: 1999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP H 47 HIS 0.004 0.001 HIS B1048 PHE 0.017 0.002 PHE A 400 TYR 0.029 0.002 TYR A 265 ARG 0.008 0.001 ARG P 96 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 205 time to evaluate : 3.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 421 TYR cc_start: 0.8832 (m-80) cc_final: 0.8335 (m-80) REVERT: A 855 PHE cc_start: 0.6994 (m-80) cc_final: 0.6465 (m-80) REVERT: A 1017 GLU cc_start: 0.8496 (tm-30) cc_final: 0.8169 (tm-30) REVERT: B 346 ARG cc_start: 0.8949 (mtp-110) cc_final: 0.8676 (tmm-80) REVERT: B 386 LYS cc_start: 0.9310 (mmtt) cc_final: 0.9020 (ttpp) REVERT: B 425 LEU cc_start: 0.8582 (mt) cc_final: 0.8334 (mt) REVERT: B 473 TYR cc_start: 0.6202 (OUTLIER) cc_final: 0.5311 (m-10) REVERT: B 474 GLN cc_start: 0.7494 (tm-30) cc_final: 0.7166 (tm-30) REVERT: B 483 VAL cc_start: 0.5091 (OUTLIER) cc_final: 0.4788 (p) REVERT: C 200 TYR cc_start: 0.7804 (m-80) cc_final: 0.7492 (t80) REVERT: C 406 GLU cc_start: 0.8770 (mp0) cc_final: 0.8248 (mp0) REVERT: C 453 TYR cc_start: 0.8374 (p90) cc_final: 0.7462 (p90) REVERT: H 79 TYR cc_start: 0.8976 (m-80) cc_final: 0.8700 (m-80) REVERT: H 91 TYR cc_start: 0.7180 (m-10) cc_final: 0.6894 (m-10) REVERT: H 101 ASP cc_start: 0.3976 (p0) cc_final: 0.3462 (p0) REVERT: L 34 ASN cc_start: 0.8140 (m-40) cc_final: 0.7752 (m110) REVERT: L 37 GLN cc_start: 0.8037 (tt0) cc_final: 0.7727 (tt0) REVERT: L 46 LEU cc_start: 0.8585 (tp) cc_final: 0.8305 (tt) REVERT: L 47 LEU cc_start: 0.8391 (mt) cc_final: 0.7950 (mt) REVERT: L 61 ARG cc_start: 0.7782 (ptp90) cc_final: 0.7449 (ptp90) REVERT: L 79 GLN cc_start: 0.7805 (mp-120) cc_final: 0.7560 (mp10) REVERT: L 92 TYR cc_start: 0.8254 (t80) cc_final: 0.7879 (t80) REVERT: M 97 ARG cc_start: 0.6543 (mtm180) cc_final: 0.6216 (ttm110) REVERT: M 102 TYR cc_start: 0.8695 (t80) cc_final: 0.8369 (t80) REVERT: N 35 TRP cc_start: 0.3758 (m100) cc_final: 0.3369 (m100) REVERT: N 39 LYS cc_start: 0.7111 (mmpt) cc_final: 0.6248 (tmtt) REVERT: N 88 CYS cc_start: 0.4559 (OUTLIER) cc_final: 0.3915 (m) REVERT: N 105 GLU cc_start: 0.6969 (mt-10) cc_final: 0.6557 (tt0) REVERT: O 19 ARG cc_start: 0.7395 (ttp-170) cc_final: 0.6702 (tpp-160) REVERT: O 32 TYR cc_start: 0.6092 (m-10) cc_final: 0.5528 (m-10) REVERT: O 34 MET cc_start: 0.7996 (mmp) cc_final: 0.7092 (mmm) REVERT: O 80 LEU cc_start: 0.5344 (tp) cc_final: 0.4991 (tp) outliers start: 43 outliers final: 27 residues processed: 237 average time/residue: 0.4179 time to fit residues: 159.0262 Evaluate side-chains 217 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 187 time to evaluate : 3.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 429 PHE Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 88 CYS Chi-restraints excluded: chain P residue 96 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 119 optimal weight: 2.9990 chunk 318 optimal weight: 20.0000 chunk 69 optimal weight: 0.7980 chunk 207 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 chunk 354 optimal weight: 0.4980 chunk 293 optimal weight: 1.9990 chunk 163 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 117 optimal weight: 2.9990 chunk 185 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 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 81 ASN ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 30210 Z= 0.177 Angle : 0.572 13.299 41082 Z= 0.295 Chirality : 0.045 0.531 4839 Planarity : 0.004 0.085 5225 Dihedral : 5.556 59.551 5223 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.07 % Favored : 93.88 % Rotamer: Outliers : 1.56 % Allowed : 13.46 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.08 (0.14), residues: 3627 helix: 2.26 (0.20), residues: 667 sheet: 0.27 (0.16), residues: 931 loop : -1.04 (0.14), residues: 2029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP H 47 HIS 0.004 0.001 HIS B1048 PHE 0.019 0.001 PHE B 377 TYR 0.038 0.001 TYR B 380 ARG 0.009 0.000 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 210 time to evaluate : 3.274 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 421 TYR cc_start: 0.8803 (m-80) cc_final: 0.8317 (m-80) REVERT: A 1017 GLU cc_start: 0.8467 (tm-30) cc_final: 0.8154 (tm-30) REVERT: B 81 ASN cc_start: 0.8490 (OUTLIER) cc_final: 0.8032 (p0) REVERT: B 346 ARG cc_start: 0.8958 (mtp-110) cc_final: 0.8694 (tmm-80) REVERT: B 370 ASN cc_start: 0.8873 (m-40) cc_final: 0.8188 (p0) REVERT: B 386 LYS cc_start: 0.9291 (mmtt) cc_final: 0.8991 (ttpp) REVERT: B 473 TYR cc_start: 0.6327 (OUTLIER) cc_final: 0.5359 (m-10) REVERT: B 474 GLN cc_start: 0.7406 (tm-30) cc_final: 0.7128 (tm-30) REVERT: B 483 VAL cc_start: 0.5015 (OUTLIER) cc_final: 0.4685 (p) REVERT: C 200 TYR cc_start: 0.7831 (m-80) cc_final: 0.7591 (t80) REVERT: C 406 GLU cc_start: 0.8748 (mp0) cc_final: 0.8249 (mp0) REVERT: C 453 TYR cc_start: 0.8316 (p90) cc_final: 0.7405 (p90) REVERT: C 740 MET cc_start: 0.8076 (tmm) cc_final: 0.7472 (tmm) REVERT: H 79 TYR cc_start: 0.8938 (m-80) cc_final: 0.8614 (m-80) REVERT: H 91 TYR cc_start: 0.7142 (m-10) cc_final: 0.6909 (m-10) REVERT: H 101 ASP cc_start: 0.3918 (p0) cc_final: 0.3404 (p0) REVERT: L 34 ASN cc_start: 0.7950 (m-40) cc_final: 0.7617 (m110) REVERT: L 37 GLN cc_start: 0.8038 (tt0) cc_final: 0.7438 (tt0) REVERT: L 61 ARG cc_start: 0.7723 (ptp90) cc_final: 0.7422 (ptp90) REVERT: L 79 GLN cc_start: 0.7731 (mp-120) cc_final: 0.7525 (mp10) REVERT: L 92 TYR cc_start: 0.8171 (t80) cc_final: 0.7835 (t80) REVERT: M 34 MET cc_start: 0.5775 (mmm) cc_final: 0.5475 (mmm) REVERT: M 97 ARG cc_start: 0.6445 (mtm180) cc_final: 0.6203 (mtm110) REVERT: M 102 TYR cc_start: 0.8696 (t80) cc_final: 0.8373 (t80) REVERT: N 35 TRP cc_start: 0.3771 (m100) cc_final: 0.3328 (m100) REVERT: N 39 LYS cc_start: 0.7195 (mmpt) cc_final: 0.6405 (tmtt) REVERT: N 88 CYS cc_start: 0.4539 (OUTLIER) cc_final: 0.3999 (m) REVERT: N 89 GLN cc_start: 0.6785 (tm-30) cc_final: 0.6293 (tm-30) REVERT: N 105 GLU cc_start: 0.6975 (mt-10) cc_final: 0.6661 (tt0) REVERT: O 19 ARG cc_start: 0.7439 (ttp-170) cc_final: 0.6835 (tpp-160) REVERT: P 3 GLN cc_start: 0.7845 (mm110) cc_final: 0.7468 (mm-40) outliers start: 50 outliers final: 28 residues processed: 248 average time/residue: 0.4702 time to fit residues: 187.1771 Evaluate side-chains 221 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 189 time to evaluate : 3.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain C residue 429 PHE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain N residue 88 CYS Chi-restraints excluded: chain O residue 31 ILE Chi-restraints excluded: chain P residue 96 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 341 optimal weight: 50.0000 chunk 39 optimal weight: 0.9990 chunk 201 optimal weight: 4.9990 chunk 258 optimal weight: 0.9990 chunk 200 optimal weight: 9.9990 chunk 298 optimal weight: 0.8980 chunk 197 optimal weight: 6.9990 chunk 352 optimal weight: 6.9990 chunk 220 optimal weight: 2.9990 chunk 215 optimal weight: 1.9990 chunk 162 optimal weight: 0.0170 overall best weight: 0.9824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 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 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 30210 Z= 0.175 Angle : 0.562 10.694 41082 Z= 0.291 Chirality : 0.045 0.522 4839 Planarity : 0.004 0.071 5225 Dihedral : 5.373 59.662 5223 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.15 % Favored : 93.77 % Rotamer: Outliers : 1.31 % Allowed : 14.02 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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 (0.14), residues: 3627 helix: 2.31 (0.20), residues: 672 sheet: 0.29 (0.16), residues: 938 loop : -0.99 (0.14), residues: 2017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP H 47 HIS 0.008 0.001 HIS O 35 PHE 0.018 0.001 PHE C 565 TYR 0.030 0.001 TYR A 265 ARG 0.006 0.000 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 203 time to evaluate : 3.486 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 421 TYR cc_start: 0.8810 (m-80) cc_final: 0.8348 (m-80) REVERT: A 1017 GLU cc_start: 0.8467 (tm-30) cc_final: 0.8155 (tm-30) REVERT: B 81 ASN cc_start: 0.8510 (p0) cc_final: 0.8141 (p0) REVERT: B 346 ARG cc_start: 0.8980 (mtp-110) cc_final: 0.8703 (tmm-80) REVERT: B 386 LYS cc_start: 0.9278 (mmtt) cc_final: 0.8975 (ttpp) REVERT: B 473 TYR cc_start: 0.6283 (OUTLIER) cc_final: 0.5322 (m-10) REVERT: B 474 GLN cc_start: 0.7462 (tm-30) cc_final: 0.7206 (tm-30) REVERT: B 483 VAL cc_start: 0.4904 (OUTLIER) cc_final: 0.4615 (p) REVERT: C 200 TYR cc_start: 0.7815 (m-80) cc_final: 0.7606 (t80) REVERT: C 406 GLU cc_start: 0.8773 (mp0) cc_final: 0.8266 (mp0) REVERT: C 453 TYR cc_start: 0.8306 (p90) cc_final: 0.7430 (p90) REVERT: H 75 LYS cc_start: 0.8939 (mtpp) cc_final: 0.8633 (mtmm) REVERT: H 79 TYR cc_start: 0.8945 (m-80) cc_final: 0.8647 (m-80) REVERT: H 91 TYR cc_start: 0.7129 (m-10) cc_final: 0.6886 (m-10) REVERT: H 101 ASP cc_start: 0.3993 (p0) cc_final: 0.3503 (p0) REVERT: L 34 ASN cc_start: 0.7940 (m-40) cc_final: 0.7584 (m110) REVERT: L 37 GLN cc_start: 0.8045 (tt0) cc_final: 0.7468 (tt0) REVERT: L 61 ARG cc_start: 0.7717 (ptp90) cc_final: 0.7440 (ptp90) REVERT: L 92 TYR cc_start: 0.8168 (t80) cc_final: 0.7857 (t80) REVERT: M 82 MET cc_start: 0.3795 (mmp) cc_final: 0.2587 (tpp) REVERT: M 97 ARG cc_start: 0.6336 (mtm180) cc_final: 0.6102 (ttm110) REVERT: M 102 TYR cc_start: 0.8699 (t80) cc_final: 0.8368 (t80) REVERT: N 35 TRP cc_start: 0.3667 (m100) cc_final: 0.3267 (m100) REVERT: N 39 LYS cc_start: 0.7203 (mmpt) cc_final: 0.6455 (tmtt) REVERT: N 88 CYS cc_start: 0.4562 (OUTLIER) cc_final: 0.3999 (m) REVERT: N 89 GLN cc_start: 0.6797 (tm-30) cc_final: 0.6280 (tm-30) REVERT: N 105 GLU cc_start: 0.6921 (mt-10) cc_final: 0.6642 (tt0) REVERT: O 19 ARG cc_start: 0.7471 (ttp-170) cc_final: 0.6722 (tpt170) REVERT: P 3 GLN cc_start: 0.7839 (mm110) cc_final: 0.7467 (mm-40) outliers start: 42 outliers final: 28 residues processed: 236 average time/residue: 0.4286 time to fit residues: 161.2825 Evaluate side-chains 221 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 190 time to evaluate : 3.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 429 PHE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain N residue 88 CYS Chi-restraints excluded: chain O residue 31 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 218 optimal weight: 0.0970 chunk 140 optimal weight: 0.0000 chunk 210 optimal weight: 7.9990 chunk 106 optimal weight: 8.9990 chunk 69 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 224 optimal weight: 0.9980 chunk 240 optimal weight: 6.9990 chunk 174 optimal weight: 4.9990 chunk 32 optimal weight: 0.5980 chunk 277 optimal weight: 0.7980 overall best weight: 0.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 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 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN B1106 GLN C 81 ASN ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 992 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 30210 Z= 0.144 Angle : 0.559 12.225 41082 Z= 0.287 Chirality : 0.046 0.847 4839 Planarity : 0.004 0.061 5225 Dihedral : 5.158 58.605 5223 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.71 % Favored : 94.21 % Rotamer: Outliers : 1.19 % Allowed : 14.43 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.11 (0.14), residues: 3627 helix: 2.46 (0.20), residues: 672 sheet: 0.46 (0.16), residues: 925 loop : -0.97 (0.14), residues: 2030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP H 47 HIS 0.004 0.001 HIS O 35 PHE 0.018 0.001 PHE B 392 TYR 0.025 0.001 TYR A 265 ARG 0.011 0.000 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 218 time to evaluate : 3.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 421 TYR cc_start: 0.8794 (m-80) cc_final: 0.8371 (m-80) REVERT: B 81 ASN cc_start: 0.8405 (p0) cc_final: 0.7996 (p0) REVERT: B 346 ARG cc_start: 0.8964 (mtp-110) cc_final: 0.8717 (tmm-80) REVERT: B 386 LYS cc_start: 0.9304 (mmtt) cc_final: 0.8981 (ttpp) REVERT: B 473 TYR cc_start: 0.6376 (OUTLIER) cc_final: 0.5464 (m-10) REVERT: B 474 GLN cc_start: 0.7372 (tm-30) cc_final: 0.7104 (tm-30) REVERT: B 483 VAL cc_start: 0.4642 (OUTLIER) cc_final: 0.4193 (p) REVERT: C 269 TYR cc_start: 0.7820 (m-80) cc_final: 0.7343 (m-10) REVERT: C 406 GLU cc_start: 0.8785 (mp0) cc_final: 0.8296 (mp0) REVERT: C 453 TYR cc_start: 0.8227 (p90) cc_final: 0.7344 (p90) REVERT: H 79 TYR cc_start: 0.8936 (m-80) cc_final: 0.8603 (m-80) REVERT: H 91 TYR cc_start: 0.7139 (m-10) cc_final: 0.6898 (m-10) REVERT: H 101 ASP cc_start: 0.3719 (p0) cc_final: 0.3184 (p0) REVERT: L 34 ASN cc_start: 0.7847 (m-40) cc_final: 0.7562 (m-40) REVERT: L 37 GLN cc_start: 0.8000 (tt0) cc_final: 0.7441 (tt0) REVERT: L 92 TYR cc_start: 0.8135 (t80) cc_final: 0.7812 (t80) REVERT: M 34 MET cc_start: 0.6170 (mmm) cc_final: 0.5596 (mmm) REVERT: M 102 TYR cc_start: 0.8705 (t80) cc_final: 0.8356 (t80) REVERT: N 35 TRP cc_start: 0.3748 (m100) cc_final: 0.3344 (m100) REVERT: N 39 LYS cc_start: 0.7353 (mmpt) cc_final: 0.6545 (tmtt) REVERT: N 88 CYS cc_start: 0.4478 (OUTLIER) cc_final: 0.4021 (m) REVERT: N 89 GLN cc_start: 0.6790 (tm-30) cc_final: 0.6265 (tm-30) REVERT: O 19 ARG cc_start: 0.7482 (ttp-170) cc_final: 0.6737 (tpt170) REVERT: O 34 MET cc_start: 0.7628 (mmm) cc_final: 0.7155 (mmm) REVERT: P 3 GLN cc_start: 0.7827 (mm110) cc_final: 0.7453 (mm-40) outliers start: 38 outliers final: 28 residues processed: 247 average time/residue: 0.4522 time to fit residues: 177.2429 Evaluate side-chains 233 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 202 time to evaluate : 3.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain C residue 429 PHE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain N residue 88 CYS Chi-restraints excluded: chain O residue 31 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 320 optimal weight: 8.9990 chunk 337 optimal weight: 20.0000 chunk 308 optimal weight: 9.9990 chunk 328 optimal weight: 20.0000 chunk 197 optimal weight: 4.9990 chunk 143 optimal weight: 4.9990 chunk 258 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 chunk 297 optimal weight: 4.9990 chunk 310 optimal weight: 0.6980 chunk 327 optimal weight: 20.0000 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 925 ASN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN B 901 GLN B1106 GLN ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 30210 Z= 0.446 Angle : 0.688 11.750 41082 Z= 0.355 Chirality : 0.048 0.593 4839 Planarity : 0.004 0.075 5225 Dihedral : 5.673 59.467 5223 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.14 % Favored : 92.78 % Rotamer: Outliers : 1.47 % Allowed : 14.46 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 3627 helix: 1.91 (0.20), residues: 673 sheet: 0.25 (0.16), residues: 984 loop : -1.07 (0.14), residues: 1970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP H 47 HIS 0.004 0.001 HIS B 49 PHE 0.023 0.002 PHE C 32 TYR 0.029 0.002 TYR A 265 ARG 0.008 0.001 ARG P 96 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 198 time to evaluate : 3.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 421 TYR cc_start: 0.8840 (m-80) cc_final: 0.8488 (m-80) REVERT: B 81 ASN cc_start: 0.8505 (p0) cc_final: 0.8005 (p0) REVERT: B 346 ARG cc_start: 0.8987 (mtp-110) cc_final: 0.8765 (tmm-80) REVERT: B 380 TYR cc_start: 0.8131 (m-80) cc_final: 0.7677 (m-10) REVERT: B 473 TYR cc_start: 0.6350 (OUTLIER) cc_final: 0.5585 (m-10) REVERT: B 474 GLN cc_start: 0.7397 (tm-30) cc_final: 0.7123 (tm-30) REVERT: B 483 VAL cc_start: 0.4561 (OUTLIER) cc_final: 0.4004 (p) REVERT: C 200 TYR cc_start: 0.7929 (OUTLIER) cc_final: 0.7567 (t80) REVERT: C 406 GLU cc_start: 0.8813 (mp0) cc_final: 0.8352 (mp0) REVERT: H 34 MET cc_start: 0.7390 (mmm) cc_final: 0.7042 (mmm) REVERT: H 75 LYS cc_start: 0.8918 (mtpp) cc_final: 0.8666 (mtmm) REVERT: H 79 TYR cc_start: 0.8964 (m-80) cc_final: 0.8620 (m-80) REVERT: H 91 TYR cc_start: 0.7192 (m-10) cc_final: 0.6956 (m-10) REVERT: H 101 ASP cc_start: 0.3982 (p0) cc_final: 0.3400 (p0) REVERT: L 34 ASN cc_start: 0.8204 (m-40) cc_final: 0.7896 (m-40) REVERT: L 37 GLN cc_start: 0.7890 (tt0) cc_final: 0.7329 (tt0) REVERT: L 92 TYR cc_start: 0.8263 (t80) cc_final: 0.7986 (t80) REVERT: M 82 MET cc_start: 0.3838 (mmp) cc_final: 0.2654 (tpp) REVERT: M 97 ARG cc_start: 0.6096 (mtm110) cc_final: 0.5440 (ttm110) REVERT: M 102 TYR cc_start: 0.8741 (t80) cc_final: 0.8405 (t80) REVERT: N 35 TRP cc_start: 0.3907 (m100) cc_final: 0.3514 (m100) REVERT: N 39 LYS cc_start: 0.7270 (mmpt) cc_final: 0.6588 (tmtt) REVERT: N 88 CYS cc_start: 0.3906 (OUTLIER) cc_final: 0.3327 (m) REVERT: N 89 GLN cc_start: 0.6764 (tm-30) cc_final: 0.6226 (tm-30) REVERT: O 19 ARG cc_start: 0.7486 (ttp-170) cc_final: 0.6733 (tpt170) REVERT: P 3 GLN cc_start: 0.7760 (mm110) cc_final: 0.7452 (mm-40) REVERT: P 95 PRO cc_start: 0.8077 (Cg_endo) cc_final: 0.7816 (Cg_exo) outliers start: 47 outliers final: 35 residues processed: 236 average time/residue: 0.4410 time to fit residues: 165.8027 Evaluate side-chains 226 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 187 time to evaluate : 3.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 429 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain N residue 88 CYS Chi-restraints excluded: chain O residue 31 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 215 optimal weight: 3.9990 chunk 347 optimal weight: 6.9990 chunk 212 optimal weight: 4.9990 chunk 164 optimal weight: 0.7980 chunk 241 optimal weight: 7.9990 chunk 364 optimal weight: 7.9990 chunk 335 optimal weight: 5.9990 chunk 290 optimal weight: 0.5980 chunk 30 optimal weight: 7.9990 chunk 224 optimal weight: 0.2980 chunk 178 optimal weight: 0.9980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 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 87 ASN ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1011 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 30210 Z= 0.206 Angle : 0.584 11.814 41082 Z= 0.301 Chirality : 0.046 0.526 4839 Planarity : 0.004 0.044 5225 Dihedral : 5.408 59.351 5223 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.12 % Favored : 93.80 % Rotamer: Outliers : 1.22 % Allowed : 15.09 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.03 (0.14), residues: 3627 helix: 2.25 (0.20), residues: 674 sheet: 0.35 (0.16), residues: 953 loop : -1.05 (0.14), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP H 47 HIS 0.004 0.001 HIS A1048 PHE 0.022 0.001 PHE A 168 TYR 0.027 0.001 TYR A 265 ARG 0.008 0.000 ARG L 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 193 time to evaluate : 3.579 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 421 TYR cc_start: 0.8813 (m-80) cc_final: 0.8473 (m-80) REVERT: A 740 MET cc_start: 0.8281 (tpp) cc_final: 0.8002 (mmm) REVERT: A 869 MET cc_start: 0.8622 (OUTLIER) cc_final: 0.8371 (mtm) REVERT: B 81 ASN cc_start: 0.8513 (p0) cc_final: 0.7981 (p0) REVERT: B 346 ARG cc_start: 0.8980 (mtp-110) cc_final: 0.8777 (tmm-80) REVERT: B 380 TYR cc_start: 0.8072 (m-80) cc_final: 0.7717 (m-10) REVERT: B 386 LYS cc_start: 0.9294 (mmtt) cc_final: 0.8998 (ttpp) REVERT: B 473 TYR cc_start: 0.6304 (OUTLIER) cc_final: 0.5435 (m-10) REVERT: B 483 VAL cc_start: 0.4582 (OUTLIER) cc_final: 0.4060 (p) REVERT: C 200 TYR cc_start: 0.7853 (OUTLIER) cc_final: 0.7483 (t80) REVERT: C 406 GLU cc_start: 0.8777 (mp0) cc_final: 0.8299 (mp0) REVERT: H 79 TYR cc_start: 0.8958 (m-80) cc_final: 0.8601 (m-80) REVERT: H 91 TYR cc_start: 0.7236 (m-10) cc_final: 0.7035 (m-10) REVERT: H 101 ASP cc_start: 0.3874 (p0) cc_final: 0.3267 (p0) REVERT: L 34 ASN cc_start: 0.8009 (m-40) cc_final: 0.7764 (m-40) REVERT: L 37 GLN cc_start: 0.7877 (tt0) cc_final: 0.7288 (tt0) REVERT: L 92 TYR cc_start: 0.8201 (t80) cc_final: 0.7911 (t80) REVERT: M 82 MET cc_start: 0.3873 (mmp) cc_final: 0.2701 (tpp) REVERT: M 97 ARG cc_start: 0.5953 (mtm110) cc_final: 0.5339 (ttm110) REVERT: M 102 TYR cc_start: 0.8748 (t80) cc_final: 0.8373 (t80) REVERT: N 35 TRP cc_start: 0.3922 (m100) cc_final: 0.3530 (m100) REVERT: N 39 LYS cc_start: 0.7247 (mmpt) cc_final: 0.6613 (tmtt) REVERT: N 88 CYS cc_start: 0.4208 (OUTLIER) cc_final: 0.3758 (m) REVERT: N 89 GLN cc_start: 0.6777 (tm-30) cc_final: 0.6226 (tm-30) REVERT: O 19 ARG cc_start: 0.7471 (ttp-170) cc_final: 0.6725 (tpt170) REVERT: O 80 LEU cc_start: 0.5368 (tp) cc_final: 0.4998 (mt) REVERT: P 3 GLN cc_start: 0.7752 (mm110) cc_final: 0.7454 (mm-40) outliers start: 39 outliers final: 31 residues processed: 224 average time/residue: 0.4448 time to fit residues: 157.6714 Evaluate side-chains 226 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 190 time to evaluate : 3.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 429 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain N residue 88 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 230 optimal weight: 4.9990 chunk 309 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 267 optimal weight: 0.0970 chunk 42 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 290 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 298 optimal weight: 1.9990 chunk 36 optimal weight: 20.0000 chunk 53 optimal weight: 8.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 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 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.111703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.074008 restraints weight = 76480.484| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 3.34 r_work: 0.3114 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 30210 Z= 0.266 Angle : 0.593 11.721 41082 Z= 0.305 Chirality : 0.046 0.513 4839 Planarity : 0.004 0.045 5225 Dihedral : 5.372 59.975 5223 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.73 % Favored : 93.19 % Rotamer: Outliers : 1.35 % Allowed : 14.96 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.05 (0.14), residues: 3627 helix: 2.25 (0.20), residues: 676 sheet: 0.34 (0.16), residues: 951 loop : -1.06 (0.14), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP H 47 HIS 0.003 0.001 HIS B 49 PHE 0.018 0.001 PHE C 201 TYR 0.026 0.001 TYR A 265 ARG 0.007 0.000 ARG L 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6113.90 seconds wall clock time: 113 minutes 9.76 seconds (6789.76 seconds total)