Starting phenix.real_space_refine on Mon Mar 25 15:46:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h3c_0132/03_2024/6h3c_0132.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h3c_0132/03_2024/6h3c_0132.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h3c_0132/03_2024/6h3c_0132.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h3c_0132/03_2024/6h3c_0132.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h3c_0132/03_2024/6h3c_0132.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h3c_0132/03_2024/6h3c_0132.pdb" } resolution = 3.9 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= 0.003 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 S 136 5.16 5 C 15942 2.51 5 N 4334 2.21 5 O 4708 1.98 5 H 24860 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 242": "OE1" <-> "OE2" Residue "C PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 347": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 369": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 242": "OE1" <-> "OE2" Residue "H PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 347": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 369": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 420": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 420": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 49982 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 4134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 4134 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 5, 'TRANS': 249} Chain: "B" Number of atoms: 4122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 4122 Classifications: {'peptide': 258} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 249} Chain breaks: 2 Chain: "C" Number of atoms: 6077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 6077 Classifications: {'peptide': 383} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 354} Chain: "D" Number of atoms: 3761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 3761 Classifications: {'peptide': 237} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 220} Chain: "F" Number of atoms: 4134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 4134 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 5, 'TRANS': 249} Chain: "G" Number of atoms: 4122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 4122 Classifications: {'peptide': 258} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 249} Chain breaks: 2 Chain: "H" Number of atoms: 6077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 6077 Classifications: {'peptide': 383} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 354} Chain: "I" Number of atoms: 3761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 3761 Classifications: {'peptide': 237} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 220} Chain: "E" Number of atoms: 6893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 6893 Classifications: {'peptide': 440} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 417} Chain breaks: 1 Chain: "J" Number of atoms: 6893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 6893 Classifications: {'peptide': 440} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 417} Chain breaks: 1 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Time building chain proxies: 20.55, per 1000 atoms: 0.41 Number of scatterers: 49982 At special positions: 0 Unit cell: (165.98, 181.46, 149.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 136 16.00 O 4708 8.00 N 4334 7.00 C 15942 6.00 H 24860 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 42.28 Conformation dependent library (CDL) restraints added in 4.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 401 " pdb="ZN ZN B 401 " - pdb=" NE2 HIS B 122 " pdb="ZN ZN B 401 " - pdb=" NE2 HIS B 124 " pdb=" ZN G 401 " pdb="ZN ZN G 401 " - pdb=" NE2 HIS G 122 " pdb="ZN ZN G 401 " - pdb=" NE2 HIS G 124 " 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5980 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 24 sheets defined 45.7% alpha, 16.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.80 Creating SS restraints... Processing helix chain 'A' and resid 6 through 19 removed outlier: 3.504A pdb=" N ASN A 19 " --> pdb=" O PHE A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 85 Processing helix chain 'A' and resid 106 through 120 removed outlier: 3.543A pdb=" N ARG A 118 " --> pdb=" O LYS A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 168 Processing helix chain 'A' and resid 182 through 192 removed outlier: 3.526A pdb=" N LYS A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 196 Processing helix chain 'A' and resid 203 through 255 removed outlier: 3.613A pdb=" N ARG A 207 " --> pdb=" O MET A 203 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N TYR A 213 " --> pdb=" O ILE A 209 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N LEU A 216 " --> pdb=" O VAL A 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 27 Processing helix chain 'B' and resid 93 through 112 Processing helix chain 'B' and resid 132 through 146 Processing helix chain 'B' and resid 225 through 232 Processing helix chain 'B' and resid 234 through 252 removed outlier: 3.521A pdb=" N CYS B 240 " --> pdb=" O PRO B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 279 Processing helix chain 'B' and resid 279 through 316 Processing helix chain 'C' and resid 2 through 9 Processing helix chain 'C' and resid 14 through 24 Processing helix chain 'C' and resid 86 through 90 Processing helix chain 'C' and resid 99 through 104 Processing helix chain 'C' and resid 109 through 111 No H-bonds generated for 'chain 'C' and resid 109 through 111' Processing helix chain 'C' and resid 112 through 133 removed outlier: 3.537A pdb=" N ARG C 131 " --> pdb=" O PHE C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 147 removed outlier: 4.017A pdb=" N THR C 144 " --> pdb=" O PHE C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 154 removed outlier: 3.575A pdb=" N GLU C 153 " --> pdb=" O GLN C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 230 Processing helix chain 'C' and resid 231 through 234 Processing helix chain 'C' and resid 245 through 280 Proline residue: C 251 - end of helix removed outlier: 5.109A pdb=" N HIS C 255 " --> pdb=" O PRO C 251 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ARG C 272 " --> pdb=" O TYR C 268 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N GLU C 273 " --> pdb=" O HIS C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 377 Proline residue: C 371 - end of helix Processing helix chain 'D' and resid 102 through 107 Processing helix chain 'D' and resid 119 through 135 Processing helix chain 'D' and resid 162 through 171 removed outlier: 3.686A pdb=" N LEU D 166 " --> pdb=" O ASP D 162 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N TYR D 171 " --> pdb=" O CYS D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 192 Processing helix chain 'D' and resid 229 through 238 removed outlier: 5.620A pdb=" N MET D 235 " --> pdb=" O PRO D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 255 removed outlier: 3.604A pdb=" N GLU D 254 " --> pdb=" O ASN D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 269 Processing helix chain 'D' and resid 270 through 272 No H-bonds generated for 'chain 'D' and resid 270 through 272' Processing helix chain 'D' and resid 287 through 292 Processing helix chain 'D' and resid 292 through 299 Processing helix chain 'D' and resid 307 through 311 Processing helix chain 'F' and resid 6 through 19 removed outlier: 3.503A pdb=" N ASN F 19 " --> pdb=" O PHE F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 85 Processing helix chain 'F' and resid 106 through 120 removed outlier: 3.544A pdb=" N ARG F 118 " --> pdb=" O LYS F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 168 Processing helix chain 'F' and resid 182 through 192 removed outlier: 3.526A pdb=" N LYS F 190 " --> pdb=" O ALA F 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 196 Processing helix chain 'F' and resid 203 through 255 removed outlier: 3.614A pdb=" N ARG F 207 " --> pdb=" O MET F 203 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N TYR F 213 " --> pdb=" O ILE F 209 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N LEU F 216 " --> pdb=" O VAL F 212 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 27 Processing helix chain 'G' and resid 93 through 112 Processing helix chain 'G' and resid 132 through 146 Processing helix chain 'G' and resid 225 through 232 Processing helix chain 'G' and resid 234 through 252 removed outlier: 3.521A pdb=" N CYS G 240 " --> pdb=" O PRO G 236 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLU G 243 " --> pdb=" O LEU G 239 " (cutoff:3.500A) Processing helix chain 'G' and resid 257 through 279 Processing helix chain 'G' and resid 279 through 316 Processing helix chain 'H' and resid 2 through 9 Processing helix chain 'H' and resid 14 through 24 Processing helix chain 'H' and resid 86 through 90 Processing helix chain 'H' and resid 99 through 104 Processing helix chain 'H' and resid 109 through 111 No H-bonds generated for 'chain 'H' and resid 109 through 111' Processing helix chain 'H' and resid 112 through 133 removed outlier: 3.538A pdb=" N ARG H 131 " --> pdb=" O PHE H 127 " (cutoff:3.500A) Processing helix chain 'H' and resid 135 through 147 removed outlier: 4.018A pdb=" N THR H 144 " --> pdb=" O PHE H 140 " (cutoff:3.500A) Processing helix chain 'H' and resid 148 through 154 removed outlier: 3.576A pdb=" N GLU H 153 " --> pdb=" O GLN H 150 " (cutoff:3.500A) Processing helix chain 'H' and resid 224 through 230 Processing helix chain 'H' and resid 231 through 234 Processing helix chain 'H' and resid 245 through 280 Proline residue: H 251 - end of helix removed outlier: 5.110A pdb=" N HIS H 255 " --> pdb=" O PRO H 251 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ARG H 272 " --> pdb=" O TYR H 268 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N GLU H 273 " --> pdb=" O HIS H 269 " (cutoff:3.500A) Processing helix chain 'H' and resid 354 through 377 Proline residue: H 371 - end of helix Processing helix chain 'I' and resid 102 through 107 Processing helix chain 'I' and resid 119 through 135 Processing helix chain 'I' and resid 162 through 171 removed outlier: 3.687A pdb=" N LEU I 166 " --> pdb=" O ASP I 162 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N TYR I 171 " --> pdb=" O CYS I 167 " (cutoff:3.500A) Processing helix chain 'I' and resid 183 through 192 Processing helix chain 'I' and resid 229 through 238 removed outlier: 5.620A pdb=" N MET I 235 " --> pdb=" O PRO I 231 " (cutoff:3.500A) Processing helix chain 'I' and resid 250 through 255 removed outlier: 3.604A pdb=" N GLU I 254 " --> pdb=" O ASN I 250 " (cutoff:3.500A) Processing helix chain 'I' and resid 259 through 269 Processing helix chain 'I' and resid 270 through 272 No H-bonds generated for 'chain 'I' and resid 270 through 272' Processing helix chain 'I' and resid 287 through 292 Processing helix chain 'I' and resid 292 through 299 Processing helix chain 'I' and resid 307 through 311 Processing helix chain 'E' and resid 27 through 32 Processing helix chain 'E' and resid 32 through 48 Processing helix chain 'E' and resid 60 through 68 Processing helix chain 'E' and resid 69 through 74 Processing helix chain 'E' and resid 88 through 105 removed outlier: 3.770A pdb=" N LEU E 103 " --> pdb=" O GLN E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 134 Processing helix chain 'E' and resid 184 through 196 Processing helix chain 'E' and resid 212 through 223 Processing helix chain 'E' and resid 234 through 240 Processing helix chain 'E' and resid 245 through 249 Processing helix chain 'E' and resid 290 through 295 Processing helix chain 'E' and resid 296 through 298 No H-bonds generated for 'chain 'E' and resid 296 through 298' Processing helix chain 'E' and resid 307 through 322 Processing helix chain 'E' and resid 323 through 347 Processing helix chain 'E' and resid 353 through 355 No H-bonds generated for 'chain 'E' and resid 353 through 355' Processing helix chain 'E' and resid 366 through 369 Processing helix chain 'E' and resid 371 through 381 removed outlier: 4.645A pdb=" N ARG E 377 " --> pdb=" O ALA E 373 " (cutoff:3.500A) Processing helix chain 'E' and resid 407 through 412 Processing helix chain 'E' and resid 416 through 439 removed outlier: 3.585A pdb=" N ILE E 433 " --> pdb=" O GLU E 429 " (cutoff:3.500A) Processing helix chain 'E' and resid 443 through 454 removed outlier: 4.307A pdb=" N SER E 449 " --> pdb=" O GLN E 445 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU E 452 " --> pdb=" O LYS E 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 454 through 473 Processing helix chain 'J' and resid 27 through 32 Processing helix chain 'J' and resid 32 through 48 Processing helix chain 'J' and resid 60 through 68 Processing helix chain 'J' and resid 69 through 74 Processing helix chain 'J' and resid 88 through 105 removed outlier: 3.770A pdb=" N LEU J 103 " --> pdb=" O GLN J 99 " (cutoff:3.500A) Processing helix chain 'J' and resid 124 through 134 Processing helix chain 'J' and resid 184 through 196 Processing helix chain 'J' and resid 212 through 223 Processing helix chain 'J' and resid 234 through 240 Processing helix chain 'J' and resid 245 through 249 Processing helix chain 'J' and resid 290 through 295 Processing helix chain 'J' and resid 296 through 298 No H-bonds generated for 'chain 'J' and resid 296 through 298' Processing helix chain 'J' and resid 307 through 322 Processing helix chain 'J' and resid 323 through 347 Processing helix chain 'J' and resid 353 through 355 No H-bonds generated for 'chain 'J' and resid 353 through 355' Processing helix chain 'J' and resid 366 through 369 Processing helix chain 'J' and resid 371 through 381 removed outlier: 4.645A pdb=" N ARG J 377 " --> pdb=" O ALA J 373 " (cutoff:3.500A) Processing helix chain 'J' and resid 407 through 412 Processing helix chain 'J' and resid 416 through 439 removed outlier: 3.585A pdb=" N ILE J 433 " --> pdb=" O GLU J 429 " (cutoff:3.500A) Processing helix chain 'J' and resid 443 through 454 removed outlier: 4.307A pdb=" N SER J 449 " --> pdb=" O GLN J 445 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU J 452 " --> pdb=" O LYS J 448 " (cutoff:3.500A) Processing helix chain 'J' and resid 454 through 473 Processing sheet with id=AA1, first strand: chain 'A' and resid 154 through 157 removed outlier: 3.536A pdb=" N GLN A 156 " --> pdb=" O ARG A 149 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 160 through 161 removed outlier: 6.736A pdb=" N ALA A 3 " --> pdb=" O ALA A 161 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ALA A 2 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N ILE A 56 " --> pdb=" O ALA A 2 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N SER A 4 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N ASN A 58 " --> pdb=" O SER A 4 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N LEU A 29 " --> pdb=" O HIS A 57 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N HIS A 59 " --> pdb=" O PHE A 27 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N PHE A 27 " --> pdb=" O HIS A 59 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N GLU A 25 " --> pdb=" O PRO A 61 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N TRP A 94 " --> pdb=" O LEU A 128 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N PHE A 130 " --> pdb=" O TRP A 94 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ARG A 96 " --> pdb=" O PHE A 130 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N PHE A 132 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N ARG A 98 " --> pdb=" O PHE A 132 " (cutoff:3.500A) removed outlier: 9.029A pdb=" N SER A 134 " --> pdb=" O ARG A 98 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ARG B 167 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N PHE B 157 " --> pdb=" O ARG B 167 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N VAL B 117 " --> pdb=" O GLY B 40 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N GLY B 40 " --> pdb=" O VAL B 117 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLY B 119 " --> pdb=" O CYS B 38 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LEU B 37 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N VAL B 77 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ILE B 39 " --> pdb=" O HIS B 75 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N SER B 76 " --> pdb=" O GLU B 15 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N VAL B 12 " --> pdb=" O HIS B 217 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N VAL B 219 " --> pdb=" O VAL B 12 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU B 14 " --> pdb=" O VAL B 219 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 69 through 70 removed outlier: 3.510A pdb=" N LYS A 74 " --> pdb=" O ASP A 70 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 36 through 41 removed outlier: 4.755A pdb=" N LEU C 40 " --> pdb=" O ARG C 55 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N ARG C 55 " --> pdb=" O LEU C 40 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 156 through 159 Processing sheet with id=AA6, first strand: chain 'C' and resid 286 through 288 removed outlier: 6.778A pdb=" N THR C 298 " --> pdb=" O VAL C 287 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU C 297 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU C 325 " --> pdb=" O GLN C 344 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N TYR C 340 " --> pdb=" O SER C 329 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 155 through 160 removed outlier: 4.310A pdb=" N GLY D 158 " --> pdb=" O PHE D 144 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N PHE D 144 " --> pdb=" O GLY D 158 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU D 143 " --> pdb=" O GLU D 93 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LYS D 94 " --> pdb=" O VAL D 210 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N VAL D 216 " --> pdb=" O CYS D 98 " (cutoff:3.500A) removed outlier: 9.004A pdb=" N TYR D 280 " --> pdb=" O PHE D 243 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL D 245 " --> pdb=" O TYR D 280 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N VAL D 282 " --> pdb=" O VAL D 245 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N TYR D 247 " --> pdb=" O VAL D 282 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 110 through 111 Processing sheet with id=AA9, first strand: chain 'F' and resid 154 through 157 removed outlier: 3.537A pdb=" N GLN F 156 " --> pdb=" O ARG F 149 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 160 through 161 removed outlier: 6.735A pdb=" N ALA F 3 " --> pdb=" O ALA F 161 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ALA F 2 " --> pdb=" O ILE F 54 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N ILE F 56 " --> pdb=" O ALA F 2 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N SER F 4 " --> pdb=" O ILE F 56 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N ASN F 58 " --> pdb=" O SER F 4 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N LEU F 29 " --> pdb=" O HIS F 57 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N HIS F 59 " --> pdb=" O PHE F 27 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N PHE F 27 " --> pdb=" O HIS F 59 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N GLU F 25 " --> pdb=" O PRO F 61 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N TRP F 94 " --> pdb=" O LEU F 128 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N PHE F 130 " --> pdb=" O TRP F 94 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ARG F 96 " --> pdb=" O PHE F 130 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N PHE F 132 " --> pdb=" O ARG F 96 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N ARG F 98 " --> pdb=" O PHE F 132 " (cutoff:3.500A) removed outlier: 9.029A pdb=" N SER F 134 " --> pdb=" O ARG F 98 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ARG G 167 " --> pdb=" O PHE G 157 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N PHE G 157 " --> pdb=" O ARG G 167 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N VAL G 117 " --> pdb=" O GLY G 40 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N GLY G 40 " --> pdb=" O VAL G 117 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N GLY G 119 " --> pdb=" O CYS G 38 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LEU G 37 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N VAL G 77 " --> pdb=" O LEU G 37 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ILE G 39 " --> pdb=" O HIS G 75 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N SER G 76 " --> pdb=" O GLU G 15 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N VAL G 12 " --> pdb=" O HIS G 217 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N VAL G 219 " --> pdb=" O VAL G 12 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU G 14 " --> pdb=" O VAL G 219 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 69 through 70 removed outlier: 3.510A pdb=" N LYS F 74 " --> pdb=" O ASP F 70 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 36 through 41 removed outlier: 4.754A pdb=" N LEU H 40 " --> pdb=" O ARG H 55 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N ARG H 55 " --> pdb=" O LEU H 40 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 156 through 159 Processing sheet with id=AB5, first strand: chain 'H' and resid 286 through 288 removed outlier: 6.779A pdb=" N THR H 298 " --> pdb=" O VAL H 287 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU H 297 " --> pdb=" O ILE H 312 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU H 325 " --> pdb=" O GLN H 344 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N TYR H 340 " --> pdb=" O SER H 329 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 155 through 160 removed outlier: 4.310A pdb=" N GLY I 158 " --> pdb=" O PHE I 144 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N PHE I 144 " --> pdb=" O GLY I 158 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU I 143 " --> pdb=" O GLU I 93 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LYS I 94 " --> pdb=" O VAL I 210 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N VAL I 216 " --> pdb=" O CYS I 98 " (cutoff:3.500A) removed outlier: 9.003A pdb=" N TYR I 280 " --> pdb=" O PHE I 243 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N VAL I 245 " --> pdb=" O TYR I 280 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N VAL I 282 " --> pdb=" O VAL I 245 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N TYR I 247 " --> pdb=" O VAL I 282 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 110 through 111 Processing sheet with id=AB8, first strand: chain 'E' and resid 50 through 51 removed outlier: 6.972A pdb=" N LEU E 50 " --> pdb=" O THR E 385 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'E' and resid 113 through 116 removed outlier: 6.408A pdb=" N LEU E 227 " --> pdb=" O ILE E 252 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N THR E 254 " --> pdb=" O LEU E 227 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ALA E 229 " --> pdb=" O THR E 254 " (cutoff:3.500A) removed outlier: 8.543A pdb=" N THR E 256 " --> pdb=" O ALA E 229 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 275 through 278 Processing sheet with id=AC2, first strand: chain 'E' and resid 350 through 351 removed outlier: 4.021A pdb=" N SER E 350 " --> pdb=" O ASP E 364 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 50 through 51 removed outlier: 6.971A pdb=" N LEU J 50 " --> pdb=" O THR J 385 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'J' and resid 113 through 116 removed outlier: 6.408A pdb=" N LEU J 227 " --> pdb=" O ILE J 252 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N THR J 254 " --> pdb=" O LEU J 227 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ALA J 229 " --> pdb=" O THR J 254 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N THR J 256 " --> pdb=" O ALA J 229 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 275 through 278 Processing sheet with id=AC6, first strand: chain 'J' and resid 350 through 351 removed outlier: 4.020A pdb=" N SER J 350 " --> pdb=" O ASP J 364 " (cutoff:3.500A) 1249 hydrogen bonds defined for protein. 3507 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: 21.05 Time building geometry restraints manager: 43.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 24790 1.04 - 1.24: 4081 1.24 - 1.44: 7957 1.44 - 1.64: 13502 1.64 - 1.85: 202 Bond restraints: 50532 Sorted by residual: bond pdb=" CB HIS E 359 " pdb=" CG HIS E 359 " ideal model delta sigma weight residual 1.497 1.382 0.115 1.40e-02 5.10e+03 6.72e+01 bond pdb=" CB HIS J 359 " pdb=" CG HIS J 359 " ideal model delta sigma weight residual 1.497 1.382 0.115 1.40e-02 5.10e+03 6.72e+01 bond pdb=" CB HIS G 122 " pdb=" CG HIS G 122 " ideal model delta sigma weight residual 1.497 1.394 0.103 1.40e-02 5.10e+03 5.37e+01 bond pdb=" CB HIS B 122 " pdb=" CG HIS B 122 " ideal model delta sigma weight residual 1.497 1.395 0.102 1.40e-02 5.10e+03 5.28e+01 bond pdb=" CA PRO I 220 " pdb=" C PRO I 220 " ideal model delta sigma weight residual 1.514 1.551 -0.036 5.50e-03 3.31e+04 4.34e+01 ... (remaining 50527 not shown) Histogram of bond angle deviations from ideal: 93.57 - 101.68: 72 101.68 - 109.79: 38747 109.79 - 117.89: 28931 117.89 - 126.00: 22642 126.00 - 134.11: 874 Bond angle restraints: 91266 Sorted by residual: angle pdb=" N GLU B 210 " pdb=" CA GLU B 210 " pdb=" C GLU B 210 " ideal model delta sigma weight residual 113.20 124.14 -10.94 1.21e+00 6.83e-01 8.17e+01 angle pdb=" N GLU G 210 " pdb=" CA GLU G 210 " pdb=" C GLU G 210 " ideal model delta sigma weight residual 113.20 124.12 -10.92 1.21e+00 6.83e-01 8.14e+01 angle pdb=" N SER H 42 " pdb=" CA SER H 42 " pdb=" C SER H 42 " ideal model delta sigma weight residual 111.71 121.91 -10.20 1.15e+00 7.56e-01 7.86e+01 angle pdb=" N SER C 42 " pdb=" CA SER C 42 " pdb=" C SER C 42 " ideal model delta sigma weight residual 111.71 121.90 -10.19 1.15e+00 7.56e-01 7.85e+01 angle pdb=" CA HIS I 249 " pdb=" CB HIS I 249 " pdb=" CG HIS I 249 " ideal model delta sigma weight residual 113.80 122.65 -8.85 1.00e+00 1.00e+00 7.84e+01 ... (remaining 91261 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.86: 22547 16.86 - 33.73: 903 33.73 - 50.59: 285 50.59 - 67.46: 119 67.46 - 84.32: 30 Dihedral angle restraints: 23884 sinusoidal: 13002 harmonic: 10882 Sorted by residual: dihedral pdb=" C TYR I 240 " pdb=" N TYR I 240 " pdb=" CA TYR I 240 " pdb=" CB TYR I 240 " ideal model delta harmonic sigma weight residual -122.60 -112.33 -10.27 0 2.50e+00 1.60e-01 1.69e+01 dihedral pdb=" C TYR D 240 " pdb=" N TYR D 240 " pdb=" CA TYR D 240 " pdb=" CB TYR D 240 " ideal model delta harmonic sigma weight residual -122.60 -112.35 -10.25 0 2.50e+00 1.60e-01 1.68e+01 dihedral pdb=" N PHE C 73 " pdb=" C PHE C 73 " pdb=" CA PHE C 73 " pdb=" CB PHE C 73 " ideal model delta harmonic sigma weight residual 122.80 132.23 -9.43 0 2.50e+00 1.60e-01 1.42e+01 ... (remaining 23881 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 2801 0.104 - 0.209: 868 0.209 - 0.313: 159 0.313 - 0.418: 10 0.418 - 0.522: 4 Chirality restraints: 3842 Sorted by residual: chirality pdb=" CA PHE C 73 " pdb=" N PHE C 73 " pdb=" C PHE C 73 " pdb=" CB PHE C 73 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.81e+00 chirality pdb=" CA PHE H 73 " pdb=" N PHE H 73 " pdb=" C PHE H 73 " pdb=" CB PHE H 73 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.73e+00 chirality pdb=" CA SER I 102 " pdb=" N SER I 102 " pdb=" C SER I 102 " pdb=" CB SER I 102 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.57e+00 ... (remaining 3839 not shown) Planarity restraints: 7496 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU G 316 " 0.041 2.00e-02 2.50e+03 8.34e-02 6.95e+01 pdb=" C GLU G 316 " -0.144 2.00e-02 2.50e+03 pdb=" O GLU G 316 " 0.052 2.00e-02 2.50e+03 pdb=" OXT GLU G 316 " 0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 316 " -0.041 2.00e-02 2.50e+03 8.32e-02 6.92e+01 pdb=" C GLU B 316 " 0.144 2.00e-02 2.50e+03 pdb=" O GLU B 316 " -0.052 2.00e-02 2.50e+03 pdb=" OXT GLU B 316 " -0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR I 240 " -0.093 2.00e-02 2.50e+03 4.09e-02 5.02e+01 pdb=" CG TYR I 240 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR I 240 " 0.045 2.00e-02 2.50e+03 pdb=" CD2 TYR I 240 " 0.041 2.00e-02 2.50e+03 pdb=" CE1 TYR I 240 " 0.025 2.00e-02 2.50e+03 pdb=" CE2 TYR I 240 " 0.027 2.00e-02 2.50e+03 pdb=" CZ TYR I 240 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR I 240 " -0.076 2.00e-02 2.50e+03 pdb=" HD1 TYR I 240 " 0.003 2.00e-02 2.50e+03 pdb=" HD2 TYR I 240 " 0.002 2.00e-02 2.50e+03 pdb=" HE1 TYR I 240 " 0.003 2.00e-02 2.50e+03 pdb=" HE2 TYR I 240 " 0.003 2.00e-02 2.50e+03 ... (remaining 7493 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 1983 2.15 - 2.77: 99431 2.77 - 3.38: 145524 3.38 - 3.99: 191440 3.99 - 4.60: 300410 Nonbonded interactions: 738788 Sorted by model distance: nonbonded pdb=" H ARG H 224 " pdb=" H ILE H 225 " model vdw 1.542 2.100 nonbonded pdb=" H ARG C 224 " pdb=" H ILE C 225 " model vdw 1.542 2.100 nonbonded pdb=" H GLY E 393 " pdb=" H ASP E 394 " model vdw 1.577 2.100 nonbonded pdb=" H GLY J 393 " pdb=" H ASP J 394 " model vdw 1.578 2.100 nonbonded pdb=" H THR G 163 " pdb=" H LYS G 164 " model vdw 1.636 2.100 ... (remaining 738783 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' selection = chain 'F' } ncs_group { reference = chain 'B' selection = chain 'G' } ncs_group { reference = chain 'C' selection = chain 'H' } ncs_group { reference = chain 'D' selection = chain 'I' } ncs_group { reference = chain 'E' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.510 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: 0.780 Extract box with map and model: 11.620 Check model and map are aligned: 0.780 Set scattering table: 0.460 Process input model: 169.610 Find NCS groups from input model: 1.960 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 191.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6879 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 : 0.020 0.142 25672 Z= 1.323 Angle : 1.861 15.244 34764 Z= 1.261 Chirality : 0.100 0.522 3842 Planarity : 0.009 0.083 4526 Dihedral : 10.539 84.319 9598 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.33 % Favored : 94.22 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.15), residues: 3114 helix: 0.10 (0.14), residues: 1244 sheet: 0.31 (0.24), residues: 456 loop : -0.63 (0.17), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.008 TRP G 130 HIS 0.013 0.003 HIS D 292 PHE 0.050 0.007 PHE C 369 TYR 0.092 0.009 TYR I 240 ARG 0.009 0.001 ARG F 108 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 2774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 720 time to evaluate : 4.340 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: 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: 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: 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: 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: 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: 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: 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 128 LEU cc_start: 0.8654 (tp) cc_final: 0.8232 (tp) REVERT: A 173 TYR cc_start: 0.8450 (m-80) cc_final: 0.7873 (m-80) REVERT: A 205 ASP cc_start: 0.7605 (p0) cc_final: 0.7176 (p0) REVERT: B 85 LYS cc_start: 0.7893 (mttm) cc_final: 0.6928 (tmtt) REVERT: B 97 LEU cc_start: 0.8922 (mt) cc_final: 0.8649 (tt) REVERT: B 161 LYS cc_start: 0.8837 (pttt) cc_final: 0.8314 (mttt) REVERT: B 243 GLU cc_start: 0.8620 (mm-30) cc_final: 0.8052 (mm-30) REVERT: C 1 MET cc_start: 0.4558 (ttm) cc_final: 0.3841 (ttp) REVERT: C 111 GLU cc_start: 0.6939 (pm20) cc_final: 0.6477 (tm-30) REVERT: C 216 TYR cc_start: 0.7390 (m-80) cc_final: 0.6975 (t80) REVERT: C 302 MET cc_start: -0.1096 (ttm) cc_final: -0.1609 (ttp) REVERT: D 105 MET cc_start: 0.3706 (mmm) cc_final: 0.3279 (mmt) REVERT: D 135 LYS cc_start: 0.2158 (mttm) cc_final: 0.1910 (tppt) REVERT: D 186 LEU cc_start: 0.6483 (tp) cc_final: 0.6035 (mm) REVERT: F 128 LEU cc_start: 0.8627 (tp) cc_final: 0.8223 (tp) REVERT: F 173 TYR cc_start: 0.8475 (m-80) cc_final: 0.7914 (m-80) REVERT: F 205 ASP cc_start: 0.7569 (p0) cc_final: 0.7147 (p0) REVERT: G 85 LYS cc_start: 0.7858 (mttm) cc_final: 0.6949 (tmtt) REVERT: G 97 LEU cc_start: 0.8916 (mt) cc_final: 0.8644 (tt) REVERT: G 161 LYS cc_start: 0.8777 (pttt) cc_final: 0.8324 (mttt) REVERT: G 243 GLU cc_start: 0.8621 (mm-30) cc_final: 0.8060 (mm-30) REVERT: H 1 MET cc_start: 0.4518 (ttm) cc_final: 0.3815 (ttp) REVERT: H 111 GLU cc_start: 0.6842 (pm20) cc_final: 0.6455 (tm-30) REVERT: H 216 TYR cc_start: 0.7353 (m-80) cc_final: 0.6945 (t80) REVERT: H 302 MET cc_start: -0.1144 (ttm) cc_final: -0.1630 (ttp) REVERT: I 105 MET cc_start: 0.3567 (mmm) cc_final: 0.3183 (mmt) REVERT: I 135 LYS cc_start: 0.2208 (mttm) cc_final: 0.1977 (tppt) REVERT: I 186 LEU cc_start: 0.6512 (tp) cc_final: 0.6064 (mm) REVERT: E 443 LYS cc_start: 0.8748 (mmtt) cc_final: 0.8464 (mmmm) REVERT: J 443 LYS cc_start: 0.8735 (mmtt) cc_final: 0.8453 (mmmm) REVERT: J 447 PHE cc_start: 0.6082 (p90) cc_final: 0.5607 (p90) outliers start: 0 outliers final: 0 residues processed: 720 average time/residue: 0.9448 time to fit residues: 1046.4624 Evaluate side-chains 433 residues out of total 2774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 433 time to evaluate : 3.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 261 optimal weight: 0.5980 chunk 234 optimal weight: 0.6980 chunk 130 optimal weight: 0.9980 chunk 80 optimal weight: 6.9990 chunk 158 optimal weight: 0.7980 chunk 125 optimal weight: 0.7980 chunk 242 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 147 optimal weight: 0.5980 chunk 180 optimal weight: 10.0000 chunk 281 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 ASN C 100 GLN C 338 GLN ** G 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 294 ASN H 100 GLN ** H 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 338 GLN ** E 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 332 GLN E 336 ASN ** J 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6892 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 25672 Z= 0.242 Angle : 0.775 8.004 34764 Z= 0.429 Chirality : 0.045 0.215 3842 Planarity : 0.005 0.055 4526 Dihedral : 6.034 76.755 3424 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.39 % Allowed : 4.91 % Favored : 94.70 % Rotamer: Outliers : 2.05 % Allowed : 8.87 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.15), residues: 3114 helix: 0.44 (0.14), residues: 1258 sheet: -0.01 (0.24), residues: 462 loop : -1.00 (0.16), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP J 36 HIS 0.010 0.002 HIS D 249 PHE 0.030 0.002 PHE A 148 TYR 0.031 0.002 TYR D 240 ARG 0.005 0.001 ARG E 327 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 2774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 476 time to evaluate : 3.692 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: 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: 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 ASP cc_start: 0.7368 (p0) cc_final: 0.6732 (p0) REVERT: B 85 LYS cc_start: 0.7526 (mttm) cc_final: 0.6673 (tmtt) REVERT: B 88 ASP cc_start: 0.6741 (OUTLIER) cc_final: 0.6421 (t0) REVERT: B 97 LEU cc_start: 0.8889 (mt) cc_final: 0.8663 (tt) REVERT: B 161 LYS cc_start: 0.8827 (pttt) cc_final: 0.8324 (mttt) REVERT: B 304 GLU cc_start: 0.6722 (mm-30) cc_final: 0.6369 (tm-30) REVERT: B 309 MET cc_start: 0.7922 (tpp) cc_final: 0.7631 (tpp) REVERT: C 216 TYR cc_start: 0.7471 (m-80) cc_final: 0.7205 (t80) REVERT: C 302 MET cc_start: -0.0589 (ttm) cc_final: -0.1266 (ttp) REVERT: C 349 TYR cc_start: 0.4351 (p90) cc_final: 0.2335 (t80) REVERT: C 358 MET cc_start: 0.2554 (tmm) cc_final: 0.1912 (tmm) REVERT: D 105 MET cc_start: 0.3349 (mmm) cc_final: 0.2792 (mmt) REVERT: D 186 LEU cc_start: 0.6397 (tp) cc_final: 0.5980 (mm) REVERT: F 128 LEU cc_start: 0.8576 (tp) cc_final: 0.8336 (tp) REVERT: F 131 SER cc_start: 0.9002 (t) cc_final: 0.8614 (m) REVERT: F 205 ASP cc_start: 0.7321 (p0) cc_final: 0.6708 (p0) REVERT: G 85 LYS cc_start: 0.7523 (mttm) cc_final: 0.6681 (tmtt) REVERT: G 88 ASP cc_start: 0.6725 (OUTLIER) cc_final: 0.6407 (t0) REVERT: G 97 LEU cc_start: 0.8863 (mt) cc_final: 0.8642 (tt) REVERT: G 161 LYS cc_start: 0.8783 (pttt) cc_final: 0.8354 (mttt) REVERT: G 304 GLU cc_start: 0.6709 (mm-30) cc_final: 0.6340 (tm-30) REVERT: G 309 MET cc_start: 0.7943 (tpp) cc_final: 0.7647 (tpp) REVERT: H 216 TYR cc_start: 0.7423 (m-80) cc_final: 0.7185 (t80) REVERT: H 302 MET cc_start: -0.0483 (ttm) cc_final: -0.1217 (ttp) REVERT: H 349 TYR cc_start: 0.4435 (p90) cc_final: 0.2354 (t80) REVERT: I 186 LEU cc_start: 0.6500 (tp) cc_final: 0.6048 (mm) REVERT: E 221 ASP cc_start: 0.6690 (m-30) cc_final: 0.6404 (m-30) REVERT: E 230 ASP cc_start: 0.7006 (OUTLIER) cc_final: 0.6568 (m-30) REVERT: E 443 LYS cc_start: 0.8700 (mmtt) cc_final: 0.8465 (mmmm) REVERT: J 51 GLU cc_start: 0.6310 (mt-10) cc_final: 0.5910 (mt-10) REVERT: J 221 ASP cc_start: 0.7158 (m-30) cc_final: 0.6691 (m-30) REVERT: J 230 ASP cc_start: 0.6984 (OUTLIER) cc_final: 0.6496 (m-30) REVERT: J 443 LYS cc_start: 0.8744 (mmtt) cc_final: 0.8512 (mmmm) outliers start: 57 outliers final: 42 residues processed: 513 average time/residue: 0.7694 time to fit residues: 629.6369 Evaluate side-chains 447 residues out of total 2774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 401 time to evaluate : 4.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 294 ASN Chi-restraints excluded: chain B residue 303 GLN Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain C residue 151 TYR Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain D residue 281 GLU Chi-restraints excluded: chain F residue 11 SER Chi-restraints excluded: chain F residue 58 ASN Chi-restraints excluded: chain F residue 107 TYR Chi-restraints excluded: chain F residue 200 ASP Chi-restraints excluded: chain F residue 224 CYS Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain G residue 146 ASP Chi-restraints excluded: chain G residue 294 ASN Chi-restraints excluded: chain G residue 303 GLN Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 142 TYR Chi-restraints excluded: chain H residue 151 TYR Chi-restraints excluded: chain H residue 204 SER Chi-restraints excluded: chain H residue 253 VAL Chi-restraints excluded: chain H residue 258 THR Chi-restraints excluded: chain H residue 279 LEU Chi-restraints excluded: chain I residue 281 GLU Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain E residue 230 ASP Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 104 GLU Chi-restraints excluded: chain J residue 230 ASP Chi-restraints excluded: chain J residue 255 THR Chi-restraints excluded: chain J residue 261 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 156 optimal weight: 2.9990 chunk 87 optimal weight: 9.9990 chunk 234 optimal weight: 4.9990 chunk 191 optimal weight: 8.9990 chunk 77 optimal weight: 0.9990 chunk 282 optimal weight: 3.9990 chunk 304 optimal weight: 6.9990 chunk 251 optimal weight: 3.9990 chunk 279 optimal weight: 2.9990 chunk 96 optimal weight: 8.9990 chunk 226 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN ** B 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 GLN ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 136 HIS F 155 ASN ** G 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 177 GLN G 285 GLN ** G 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 332 GLN J 336 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 25672 Z= 0.386 Angle : 0.722 7.460 34764 Z= 0.400 Chirality : 0.044 0.185 3842 Planarity : 0.005 0.060 4526 Dihedral : 6.017 84.622 3424 Min Nonbonded Distance : 1.682 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.39 % Allowed : 6.42 % Favored : 93.19 % Rotamer: Outliers : 2.52 % Allowed : 10.02 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.14), residues: 3114 helix: 0.41 (0.14), residues: 1252 sheet: -0.35 (0.23), residues: 482 loop : -1.34 (0.16), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 261 HIS 0.014 0.002 HIS H 227 PHE 0.035 0.002 PHE E 450 TYR 0.023 0.002 TYR D 240 ARG 0.008 0.001 ARG E 377 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 2774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 395 time to evaluate : 4.280 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: 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: 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: 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: 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: 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: symmetry clash REVERT: A 131 SER cc_start: 0.8907 (t) cc_final: 0.8245 (p) REVERT: A 205 ASP cc_start: 0.7342 (p0) cc_final: 0.7016 (p0) REVERT: B 85 LYS cc_start: 0.7668 (mttm) cc_final: 0.6674 (tmtt) REVERT: B 88 ASP cc_start: 0.7085 (OUTLIER) cc_final: 0.6757 (t0) REVERT: B 161 LYS cc_start: 0.8854 (pttt) cc_final: 0.8427 (mttt) REVERT: B 304 GLU cc_start: 0.6708 (mm-30) cc_final: 0.6333 (mm-30) REVERT: B 309 MET cc_start: 0.7918 (tpp) cc_final: 0.7676 (tpp) REVERT: C 216 TYR cc_start: 0.7570 (m-80) cc_final: 0.7264 (t80) REVERT: C 236 HIS cc_start: 0.6028 (t70) cc_final: 0.5757 (t70) REVERT: C 302 MET cc_start: -0.0312 (ttm) cc_final: -0.1163 (ttp) REVERT: D 105 MET cc_start: 0.3688 (mmm) cc_final: 0.3303 (mmt) REVERT: D 186 LEU cc_start: 0.6481 (tp) cc_final: 0.6079 (mm) REVERT: F 128 LEU cc_start: 0.8716 (tp) cc_final: 0.8450 (tp) REVERT: F 131 SER cc_start: 0.8950 (t) cc_final: 0.8365 (p) REVERT: F 205 ASP cc_start: 0.7351 (p0) cc_final: 0.7052 (p0) REVERT: G 85 LYS cc_start: 0.7701 (mttm) cc_final: 0.6866 (tmtt) REVERT: G 88 ASP cc_start: 0.7038 (OUTLIER) cc_final: 0.6717 (t0) REVERT: G 161 LYS cc_start: 0.8802 (pttt) cc_final: 0.8447 (mttt) REVERT: G 309 MET cc_start: 0.7919 (tpp) cc_final: 0.7664 (tpp) REVERT: H 236 HIS cc_start: 0.5982 (t70) cc_final: 0.5723 (t70) REVERT: H 302 MET cc_start: -0.0325 (ttm) cc_final: -0.1203 (ttp) REVERT: H 349 TYR cc_start: 0.4161 (p90) cc_final: 0.2430 (t80) REVERT: I 105 MET cc_start: 0.3563 (mmm) cc_final: 0.2982 (mmt) REVERT: I 186 LEU cc_start: 0.6473 (tp) cc_final: 0.6033 (mm) REVERT: E 230 ASP cc_start: 0.7618 (OUTLIER) cc_final: 0.7207 (m-30) REVERT: E 443 LYS cc_start: 0.8735 (mmtt) cc_final: 0.8482 (mmmm) REVERT: E 447 PHE cc_start: 0.6177 (OUTLIER) cc_final: 0.5397 (p90) REVERT: J 230 ASP cc_start: 0.7439 (OUTLIER) cc_final: 0.7080 (m-30) REVERT: J 443 LYS cc_start: 0.8757 (mmtt) cc_final: 0.8504 (mmmm) outliers start: 70 outliers final: 52 residues processed: 449 average time/residue: 0.7773 time to fit residues: 555.3620 Evaluate side-chains 412 residues out of total 2774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 355 time to evaluate : 4.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 303 GLN Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain F residue 58 ASN Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 107 TYR Chi-restraints excluded: chain F residue 200 ASP Chi-restraints excluded: chain F residue 224 CYS Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 146 ASP Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 171 THR Chi-restraints excluded: chain G residue 280 SER Chi-restraints excluded: chain G residue 303 GLN Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 142 TYR Chi-restraints excluded: chain H residue 204 SER Chi-restraints excluded: chain H residue 253 VAL Chi-restraints excluded: chain H residue 258 THR Chi-restraints excluded: chain H residue 279 LEU Chi-restraints excluded: chain I residue 166 LEU Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain E residue 230 ASP Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 447 PHE Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 104 GLU Chi-restraints excluded: chain J residue 230 ASP Chi-restraints excluded: chain J residue 255 THR Chi-restraints excluded: chain J residue 261 LEU Chi-restraints excluded: chain J residue 447 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 278 optimal weight: 3.9990 chunk 212 optimal weight: 9.9990 chunk 146 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 134 optimal weight: 3.9990 chunk 189 optimal weight: 20.0000 chunk 283 optimal weight: 2.9990 chunk 299 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 268 optimal weight: 2.9990 chunk 80 optimal weight: 20.0000 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 HIS ** B 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 HIS ** G 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 217 HIS ** G 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 136 HIS E 389 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.4173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 25672 Z= 0.268 Angle : 0.639 6.619 34764 Z= 0.349 Chirality : 0.042 0.166 3842 Planarity : 0.005 0.063 4526 Dihedral : 5.886 86.501 3424 Min Nonbonded Distance : 1.730 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.62 % Favored : 92.94 % Rotamer: Outliers : 2.81 % Allowed : 10.96 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.15), residues: 3114 helix: 0.49 (0.14), residues: 1272 sheet: -0.69 (0.23), residues: 472 loop : -1.46 (0.16), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 261 HIS 0.009 0.002 HIS B 73 PHE 0.039 0.002 PHE J 450 TYR 0.021 0.002 TYR I 240 ARG 0.004 0.000 ARG J 215 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 2774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 371 time to evaluate : 3.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 SER cc_start: 0.8854 (t) cc_final: 0.8256 (p) REVERT: A 205 ASP cc_start: 0.7269 (p0) cc_final: 0.6930 (p0) REVERT: B 85 LYS cc_start: 0.7652 (mttm) cc_final: 0.6688 (tmtt) REVERT: B 88 ASP cc_start: 0.7156 (OUTLIER) cc_final: 0.6794 (t0) REVERT: B 161 LYS cc_start: 0.8773 (pttt) cc_final: 0.8462 (mttm) REVERT: C 216 TYR cc_start: 0.7572 (m-80) cc_final: 0.7261 (t80) REVERT: C 302 MET cc_start: -0.0319 (ttm) cc_final: -0.1163 (ttp) REVERT: D 105 MET cc_start: 0.3745 (mmm) cc_final: 0.3467 (mmt) REVERT: D 186 LEU cc_start: 0.6334 (tp) cc_final: 0.5878 (mm) REVERT: F 131 SER cc_start: 0.8969 (t) cc_final: 0.8361 (p) REVERT: F 205 ASP cc_start: 0.7288 (p0) cc_final: 0.6903 (p0) REVERT: G 85 LYS cc_start: 0.7650 (mttm) cc_final: 0.6760 (tmtt) REVERT: G 88 ASP cc_start: 0.7093 (OUTLIER) cc_final: 0.6728 (t0) REVERT: G 161 LYS cc_start: 0.8730 (pttt) cc_final: 0.8505 (mttm) REVERT: H 302 MET cc_start: -0.0282 (ttm) cc_final: -0.1146 (ttp) REVERT: I 105 MET cc_start: 0.3840 (mmm) cc_final: 0.3553 (mmt) REVERT: I 186 LEU cc_start: 0.6403 (tp) cc_final: 0.5976 (mm) REVERT: E 230 ASP cc_start: 0.7540 (OUTLIER) cc_final: 0.7107 (m-30) REVERT: E 443 LYS cc_start: 0.8765 (mmtt) cc_final: 0.8541 (mmmm) REVERT: J 230 ASP cc_start: 0.7416 (OUTLIER) cc_final: 0.6975 (m-30) REVERT: J 443 LYS cc_start: 0.8779 (mmtt) cc_final: 0.8535 (mmmm) outliers start: 78 outliers final: 61 residues processed: 426 average time/residue: 0.8356 time to fit residues: 563.7125 Evaluate side-chains 410 residues out of total 2774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 345 time to evaluate : 3.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 232 MET Chi-restraints excluded: chain F residue 58 ASN Chi-restraints excluded: chain F residue 107 TYR Chi-restraints excluded: chain F residue 200 ASP Chi-restraints excluded: chain F residue 224 CYS Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 146 ASP Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 171 THR Chi-restraints excluded: chain G residue 240 CYS Chi-restraints excluded: chain G residue 280 SER Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 142 TYR Chi-restraints excluded: chain H residue 203 LEU Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain H residue 258 THR Chi-restraints excluded: chain H residue 279 LEU Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 166 LEU Chi-restraints excluded: chain E residue 70 CYS Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain E residue 230 ASP Chi-restraints excluded: chain E residue 251 ASP Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 447 PHE Chi-restraints excluded: chain E residue 469 GLU Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 104 GLU Chi-restraints excluded: chain J residue 230 ASP Chi-restraints excluded: chain J residue 251 ASP Chi-restraints excluded: chain J residue 255 THR Chi-restraints excluded: chain J residue 261 LEU Chi-restraints excluded: chain J residue 447 PHE Chi-restraints excluded: chain J residue 469 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 249 optimal weight: 2.9990 chunk 170 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 223 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 chunk 255 optimal weight: 3.9990 chunk 207 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 153 optimal weight: 0.8980 chunk 268 optimal weight: 4.9990 chunk 75 optimal weight: 9.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 HIS ** B 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 HIS ** B 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 GLN ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 HIS ** G 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 389 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.4624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 25672 Z= 0.317 Angle : 0.648 7.085 34764 Z= 0.353 Chirality : 0.042 0.159 3842 Planarity : 0.005 0.066 4526 Dihedral : 5.767 76.550 3424 Min Nonbonded Distance : 1.694 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.45 % Allowed : 7.39 % Favored : 92.16 % Rotamer: Outliers : 2.85 % Allowed : 11.18 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.15), residues: 3114 helix: 0.52 (0.14), residues: 1270 sheet: -0.98 (0.23), residues: 456 loop : -1.68 (0.16), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 113 HIS 0.011 0.001 HIS H 236 PHE 0.023 0.002 PHE J 450 TYR 0.026 0.002 TYR C 124 ARG 0.005 0.000 ARG H 55 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 351 time to evaluate : 3.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 SER cc_start: 0.8831 (t) cc_final: 0.8205 (p) REVERT: B 85 LYS cc_start: 0.7692 (mttm) cc_final: 0.6767 (tmtt) REVERT: B 88 ASP cc_start: 0.7168 (OUTLIER) cc_final: 0.6898 (t0) REVERT: B 113 ARG cc_start: 0.7592 (mmm-85) cc_final: 0.7163 (mmt-90) REVERT: B 161 LYS cc_start: 0.8690 (pttt) cc_final: 0.8390 (mttt) REVERT: B 309 MET cc_start: 0.7772 (tpp) cc_final: 0.7545 (tpp) REVERT: C 13 MET cc_start: 0.7470 (OUTLIER) cc_final: 0.7219 (ttm) REVERT: C 302 MET cc_start: -0.0205 (ttm) cc_final: -0.1070 (ttp) REVERT: D 186 LEU cc_start: 0.6380 (tp) cc_final: 0.5967 (mm) REVERT: F 51 LEU cc_start: 0.7759 (tp) cc_final: 0.7442 (mm) REVERT: F 131 SER cc_start: 0.8893 (t) cc_final: 0.8306 (p) REVERT: F 205 ASP cc_start: 0.7320 (p0) cc_final: 0.7087 (p0) REVERT: G 85 LYS cc_start: 0.7699 (mttm) cc_final: 0.6795 (tmtt) REVERT: G 88 ASP cc_start: 0.7197 (OUTLIER) cc_final: 0.6930 (t0) REVERT: G 309 MET cc_start: 0.7801 (tpp) cc_final: 0.7559 (tpp) REVERT: H 13 MET cc_start: 0.7475 (OUTLIER) cc_final: 0.7239 (ttm) REVERT: H 302 MET cc_start: -0.0219 (ttm) cc_final: -0.1080 (ttp) REVERT: I 105 MET cc_start: 0.3909 (mmm) cc_final: 0.3708 (mmt) REVERT: I 186 LEU cc_start: 0.6415 (tp) cc_final: 0.5984 (mm) REVERT: E 230 ASP cc_start: 0.7517 (OUTLIER) cc_final: 0.7020 (m-30) REVERT: E 379 LEU cc_start: 0.8729 (mm) cc_final: 0.8519 (mm) REVERT: E 384 ILE cc_start: 0.8067 (mt) cc_final: 0.7857 (mt) REVERT: E 443 LYS cc_start: 0.8813 (mmtt) cc_final: 0.8531 (mmmt) REVERT: E 444 LEU cc_start: 0.8511 (mt) cc_final: 0.8246 (mp) REVERT: E 447 PHE cc_start: 0.6067 (OUTLIER) cc_final: 0.5062 (p90) REVERT: E 477 MET cc_start: 0.8144 (mtp) cc_final: 0.7850 (mtp) REVERT: J 230 ASP cc_start: 0.7506 (OUTLIER) cc_final: 0.6992 (m-30) REVERT: J 443 LYS cc_start: 0.8788 (mmtt) cc_final: 0.8544 (mmmm) outliers start: 79 outliers final: 59 residues processed: 408 average time/residue: 0.8331 time to fit residues: 538.9520 Evaluate side-chains 398 residues out of total 2774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 332 time to evaluate : 4.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain C residue 151 TYR Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain F residue 58 ASN Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 107 TYR Chi-restraints excluded: chain F residue 200 ASP Chi-restraints excluded: chain F residue 224 CYS Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 146 ASP Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 171 THR Chi-restraints excluded: chain G residue 280 SER Chi-restraints excluded: chain H residue 13 MET Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 70 ASP Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 142 TYR Chi-restraints excluded: chain H residue 151 TYR Chi-restraints excluded: chain H residue 203 LEU Chi-restraints excluded: chain H residue 204 SER Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain H residue 258 THR Chi-restraints excluded: chain H residue 279 LEU Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 106 SER Chi-restraints excluded: chain I residue 166 LEU Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain E residue 230 ASP Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 447 PHE Chi-restraints excluded: chain E residue 469 GLU Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 47 CYS Chi-restraints excluded: chain J residue 104 GLU Chi-restraints excluded: chain J residue 230 ASP Chi-restraints excluded: chain J residue 447 PHE Chi-restraints excluded: chain J residue 469 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 100 optimal weight: 8.9990 chunk 269 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 175 optimal weight: 9.9990 chunk 73 optimal weight: 1.9990 chunk 299 optimal weight: 4.9990 chunk 248 optimal weight: 8.9990 chunk 138 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 99 optimal weight: 5.9990 chunk 157 optimal weight: 1.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** B 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 GLN ** B 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 310 HIS ** F 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 GLN ** G 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 244 GLN ** G 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 GLN J 40 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.5083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 25672 Z= 0.432 Angle : 0.711 9.433 34764 Z= 0.388 Chirality : 0.045 0.179 3842 Planarity : 0.006 0.073 4526 Dihedral : 5.908 68.355 3424 Min Nonbonded Distance : 1.611 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.45 % Allowed : 7.68 % Favored : 91.88 % Rotamer: Outliers : 3.39 % Allowed : 12.15 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.14), residues: 3114 helix: 0.25 (0.14), residues: 1264 sheet: -1.11 (0.23), residues: 462 loop : -1.95 (0.15), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 113 HIS 0.010 0.002 HIS B 25 PHE 0.035 0.002 PHE J 450 TYR 0.031 0.002 TYR E 174 ARG 0.005 0.001 ARG A 96 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 320 time to evaluate : 3.388 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: 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: 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: 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: 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 51 LEU cc_start: 0.7542 (tp) cc_final: 0.7311 (mm) REVERT: B 85 LYS cc_start: 0.7800 (mttm) cc_final: 0.6701 (tmtt) REVERT: B 88 ASP cc_start: 0.7335 (OUTLIER) cc_final: 0.7083 (t0) REVERT: B 161 LYS cc_start: 0.8761 (pttt) cc_final: 0.8444 (mttt) REVERT: C 13 MET cc_start: 0.7577 (OUTLIER) cc_final: 0.7138 (ttm) REVERT: C 302 MET cc_start: 0.0008 (ttm) cc_final: -0.0914 (ttp) REVERT: D 186 LEU cc_start: 0.6409 (tp) cc_final: 0.6040 (mm) REVERT: F 51 LEU cc_start: 0.7521 (tp) cc_final: 0.7275 (mm) REVERT: G 85 LYS cc_start: 0.7816 (mttm) cc_final: 0.6729 (tmtt) REVERT: G 88 ASP cc_start: 0.7349 (OUTLIER) cc_final: 0.7092 (t0) REVERT: H 13 MET cc_start: 0.7574 (OUTLIER) cc_final: 0.7096 (ttm) REVERT: H 302 MET cc_start: -0.0031 (ttm) cc_final: -0.0903 (ttp) REVERT: I 105 MET cc_start: 0.3954 (mmm) cc_final: 0.3691 (mmt) REVERT: E 230 ASP cc_start: 0.7572 (OUTLIER) cc_final: 0.7191 (m-30) REVERT: E 443 LYS cc_start: 0.8762 (mmtt) cc_final: 0.8509 (mmmt) REVERT: E 477 MET cc_start: 0.8254 (mtp) cc_final: 0.7961 (mtp) REVERT: J 51 GLU cc_start: 0.6921 (mt-10) cc_final: 0.6319 (mt-10) REVERT: J 230 ASP cc_start: 0.7539 (OUTLIER) cc_final: 0.7172 (m-30) REVERT: J 443 LYS cc_start: 0.8795 (mmtt) cc_final: 0.8494 (mmmm) outliers start: 94 outliers final: 78 residues processed: 390 average time/residue: 0.8481 time to fit residues: 525.5181 Evaluate side-chains 387 residues out of total 2774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 303 time to evaluate : 3.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASN Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 92 PHE Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain C residue 151 TYR Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 232 MET Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 58 ASN Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 107 TYR Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain F residue 200 ASP Chi-restraints excluded: chain F residue 224 CYS Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 123 SER Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 146 ASP Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 171 THR Chi-restraints excluded: chain G residue 280 SER Chi-restraints excluded: chain H residue 13 MET Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 72 ILE Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 142 TYR Chi-restraints excluded: chain H residue 151 TYR Chi-restraints excluded: chain H residue 202 LEU Chi-restraints excluded: chain H residue 203 LEU Chi-restraints excluded: chain H residue 204 SER Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain H residue 258 THR Chi-restraints excluded: chain H residue 279 LEU Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 106 SER Chi-restraints excluded: chain E residue 70 CYS Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain E residue 177 ASN Chi-restraints excluded: chain E residue 193 ARG Chi-restraints excluded: chain E residue 230 ASP Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 353 SER Chi-restraints excluded: chain E residue 447 PHE Chi-restraints excluded: chain E residue 469 GLU Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 47 CYS Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 104 GLU Chi-restraints excluded: chain J residue 177 ASN Chi-restraints excluded: chain J residue 230 ASP Chi-restraints excluded: chain J residue 261 LEU Chi-restraints excluded: chain J residue 353 SER Chi-restraints excluded: chain J residue 447 PHE Chi-restraints excluded: chain J residue 469 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 289 optimal weight: 3.9990 chunk 33 optimal weight: 0.0670 chunk 170 optimal weight: 2.9990 chunk 219 optimal weight: 20.0000 chunk 169 optimal weight: 0.5980 chunk 252 optimal weight: 5.9990 chunk 167 optimal weight: 0.3980 chunk 298 optimal weight: 0.6980 chunk 186 optimal weight: 9.9990 chunk 182 optimal weight: 7.9990 chunk 137 optimal weight: 0.9990 overall best weight: 0.5520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7117 moved from start: 0.5180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25672 Z= 0.178 Angle : 0.591 6.571 34764 Z= 0.314 Chirality : 0.041 0.161 3842 Planarity : 0.005 0.066 4526 Dihedral : 5.541 63.663 3424 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.36 % Favored : 93.19 % Rotamer: Outliers : 2.49 % Allowed : 12.65 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.15), residues: 3114 helix: 0.77 (0.14), residues: 1272 sheet: -0.97 (0.23), residues: 464 loop : -1.78 (0.16), residues: 1378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 36 HIS 0.011 0.001 HIS B 25 PHE 0.030 0.001 PHE E 450 TYR 0.025 0.002 TYR C 289 ARG 0.007 0.000 ARG B 113 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 334 time to evaluate : 3.886 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: 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: 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: 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: 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 51 LEU cc_start: 0.7448 (tp) cc_final: 0.7172 (mm) REVERT: A 131 SER cc_start: 0.8778 (t) cc_final: 0.8194 (p) REVERT: B 85 LYS cc_start: 0.7718 (mttm) cc_final: 0.6601 (tmtt) REVERT: B 88 ASP cc_start: 0.7212 (OUTLIER) cc_final: 0.6958 (t0) REVERT: B 161 LYS cc_start: 0.8752 (pttt) cc_final: 0.8400 (mttt) REVERT: B 223 THR cc_start: 0.6246 (p) cc_final: 0.6012 (t) REVERT: C 13 MET cc_start: 0.7435 (OUTLIER) cc_final: 0.7162 (ttm) REVERT: C 302 MET cc_start: -0.0105 (ttm) cc_final: -0.0979 (ttp) REVERT: D 186 LEU cc_start: 0.6404 (tp) cc_final: 0.5999 (mm) REVERT: F 51 LEU cc_start: 0.7424 (tp) cc_final: 0.7131 (mm) REVERT: F 131 SER cc_start: 0.8806 (t) cc_final: 0.8257 (p) REVERT: F 205 ASP cc_start: 0.7284 (p0) cc_final: 0.6943 (p0) REVERT: G 85 LYS cc_start: 0.7725 (mttm) cc_final: 0.6648 (tmtt) REVERT: G 88 ASP cc_start: 0.7206 (OUTLIER) cc_final: 0.6925 (t0) REVERT: G 223 THR cc_start: 0.6208 (p) cc_final: 0.5951 (t) REVERT: H 302 MET cc_start: -0.0169 (ttm) cc_final: -0.1007 (ttp) REVERT: E 42 GLU cc_start: 0.7522 (tp30) cc_final: 0.6815 (tp30) REVERT: E 443 LYS cc_start: 0.8681 (mmtt) cc_final: 0.8439 (mmmt) REVERT: E 477 MET cc_start: 0.8205 (mtp) cc_final: 0.7930 (mtp) REVERT: J 42 GLU cc_start: 0.7497 (tp30) cc_final: 0.6867 (tp30) REVERT: J 51 GLU cc_start: 0.6757 (mt-10) cc_final: 0.6229 (mt-10) REVERT: J 230 ASP cc_start: 0.7266 (OUTLIER) cc_final: 0.6827 (m-30) REVERT: J 443 LYS cc_start: 0.8786 (mmtt) cc_final: 0.8507 (mmmt) outliers start: 69 outliers final: 56 residues processed: 383 average time/residue: 0.8314 time to fit residues: 501.5905 Evaluate side-chains 379 residues out of total 2774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 319 time to evaluate : 3.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain C residue 151 TYR Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 169 CYS Chi-restraints excluded: chain F residue 58 ASN Chi-restraints excluded: chain F residue 107 TYR Chi-restraints excluded: chain F residue 224 CYS Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 146 ASP Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 301 LEU Chi-restraints excluded: chain H residue 70 ASP Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 142 TYR Chi-restraints excluded: chain H residue 151 TYR Chi-restraints excluded: chain H residue 203 LEU Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain H residue 258 THR Chi-restraints excluded: chain H residue 279 LEU Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 106 SER Chi-restraints excluded: chain I residue 169 CYS Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain E residue 193 ARG Chi-restraints excluded: chain E residue 251 ASP Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 444 LEU Chi-restraints excluded: chain E residue 447 PHE Chi-restraints excluded: chain E residue 469 GLU Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 70 CYS Chi-restraints excluded: chain J residue 104 GLU Chi-restraints excluded: chain J residue 193 ARG Chi-restraints excluded: chain J residue 230 ASP Chi-restraints excluded: chain J residue 251 ASP Chi-restraints excluded: chain J residue 447 PHE Chi-restraints excluded: chain J residue 469 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 184 optimal weight: 10.0000 chunk 119 optimal weight: 1.9990 chunk 178 optimal weight: 5.9990 chunk 90 optimal weight: 9.9990 chunk 58 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 189 optimal weight: 40.0000 chunk 203 optimal weight: 20.0000 chunk 147 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 234 optimal weight: 4.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 GLN ** G 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.5311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 25672 Z= 0.240 Angle : 0.593 8.289 34764 Z= 0.317 Chirality : 0.041 0.176 3842 Planarity : 0.005 0.066 4526 Dihedral : 5.469 59.414 3424 Min Nonbonded Distance : 1.727 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.39 % Allowed : 6.87 % Favored : 92.74 % Rotamer: Outliers : 2.45 % Allowed : 13.23 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.15), residues: 3114 helix: 0.82 (0.14), residues: 1272 sheet: -1.02 (0.23), residues: 460 loop : -1.79 (0.16), residues: 1382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 261 HIS 0.014 0.001 HIS G 25 PHE 0.028 0.001 PHE E 450 TYR 0.018 0.002 TYR C 289 ARG 0.013 0.000 ARG G 81 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 315 time to evaluate : 4.052 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: 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: 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: 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: 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 131 SER cc_start: 0.8750 (t) cc_final: 0.8171 (p) REVERT: A 205 ASP cc_start: 0.7379 (p0) cc_final: 0.7174 (p0) REVERT: B 85 LYS cc_start: 0.7732 (mttm) cc_final: 0.6605 (tmtt) REVERT: B 88 ASP cc_start: 0.7217 (OUTLIER) cc_final: 0.6953 (t0) REVERT: B 161 LYS cc_start: 0.8729 (pttt) cc_final: 0.8399 (mttt) REVERT: B 223 THR cc_start: 0.6280 (p) cc_final: 0.6067 (t) REVERT: C 13 MET cc_start: 0.7512 (OUTLIER) cc_final: 0.7293 (ttm) REVERT: C 302 MET cc_start: -0.0018 (ttm) cc_final: -0.0912 (ttp) REVERT: D 186 LEU cc_start: 0.6446 (tp) cc_final: 0.6020 (mm) REVERT: F 131 SER cc_start: 0.8811 (t) cc_final: 0.8254 (p) REVERT: F 205 ASP cc_start: 0.7344 (p0) cc_final: 0.7017 (p0) REVERT: G 85 LYS cc_start: 0.7736 (mttm) cc_final: 0.6608 (tmtt) REVERT: G 88 ASP cc_start: 0.7226 (OUTLIER) cc_final: 0.6937 (t0) REVERT: G 223 THR cc_start: 0.6264 (p) cc_final: 0.6031 (t) REVERT: H 302 MET cc_start: -0.0040 (ttm) cc_final: -0.0894 (ttp) REVERT: E 443 LYS cc_start: 0.8633 (mmtt) cc_final: 0.8382 (mmmt) REVERT: E 477 MET cc_start: 0.8197 (mtp) cc_final: 0.7890 (mtp) REVERT: J 51 GLU cc_start: 0.6833 (mt-10) cc_final: 0.6262 (mt-10) REVERT: J 193 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7912 (mtm110) REVERT: J 230 ASP cc_start: 0.7300 (OUTLIER) cc_final: 0.6838 (m-30) REVERT: J 231 MET cc_start: 0.7302 (mtp) cc_final: 0.7091 (mtp) REVERT: J 443 LYS cc_start: 0.8788 (mmtt) cc_final: 0.8502 (mmmt) outliers start: 68 outliers final: 57 residues processed: 367 average time/residue: 0.8408 time to fit residues: 489.8252 Evaluate side-chains 374 residues out of total 2774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 312 time to evaluate : 3.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 92 PHE Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain C residue 151 TYR Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 169 CYS Chi-restraints excluded: chain D residue 232 MET Chi-restraints excluded: chain F residue 58 ASN Chi-restraints excluded: chain F residue 107 TYR Chi-restraints excluded: chain F residue 224 CYS Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 146 ASP Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 301 LEU Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 142 TYR Chi-restraints excluded: chain H residue 151 TYR Chi-restraints excluded: chain H residue 203 LEU Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain H residue 258 THR Chi-restraints excluded: chain H residue 279 LEU Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 106 SER Chi-restraints excluded: chain I residue 169 CYS Chi-restraints excluded: chain E residue 47 CYS Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain E residue 193 ARG Chi-restraints excluded: chain E residue 428 ASP Chi-restraints excluded: chain E residue 444 LEU Chi-restraints excluded: chain E residue 447 PHE Chi-restraints excluded: chain E residue 469 GLU Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 104 GLU Chi-restraints excluded: chain J residue 193 ARG Chi-restraints excluded: chain J residue 230 ASP Chi-restraints excluded: chain J residue 381 LEU Chi-restraints excluded: chain J residue 447 PHE Chi-restraints excluded: chain J residue 469 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 271 optimal weight: 7.9990 chunk 286 optimal weight: 0.2980 chunk 261 optimal weight: 0.5980 chunk 278 optimal weight: 1.9990 chunk 167 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 218 optimal weight: 30.0000 chunk 85 optimal weight: 20.0000 chunk 251 optimal weight: 3.9990 chunk 263 optimal weight: 0.9980 chunk 277 optimal weight: 0.5980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 GLN ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.5431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25672 Z= 0.175 Angle : 0.572 10.400 34764 Z= 0.301 Chirality : 0.040 0.155 3842 Planarity : 0.005 0.063 4526 Dihedral : 5.283 53.115 3424 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.74 % Favored : 92.94 % Rotamer: Outliers : 2.27 % Allowed : 13.41 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.15), residues: 3114 helix: 0.98 (0.14), residues: 1268 sheet: -0.92 (0.23), residues: 460 loop : -1.77 (0.16), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 36 HIS 0.017 0.001 HIS B 25 PHE 0.021 0.001 PHE E 450 TYR 0.013 0.001 TYR E 349 ARG 0.009 0.000 ARG G 113 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 325 time to evaluate : 4.242 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: 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: 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: 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: 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: symmetry clash REVERT: A 1 MET cc_start: 0.6498 (tpp) cc_final: 0.5884 (tpp) REVERT: A 131 SER cc_start: 0.8715 (t) cc_final: 0.8103 (p) REVERT: B 85 LYS cc_start: 0.7691 (mttm) cc_final: 0.6581 (tmtt) REVERT: B 88 ASP cc_start: 0.7216 (OUTLIER) cc_final: 0.6914 (t0) REVERT: B 161 LYS cc_start: 0.8732 (pttt) cc_final: 0.8374 (mttt) REVERT: C 216 TYR cc_start: 0.7638 (m-80) cc_final: 0.7278 (m-80) REVERT: C 302 MET cc_start: 0.0013 (ttm) cc_final: -0.0831 (ttp) REVERT: D 186 LEU cc_start: 0.6412 (tp) cc_final: 0.5930 (mm) REVERT: F 1 MET cc_start: 0.6512 (tpp) cc_final: 0.5882 (tpp) REVERT: F 131 SER cc_start: 0.8784 (t) cc_final: 0.8213 (p) REVERT: F 205 ASP cc_start: 0.7327 (p0) cc_final: 0.7005 (p0) REVERT: G 85 LYS cc_start: 0.7685 (mttm) cc_final: 0.6561 (tmtt) REVERT: G 88 ASP cc_start: 0.7232 (OUTLIER) cc_final: 0.6958 (t0) REVERT: G 223 THR cc_start: 0.6140 (p) cc_final: 0.5916 (t) REVERT: H 216 TYR cc_start: 0.7631 (m-80) cc_final: 0.7037 (m-80) REVERT: H 302 MET cc_start: -0.0037 (ttm) cc_final: -0.0883 (ttp) REVERT: E 443 LYS cc_start: 0.8588 (mmtt) cc_final: 0.8347 (mmmt) REVERT: E 477 MET cc_start: 0.8193 (mtp) cc_final: 0.7885 (mtp) REVERT: J 51 GLU cc_start: 0.6814 (mt-10) cc_final: 0.6245 (mt-10) REVERT: J 230 ASP cc_start: 0.7333 (OUTLIER) cc_final: 0.6852 (m-30) REVERT: J 231 MET cc_start: 0.7007 (mtp) cc_final: 0.6771 (mtp) REVERT: J 443 LYS cc_start: 0.8734 (mmtt) cc_final: 0.8468 (mmmt) outliers start: 63 outliers final: 53 residues processed: 372 average time/residue: 0.8390 time to fit residues: 498.1723 Evaluate side-chains 372 residues out of total 2774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 316 time to evaluate : 3.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain C residue 151 TYR Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 169 CYS Chi-restraints excluded: chain D residue 232 MET Chi-restraints excluded: chain F residue 58 ASN Chi-restraints excluded: chain F residue 94 TRP Chi-restraints excluded: chain F residue 107 TYR Chi-restraints excluded: chain F residue 224 CYS Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 146 ASP Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 301 LEU Chi-restraints excluded: chain H residue 70 ASP Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 142 TYR Chi-restraints excluded: chain H residue 151 TYR Chi-restraints excluded: chain H residue 203 LEU Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain H residue 258 THR Chi-restraints excluded: chain H residue 279 LEU Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 106 SER Chi-restraints excluded: chain I residue 169 CYS Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain E residue 251 ASP Chi-restraints excluded: chain E residue 444 LEU Chi-restraints excluded: chain E residue 447 PHE Chi-restraints excluded: chain E residue 469 GLU Chi-restraints excluded: chain J residue 104 GLU Chi-restraints excluded: chain J residue 230 ASP Chi-restraints excluded: chain J residue 381 LEU Chi-restraints excluded: chain J residue 447 PHE Chi-restraints excluded: chain J residue 469 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 182 optimal weight: 9.9990 chunk 294 optimal weight: 0.7980 chunk 179 optimal weight: 0.7980 chunk 139 optimal weight: 4.9990 chunk 204 optimal weight: 8.9990 chunk 308 optimal weight: 2.9990 chunk 284 optimal weight: 3.9990 chunk 245 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 189 optimal weight: 30.0000 chunk 150 optimal weight: 2.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.5551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 25672 Z= 0.276 Angle : 0.599 9.990 34764 Z= 0.320 Chirality : 0.041 0.156 3842 Planarity : 0.005 0.066 4526 Dihedral : 5.306 48.819 3424 Min Nonbonded Distance : 1.704 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.39 % Allowed : 7.61 % Favored : 92.00 % Rotamer: Outliers : 2.27 % Allowed : 13.84 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.15), residues: 3114 helix: 0.95 (0.14), residues: 1272 sheet: -0.98 (0.23), residues: 460 loop : -1.83 (0.16), residues: 1382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 113 HIS 0.015 0.001 HIS B 25 PHE 0.024 0.002 PHE J 450 TYR 0.015 0.002 TYR J 174 ARG 0.008 0.000 ARG G 113 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 309 time to evaluate : 3.957 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6772 (tpp) cc_final: 0.6559 (tpp) REVERT: A 131 SER cc_start: 0.8720 (t) cc_final: 0.8097 (p) REVERT: B 85 LYS cc_start: 0.7694 (mttm) cc_final: 0.6568 (tmtt) REVERT: B 88 ASP cc_start: 0.7330 (OUTLIER) cc_final: 0.7060 (t0) REVERT: B 161 LYS cc_start: 0.8732 (pttt) cc_final: 0.8376 (mttt) REVERT: C 302 MET cc_start: 0.0099 (ttm) cc_final: -0.0662 (ttp) REVERT: D 186 LEU cc_start: 0.6426 (tp) cc_final: 0.5949 (mm) REVERT: F 1 MET cc_start: 0.6795 (tpp) cc_final: 0.6559 (tpp) REVERT: F 131 SER cc_start: 0.8777 (t) cc_final: 0.8210 (p) REVERT: F 205 ASP cc_start: 0.7372 (p0) cc_final: 0.7039 (p0) REVERT: G 85 LYS cc_start: 0.7727 (mttm) cc_final: 0.6562 (tmtt) REVERT: G 88 ASP cc_start: 0.7362 (OUTLIER) cc_final: 0.7074 (t0) REVERT: H 302 MET cc_start: 0.0036 (ttm) cc_final: -0.0828 (ttp) REVERT: E 443 LYS cc_start: 0.8568 (mmtt) cc_final: 0.8311 (mmmt) REVERT: E 477 MET cc_start: 0.8215 (mtp) cc_final: 0.7903 (mtp) REVERT: J 51 GLU cc_start: 0.6880 (mt-10) cc_final: 0.6263 (mt-10) REVERT: J 230 ASP cc_start: 0.7355 (OUTLIER) cc_final: 0.6898 (m-30) REVERT: J 443 LYS cc_start: 0.8665 (mmtt) cc_final: 0.8361 (mmmt) outliers start: 63 outliers final: 59 residues processed: 354 average time/residue: 0.8100 time to fit residues: 455.2411 Evaluate side-chains 368 residues out of total 2774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 306 time to evaluate : 3.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain C residue 151 TYR Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 169 CYS Chi-restraints excluded: chain D residue 232 MET Chi-restraints excluded: chain F residue 58 ASN Chi-restraints excluded: chain F residue 94 TRP Chi-restraints excluded: chain F residue 107 TYR Chi-restraints excluded: chain F residue 213 TYR Chi-restraints excluded: chain F residue 224 CYS Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 123 SER Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 146 ASP Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 301 LEU Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 142 TYR Chi-restraints excluded: chain H residue 151 TYR Chi-restraints excluded: chain H residue 203 LEU Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain H residue 258 THR Chi-restraints excluded: chain H residue 279 LEU Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 106 SER Chi-restraints excluded: chain I residue 169 CYS Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain E residue 444 LEU Chi-restraints excluded: chain E residue 447 PHE Chi-restraints excluded: chain E residue 469 GLU Chi-restraints excluded: chain J residue 104 GLU Chi-restraints excluded: chain J residue 230 ASP Chi-restraints excluded: chain J residue 381 LEU Chi-restraints excluded: chain J residue 447 PHE Chi-restraints excluded: chain J residue 469 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 195 optimal weight: 1.9990 chunk 261 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 226 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 246 optimal weight: 0.8980 chunk 103 optimal weight: 9.9990 chunk 252 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 126 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 = 0.4444 r_free = 0.4444 target = 0.176630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.136258 restraints weight = 154082.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.133611 restraints weight = 91933.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.135130 restraints weight = 66356.916| |-----------------------------------------------------------------------------| r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.5669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25672 Z= 0.218 Angle : 0.580 10.009 34764 Z= 0.307 Chirality : 0.040 0.155 3842 Planarity : 0.005 0.067 4526 Dihedral : 5.239 42.844 3424 Min Nonbonded Distance : 1.722 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.42 % Favored : 92.26 % Rotamer: Outliers : 2.38 % Allowed : 13.81 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.15), residues: 3114 helix: 1.04 (0.14), residues: 1266 sheet: -1.00 (0.23), residues: 462 loop : -1.84 (0.16), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 261 HIS 0.016 0.001 HIS G 25 PHE 0.030 0.001 PHE J 450 TYR 0.013 0.001 TYR C 274 ARG 0.008 0.000 ARG G 113 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11095.91 seconds wall clock time: 196 minutes 41.03 seconds (11801.03 seconds total)