Starting phenix.real_space_refine on Fri Feb 23 00:45:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g0e_29655/02_2024/8g0e_29655_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g0e_29655/02_2024/8g0e_29655.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g0e_29655/02_2024/8g0e_29655_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g0e_29655/02_2024/8g0e_29655_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g0e_29655/02_2024/8g0e_29655_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g0e_29655/02_2024/8g0e_29655.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g0e_29655/02_2024/8g0e_29655.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g0e_29655/02_2024/8g0e_29655_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g0e_29655/02_2024/8g0e_29655_updated.pdb" } resolution = 2.6 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= 0.013 sd= 0.126 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: 7 Type Number sf(0) Gaussians Br 7 7.06 5 P 13 5.49 5 Mg 4 5.21 5 S 104 5.16 5 C 22946 2.51 5 N 6273 2.21 5 O 6612 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 28": "NH1" <-> "NH2" Residue "A ARG 93": "NH1" <-> "NH2" Residue "A ARG 109": "NH1" <-> "NH2" Residue "A ARG 129": "NH1" <-> "NH2" Residue "A ARG 130": "NH1" <-> "NH2" Residue "A ARG 142": "NH1" <-> "NH2" Residue "A ARG 164": "NH1" <-> "NH2" Residue "A ARG 167": "NH1" <-> "NH2" Residue "A ARG 174": "NH1" <-> "NH2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A ARG 203": "NH1" <-> "NH2" Residue "A ARG 221": "NH1" <-> "NH2" Residue "A ARG 282": "NH1" <-> "NH2" Residue "A ARG 289": "NH1" <-> "NH2" Residue "A ARG 290": "NH1" <-> "NH2" Residue "A ARG 294": "NH1" <-> "NH2" Residue "A ARG 307": "NH1" <-> "NH2" Residue "A ARG 311": "NH1" <-> "NH2" Residue "A ARG 365": "NH1" <-> "NH2" Residue "A ARG 376": "NH1" <-> "NH2" Residue "A ARG 394": "NH1" <-> "NH2" Residue "A ARG 401": "NH1" <-> "NH2" Residue "A ARG 423": "NH1" <-> "NH2" Residue "A ARG 426": "NH1" <-> "NH2" Residue "A ARG 466": "NH1" <-> "NH2" Residue "A ARG 487": "NH1" <-> "NH2" Residue "B ARG 93": "NH1" <-> "NH2" Residue "B ARG 109": "NH1" <-> "NH2" Residue "B ARG 129": "NH1" <-> "NH2" Residue "B ARG 130": "NH1" <-> "NH2" Residue "B ARG 142": "NH1" <-> "NH2" Residue "B ARG 164": "NH1" <-> "NH2" Residue "B ARG 167": "NH1" <-> "NH2" Residue "B ARG 174": "NH1" <-> "NH2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B ARG 203": "NH1" <-> "NH2" Residue "B ARG 221": "NH1" <-> "NH2" Residue "B ARG 282": "NH1" <-> "NH2" Residue "B ARG 289": "NH1" <-> "NH2" Residue "B ARG 290": "NH1" <-> "NH2" Residue "B ARG 294": "NH1" <-> "NH2" Residue "B ARG 307": "NH1" <-> "NH2" Residue "B ARG 311": "NH1" <-> "NH2" Residue "B GLU 331": "OE1" <-> "OE2" Residue "B ARG 365": "NH1" <-> "NH2" Residue "B ARG 376": "NH1" <-> "NH2" Residue "B ARG 394": "NH1" <-> "NH2" Residue "B ARG 401": "NH1" <-> "NH2" Residue "B ARG 423": "NH1" <-> "NH2" Residue "B ARG 426": "NH1" <-> "NH2" Residue "B ARG 466": "NH1" <-> "NH2" Residue "B ARG 487": "NH1" <-> "NH2" Residue "C ARG 93": "NH1" <-> "NH2" Residue "C ARG 109": "NH1" <-> "NH2" Residue "C ARG 129": "NH1" <-> "NH2" Residue "C ARG 130": "NH1" <-> "NH2" Residue "C ARG 142": "NH1" <-> "NH2" Residue "C ARG 164": "NH1" <-> "NH2" Residue "C ARG 167": "NH1" <-> "NH2" Residue "C ARG 174": "NH1" <-> "NH2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "C ARG 203": "NH1" <-> "NH2" Residue "C ARG 221": "NH1" <-> "NH2" Residue "C ARG 282": "NH1" <-> "NH2" Residue "C ARG 289": "NH1" <-> "NH2" Residue "C ARG 290": "NH1" <-> "NH2" Residue "C ARG 294": "NH1" <-> "NH2" Residue "C ARG 307": "NH1" <-> "NH2" Residue "C ARG 311": "NH1" <-> "NH2" Residue "C ARG 365": "NH1" <-> "NH2" Residue "C ARG 376": "NH1" <-> "NH2" Residue "C ARG 394": "NH1" <-> "NH2" Residue "C ARG 401": "NH1" <-> "NH2" Residue "C ARG 423": "NH1" <-> "NH2" Residue "C ARG 426": "NH1" <-> "NH2" Residue "C PHE 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 466": "NH1" <-> "NH2" Residue "C ARG 487": "NH1" <-> "NH2" Residue "C ARG 541": "NH1" <-> "NH2" Residue "D ARG 11": "NH1" <-> "NH2" Residue "D ARG 14": "NH1" <-> "NH2" Residue "D ARG 26": "NH1" <-> "NH2" Residue "D ARG 63": "NH1" <-> "NH2" Residue "D ARG 75": "NH1" <-> "NH2" Residue "D ARG 122": "NH1" <-> "NH2" Residue "D ARG 133": "NH1" <-> "NH2" Residue "D ARG 152": "NH1" <-> "NH2" Residue "D ARG 176": "NH1" <-> "NH2" Residue "D ARG 179": "NH1" <-> "NH2" Residue "D ARG 193": "NH1" <-> "NH2" Residue "D ARG 195": "NH1" <-> "NH2" Residue "D ARG 227": "NH1" <-> "NH2" Residue "D ARG 229": "NH1" <-> "NH2" Residue "D ARG 242": "NH1" <-> "NH2" Residue "D ARG 258": "NH1" <-> "NH2" Residue "D ARG 272": "NH1" <-> "NH2" Residue "D ARG 293": "NH1" <-> "NH2" Residue "D ARG 298": "NH1" <-> "NH2" Residue "D ARG 300": "NH1" <-> "NH2" Residue "D ARG 335": "NH1" <-> "NH2" Residue "D ARG 367": "NH1" <-> "NH2" Residue "D ARG 374": "NH1" <-> "NH2" Residue "D ARG 378": "NH1" <-> "NH2" Residue "D ARG 404": "NH1" <-> "NH2" Residue "D ARG 406": "NH1" <-> "NH2" Residue "D ARG 407": "NH1" <-> "NH2" Residue "D ARG 410": "NH1" <-> "NH2" Residue "E ARG 11": "NH1" <-> "NH2" Residue "E ARG 14": "NH1" <-> "NH2" Residue "E ARG 26": "NH1" <-> "NH2" Residue "E ARG 63": "NH1" <-> "NH2" Residue "E ARG 75": "NH1" <-> "NH2" Residue "E ARG 122": "NH1" <-> "NH2" Residue "E ARG 133": "NH1" <-> "NH2" Residue "E ARG 152": "NH1" <-> "NH2" Residue "E ARG 176": "NH1" <-> "NH2" Residue "E ARG 179": "NH1" <-> "NH2" Residue "E ARG 193": "NH1" <-> "NH2" Residue "E ARG 195": "NH1" <-> "NH2" Residue "E ARG 227": "NH1" <-> "NH2" Residue "E ARG 229": "NH1" <-> "NH2" Residue "E ARG 242": "NH1" <-> "NH2" Residue "E ARG 258": "NH1" <-> "NH2" Residue "E ARG 272": "NH1" <-> "NH2" Residue "E ARG 293": "NH1" <-> "NH2" Residue "E ARG 298": "NH1" <-> "NH2" Residue "E ARG 300": "NH1" <-> "NH2" Residue "E TYR 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 335": "NH1" <-> "NH2" Residue "E ARG 367": "NH1" <-> "NH2" Residue "E ARG 374": "NH1" <-> "NH2" Residue "E ARG 378": "NH1" <-> "NH2" Residue "E ARG 404": "NH1" <-> "NH2" Residue "E ARG 406": "NH1" <-> "NH2" Residue "E ARG 407": "NH1" <-> "NH2" Residue "E ARG 410": "NH1" <-> "NH2" Residue "F ARG 11": "NH1" <-> "NH2" Residue "F ARG 14": "NH1" <-> "NH2" Residue "F ARG 26": "NH1" <-> "NH2" Residue "F ARG 63": "NH1" <-> "NH2" Residue "F ARG 75": "NH1" <-> "NH2" Residue "F ARG 122": "NH1" <-> "NH2" Residue "F ARG 133": "NH1" <-> "NH2" Residue "F ARG 152": "NH1" <-> "NH2" Residue "F ARG 176": "NH1" <-> "NH2" Residue "F ARG 179": "NH1" <-> "NH2" Residue "F ARG 193": "NH1" <-> "NH2" Residue "F ARG 195": "NH1" <-> "NH2" Residue "F ARG 227": "NH1" <-> "NH2" Residue "F ARG 229": "NH1" <-> "NH2" Residue "F ARG 242": "NH1" <-> "NH2" Residue "F ARG 258": "NH1" <-> "NH2" Residue "F ARG 272": "NH1" <-> "NH2" Residue "F ARG 293": "NH1" <-> "NH2" Residue "F ARG 298": "NH1" <-> "NH2" Residue "F ARG 300": "NH1" <-> "NH2" Residue "F ARG 335": "NH1" <-> "NH2" Residue "F ARG 367": "NH1" <-> "NH2" Residue "F ARG 374": "NH1" <-> "NH2" Residue "F ARG 378": "NH1" <-> "NH2" Residue "F ARG 404": "NH1" <-> "NH2" Residue "F ARG 406": "NH1" <-> "NH2" Residue "F ARG 407": "NH1" <-> "NH2" Residue "F ARG 410": "NH1" <-> "NH2" Residue "G ARG 6": "NH1" <-> "NH2" Residue "G ARG 9": "NH1" <-> "NH2" Residue "G ARG 11": "NH1" <-> "NH2" Residue "G ARG 13": "NH1" <-> "NH2" Residue "G ARG 32": "NH1" <-> "NH2" Residue "G ARG 39": "NH1" <-> "NH2" Residue "G ARG 44": "NH1" <-> "NH2" Residue "G ARG 71": "NH1" <-> "NH2" Residue "G ARG 76": "NH1" <-> "NH2" Residue "G ARG 86": "NH1" <-> "NH2" Residue "G ARG 98": "NH1" <-> "NH2" Residue "G ARG 99": "NH1" <-> "NH2" Residue "G ARG 108": "NH1" <-> "NH2" Residue "G ARG 121": "NH1" <-> "NH2" Residue "G ARG 130": "NH1" <-> "NH2" Residue "G ARG 132": "NH1" <-> "NH2" Residue "G ARG 144": "NH1" <-> "NH2" Residue "G ARG 151": "NH1" <-> "NH2" Residue "G ARG 191": "NH1" <-> "NH2" Residue "G ARG 201": "NH1" <-> "NH2" Residue "G ARG 202": "NH1" <-> "NH2" Residue "G ARG 238": "NH1" <-> "NH2" Residue "G ARG 243": "NH1" <-> "NH2" Residue "G ARG 259": "NH1" <-> "NH2" Residue "G ARG 260": "NH1" <-> "NH2" Residue "G ARG 261": "NH1" <-> "NH2" Residue "G ARG 283": "NH1" <-> "NH2" Residue "G ARG 285": "NH1" <-> "NH2" Residue "H ARG 13": "NH1" <-> "NH2" Residue "H ARG 26": "NH1" <-> "NH2" Residue "H ARG 37": "NH1" <-> "NH2" Residue "H ARG 52": "NH1" <-> "NH2" Residue "H ARG 55": "NH1" <-> "NH2" Residue "H ARG 62": "NH1" <-> "NH2" Residue "H ARG 78": "NH1" <-> "NH2" Residue "H ARG 105": "NH1" <-> "NH2" Residue "H ARG 111": "NH1" <-> "NH2" Residue "H ARG 113": "NH1" <-> "NH2" Residue "H ARG 115": "NH1" <-> "NH2" Residue "b ARG 60": "NH1" <-> "NH2" Residue "b ARG 72": "NH1" <-> "NH2" Residue "b ARG 93": "NH1" <-> "NH2" Residue "b ARG 100": "NH1" <-> "NH2" Residue "b ARG 104": "NH1" <-> "NH2" Residue "b ARG 115": "NH1" <-> "NH2" Residue "b ARG 141": "NH1" <-> "NH2" Residue "b ARG 158": "NH1" <-> "NH2" Residue "d ARG 27": "NH1" <-> "NH2" Residue "d ARG 38": "NH1" <-> "NH2" Residue "d ARG 82": "NH1" <-> "NH2" Residue "d ARG 97": "NH1" <-> "NH2" Residue "d ARG 110": "NH1" <-> "NH2" Residue "d ARG 115": "NH1" <-> "NH2" Residue "d ARG 118": "NH1" <-> "NH2" Residue "d ARG 134": "NH1" <-> "NH2" Residue "d ARG 149": "NH1" <-> "NH2" Residue "d ARG 173": "NH1" <-> "NH2" Residue "d ARG 177": "NH1" <-> "NH2" Residue "d ARG 239": "NH1" <-> "NH2" Residue "d ARG 260": "NH1" <-> "NH2" Residue "d ARG 276": "NH1" <-> "NH2" Residue "d ARG 282": "NH1" <-> "NH2" Residue "d ARG 298": "NH1" <-> "NH2" Residue "d ARG 301": "NH1" <-> "NH2" Residue "d ARG 334": "NH1" <-> "NH2" Residue "d ARG 353": "NH1" <-> "NH2" Residue "d ARG 356": "NH1" <-> "NH2" Residue "d ARG 371": "NH1" <-> "NH2" Residue "d ARG 372": "NH1" <-> "NH2" Residue "d ARG 390": "NH1" <-> "NH2" Residue "d ARG 399": "NH1" <-> "NH2" Residue "d ARG 403": "NH1" <-> "NH2" Residue "d ARG 435": "NH1" <-> "NH2" Residue "9 ARG 45": "NH1" <-> "NH2" Residue "9 ARG 52": "NH1" <-> "NH2" Residue "1 ARG 45": "NH1" <-> "NH2" Residue "1 ARG 52": "NH1" <-> "NH2" Residue "2 ARG 45": "NH1" <-> "NH2" Residue "2 ARG 52": "NH1" <-> "NH2" Residue "3 ARG 45": "NH1" <-> "NH2" Residue "4 ARG 45": "NH1" <-> "NH2" Residue "4 ARG 52": "NH1" <-> "NH2" Residue "5 ARG 45": "NH1" <-> "NH2" Residue "5 ARG 52": "NH1" <-> "NH2" Residue "6 ARG 45": "NH1" <-> "NH2" Residue "6 ARG 52": "NH1" <-> "NH2" Residue "7 ARG 45": "NH1" <-> "NH2" Residue "7 ARG 52": "NH1" <-> "NH2" Residue "8 ARG 45": "NH1" <-> "NH2" Residue "8 ARG 52": "NH1" <-> "NH2" Residue "a ARG 50": "NH1" <-> "NH2" Residue "a ARG 74": "NH1" <-> "NH2" Residue "a PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 152": "NH1" <-> "NH2" Residue "a ARG 153": "NH1" <-> "NH2" Residue "a ARG 188": "NH1" <-> "NH2" Residue "a GLU 246": "OE1" <-> "OE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 35959 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 3837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 3837 Classifications: {'peptide': 514} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 492} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 44 Chain: "B" Number of atoms: 3735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3735 Classifications: {'peptide': 506} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 484} Chain breaks: 1 Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 8, 'ASP:plan': 14} Unresolved non-hydrogen planarities: 80 Chain: "C" Number of atoms: 3781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 3781 Classifications: {'peptide': 514} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 490} Chain breaks: 2 Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 152 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 14, 'ASP:plan': 15} Unresolved non-hydrogen planarities: 107 Chain: "D" Number of atoms: 3508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3508 Classifications: {'peptide': 464} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 439} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASP:plan': 10} Unresolved non-hydrogen planarities: 46 Chain: "E" Number of atoms: 3522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3522 Classifications: {'peptide': 464} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 439} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 31 Chain: "F" Number of atoms: 3512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3512 Classifications: {'peptide': 464} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 439} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 42 Chain: "G" Number of atoms: 2103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2103 Classifications: {'peptide': 279} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 269} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 10, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 55 Chain: "H" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 835 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 3, 'TRANS': 113} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 59 Chain: "b" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 966 Classifications: {'peptide': 141} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 3, 'TRANS': 137} Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 57 Chain: "d" Number of atoms: 2893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 2893 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 108} Link IDs: {'PTRANS': 11, 'TRANS': 420} Chain breaks: 1 Unresolved non-hydrogen bonds: 354 Unresolved non-hydrogen angles: 440 Unresolved non-hydrogen dihedrals: 268 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 32, 'ARG:plan': 7, 'ASN:plan1': 2, 'ASP:plan': 20} Unresolved non-hydrogen planarities: 245 Chain: "9" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 560 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "1" Number of atoms: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 556 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "2" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 560 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "3" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 554 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "4" Number of atoms: 564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 564 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "5" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 560 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "6" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 560 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "7" Number of atoms: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 556 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "8" Number of atoms: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 556 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "a" Number of atoms: 1807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1807 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 10, 'TRANS': 223} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Chain: "9" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'YGR': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'YGR': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'YGR': 1} Classifications: {'undetermined': 1} Chain: "5" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'YGR': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'YGR': 1} Classifications: {'undetermined': 1} Chain: "7" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'YGR': 1} Classifications: {'undetermined': 1} Chain: "8" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'YGR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 19.21, per 1000 atoms: 0.53 Number of scatterers: 35959 At special positions: 0 Unit cell: (122.57, 132.87, 242.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Br 7 34.99 S 104 16.00 P 13 15.00 Mg 4 11.99 O 6612 8.00 N 6273 7.00 C 22946 6.00 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: 16.13 Conformation dependent library (CDL) restraints added in 6.7 seconds 9608 Ramachandran restraints generated. 4804 Oldfield, 0 Emsley, 4804 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8742 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 187 helices and 29 sheets defined 56.7% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.48 Creating SS restraints... Processing helix chain 'A' and resid 9 through 21 removed outlier: 4.956A pdb=" N ALA A 14 " --> pdb=" O ILE A 11 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER A 20 " --> pdb=" O ASP A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 84 No H-bonds generated for 'chain 'A' and resid 82 through 84' Processing helix chain 'A' and resid 104 through 106 No H-bonds generated for 'chain 'A' and resid 104 through 106' Processing helix chain 'A' and resid 139 through 141 No H-bonds generated for 'chain 'A' and resid 139 through 141' Processing helix chain 'A' and resid 154 through 159 Processing helix chain 'A' and resid 178 through 195 removed outlier: 3.684A pdb=" N GLN A 189 " --> pdb=" O THR A 185 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ARG A 190 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N GLU A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ALA A 192 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR A 195 " --> pdb=" O GLU A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 225 Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 243 through 263 Proline residue: A 250 - end of helix removed outlier: 3.699A pdb=" N TRP A 260 " --> pdb=" O ILE A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 287 Processing helix chain 'A' and resid 294 through 296 No H-bonds generated for 'chain 'A' and resid 294 through 296' Processing helix chain 'A' and resid 301 through 311 removed outlier: 4.277A pdb=" N ARG A 311 " --> pdb=" O ARG A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 319 No H-bonds generated for 'chain 'A' and resid 317 through 319' Processing helix chain 'A' and resid 333 through 335 No H-bonds generated for 'chain 'A' and resid 333 through 335' Processing helix chain 'A' and resid 340 through 348 Processing helix chain 'A' and resid 357 through 361 Processing helix chain 'A' and resid 378 through 381 Processing helix chain 'A' and resid 384 through 389 Processing helix chain 'A' and resid 393 through 409 removed outlier: 5.020A pdb=" N ALA A 405 " --> pdb=" O ARG A 401 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N PHE A 406 " --> pdb=" O GLU A 402 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ALA A 407 " --> pdb=" O LEU A 403 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N ALA A 408 " --> pdb=" O GLU A 404 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N PHE A 409 " --> pdb=" O ALA A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 431 Processing helix chain 'A' and resid 441 through 452 Processing helix chain 'A' and resid 461 through 478 removed outlier: 4.546A pdb=" N GLN A 465 " --> pdb=" O VAL A 461 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N ARG A 466 " --> pdb=" O GLU A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 489 Processing helix chain 'A' and resid 494 through 510 removed outlier: 3.511A pdb=" N LYS A 509 " --> pdb=" O ASN A 505 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLY A 510 " --> pdb=" O GLU A 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 21 Processing helix chain 'B' and resid 82 through 84 No H-bonds generated for 'chain 'B' and resid 82 through 84' Processing helix chain 'B' and resid 104 through 106 No H-bonds generated for 'chain 'B' and resid 104 through 106' Processing helix chain 'B' and resid 139 through 141 No H-bonds generated for 'chain 'B' and resid 139 through 141' Processing helix chain 'B' and resid 154 through 159 Processing helix chain 'B' and resid 178 through 195 removed outlier: 3.667A pdb=" N THR B 185 " --> pdb=" O VAL B 181 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN B 189 " --> pdb=" O THR B 185 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ARG B 190 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N GLU B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N ALA B 192 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR B 195 " --> pdb=" O GLU B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 225 Processing helix chain 'B' and resid 229 through 231 No H-bonds generated for 'chain 'B' and resid 229 through 231' Processing helix chain 'B' and resid 243 through 263 Proline residue: B 250 - end of helix removed outlier: 3.709A pdb=" N TRP B 260 " --> pdb=" O ILE B 256 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN B 263 " --> pdb=" O HIS B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 287 Processing helix chain 'B' and resid 294 through 296 No H-bonds generated for 'chain 'B' and resid 294 through 296' Processing helix chain 'B' and resid 299 through 311 removed outlier: 4.071A pdb=" N PHE B 302 " --> pdb=" O GLY B 299 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ARG B 307 " --> pdb=" O LEU B 304 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU B 309 " --> pdb=" O SER B 306 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLU B 310 " --> pdb=" O ARG B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 319 No H-bonds generated for 'chain 'B' and resid 317 through 319' Processing helix chain 'B' and resid 340 through 348 Processing helix chain 'B' and resid 357 through 361 Processing helix chain 'B' and resid 384 through 389 Processing helix chain 'B' and resid 393 through 407 Processing helix chain 'B' and resid 415 through 431 Processing helix chain 'B' and resid 441 through 452 Processing helix chain 'B' and resid 461 through 478 removed outlier: 4.567A pdb=" N GLN B 465 " --> pdb=" O VAL B 461 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ARG B 466 " --> pdb=" O GLU B 462 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU B 473 " --> pdb=" O SER B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 489 Processing helix chain 'B' and resid 494 through 510 removed outlier: 3.784A pdb=" N GLY B 510 " --> pdb=" O GLU B 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 20 Processing helix chain 'C' and resid 82 through 84 No H-bonds generated for 'chain 'C' and resid 82 through 84' Processing helix chain 'C' and resid 104 through 106 No H-bonds generated for 'chain 'C' and resid 104 through 106' Processing helix chain 'C' and resid 139 through 141 No H-bonds generated for 'chain 'C' and resid 139 through 141' Processing helix chain 'C' and resid 154 through 158 Processing helix chain 'C' and resid 178 through 195 removed outlier: 3.798A pdb=" N GLN C 189 " --> pdb=" O THR C 185 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ARG C 190 " --> pdb=" O ILE C 186 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N GLU C 191 " --> pdb=" O LEU C 187 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N ALA C 192 " --> pdb=" O ASN C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 225 Processing helix chain 'C' and resid 243 through 263 Proline residue: C 250 - end of helix removed outlier: 3.631A pdb=" N TRP C 260 " --> pdb=" O ILE C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 287 Processing helix chain 'C' and resid 294 through 296 No H-bonds generated for 'chain 'C' and resid 294 through 296' Processing helix chain 'C' and resid 299 through 311 removed outlier: 3.877A pdb=" N PHE C 302 " --> pdb=" O GLY C 299 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ARG C 307 " --> pdb=" O LEU C 304 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU C 308 " --> pdb=" O HIS C 305 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N GLU C 310 " --> pdb=" O ARG C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 319 No H-bonds generated for 'chain 'C' and resid 317 through 319' Processing helix chain 'C' and resid 340 through 348 Processing helix chain 'C' and resid 357 through 362 Processing helix chain 'C' and resid 378 through 381 Processing helix chain 'C' and resid 384 through 389 Processing helix chain 'C' and resid 393 through 408 Processing helix chain 'C' and resid 415 through 431 Processing helix chain 'C' and resid 441 through 452 removed outlier: 3.660A pdb=" N GLY C 451 " --> pdb=" O ALA C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 478 removed outlier: 4.558A pdb=" N GLN C 465 " --> pdb=" O VAL C 461 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N ARG C 466 " --> pdb=" O GLU C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 489 Processing helix chain 'C' and resid 494 through 510 removed outlier: 3.779A pdb=" N GLY C 510 " --> pdb=" O GLU C 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 28 No H-bonds generated for 'chain 'D' and resid 26 through 28' Processing helix chain 'D' and resid 92 through 94 No H-bonds generated for 'chain 'D' and resid 92 through 94' Processing helix chain 'D' and resid 127 through 129 No H-bonds generated for 'chain 'D' and resid 127 through 129' Processing helix chain 'D' and resid 142 through 146 Processing helix chain 'D' and resid 166 through 179 Processing helix chain 'D' and resid 194 through 207 Processing helix chain 'D' and resid 210 through 212 No H-bonds generated for 'chain 'D' and resid 210 through 212' Processing helix chain 'D' and resid 224 through 243 removed outlier: 4.803A pdb=" N ALA D 231 " --> pdb=" O ARG D 227 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N LEU D 232 " --> pdb=" O MET D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 270 Processing helix chain 'D' and resid 283 through 293 removed outlier: 4.450A pdb=" N ARG D 293 " --> pdb=" O GLU D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 313 No H-bonds generated for 'chain 'D' and resid 311 through 313' Processing helix chain 'D' and resid 318 through 324 Processing helix chain 'D' and resid 335 through 340 Processing helix chain 'D' and resid 363 through 389 removed outlier: 4.406A pdb=" N ASP D 384 " --> pdb=" O LYS D 380 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ILE D 385 " --> pdb=" O ASP D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 393 No H-bonds generated for 'chain 'D' and resid 391 through 393' Processing helix chain 'D' and resid 396 through 411 Processing helix chain 'D' and resid 417 through 423 removed outlier: 3.976A pdb=" N GLN D 421 " --> pdb=" O ALA D 418 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR D 423 " --> pdb=" O GLU D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 443 Processing helix chain 'D' and resid 452 through 455 Processing helix chain 'D' and resid 460 through 469 Processing helix chain 'E' and resid 26 through 28 No H-bonds generated for 'chain 'E' and resid 26 through 28' Processing helix chain 'E' and resid 43 through 45 No H-bonds generated for 'chain 'E' and resid 43 through 45' Processing helix chain 'E' and resid 92 through 94 No H-bonds generated for 'chain 'E' and resid 92 through 94' Processing helix chain 'E' and resid 127 through 129 No H-bonds generated for 'chain 'E' and resid 127 through 129' Processing helix chain 'E' and resid 142 through 147 Processing helix chain 'E' and resid 166 through 176 Processing helix chain 'E' and resid 194 through 207 Processing helix chain 'E' and resid 210 through 212 No H-bonds generated for 'chain 'E' and resid 210 through 212' Processing helix chain 'E' and resid 224 through 243 removed outlier: 5.211A pdb=" N ALA E 231 " --> pdb=" O ARG E 227 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N LEU E 232 " --> pdb=" O MET E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 256 through 270 Processing helix chain 'E' and resid 283 through 294 removed outlier: 4.074A pdb=" N ARG E 293 " --> pdb=" O GLU E 289 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE E 294 " --> pdb=" O LEU E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 313 No H-bonds generated for 'chain 'E' and resid 311 through 313' Processing helix chain 'E' and resid 318 through 326 removed outlier: 4.546A pdb=" N ALA E 325 " --> pdb=" O ALA E 321 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N HIS E 326 " --> pdb=" O THR E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 339 Processing helix chain 'E' and resid 358 through 361 No H-bonds generated for 'chain 'E' and resid 358 through 361' Processing helix chain 'E' and resid 363 through 388 removed outlier: 4.452A pdb=" N ASP E 384 " --> pdb=" O LYS E 380 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N ILE E 385 " --> pdb=" O ASP E 381 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE E 388 " --> pdb=" O ASP E 384 " (cutoff:3.500A) Processing helix chain 'E' and resid 391 through 393 No H-bonds generated for 'chain 'E' and resid 391 through 393' Processing helix chain 'E' and resid 398 through 411 Processing helix chain 'E' and resid 417 through 423 removed outlier: 3.523A pdb=" N GLU E 420 " --> pdb=" O MET E 417 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLN E 421 " --> pdb=" O ALA E 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 432 through 444 Processing helix chain 'E' and resid 452 through 455 Processing helix chain 'E' and resid 462 through 470 Processing helix chain 'F' and resid 26 through 28 No H-bonds generated for 'chain 'F' and resid 26 through 28' Processing helix chain 'F' and resid 43 through 45 No H-bonds generated for 'chain 'F' and resid 43 through 45' Processing helix chain 'F' and resid 112 through 114 No H-bonds generated for 'chain 'F' and resid 112 through 114' Processing helix chain 'F' and resid 127 through 129 No H-bonds generated for 'chain 'F' and resid 127 through 129' Processing helix chain 'F' and resid 142 through 147 Processing helix chain 'F' and resid 166 through 177 Processing helix chain 'F' and resid 194 through 206 Processing helix chain 'F' and resid 210 through 212 No H-bonds generated for 'chain 'F' and resid 210 through 212' Processing helix chain 'F' and resid 224 through 243 removed outlier: 5.262A pdb=" N ALA F 231 " --> pdb=" O ARG F 227 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LEU F 232 " --> pdb=" O MET F 228 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET F 237 " --> pdb=" O SER F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 265 Processing helix chain 'F' and resid 276 through 278 No H-bonds generated for 'chain 'F' and resid 276 through 278' Processing helix chain 'F' and resid 283 through 294 removed outlier: 3.654A pdb=" N LEU F 290 " --> pdb=" O GLU F 286 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE F 294 " --> pdb=" O LEU F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 311 through 313 No H-bonds generated for 'chain 'F' and resid 311 through 313' Processing helix chain 'F' and resid 318 through 326 removed outlier: 4.208A pdb=" N ALA F 325 " --> pdb=" O ALA F 321 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N HIS F 326 " --> pdb=" O THR F 322 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 339 Processing helix chain 'F' and resid 363 through 389 removed outlier: 4.378A pdb=" N ASP F 384 " --> pdb=" O LYS F 380 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ILE F 385 " --> pdb=" O ASP F 381 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE F 388 " --> pdb=" O ASP F 384 " (cutoff:3.500A) Processing helix chain 'F' and resid 391 through 393 No H-bonds generated for 'chain 'F' and resid 391 through 393' Processing helix chain 'F' and resid 396 through 412 Processing helix chain 'F' and resid 417 through 423 removed outlier: 4.830A pdb=" N GLN F 421 " --> pdb=" O ALA F 418 " (cutoff:3.500A) Processing helix chain 'F' and resid 432 through 444 Processing helix chain 'F' and resid 452 through 455 Processing helix chain 'F' and resid 461 through 470 Processing helix chain 'G' and resid 5 through 42 Processing helix chain 'G' and resid 44 through 60 Processing helix chain 'G' and resid 66 through 68 No H-bonds generated for 'chain 'G' and resid 66 through 68' Processing helix chain 'G' and resid 92 through 109 Processing helix chain 'G' and resid 121 through 129 Processing helix chain 'G' and resid 147 through 162 Processing helix chain 'G' and resid 228 through 302 Proline residue: G 237 - end of helix Processing helix chain 'H' and resid 87 through 89 No H-bonds generated for 'chain 'H' and resid 87 through 89' Processing helix chain 'H' and resid 92 through 100 removed outlier: 3.781A pdb=" N ALA H 100 " --> pdb=" O LYS H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 117 Processing helix chain 'b' and resid 29 through 47 removed outlier: 4.292A pdb=" N ILE b 36 " --> pdb=" O ALA b 33 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ILE b 45 " --> pdb=" O LEU b 42 " (cutoff:3.500A) Processing helix chain 'b' and resid 50 through 160 removed outlier: 3.745A pdb=" N ALA b 79 " --> pdb=" O ALA b 75 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY b 143 " --> pdb=" O GLN b 139 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ASP b 149 " --> pdb=" O GLU b 145 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N GLY b 150 " --> pdb=" O SER b 146 " (cutoff:3.500A) Processing helix chain 'd' and resid 2 through 21 Processing helix chain 'd' and resid 23 through 137 Processing helix chain 'd' and resid 140 through 156 removed outlier: 3.791A pdb=" N GLN d 156 " --> pdb=" O SER d 152 " (cutoff:3.500A) Processing helix chain 'd' and resid 174 through 193 removed outlier: 3.898A pdb=" N GLY d 192 " --> pdb=" O ASP d 188 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N GLY d 193 " --> pdb=" O SER d 189 " (cutoff:3.500A) Processing helix chain 'd' and resid 196 through 215 Processing helix chain 'd' and resid 217 through 223 Processing helix chain 'd' and resid 231 through 244 removed outlier: 6.625A pdb=" N ASP d 243 " --> pdb=" O ARG d 239 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LYS d 244 " --> pdb=" O LEU d 240 " (cutoff:3.500A) Processing helix chain 'd' and resid 247 through 258 removed outlier: 4.150A pdb=" N VAL d 257 " --> pdb=" O LEU d 253 " (cutoff:3.500A) Processing helix chain 'd' and resid 264 through 286 removed outlier: 3.812A pdb=" N ILE d 268 " --> pdb=" O GLU d 264 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU d 279 " --> pdb=" O ALA d 275 " (cutoff:3.500A) Processing helix chain 'd' and resid 289 through 304 Processing helix chain 'd' and resid 307 through 314 Processing helix chain 'd' and resid 320 through 330 Processing helix chain 'd' and resid 339 through 351 Processing helix chain 'd' and resid 357 through 372 removed outlier: 3.704A pdb=" N ARG d 372 " --> pdb=" O ALA d 368 " (cutoff:3.500A) Processing helix chain 'd' and resid 387 through 401 Processing helix chain 'd' and resid 413 through 415 No H-bonds generated for 'chain 'd' and resid 413 through 415' Processing helix chain 'd' and resid 432 through 441 Processing helix chain '9' and resid 6 through 45 Processing helix chain '9' and resid 47 through 79 removed outlier: 3.779A pdb=" N GLN 9 50 " --> pdb=" O PRO 9 47 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N GLY 9 51 " --> pdb=" O GLU 9 48 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE 9 54 " --> pdb=" O GLY 9 51 " (cutoff:3.500A) Proline residue: 9 56 - end of helix removed outlier: 3.601A pdb=" N ILE 9 59 " --> pdb=" O PRO 9 56 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL 9 61 " --> pdb=" O PHE 9 58 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL 9 64 " --> pdb=" O VAL 9 61 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLU 9 65 " --> pdb=" O GLY 9 62 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA 9 66 " --> pdb=" O LEU 9 63 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR 9 68 " --> pdb=" O GLU 9 65 " (cutoff:3.500A) Processing helix chain '1' and resid 6 through 45 Processing helix chain '1' and resid 47 through 79 removed outlier: 4.334A pdb=" N GLY 1 51 " --> pdb=" O GLU 1 48 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE 1 54 " --> pdb=" O GLY 1 51 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR 1 55 " --> pdb=" O ARG 1 52 " (cutoff:3.500A) Proline residue: 1 56 - end of helix removed outlier: 4.259A pdb=" N VAL 1 61 " --> pdb=" O PHE 1 58 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLU 1 65 " --> pdb=" O GLY 1 62 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N PHE 1 69 " --> pdb=" O ALA 1 66 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ILE 1 70 " --> pdb=" O ALA 1 67 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA 1 76 " --> pdb=" O ALA 1 73 " (cutoff:3.500A) Processing helix chain '2' and resid 6 through 45 Processing helix chain '2' and resid 47 through 79 removed outlier: 3.796A pdb=" N GLN 2 50 " --> pdb=" O PRO 2 47 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N GLY 2 51 " --> pdb=" O GLU 2 48 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE 2 54 " --> pdb=" O GLY 2 51 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N THR 2 55 " --> pdb=" O ARG 2 52 " (cutoff:3.500A) Proline residue: 2 56 - end of helix removed outlier: 3.881A pdb=" N ILE 2 59 " --> pdb=" O PRO 2 56 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL 2 61 " --> pdb=" O PHE 2 58 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU 2 65 " --> pdb=" O GLY 2 62 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ILE 2 70 " --> pdb=" O ALA 2 67 " (cutoff:3.500A) Processing helix chain '3' and resid 6 through 45 Processing helix chain '3' and resid 47 through 80 removed outlier: 4.565A pdb=" N GLY 3 51 " --> pdb=" O GLU 3 48 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N THR 3 55 " --> pdb=" O ARG 3 52 " (cutoff:3.500A) Proline residue: 3 56 - end of helix removed outlier: 3.713A pdb=" N ILE 3 59 " --> pdb=" O PRO 3 56 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL 3 61 " --> pdb=" O PHE 3 58 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL 3 64 " --> pdb=" O VAL 3 61 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU 3 65 " --> pdb=" O GLY 3 62 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA 3 66 " --> pdb=" O LEU 3 63 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR 3 68 " --> pdb=" O GLU 3 65 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N MET 3 75 " --> pdb=" O LEU 3 72 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL 3 79 " --> pdb=" O ALA 3 76 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N PHE 3 80 " --> pdb=" O LEU 3 77 " (cutoff:3.500A) Processing helix chain '4' and resid 6 through 45 Processing helix chain '4' and resid 47 through 80 removed outlier: 3.769A pdb=" N GLY 4 51 " --> pdb=" O GLU 4 48 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE 4 54 " --> pdb=" O GLY 4 51 " (cutoff:3.500A) Proline residue: 4 56 - end of helix removed outlier: 3.500A pdb=" N ILE 4 59 " --> pdb=" O PRO 4 56 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL 4 61 " --> pdb=" O PHE 4 58 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLU 4 65 " --> pdb=" O GLY 4 62 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA 4 66 " --> pdb=" O LEU 4 63 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA 4 67 " --> pdb=" O VAL 4 64 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR 4 68 " --> pdb=" O GLU 4 65 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N MET 4 75 " --> pdb=" O LEU 4 72 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL 4 79 " --> pdb=" O ALA 4 76 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N PHE 4 80 " --> pdb=" O LEU 4 77 " (cutoff:3.500A) Processing helix chain '5' and resid 7 through 45 Processing helix chain '5' and resid 47 through 80 removed outlier: 3.876A pdb=" N GLN 5 50 " --> pdb=" O PRO 5 47 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N GLY 5 51 " --> pdb=" O GLU 5 48 " (cutoff:3.500A) Proline residue: 5 56 - end of helix removed outlier: 4.010A pdb=" N VAL 5 61 " --> pdb=" O PHE 5 58 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL 5 64 " --> pdb=" O VAL 5 61 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU 5 65 " --> pdb=" O GLY 5 62 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA 5 66 " --> pdb=" O LEU 5 63 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA 5 67 " --> pdb=" O VAL 5 64 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR 5 68 " --> pdb=" O GLU 5 65 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE 5 70 " --> pdb=" O ALA 5 67 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N MET 5 75 " --> pdb=" O LEU 5 72 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ALA 5 76 " --> pdb=" O ALA 5 73 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL 5 79 " --> pdb=" O ALA 5 76 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N PHE 5 80 " --> pdb=" O LEU 5 77 " (cutoff:3.500A) Processing helix chain '6' and resid 6 through 45 Processing helix chain '6' and resid 47 through 79 removed outlier: 5.130A pdb=" N GLY 6 51 " --> pdb=" O GLU 6 48 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N THR 6 55 " --> pdb=" O ARG 6 52 " (cutoff:3.500A) Proline residue: 6 56 - end of helix removed outlier: 4.001A pdb=" N ILE 6 59 " --> pdb=" O PRO 6 56 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL 6 61 " --> pdb=" O PHE 6 58 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLU 6 65 " --> pdb=" O GLY 6 62 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TYR 6 68 " --> pdb=" O GLU 6 65 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE 6 70 " --> pdb=" O ALA 6 67 " (cutoff:3.500A) Processing helix chain '7' and resid 6 through 45 Processing helix chain '7' and resid 47 through 79 removed outlier: 3.809A pdb=" N GLN 7 50 " --> pdb=" O PRO 7 47 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLY 7 51 " --> pdb=" O GLU 7 48 " (cutoff:3.500A) Proline residue: 7 56 - end of helix removed outlier: 3.668A pdb=" N VAL 7 61 " --> pdb=" O PHE 7 58 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL 7 64 " --> pdb=" O VAL 7 61 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLU 7 65 " --> pdb=" O GLY 7 62 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA 7 66 " --> pdb=" O LEU 7 63 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N MET 7 75 " --> pdb=" O LEU 7 72 " (cutoff:3.500A) Processing helix chain '8' and resid 6 through 45 Processing helix chain '8' and resid 47 through 80 removed outlier: 4.187A pdb=" N GLY 8 51 " --> pdb=" O GLU 8 48 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU 8 53 " --> pdb=" O GLN 8 50 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE 8 54 " --> pdb=" O GLY 8 51 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR 8 55 " --> pdb=" O ARG 8 52 " (cutoff:3.500A) Proline residue: 8 56 - end of helix removed outlier: 3.511A pdb=" N VAL 8 61 " --> pdb=" O PHE 8 58 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU 8 65 " --> pdb=" O GLY 8 62 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA 8 66 " --> pdb=" O LEU 8 63 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N PHE 8 80 " --> pdb=" O LEU 8 77 " (cutoff:3.500A) Processing helix chain 'a' and resid 29 through 51 Processing helix chain 'a' and resid 61 through 80 Processing helix chain 'a' and resid 88 through 108 removed outlier: 3.687A pdb=" N LEU a 92 " --> pdb=" O PHE a 88 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA a 107 " --> pdb=" O SER a 103 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N VAL a 108 " --> pdb=" O ASN a 104 " (cutoff:3.500A) Processing helix chain 'a' and resid 127 through 129 No H-bonds generated for 'chain 'a' and resid 127 through 129' Processing helix chain 'a' and resid 131 through 153 Processing helix chain 'a' and resid 155 through 164 Proline residue: a 159 - end of helix Processing helix chain 'a' and resid 168 through 205 Proline residue: a 172 - end of helix removed outlier: 4.152A pdb=" N GLU a 178 " --> pdb=" O ILE a 175 " (cutoff:3.500A) Proline residue: a 182 - end of helix removed outlier: 4.456A pdb=" N ARG a 188 " --> pdb=" O LEU a 185 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLY a 191 " --> pdb=" O ARG a 188 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN a 192 " --> pdb=" O LEU a 189 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE a 194 " --> pdb=" O GLY a 191 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA a 195 " --> pdb=" O ASN a 192 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N VAL a 200 " --> pdb=" O GLY a 197 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE a 203 " --> pdb=" O VAL a 200 " (cutoff:3.500A) Processing helix chain 'a' and resid 208 through 245 removed outlier: 3.871A pdb=" N TRP a 212 " --> pdb=" O TRP a 208 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N PHE a 213 " --> pdb=" O TYR a 209 " (cutoff:3.500A) Proline residue: a 214 - end of helix removed outlier: 3.972A pdb=" N PHE a 224 " --> pdb=" O THR a 220 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 90 through 92 removed outlier: 6.614A pdb=" N HIS A 43 " --> pdb=" O ILE A 35 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ALA A 37 " --> pdb=" O ILE A 41 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ILE A 41 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL A 77 " --> pdb=" O ALA A 66 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N ALA A 66 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU A 54 " --> pdb=" O ALA A 66 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N GLU A 96 " --> pdb=" O LEU A 55 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N GLU A 57 " --> pdb=" O THR A 94 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N THR A 94 " --> pdb=" O GLU A 57 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 99 through 102 Processing sheet with id= C, first strand: chain 'A' and resid 351 through 355 Processing sheet with id= D, first strand: chain 'A' and resid 232 through 237 removed outlier: 8.644A pdb=" N THR A 233 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N CYS A 204 " --> pdb=" O THR A 233 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N VAL A 235 " --> pdb=" O CYS A 204 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N TYR A 206 " --> pdb=" O VAL A 235 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N ALA A 237 " --> pdb=" O TYR A 206 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ALA A 208 " --> pdb=" O ALA A 237 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N HIS A 266 " --> pdb=" O ARG A 203 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N VAL A 205 " --> pdb=" O HIS A 266 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LEU A 268 " --> pdb=" O VAL A 205 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N VAL A 207 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N VAL A 270 " --> pdb=" O VAL A 207 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ILE A 209 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ASP A 272 " --> pdb=" O ILE A 209 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N SER A 323 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N ILE A 269 " --> pdb=" O SER A 323 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N THR A 325 " --> pdb=" O ILE A 269 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N PHE A 271 " --> pdb=" O THR A 325 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEU A 327 " --> pdb=" O PHE A 271 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 90 through 92 removed outlier: 6.671A pdb=" N HIS B 43 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ALA B 37 " --> pdb=" O ILE B 41 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ILE B 41 " --> pdb=" O ALA B 37 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL B 77 " --> pdb=" O ALA B 66 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N ALA B 66 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N LEU B 79 " --> pdb=" O GLY B 64 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N GLY B 64 " --> pdb=" O LEU B 79 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 99 through 102 Processing sheet with id= G, first strand: chain 'B' and resid 352 through 355 removed outlier: 6.549A pdb=" N LEU B 169 " --> pdb=" O CYS B 353 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N LEU B 355 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ILE B 171 " --> pdb=" O LEU B 355 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 232 through 237 removed outlier: 8.626A pdb=" N THR B 233 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N CYS B 204 " --> pdb=" O THR B 233 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N VAL B 235 " --> pdb=" O CYS B 204 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N TYR B 206 " --> pdb=" O VAL B 235 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ALA B 237 " --> pdb=" O TYR B 206 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ALA B 208 " --> pdb=" O ALA B 237 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N HIS B 266 " --> pdb=" O ARG B 203 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N VAL B 205 " --> pdb=" O HIS B 266 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU B 268 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N VAL B 207 " --> pdb=" O LEU B 268 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N VAL B 270 " --> pdb=" O VAL B 207 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ILE B 209 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ASP B 272 " --> pdb=" O ILE B 209 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N SER B 323 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N ILE B 269 " --> pdb=" O SER B 323 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N THR B 325 " --> pdb=" O ILE B 269 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N PHE B 271 " --> pdb=" O THR B 325 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'C' and resid 90 through 92 removed outlier: 6.671A pdb=" N HIS C 43 " --> pdb=" O ILE C 35 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ALA C 37 " --> pdb=" O ILE C 41 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ILE C 41 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL C 77 " --> pdb=" O ALA C 66 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ALA C 66 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N LEU C 79 " --> pdb=" O GLY C 64 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N GLY C 64 " --> pdb=" O LEU C 79 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 99 through 102 Processing sheet with id= K, first strand: chain 'C' and resid 351 through 355 Processing sheet with id= L, first strand: chain 'C' and resid 232 through 237 removed outlier: 8.527A pdb=" N THR C 233 " --> pdb=" O VAL C 202 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N CYS C 204 " --> pdb=" O THR C 233 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N VAL C 235 " --> pdb=" O CYS C 204 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N TYR C 206 " --> pdb=" O VAL C 235 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ALA C 237 " --> pdb=" O TYR C 206 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ALA C 208 " --> pdb=" O ALA C 237 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N HIS C 266 " --> pdb=" O ARG C 203 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N VAL C 205 " --> pdb=" O HIS C 266 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU C 268 " --> pdb=" O VAL C 205 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N VAL C 207 " --> pdb=" O LEU C 268 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N VAL C 270 " --> pdb=" O VAL C 207 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N ILE C 209 " --> pdb=" O VAL C 270 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ASP C 272 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N SER C 323 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N ILE C 269 " --> pdb=" O SER C 323 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N THR C 325 " --> pdb=" O ILE C 269 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N PHE C 271 " --> pdb=" O THR C 325 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'D' and resid 11 through 16 removed outlier: 6.513A pdb=" N ASP D 21 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ILE D 15 " --> pdb=" O VAL D 19 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N VAL D 19 " --> pdb=" O ILE D 15 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ILE D 65 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N VAL D 53 " --> pdb=" O ILE D 65 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 87 through 89 Processing sheet with id= O, first strand: chain 'D' and resid 135 through 137 removed outlier: 4.756A pdb=" N GLU D 135 " --> pdb=" O ARG D 152 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N TYR D 150 " --> pdb=" O LEU D 137 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 304 through 306 removed outlier: 6.659A pdb=" N ALA D 329 " --> pdb=" O ALA D 157 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N PHE D 159 " --> pdb=" O ALA D 329 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N THR D 331 " --> pdb=" O PHE D 159 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 249 through 254 removed outlier: 7.005A pdb=" N THR D 184 " --> pdb=" O LEU D 250 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N PHE D 252 " --> pdb=" O THR D 184 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N VAL D 186 " --> pdb=" O PHE D 252 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ASP D 254 " --> pdb=" O VAL D 186 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ALA D 188 " --> pdb=" O ASP D 254 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 11 through 16 removed outlier: 6.584A pdb=" N ASP E 21 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ILE E 15 " --> pdb=" O VAL E 19 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N VAL E 19 " --> pdb=" O ILE E 15 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ILE E 65 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N VAL E 53 " --> pdb=" O ILE E 65 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 87 through 90 removed outlier: 3.967A pdb=" N GLU E 116 " --> pdb=" O VAL E 90 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 329 through 332 removed outlier: 7.416A pdb=" N ILE E 156 " --> pdb=" O ILE E 302 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N SER E 304 " --> pdb=" O ILE E 156 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N LEU E 158 " --> pdb=" O SER E 304 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLN E 306 " --> pdb=" O LEU E 158 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N GLY E 160 " --> pdb=" O GLN E 306 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N VAL E 308 " --> pdb=" O GLY E 160 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N VAL E 249 " --> pdb=" O THR E 303 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N MET E 305 " --> pdb=" O VAL E 249 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N LEU E 251 " --> pdb=" O MET E 305 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N ALA E 307 " --> pdb=" O LEU E 251 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE E 253 " --> pdb=" O ALA E 307 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N TYR E 309 " --> pdb=" O ILE E 253 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N THR E 184 " --> pdb=" O LEU E 250 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N PHE E 252 " --> pdb=" O THR E 184 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N VAL E 186 " --> pdb=" O PHE E 252 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N ASP E 254 " --> pdb=" O VAL E 186 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ALA E 188 " --> pdb=" O ASP E 254 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'F' and resid 11 through 16 removed outlier: 6.634A pdb=" N ASP F 21 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ILE F 15 " --> pdb=" O VAL F 19 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N VAL F 19 " --> pdb=" O ILE F 15 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ILE F 65 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N VAL F 53 " --> pdb=" O ILE F 65 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 87 through 90 removed outlier: 4.043A pdb=" N GLU F 116 " --> pdb=" O VAL F 90 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'F' and resid 98 through 100 removed outlier: 8.427A pdb=" N PHE F 99 " --> pdb=" O THR F 213 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LEU F 215 " --> pdb=" O PHE F 99 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N SER F 185 " --> pdb=" O ALA F 214 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N VAL F 216 " --> pdb=" O SER F 185 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N PHE F 187 " --> pdb=" O VAL F 216 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ALA F 329 " --> pdb=" O ALA F 157 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N PHE F 159 " --> pdb=" O ALA F 329 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N THR F 331 " --> pdb=" O PHE F 159 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'G' and resid 197 through 204 removed outlier: 6.756A pdb=" N LEU G 183 " --> pdb=" O ALA G 203 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N HIS G 184 " --> pdb=" O ARG G 76 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLY G 78 " --> pdb=" O HIS G 184 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N VAL G 186 " --> pdb=" O GLY G 78 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N LEU G 80 " --> pdb=" O VAL G 186 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N THR G 188 " --> pdb=" O LEU G 80 " (cutoff:3.500A) removed outlier: 9.118A pdb=" N VAL G 82 " --> pdb=" O THR G 188 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ASP G 113 " --> pdb=" O ALA G 77 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N VAL G 79 " --> pdb=" O ASP G 113 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N VAL G 115 " --> pdb=" O VAL G 79 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N VAL G 81 " --> pdb=" O VAL G 115 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N TYR G 117 " --> pdb=" O VAL G 81 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N VAL G 118 " --> pdb=" O VAL G 135 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N SER G 137 " --> pdb=" O VAL G 118 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'H' and resid 6 through 10 removed outlier: 6.018A pdb=" N VAL H 77 " --> pdb=" O GLU H 7 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N VAL H 9 " --> pdb=" O VAL H 77 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ILE H 79 " --> pdb=" O VAL H 9 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'H' and resid 30 through 34 removed outlier: 4.180A pdb=" N ARG H 26 " --> pdb=" O MET H 50 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N MET H 50 " --> pdb=" O ARG H 26 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ASN H 83 " --> pdb=" O ASP H 66 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'd' and resid 405 through 411 removed outlier: 6.558A pdb=" N VAL d 375 " --> pdb=" O SER d 406 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N GLN d 408 " --> pdb=" O VAL d 375 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ALA d 377 " --> pdb=" O GLN d 408 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N HIS d 410 " --> pdb=" O ALA d 377 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL d 379 " --> pdb=" O HIS d 410 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'a' and resid 20 through 22 Processing sheet with id= AC, first strand: chain 'a' and resid 112 through 114 2036 hydrogen bonds defined for protein. 5328 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.88 Time building geometry restraints manager: 16.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.31: 6084 1.31 - 1.47: 14259 1.47 - 1.63: 16038 1.63 - 1.78: 21 1.78 - 1.94: 180 Bond restraints: 36582 Sorted by residual: bond pdb=" CA ARG B 365 " pdb=" C ARG B 365 " ideal model delta sigma weight residual 1.522 1.444 0.079 8.40e-03 1.42e+04 8.76e+01 bond pdb=" CA GLU B 71 " pdb=" C GLU B 71 " ideal model delta sigma weight residual 1.524 1.408 0.115 1.26e-02 6.30e+03 8.38e+01 bond pdb=" CA ASP B 173 " pdb=" C ASP B 173 " ideal model delta sigma weight residual 1.528 1.413 0.114 1.33e-02 5.65e+03 7.41e+01 bond pdb=" CA ASN B 369 " pdb=" C ASN B 369 " ideal model delta sigma weight residual 1.525 1.420 0.104 1.25e-02 6.40e+03 6.95e+01 bond pdb=" C5 ATP B 600 " pdb=" N7 ATP B 600 " ideal model delta sigma weight residual 1.387 1.305 0.082 1.00e-02 1.00e+04 6.78e+01 ... (remaining 36577 not shown) Histogram of bond angle deviations from ideal: 98.76 - 106.97: 1170 106.97 - 115.18: 22001 115.18 - 123.38: 25525 123.38 - 131.59: 971 131.59 - 139.80: 47 Bond angle restraints: 49714 Sorted by residual: angle pdb=" PB ATP B 600 " pdb=" O3B ATP B 600 " pdb=" PG ATP B 600 " ideal model delta sigma weight residual 139.87 121.82 18.05 1.00e+00 1.00e+00 3.26e+02 angle pdb=" PA ATP B 600 " pdb=" O3A ATP B 600 " pdb=" PB ATP B 600 " ideal model delta sigma weight residual 136.83 122.89 13.94 1.00e+00 1.00e+00 1.94e+02 angle pdb=" N ALA D 359 " pdb=" CA ALA D 359 " pdb=" C ALA D 359 " ideal model delta sigma weight residual 111.28 123.86 -12.58 1.09e+00 8.42e-01 1.33e+02 angle pdb=" N LYS B 178 " pdb=" CA LYS B 178 " pdb=" C LYS B 178 " ideal model delta sigma weight residual 111.28 122.09 -10.81 1.09e+00 8.42e-01 9.83e+01 angle pdb=" N GLU B 71 " pdb=" CA GLU B 71 " pdb=" C GLU B 71 " ideal model delta sigma weight residual 111.14 101.62 9.52 1.08e+00 8.57e-01 7.77e+01 ... (remaining 49709 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.85: 20759 25.85 - 51.71: 799 51.71 - 77.56: 139 77.56 - 103.41: 23 103.41 - 129.27: 2 Dihedral angle restraints: 21722 sinusoidal: 8074 harmonic: 13648 Sorted by residual: dihedral pdb=" CA PRO C 366 " pdb=" C PRO C 366 " pdb=" N ALA C 367 " pdb=" CA ALA C 367 " ideal model delta harmonic sigma weight residual 180.00 152.33 27.67 0 5.00e+00 4.00e-02 3.06e+01 dihedral pdb=" CA GLU D 192 " pdb=" C GLU D 192 " pdb=" N ARG D 193 " pdb=" CA ARG D 193 " ideal model delta harmonic sigma weight residual 180.00 154.31 25.69 0 5.00e+00 4.00e-02 2.64e+01 dihedral pdb=" CA ARG A 365 " pdb=" C ARG A 365 " pdb=" N PRO A 366 " pdb=" CA PRO A 366 " ideal model delta harmonic sigma weight residual 0.00 25.61 -25.61 0 5.00e+00 4.00e-02 2.62e+01 ... (remaining 21719 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.151: 5765 0.151 - 0.302: 64 0.302 - 0.453: 12 0.453 - 0.604: 2 0.604 - 0.755: 1 Chirality restraints: 5844 Sorted by residual: chirality pdb=" CB VAL B 370 " pdb=" CA VAL B 370 " pdb=" CG1 VAL B 370 " pdb=" CG2 VAL B 370 " both_signs ideal model delta sigma weight residual False -2.63 -1.87 -0.75 2.00e-01 2.50e+01 1.42e+01 chirality pdb=" CA LYS B 175 " pdb=" N LYS B 175 " pdb=" C LYS B 175 " pdb=" CB LYS B 175 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.42e+00 chirality pdb=" CA THR B 176 " pdb=" N THR B 176 " pdb=" C THR B 176 " pdb=" CB THR B 176 " both_signs ideal model delta sigma weight residual False 2.53 2.05 0.47 2.00e-01 2.50e+01 5.57e+00 ... (remaining 5841 not shown) Planarity restraints: 6397 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG 5 45 " 0.026 2.00e-02 2.50e+03 4.95e-02 2.45e+01 pdb=" C ARG 5 45 " -0.086 2.00e-02 2.50e+03 pdb=" O ARG 5 45 " 0.031 2.00e-02 2.50e+03 pdb=" N GLN 5 46 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN 7 50 " 0.024 2.00e-02 2.50e+03 4.71e-02 2.22e+01 pdb=" C GLN 7 50 " -0.082 2.00e-02 2.50e+03 pdb=" O GLN 7 50 " 0.030 2.00e-02 2.50e+03 pdb=" N GLY 7 51 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 343 " -0.053 2.00e-02 2.50e+03 3.30e-02 1.90e+01 pdb=" CG PHE D 343 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE D 343 " 0.037 2.00e-02 2.50e+03 pdb=" CD2 PHE D 343 " 0.031 2.00e-02 2.50e+03 pdb=" CE1 PHE D 343 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE D 343 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE D 343 " -0.035 2.00e-02 2.50e+03 ... (remaining 6394 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.41: 59 2.41 - 3.03: 24240 3.03 - 3.65: 56300 3.65 - 4.28: 88132 4.28 - 4.90: 148280 Nonbonded interactions: 317011 Sorted by model distance: nonbonded pdb=" O2G ATP E 600 " pdb="MG MG E 601 " model vdw 1.784 2.170 nonbonded pdb=" O2B ATP B 600 " pdb="MG MG B 601 " model vdw 1.845 2.170 nonbonded pdb=" OG1 THR E 167 " pdb="MG MG E 601 " model vdw 1.849 2.170 nonbonded pdb=" O2G ATP A 600 " pdb="MG MG A 601 " model vdw 1.868 2.170 nonbonded pdb=" OG1 THR A 179 " pdb="MG MG A 601 " model vdw 1.897 2.170 ... (remaining 317006 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 '1' and (resid 5 through 51 or (resid 52 and (name N or name CA or name C \ or name O or name CB )) or resid 53 through 85)) selection = (chain '2' and (resid 5 through 45 or (resid 46 and (name N or name CA or name C \ or name O or name CB )) or resid 47 through 51 or (resid 52 and (name N or name \ CA or name C or name O or name CB )) or resid 53 through 85)) selection = (chain '3' and (resid 5 through 45 or (resid 46 and (name N or name CA or name C \ or name O or name CB )) or resid 47 through 85)) selection = (chain '4' and (resid 5 through 45 or (resid 46 and (name N or name CA or name C \ or name O or name CB )) or resid 47 or (resid 48 through 49 and (name N or name \ CA or name C or name O or name CB )) or resid 50 through 51 or (resid 52 and (n \ ame N or name CA or name C or name O or name CB )) or resid 53 through 85)) selection = (chain '5' and (resid 5 through 45 or (resid 46 and (name N or name CA or name C \ or name O or name CB )) or resid 47 through 51 or (resid 52 and (name N or name \ CA or name C or name O or name CB )) or resid 53 through 85)) selection = (chain '6' and (resid 5 through 45 or (resid 46 and (name N or name CA or name C \ or name O or name CB )) or resid 47 through 51 or (resid 52 and (name N or name \ CA or name C or name O or name CB )) or resid 53 through 85)) selection = (chain '7' and (resid 5 through 51 or (resid 52 and (name N or name CA or name C \ or name O or name CB )) or resid 53 through 85)) selection = (chain '8' and (resid 5 through 51 or (resid 52 and (name N or name CA or name C \ or name O or name CB )) or resid 53 through 85)) selection = (chain '9' and (resid 5 through 45 or (resid 46 and (name N or name CA or name C \ or name O or name CB )) or resid 47 through 51 or (resid 52 and (name N or name \ CA or name C or name O or name CB )) or resid 53 through 85)) } ncs_group { reference = (chain 'A' and ((resid 9 through 12 and (name N or name CA or name C or name O o \ r name CB )) or (resid 13 through 17 and (name N or name CA or name C or name O \ or name CB )) or resid 18 or (resid 19 through 22 and (name N or name CA or name \ C or name O or name CB )) or (resid 29 and (name N or name CA or name C or name \ O or name CB )) or resid 30 through 38 or (resid 39 and (name N or name CA or n \ ame C or name O or name CB )) or resid 40 through 69 or (resid 70 and (name N or \ name CA or name C or name O or name CB )) or resid 71 through 172 or (resid 173 \ and (name N or name CA or name C or name O or name CB )) or resid 174 through 2 \ 40 or (resid 241 through 243 and (name N or name CA or name C or name O or name \ CB )) or resid 244 through 272 or (resid 273 and (name N or name CA or name C or \ name O or name CB )) or resid 274 through 278 or (resid 279 through 280 and (na \ me N or name CA or name C or name O or name CB )) or resid 281 through 294 or (r \ esid 295 through 296 and (name N or name CA or name C or name O or name CB )) or \ resid 297 through 299 or (resid 300 and (name N or name CA or name C or name O \ or name CB )) or resid 301 through 316 or (resid 317 through 318 and (name N or \ name CA or name C or name O or name CB )) or resid 319 through 335 or (resid 336 \ and (name N or name CA or name C or name O or name CB )) or resid 337 through 3 \ 55 or (resid 356 and (name N or name CA or name C or name O or name CB )) or res \ id 357 or (resid 358 and (name N or name CA or name C or name O or name CB )) or \ resid 359 through 387 or (resid 388 and (name N or name CA or name C or name O \ or name CB )) or resid 389 through 401 or (resid 402 and (name N or name CA or n \ ame C or name O or name CB )) or resid 403 through 411 or (resid 412 through 416 \ and (name N or name CA or name C or name O or name CB )) or resid 417 through 4 \ 61 or (resid 462 through 463 and (name N or name CA or name C or name O or name \ CB )) or resid 464 through 472 or (resid 473 and (name N or name CA or name C or \ name O or name CB )) or resid 474 through 480 or (resid 481 and (name N or name \ CA or name C or name O or name CB )) or resid 482 through 483 or (resid 484 and \ (name N or name CA or name C or name O or name CB )) or resid 485 through 493 o \ r (resid 494 through 496 and (name N or name CA or name C or name O or name CB ) \ ) or resid 497 or (resid 498 and (name N or name CA or name C or name O or name \ CB )) or resid 499 through 515 or (resid 518 and (name N or name CA or name C or \ name O or name CB )) or resid 519 through 520 or resid 600 through 601)) selection = (chain 'B' and ((resid 9 through 17 and (name N or name CA or name C or name O o \ r name CB )) or resid 18 or (resid 19 through 29 and (name N or name CA or name \ C or name O or name CB )) or resid 30 through 190 or (resid 191 through 192 and \ (name N or name CA or name C or name O or name CB )) or resid 193 through 240 or \ (resid 241 through 243 and (name N or name CA or name C or name O or name CB )) \ or resid 244 through 272 or (resid 273 and (name N or name CA or name C or name \ O or name CB )) or resid 274 through 278 or (resid 279 through 280 and (name N \ or name CA or name C or name O or name CB )) or resid 281 through 294 or (resid \ 295 through 296 and (name N or name CA or name C or name O or name CB )) or resi \ d 297 through 316 or (resid 317 through 318 and (name N or name CA or name C or \ name O or name CB )) or resid 319 through 335 or (resid 336 and (name N or name \ CA or name C or name O or name CB )) or resid 337 through 387 or (resid 388 and \ (name N or name CA or name C or name O or name CB )) or resid 389 through 403 or \ (resid 404 through 405 and (name N or name CA or name C or name O or name CB )) \ or resid 406 through 461 or (resid 462 through 463 and (name N or name CA or na \ me C or name O or name CB )) or resid 464 through 493 or (resid 494 through 496 \ and (name N or name CA or name C or name O or name CB )) or resid 497 or (resid \ 498 and (name N or name CA or name C or name O or name CB )) or resid 499 throug \ h 515 or resid 518 through 520 or resid 600 through 601)) selection = (chain 'C' and (resid 9 through 38 or (resid 39 and (name N or name CA or name C \ or name O or name CB )) or resid 40 through 69 or (resid 70 and (name N or name \ CA or name C or name O or name CB )) or resid 71 through 122 or (resid 123 and \ (name N or name CA or name C or name O or name CB )) or resid 124 through 190 or \ (resid 191 through 192 and (name N or name CA or name C or name O or name CB )) \ or resid 193 through 357 or (resid 358 and (name N or name CA or name C or name \ O or name CB )) or resid 359 through 401 or (resid 402 and (name N or name CA o \ r name C or name O or name CB )) or resid 403 or (resid 404 through 405 and (nam \ e N or name CA or name C or name O or name CB )) or resid 406 through 412 or (re \ sid 413 through 416 and (name N or name CA or name C or name O or name CB )) or \ resid 417 through 421 or (resid 422 and (name N or name CA or name C or name O o \ r name CB )) or resid 423 through 505 or (resid 506 and (name N or name CA or na \ me C or name O or name CB )) or resid 507 through 515 or (resid 537 and (name N \ or name CA or name C or name O or name CB )) or resid 538 or resid 540 or resid \ 600 through 601)) } ncs_group { reference = (chain 'D' and (resid 8 through 59 or (resid 60 and (name N or name CA or name C \ or name O or name CB )) or resid 61 through 191 or (resid 192 and (name N or na \ me CA or name C or name O or name CB )) or resid 193 through 198 or (resid 199 a \ nd (name N or name CA or name C or name O or name CB )) or resid 200 through 202 \ or (resid 203 and (name N or name CA or name C or name O or name CB )) or resid \ 204 through 205 or (resid 206 through 207 and (name N or name CA or name C or n \ ame O or name CB )) or resid 208 through 211 or (resid 212 and (name N or name C \ A or name C or name O or name CB )) or resid 213 through 284 or (resid 285 and ( \ name N or name CA or name C or name O or name CB )) or resid 286 through 288 or \ (resid 289 and (name N or name CA or name C or name O or name CB )) or resid 290 \ through 291 or (resid 292 and (name N or name CA or name C or name O or name CB \ )) or resid 293 through 396 or (resid 397 through 398 and (name N or name CA or \ name C or name O or name CB )) or resid 399 through 436 or (resid 437 through 4 \ 38 and (name N or name CA or name C or name O or name CB )) or resid 439 through \ 471)) selection = (chain 'E' and (resid 8 through 198 or (resid 199 and (name N or name CA or name \ C or name O or name CB )) or resid 200 through 253 or (resid 254 and (name N or \ name CA or name C or name O or name CB )) or resid 255 through 312 or (resid 31 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 314 through \ 362 or (resid 363 through 364 and (name N or name CA or name C or name O or name \ CB )) or resid 365 through 391 or (resid 392 through 393 and (name N or name CA \ or name C or name O or name CB )) or resid 394 through 395 or (resid 396 throug \ h 398 and (name N or name CA or name C or name O or name CB )) or resid 399 thro \ ugh 436 or (resid 437 through 438 and (name N or name CA or name C or name O or \ name CB )) or resid 439 through 447 or (resid 448 and (name N or name CA or name \ C or name O or name CB )) or resid 449 through 452 or (resid 453 through 454 an \ d (name N or name CA or name C or name O or name CB )) or resid 455 through 461 \ or (resid 462 through 463 and (name N or name CA or name C or name O or name CB \ )) or resid 464 through 471)) selection = (chain 'F' and (resid 8 through 58 or (resid 59 through 60 and (name N or name C \ A or name C or name O or name CB )) or resid 61 through 211 or (resid 212 and (n \ ame N or name CA or name C or name O or name CB )) or resid 213 through 253 or ( \ resid 254 and (name N or name CA or name C or name O or name CB )) or resid 255 \ through 288 or (resid 289 and (name N or name CA or name C or name O or name CB \ )) or resid 290 through 291 or (resid 292 and (name N or name CA or name C or na \ me O or name CB )) or resid 293 through 312 or (resid 313 and (name N or name CA \ or name C or name O or name CB )) or resid 314 through 391 or (resid 392 throug \ h 393 and (name N or name CA or name C or name O or name CB )) or resid 394 thro \ ugh 397 or (resid 398 and (name N or name CA or name C or name O or name CB )) o \ r resid 399 through 447 or (resid 448 and (name N or name CA or name C or name O \ or name CB )) or resid 449 through 452 or (resid 453 through 454 and (name N or \ name CA or name C or name O or name CB )) or resid 455 through 462 or (resid 46 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 464 through \ 471)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.450 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: 0.040 Extract box with map and model: 8.950 Check model and map are aligned: 0.560 Set scattering table: 0.340 Process input model: 99.860 Find NCS groups from input model: 2.700 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 128.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 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 : 0.008 0.120 36582 Z= 0.568 Angle : 0.942 19.551 49714 Z= 0.527 Chirality : 0.052 0.755 5844 Planarity : 0.005 0.085 6397 Dihedral : 14.171 129.267 12980 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.44 % Favored : 97.50 % Rotamer: Outliers : 1.18 % Allowed : 0.92 % Favored : 97.90 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 4.12 % Cis-general : 0.13 % 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: 0.70 (0.12), residues: 4804 helix: 1.11 (0.10), residues: 2622 sheet: -0.95 (0.22), residues: 517 loop : 0.11 (0.16), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 118 HIS 0.005 0.001 HIS F 97 PHE 0.053 0.002 PHE D 343 TYR 0.020 0.001 TYR E 315 ARG 0.008 0.000 ARG G 144 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9608 Ramachandran restraints generated. 4804 Oldfield, 0 Emsley, 4804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9608 Ramachandran restraints generated. 4804 Oldfield, 0 Emsley, 4804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 3782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 338 time to evaluate : 4.400 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: D 358 PRO cc_start: 0.9079 (OUTLIER) cc_final: 0.8871 (Cg_exo) REVERT: G 155 ASP cc_start: 0.8000 (t0) cc_final: 0.7781 (t0) outliers start: 41 outliers final: 9 residues processed: 372 average time/residue: 1.6035 time to fit residues: 712.6718 Evaluate side-chains 204 residues out of total 3782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 194 time to evaluate : 4.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain D residue 358 PRO Chi-restraints excluded: chain E residue 470 SER Chi-restraints excluded: chain H residue 119 GLN Chi-restraints excluded: chain b residue 55 LYS Chi-restraints excluded: chain b residue 59 GLU Chi-restraints excluded: chain d residue 37 VAL Chi-restraints excluded: chain d residue 242 SER Chi-restraints excluded: chain 5 residue 52 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 405 optimal weight: 20.0000 chunk 363 optimal weight: 6.9990 chunk 201 optimal weight: 10.0000 chunk 124 optimal weight: 0.8980 chunk 245 optimal weight: 4.9990 chunk 194 optimal weight: 5.9990 chunk 376 optimal weight: 8.9990 chunk 145 optimal weight: 0.0980 chunk 228 optimal weight: 1.9990 chunk 280 optimal weight: 0.9980 chunk 435 optimal weight: 8.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 HIS A 512 GLN D 425 GLN E 175 ASN ** E 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 326 HIS F 326 HIS b 136 GLN d 34 GLN d 220 ASN 1 6 ASN ** 3 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 15 HIS a 76 GLN a 243 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 36582 Z= 0.251 Angle : 0.590 12.015 49714 Z= 0.297 Chirality : 0.042 0.232 5844 Planarity : 0.004 0.046 6397 Dihedral : 8.493 97.546 5405 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.87 % Favored : 98.11 % Rotamer: Outliers : 1.41 % Allowed : 7.24 % Favored : 91.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.12 % Cis-general : 0.13 % 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: 1.12 (0.12), residues: 4804 helix: 1.42 (0.10), residues: 2640 sheet: -0.71 (0.22), residues: 523 loop : 0.31 (0.17), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP d 21 HIS 0.006 0.001 HIS a 12 PHE 0.020 0.002 PHE 7 54 TYR 0.026 0.001 TYR a 145 ARG 0.008 0.000 ARG 9 45 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9608 Ramachandran restraints generated. 4804 Oldfield, 0 Emsley, 4804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9608 Ramachandran restraints generated. 4804 Oldfield, 0 Emsley, 4804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 3782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 223 time to evaluate : 4.569 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: G 155 ASP cc_start: 0.7986 (t0) cc_final: 0.7749 (t0) REVERT: H 7 GLU cc_start: 0.8624 (pt0) cc_final: 0.8307 (pm20) REVERT: H 119 GLN cc_start: 0.7181 (OUTLIER) cc_final: 0.6917 (mt0) outliers start: 49 outliers final: 11 residues processed: 253 average time/residue: 1.4927 time to fit residues: 458.6705 Evaluate side-chains 205 residues out of total 3782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 193 time to evaluate : 4.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain E residue 470 SER Chi-restraints excluded: chain F residue 287 MET Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 119 GLN Chi-restraints excluded: chain b residue 59 GLU Chi-restraints excluded: chain d residue 37 VAL Chi-restraints excluded: chain 4 residue 77 LEU Chi-restraints excluded: chain 5 residue 78 PHE Chi-restraints excluded: chain 7 residue 32 ASP Chi-restraints excluded: chain 7 residue 74 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 242 optimal weight: 5.9990 chunk 135 optimal weight: 2.9990 chunk 362 optimal weight: 3.9990 chunk 296 optimal weight: 4.9990 chunk 120 optimal weight: 0.8980 chunk 436 optimal weight: 30.0000 chunk 471 optimal weight: 20.0000 chunk 388 optimal weight: 5.9990 chunk 433 optimal weight: 50.0000 chunk 148 optimal weight: 4.9990 chunk 350 optimal weight: 3.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 305 HIS b 136 GLN ** 3 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 71 ASN a 76 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 36582 Z= 0.351 Angle : 0.591 9.347 49714 Z= 0.297 Chirality : 0.043 0.245 5844 Planarity : 0.004 0.060 6397 Dihedral : 7.865 86.068 5391 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.55 % Allowed : 9.00 % Favored : 89.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.12 % Cis-general : 0.13 % 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: 1.29 (0.12), residues: 4804 helix: 1.51 (0.10), residues: 2660 sheet: -0.56 (0.22), residues: 533 loop : 0.45 (0.17), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP d 21 HIS 0.005 0.001 HIS F 97 PHE 0.020 0.001 PHE 8 54 TYR 0.023 0.001 TYR a 145 ARG 0.006 0.000 ARG E 26 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9608 Ramachandran restraints generated. 4804 Oldfield, 0 Emsley, 4804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9608 Ramachandran restraints generated. 4804 Oldfield, 0 Emsley, 4804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 3782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 215 time to evaluate : 4.281 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: G 155 ASP cc_start: 0.8018 (t0) cc_final: 0.7776 (t0) REVERT: G 206 MET cc_start: 0.8582 (OUTLIER) cc_final: 0.8257 (mtm) outliers start: 54 outliers final: 15 residues processed: 246 average time/residue: 1.5575 time to fit residues: 465.2162 Evaluate side-chains 203 residues out of total 3782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 187 time to evaluate : 4.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain F residue 287 MET Chi-restraints excluded: chain F residue 409 GLU Chi-restraints excluded: chain G residue 206 MET Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain b residue 59 GLU Chi-restraints excluded: chain d residue 37 VAL Chi-restraints excluded: chain 4 residue 72 LEU Chi-restraints excluded: chain 4 residue 77 LEU Chi-restraints excluded: chain 5 residue 78 PHE Chi-restraints excluded: chain 7 residue 55 THR Chi-restraints excluded: chain 7 residue 60 THR Chi-restraints excluded: chain 8 residue 61 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 431 optimal weight: 40.0000 chunk 328 optimal weight: 40.0000 chunk 226 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 208 optimal weight: 10.0000 chunk 293 optimal weight: 1.9990 chunk 438 optimal weight: 20.0000 chunk 463 optimal weight: 5.9990 chunk 228 optimal weight: 4.9990 chunk 415 optimal weight: 6.9990 chunk 125 optimal weight: 0.7980 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 56 HIS b 136 GLN ** 3 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 76 GLN ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 36582 Z= 0.285 Angle : 0.573 12.407 49714 Z= 0.284 Chirality : 0.042 0.318 5844 Planarity : 0.004 0.048 6397 Dihedral : 7.439 84.464 5386 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.70 % Allowed : 10.38 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.12 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.13), residues: 4804 helix: 1.62 (0.10), residues: 2634 sheet: -0.51 (0.22), residues: 524 loop : 0.52 (0.17), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP d 21 HIS 0.005 0.001 HIS F 97 PHE 0.021 0.001 PHE 2 74 TYR 0.023 0.001 TYR 5 68 ARG 0.008 0.000 ARG a 74 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9608 Ramachandran restraints generated. 4804 Oldfield, 0 Emsley, 4804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9608 Ramachandran restraints generated. 4804 Oldfield, 0 Emsley, 4804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 3782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 200 time to evaluate : 4.618 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: G 112 LYS cc_start: 0.9054 (OUTLIER) cc_final: 0.8797 (mtmm) REVERT: G 155 ASP cc_start: 0.8034 (t0) cc_final: 0.7793 (t0) outliers start: 59 outliers final: 17 residues processed: 234 average time/residue: 1.5010 time to fit residues: 429.1351 Evaluate side-chains 199 residues out of total 3782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 181 time to evaluate : 4.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain F residue 179 ARG Chi-restraints excluded: chain F residue 409 GLU Chi-restraints excluded: chain G residue 53 MET Chi-restraints excluded: chain G residue 112 LYS Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain b residue 59 GLU Chi-restraints excluded: chain d residue 37 VAL Chi-restraints excluded: chain d residue 423 VAL Chi-restraints excluded: chain 4 residue 72 LEU Chi-restraints excluded: chain 5 residue 78 PHE Chi-restraints excluded: chain 7 residue 55 THR Chi-restraints excluded: chain 7 residue 60 THR Chi-restraints excluded: chain 8 residue 57 PHE Chi-restraints excluded: chain a residue 13 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 386 optimal weight: 7.9990 chunk 263 optimal weight: 3.9990 chunk 6 optimal weight: 8.9990 chunk 345 optimal weight: 9.9990 chunk 191 optimal weight: 7.9990 chunk 395 optimal weight: 20.0000 chunk 320 optimal weight: 10.0000 chunk 0 optimal weight: 40.0000 chunk 236 optimal weight: 7.9990 chunk 416 optimal weight: 6.9990 chunk 117 optimal weight: 0.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 HIS ** A 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 255 ASN G 131 GLN b 136 GLN ** 3 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.069 36582 Z= 0.528 Angle : 0.660 9.929 49714 Z= 0.328 Chirality : 0.044 0.216 5844 Planarity : 0.004 0.050 6397 Dihedral : 7.457 85.394 5386 Min Nonbonded Distance : 1.737 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.27 % Allowed : 10.72 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.12 % Cis-general : 0.13 % 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: 1.40 (0.13), residues: 4804 helix: 1.64 (0.10), residues: 2616 sheet: -0.51 (0.22), residues: 530 loop : 0.45 (0.17), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP d 21 HIS 0.007 0.001 HIS C 266 PHE 0.026 0.002 PHE 8 74 TYR 0.022 0.002 TYR a 145 ARG 0.010 0.001 ARG b 141 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9608 Ramachandran restraints generated. 4804 Oldfield, 0 Emsley, 4804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9608 Ramachandran restraints generated. 4804 Oldfield, 0 Emsley, 4804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 3782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 193 time to evaluate : 4.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 227 ARG cc_start: 0.9027 (OUTLIER) cc_final: 0.8780 (ttp-170) REVERT: G 112 LYS cc_start: 0.9108 (OUTLIER) cc_final: 0.8865 (mttp) REVERT: G 155 ASP cc_start: 0.8058 (t0) cc_final: 0.7812 (t0) REVERT: G 206 MET cc_start: 0.8591 (OUTLIER) cc_final: 0.8257 (mtm) REVERT: b 71 ASN cc_start: 0.8458 (m110) cc_final: 0.8231 (m110) REVERT: b 82 GLN cc_start: 0.9105 (tp-100) cc_final: 0.8275 (tm-30) REVERT: b 136 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7875 (tp40) outliers start: 79 outliers final: 27 residues processed: 243 average time/residue: 1.4357 time to fit residues: 425.6473 Evaluate side-chains 211 residues out of total 3782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 180 time to evaluate : 4.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain E residue 227 ARG Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 179 ARG Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 355 ILE Chi-restraints excluded: chain F residue 409 GLU Chi-restraints excluded: chain G residue 53 MET Chi-restraints excluded: chain G residue 112 LYS Chi-restraints excluded: chain G residue 162 MET Chi-restraints excluded: chain G residue 206 MET Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain b residue 36 ILE Chi-restraints excluded: chain b residue 44 VAL Chi-restraints excluded: chain b residue 67 THR Chi-restraints excluded: chain b residue 136 GLN Chi-restraints excluded: chain d residue 37 VAL Chi-restraints excluded: chain d residue 423 VAL Chi-restraints excluded: chain 1 residue 75 MET Chi-restraints excluded: chain 4 residue 72 LEU Chi-restraints excluded: chain 4 residue 77 LEU Chi-restraints excluded: chain 5 residue 78 PHE Chi-restraints excluded: chain 7 residue 55 THR Chi-restraints excluded: chain 7 residue 60 THR Chi-restraints excluded: chain 7 residue 74 PHE Chi-restraints excluded: chain 8 residue 57 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 156 optimal weight: 1.9990 chunk 417 optimal weight: 50.0000 chunk 91 optimal weight: 8.9990 chunk 272 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 chunk 464 optimal weight: 7.9990 chunk 385 optimal weight: 50.0000 chunk 215 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 243 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 104 ASN ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 36582 Z= 0.214 Angle : 0.565 10.641 49714 Z= 0.282 Chirality : 0.041 0.249 5844 Planarity : 0.004 0.048 6397 Dihedral : 7.121 89.775 5383 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.67 % Allowed : 12.13 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.12 % Cis-general : 0.13 % 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: 1.48 (0.13), residues: 4804 helix: 1.70 (0.10), residues: 2611 sheet: -0.57 (0.21), residues: 526 loop : 0.52 (0.17), residues: 1667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP d 21 HIS 0.007 0.001 HIS a 12 PHE 0.031 0.001 PHE 8 74 TYR 0.023 0.001 TYR a 145 ARG 0.012 0.000 ARG b 141 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9608 Ramachandran restraints generated. 4804 Oldfield, 0 Emsley, 4804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9608 Ramachandran restraints generated. 4804 Oldfield, 0 Emsley, 4804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 3782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 198 time to evaluate : 4.643 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: G 155 ASP cc_start: 0.8025 (t0) cc_final: 0.7782 (t0) REVERT: b 82 GLN cc_start: 0.8940 (tp-100) cc_final: 0.8587 (tm-30) outliers start: 58 outliers final: 22 residues processed: 235 average time/residue: 1.4893 time to fit residues: 426.8763 Evaluate side-chains 201 residues out of total 3782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 179 time to evaluate : 4.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 179 ARG Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 355 ILE Chi-restraints excluded: chain F residue 409 GLU Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain b residue 36 ILE Chi-restraints excluded: chain b residue 67 THR Chi-restraints excluded: chain d residue 72 VAL Chi-restraints excluded: chain d residue 423 VAL Chi-restraints excluded: chain 4 residue 77 LEU Chi-restraints excluded: chain 5 residue 78 PHE Chi-restraints excluded: chain 7 residue 55 THR Chi-restraints excluded: chain 7 residue 74 PHE Chi-restraints excluded: chain 8 residue 57 PHE Chi-restraints excluded: chain a residue 13 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 447 optimal weight: 6.9990 chunk 52 optimal weight: 0.6980 chunk 264 optimal weight: 9.9990 chunk 339 optimal weight: 7.9990 chunk 262 optimal weight: 6.9990 chunk 390 optimal weight: 6.9990 chunk 259 optimal weight: 0.7980 chunk 462 optimal weight: 6.9990 chunk 289 optimal weight: 6.9990 chunk 282 optimal weight: 0.1980 chunk 213 optimal weight: 6.9990 overall best weight: 3.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 131 GLN ** 3 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 36582 Z= 0.326 Angle : 0.596 11.950 49714 Z= 0.296 Chirality : 0.043 0.294 5844 Planarity : 0.004 0.046 6397 Dihedral : 6.983 89.067 5382 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.52 % Allowed : 12.56 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.12 % Cis-general : 0.13 % 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: 1.52 (0.13), residues: 4804 helix: 1.65 (0.10), residues: 2653 sheet: -0.48 (0.21), residues: 528 loop : 0.64 (0.17), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP a 105 HIS 0.005 0.001 HIS C 266 PHE 0.032 0.001 PHE 8 74 TYR 0.021 0.001 TYR a 145 ARG 0.015 0.000 ARG b 141 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9608 Ramachandran restraints generated. 4804 Oldfield, 0 Emsley, 4804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9608 Ramachandran restraints generated. 4804 Oldfield, 0 Emsley, 4804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 3782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 186 time to evaluate : 4.327 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: D 136 MET cc_start: 0.8124 (OUTLIER) cc_final: 0.7754 (ttp) REVERT: G 155 ASP cc_start: 0.8036 (t0) cc_final: 0.7797 (t0) REVERT: b 82 GLN cc_start: 0.8993 (tp-100) cc_final: 0.8336 (tm-30) REVERT: b 86 GLU cc_start: 0.8761 (mm-30) cc_final: 0.8507 (mm-30) REVERT: 8 21 MET cc_start: 0.4086 (mmm) cc_final: 0.3705 (mmm) outliers start: 53 outliers final: 28 residues processed: 222 average time/residue: 1.4755 time to fit residues: 400.3513 Evaluate side-chains 207 residues out of total 3782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 178 time to evaluate : 4.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 136 MET Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain E residue 429 THR Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 179 ARG Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 305 MET Chi-restraints excluded: chain F residue 355 ILE Chi-restraints excluded: chain F residue 409 GLU Chi-restraints excluded: chain G residue 53 MET Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain b residue 36 ILE Chi-restraints excluded: chain b residue 44 VAL Chi-restraints excluded: chain d residue 72 VAL Chi-restraints excluded: chain d residue 423 VAL Chi-restraints excluded: chain 4 residue 72 LEU Chi-restraints excluded: chain 4 residue 77 LEU Chi-restraints excluded: chain 5 residue 78 PHE Chi-restraints excluded: chain 7 residue 55 THR Chi-restraints excluded: chain 8 residue 55 THR Chi-restraints excluded: chain 8 residue 57 PHE Chi-restraints excluded: chain a residue 13 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 286 optimal weight: 3.9990 chunk 184 optimal weight: 9.9990 chunk 276 optimal weight: 6.9990 chunk 139 optimal weight: 6.9990 chunk 90 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 294 optimal weight: 0.4980 chunk 315 optimal weight: 5.9990 chunk 228 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 363 optimal weight: 0.0770 overall best weight: 2.3142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 76 GLN a 104 ASN ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 36582 Z= 0.262 Angle : 0.589 12.705 49714 Z= 0.291 Chirality : 0.042 0.272 5844 Planarity : 0.004 0.057 6397 Dihedral : 6.856 86.472 5382 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.44 % Allowed : 13.05 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.12 % Cis-general : 0.13 % 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: 1.58 (0.13), residues: 4804 helix: 1.70 (0.10), residues: 2668 sheet: -0.43 (0.21), residues: 546 loop : 0.67 (0.18), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP d 21 HIS 0.004 0.001 HIS F 97 PHE 0.040 0.001 PHE 8 74 TYR 0.022 0.001 TYR a 145 ARG 0.015 0.000 ARG b 141 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9608 Ramachandran restraints generated. 4804 Oldfield, 0 Emsley, 4804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9608 Ramachandran restraints generated. 4804 Oldfield, 0 Emsley, 4804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 3782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 189 time to evaluate : 4.229 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: D 136 MET cc_start: 0.8131 (OUTLIER) cc_final: 0.7753 (ttp) REVERT: G 112 LYS cc_start: 0.9068 (OUTLIER) cc_final: 0.8669 (mttp) REVERT: G 155 ASP cc_start: 0.8018 (t0) cc_final: 0.7780 (t0) REVERT: b 82 GLN cc_start: 0.8998 (tp-100) cc_final: 0.8393 (tp-100) REVERT: b 86 GLU cc_start: 0.8764 (mm-30) cc_final: 0.8407 (mp0) outliers start: 50 outliers final: 27 residues processed: 220 average time/residue: 1.5022 time to fit residues: 402.5356 Evaluate side-chains 203 residues out of total 3782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 174 time to evaluate : 4.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 136 MET Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain E residue 402 VAL Chi-restraints excluded: chain E residue 429 THR Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 179 ARG Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 355 ILE Chi-restraints excluded: chain F residue 409 GLU Chi-restraints excluded: chain G residue 53 MET Chi-restraints excluded: chain G residue 112 LYS Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain b residue 36 ILE Chi-restraints excluded: chain b residue 44 VAL Chi-restraints excluded: chain d residue 72 VAL Chi-restraints excluded: chain d residue 371 ARG Chi-restraints excluded: chain d residue 423 VAL Chi-restraints excluded: chain 5 residue 78 PHE Chi-restraints excluded: chain 7 residue 55 THR Chi-restraints excluded: chain 8 residue 55 THR Chi-restraints excluded: chain 8 residue 57 PHE Chi-restraints excluded: chain a residue 13 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 420 optimal weight: 6.9990 chunk 443 optimal weight: 40.0000 chunk 404 optimal weight: 5.9990 chunk 431 optimal weight: 5.9990 chunk 259 optimal weight: 2.9990 chunk 187 optimal weight: 3.9990 chunk 338 optimal weight: 20.0000 chunk 132 optimal weight: 2.9990 chunk 389 optimal weight: 0.8980 chunk 407 optimal weight: 7.9990 chunk 429 optimal weight: 0.6980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 71 ASN ** 6 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 76 GLN ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 36582 Z= 0.266 Angle : 0.603 10.961 49714 Z= 0.298 Chirality : 0.042 0.251 5844 Planarity : 0.004 0.064 6397 Dihedral : 6.772 85.805 5382 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.83 % Allowed : 14.00 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.12 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.13), residues: 4804 helix: 1.72 (0.10), residues: 2655 sheet: -0.38 (0.21), residues: 545 loop : 0.68 (0.17), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP a 105 HIS 0.004 0.001 HIS F 97 PHE 0.034 0.001 PHE 8 74 TYR 0.021 0.001 TYR a 145 ARG 0.018 0.000 ARG b 141 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9608 Ramachandran restraints generated. 4804 Oldfield, 0 Emsley, 4804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9608 Ramachandran restraints generated. 4804 Oldfield, 0 Emsley, 4804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 3782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 185 time to evaluate : 4.267 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: D 136 MET cc_start: 0.8140 (OUTLIER) cc_final: 0.7764 (ttp) outliers start: 29 outliers final: 24 residues processed: 206 average time/residue: 1.5142 time to fit residues: 380.8539 Evaluate side-chains 201 residues out of total 3782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 176 time to evaluate : 4.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 136 MET Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain E residue 402 VAL Chi-restraints excluded: chain E residue 429 THR Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 179 ARG Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 409 GLU Chi-restraints excluded: chain G residue 53 MET Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain b residue 36 ILE Chi-restraints excluded: chain b residue 44 VAL Chi-restraints excluded: chain d residue 423 VAL Chi-restraints excluded: chain 5 residue 78 PHE Chi-restraints excluded: chain 7 residue 55 THR Chi-restraints excluded: chain 8 residue 55 THR Chi-restraints excluded: chain a residue 13 VAL Chi-restraints excluded: chain a residue 78 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 283 optimal weight: 6.9990 chunk 455 optimal weight: 7.9990 chunk 278 optimal weight: 6.9990 chunk 216 optimal weight: 3.9990 chunk 316 optimal weight: 6.9990 chunk 478 optimal weight: 20.0000 chunk 440 optimal weight: 10.0000 chunk 380 optimal weight: 8.9990 chunk 39 optimal weight: 6.9990 chunk 294 optimal weight: 0.6980 chunk 233 optimal weight: 7.9990 overall best weight: 5.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 306 GLN ** b 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 76 GLN a 104 ASN ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 36582 Z= 0.489 Angle : 0.680 13.649 49714 Z= 0.338 Chirality : 0.045 0.261 5844 Planarity : 0.004 0.047 6397 Dihedral : 6.884 88.184 5382 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.92 % Allowed : 14.20 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.12 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.13), residues: 4804 helix: 1.71 (0.10), residues: 2625 sheet: -0.46 (0.21), residues: 522 loop : 0.62 (0.17), residues: 1657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP a 105 HIS 0.007 0.001 HIS C 266 PHE 0.024 0.001 PHE 7 74 TYR 0.021 0.002 TYR a 145 ARG 0.014 0.001 ARG a 74 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9608 Ramachandran restraints generated. 4804 Oldfield, 0 Emsley, 4804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9608 Ramachandran restraints generated. 4804 Oldfield, 0 Emsley, 4804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 3782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 180 time to evaluate : 4.123 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: D 136 MET cc_start: 0.8237 (OUTLIER) cc_final: 0.7922 (ttp) REVERT: G 112 LYS cc_start: 0.9032 (OUTLIER) cc_final: 0.8674 (mttp) REVERT: b 71 ASN cc_start: 0.8762 (m110) cc_final: 0.8423 (p0) REVERT: b 82 GLN cc_start: 0.9029 (tp-100) cc_final: 0.8706 (tp-100) outliers start: 32 outliers final: 23 residues processed: 205 average time/residue: 1.4287 time to fit residues: 359.4455 Evaluate side-chains 200 residues out of total 3782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 175 time to evaluate : 4.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 136 MET Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain E residue 429 THR Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 409 GLU Chi-restraints excluded: chain G residue 112 LYS Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain b residue 36 ILE Chi-restraints excluded: chain b residue 44 VAL Chi-restraints excluded: chain b residue 159 ILE Chi-restraints excluded: chain d residue 53 ASP Chi-restraints excluded: chain d residue 423 VAL Chi-restraints excluded: chain 5 residue 78 PHE Chi-restraints excluded: chain 7 residue 55 THR Chi-restraints excluded: chain 8 residue 55 THR Chi-restraints excluded: chain a residue 13 VAL Chi-restraints excluded: chain a residue 78 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 302 optimal weight: 0.9980 chunk 405 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 351 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 105 optimal weight: 10.0000 chunk 381 optimal weight: 3.9990 chunk 159 optimal weight: 0.8980 chunk 391 optimal weight: 5.9990 chunk 48 optimal weight: 9.9990 chunk 70 optimal weight: 4.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 306 GLN G 131 GLN ** b 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.069813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.042764 restraints weight = 122790.956| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 2.56 r_work: 0.2752 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2625 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 36582 Z= 0.197 Angle : 0.606 13.340 49714 Z= 0.301 Chirality : 0.042 0.275 5844 Planarity : 0.004 0.046 6397 Dihedral : 6.690 80.052 5382 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.86 % Allowed : 14.57 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.12 % Cis-general : 0.13 % 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: 1.62 (0.13), residues: 4804 helix: 1.75 (0.10), residues: 2629 sheet: -0.40 (0.21), residues: 545 loop : 0.67 (0.17), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP a 105 HIS 0.004 0.001 HIS F 97 PHE 0.023 0.001 PHE 8 74 TYR 0.022 0.001 TYR a 145 ARG 0.013 0.000 ARG a 74 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10619.30 seconds wall clock time: 191 minutes 12.12 seconds (11472.12 seconds total)