Starting phenix.real_space_refine on Tue Nov 21 23:41:42 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g0a_29651/11_2023/8g0a_29651_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g0a_29651/11_2023/8g0a_29651.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g0a_29651/11_2023/8g0a_29651_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g0a_29651/11_2023/8g0a_29651_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g0a_29651/11_2023/8g0a_29651_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g0a_29651/11_2023/8g0a_29651.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g0a_29651/11_2023/8g0a_29651.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g0a_29651/11_2023/8g0a_29651_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g0a_29651/11_2023/8g0a_29651_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.096 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 13 5.49 5 Mg 4 5.21 5 S 103 5.16 5 C 22700 2.51 5 N 6238 2.21 5 O 6572 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 ARG 365": "NH1" <-> "NH2" Residue "B ARG 376": "NH1" <-> "NH2" Residue "B ARG 394": "NH1" <-> "NH2" Residue "B TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 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 PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 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 PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 93": "NH1" <-> "NH2" Residue "b ARG 100": "NH1" <-> "NH2" Residue "b ARG 104": "NH1" <-> "NH2" Residue "b ARG 108": "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 31": "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 173": "NH1" <-> "NH2" Residue "d ARG 177": "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 "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 "9 ARG 45": "NH1" <-> "NH2" Residue "9 ARG 52": "NH1" <-> "NH2" Residue "a ARG 50": "NH1" <-> "NH2" Residue "a ARG 74": "NH1" <-> "NH2" Residue "a ARG 152": "NH1" <-> "NH2" Residue "a ARG 153": "NH1" <-> "NH2" Residue "a ARG 188": "NH1" <-> "NH2" Residue "a TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 45": "NH1" <-> "NH2" Residue "1 ARG 52": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 35630 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 3827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 3827 Classifications: {'peptide': 514} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 492} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 55 Chain: "B" Number of atoms: 3733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3733 Classifications: {'peptide': 507} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 485} Chain breaks: 1 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 9, 'PHE:plan': 1, 'ASP:plan': 10} Unresolved non-hydrogen planarities: 79 Chain: "C" Number of atoms: 3797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 3797 Classifications: {'peptide': 514} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 490} Chain breaks: 2 Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 11, 'GLN:plan1': 1, 'ASP:plan': 12} Unresolved non-hydrogen planarities: 90 Chain: "D" Number of atoms: 3505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3505 Classifications: {'peptide': 464} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 439} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 49 Chain: "E" Number of atoms: 3508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3508 Classifications: {'peptide': 464} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 439} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 46 Chain: "F" Number of atoms: 3527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3527 Classifications: {'peptide': 464} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 439} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 27 Chain: "G" Number of atoms: 2094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2094 Classifications: {'peptide': 279} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 269} Chain breaks: 2 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 53 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 63 Chain: "H" Number of atoms: 838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 838 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 3, 'TRANS': 113} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 8, 'ASN:plan1': 1, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 59 Chain: "b" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 941 Classifications: {'peptide': 141} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 3, 'TRANS': 137} Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 6, 'ASN:plan1': 1, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 84 Chain: "d" Number of atoms: 2875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 2875 Classifications: {'peptide': 433} Incomplete info: {'truncation_to_alanine': 110} Link IDs: {'PTRANS': 11, 'TRANS': 421} Chain breaks: 1 Unresolved non-hydrogen bonds: 382 Unresolved non-hydrogen angles: 480 Unresolved non-hydrogen dihedrals: 291 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 19, 'PHE:plan': 1, 'GLU:plan': 31, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 270 Chain: "2" 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: "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: 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: "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: 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: "8" 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: "9" 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: 1808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1808 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 224} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 14 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: "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: "1" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'SQC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 17.54, per 1000 atoms: 0.49 Number of scatterers: 35630 At special positions: 0 Unit cell: (136.99, 123.6, 242.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 103 16.00 P 13 15.00 Mg 4 11.99 O 6572 8.00 N 6238 7.00 C 22700 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: 15.06 Conformation dependent library (CDL) restraints added in 6.6 seconds 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8748 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 180 helices and 28 sheets defined 56.2% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.87 Creating SS restraints... Processing helix chain 'A' and resid 8 through 21 removed outlier: 3.559A pdb=" N GLU A 12 " --> pdb=" O ALA A 8 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE A 15 " --> pdb=" O ILE A 11 " (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 154 through 159 Processing helix chain 'A' and resid 178 through 195 removed outlier: 3.699A pdb=" N GLN A 189 " --> pdb=" O THR A 185 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ARG A 190 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N GLU A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ALA A 192 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 3.764A 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 229 through 231 No H-bonds generated for 'chain 'A' and resid 229 through 231' Processing helix chain 'A' and resid 243 through 262 Proline residue: A 250 - end of helix removed outlier: 3.673A 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: 3.946A 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 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 412 removed outlier: 5.055A pdb=" N SER A 392 " --> pdb=" O GLU A 388 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N LEU A 393 " --> pdb=" O VAL A 389 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ARG A 394 " --> pdb=" O ALA A 390 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N LEU A 395 " --> pdb=" O GLY A 391 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N ALA A 405 " --> pdb=" O ARG A 401 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N PHE A 406 " --> pdb=" O GLU A 402 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA A 407 " --> pdb=" O LEU A 403 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ALA A 408 " --> pdb=" O GLU A 404 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N PHE A 409 " --> pdb=" O ALA A 405 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N SER A 411 " --> pdb=" O ALA A 407 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N ASP A 412 " --> pdb=" O ALA A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 430 removed outlier: 3.804A pdb=" N GLU A 429 " --> pdb=" O ALA A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 453 Processing helix chain 'A' and resid 461 through 478 removed outlier: 3.561A pdb=" N VAL A 464 " --> pdb=" O VAL A 461 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N GLN A 465 " --> pdb=" O GLU A 462 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU A 468 " --> pdb=" O GLN A 465 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 471 " --> pdb=" O GLU A 468 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLU A 473 " --> pdb=" O GLU A 470 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N SER A 478 " --> pdb=" O VAL A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 489 Processing helix chain 'A' and resid 494 through 510 removed outlier: 3.716A pdb=" N LYS A 499 " --> pdb=" O GLU A 495 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS A 509 " --> pdb=" O ASN A 505 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY A 510 " --> pdb=" O GLU A 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 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 154 through 159 Processing helix chain 'B' and resid 178 through 195 removed outlier: 3.723A pdb=" N GLN B 189 " --> pdb=" O THR B 185 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ARG B 190 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N GLU B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ALA B 192 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 3.807A 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 228 through 230 No H-bonds generated for 'chain 'B' and resid 228 through 230' Processing helix chain 'B' and resid 243 through 263 Proline residue: B 250 - end of helix removed outlier: 3.659A pdb=" N TRP B 260 " --> pdb=" O ILE B 256 " (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 301 through 311 removed outlier: 4.060A pdb=" N ARG B 311 " --> 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 407 removed outlier: 5.136A pdb=" N SER B 392 " --> pdb=" O GLU B 388 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LEU B 393 " --> pdb=" O VAL B 389 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG B 394 " --> pdb=" O ALA B 390 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N LEU B 395 " --> pdb=" O GLY B 391 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU B 402 " --> pdb=" O SER B 398 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ALA B 405 " --> pdb=" O ARG B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 431 removed outlier: 3.781A pdb=" N GLU B 429 " --> pdb=" O ALA B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 452 removed outlier: 3.780A pdb=" N VAL B 446 " --> pdb=" O GLU B 442 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY B 451 " --> pdb=" O ALA B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 478 removed outlier: 4.639A pdb=" N GLN B 465 " --> pdb=" O GLU B 462 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU B 468 " --> pdb=" O GLN B 465 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLU B 470 " --> pdb=" O PHE B 467 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU B 473 " --> pdb=" O GLU B 470 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL B 475 " --> pdb=" O LEU B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 489 Processing helix chain 'B' and resid 494 through 510 removed outlier: 3.769A pdb=" N GLY B 510 " --> pdb=" O GLU B 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 21 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 157 No H-bonds generated for 'chain 'C' and resid 154 through 157' Processing helix chain 'C' and resid 178 through 195 removed outlier: 3.744A pdb=" N GLN C 189 " --> pdb=" O THR C 185 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ARG C 190 " --> pdb=" O ILE C 186 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N GLU C 191 " --> pdb=" O LEU C 187 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N ALA C 192 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR C 195 " --> pdb=" O GLU C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 225 Processing helix chain 'C' and resid 228 through 230 No H-bonds generated for 'chain 'C' and resid 228 through 230' Processing helix chain 'C' and resid 243 through 262 Proline residue: C 250 - end of helix removed outlier: 3.673A pdb=" N TRP C 260 " --> pdb=" O ILE C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 288 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: 4.403A pdb=" N PHE C 302 " --> pdb=" O GLY C 299 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ARG C 307 " --> pdb=" O LEU C 304 " (cutoff:3.500A) removed outlier: 4.547A 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 Processing helix chain 'C' and resid 461 through 478 removed outlier: 4.615A pdb=" N GLN C 465 " --> pdb=" O VAL C 461 " (cutoff:3.500A) removed outlier: 5.692A 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: 3.612A pdb=" N GLY C 510 " --> pdb=" O GLU C 506 " (cutoff:3.500A) 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: 4.794A pdb=" N ALA D 231 " --> pdb=" O ARG D 227 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N LEU D 232 " --> pdb=" O MET D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 269 Processing helix chain 'D' and resid 283 through 291 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 323 Processing helix chain 'D' and resid 335 through 339 Processing helix chain 'D' and resid 363 through 389 removed outlier: 4.076A pdb=" N ASP D 384 " --> pdb=" O LYS D 380 " (cutoff:3.500A) removed outlier: 4.417A 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 removed outlier: 3.523A pdb=" N ARG D 407 " --> pdb=" O ASN D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 421 removed outlier: 3.896A pdb=" N GLN D 421 " --> pdb=" O ALA D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 444 Processing helix chain 'D' and resid 452 through 454 No H-bonds generated for 'chain 'D' and resid 452 through 454' Processing helix chain 'D' and resid 462 through 468 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 178 through 180 No H-bonds generated for 'chain 'E' and resid 178 through 180' 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: 5.471A pdb=" N ALA E 231 " --> pdb=" O ARG E 227 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N LEU E 232 " --> pdb=" O MET E 228 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N MET E 237 " --> pdb=" O SER E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 256 through 270 removed outlier: 3.778A pdb=" N THR E 260 " --> pdb=" O ILE E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 283 through 292 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: 4.405A pdb=" N ALA E 325 " --> pdb=" O ALA E 321 " (cutoff:3.500A) removed outlier: 4.447A 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: 4.768A pdb=" N ASP E 384 " --> pdb=" O LYS E 380 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N ILE E 385 " --> pdb=" O ASP E 381 " (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 396 through 411 removed outlier: 3.713A pdb=" N ARG E 407 " --> pdb=" O ASN E 403 " (cutoff:3.500A) Processing helix chain 'E' and resid 418 through 423 removed outlier: 3.649A pdb=" N GLN E 421 " --> pdb=" O ALA E 418 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N THR E 423 " --> pdb=" O GLU E 420 " (cutoff:3.500A) Processing helix chain 'E' and resid 432 through 444 Processing helix chain 'E' and resid 452 through 454 No H-bonds generated for 'chain 'E' and resid 452 through 454' Processing helix chain 'E' and resid 461 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 92 through 94 No H-bonds generated for 'chain 'F' and resid 92 through 94' 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 146 Processing helix chain 'F' and resid 166 through 180 removed outlier: 4.019A pdb=" N ARG F 179 " --> pdb=" O ASN F 175 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ASN F 180 " --> pdb=" O ARG F 176 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 207 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: 4.427A pdb=" N ALA F 231 " --> pdb=" O ARG F 227 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LEU F 232 " --> pdb=" O MET F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 267 Processing helix chain 'F' and resid 283 through 294 removed outlier: 4.196A pdb=" N ARG F 293 " --> pdb=" O GLU F 289 " (cutoff:3.500A) removed outlier: 3.759A 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: 4.264A pdb=" N ALA F 325 " --> pdb=" O ALA F 321 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N HIS F 326 " --> pdb=" O THR F 322 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 340 removed outlier: 3.646A pdb=" N LYS F 340 " --> pdb=" O ALA F 336 " (cutoff:3.500A) Processing helix chain 'F' and resid 363 through 381 removed outlier: 3.712A pdb=" N ARG F 367 " --> pdb=" O ASP F 363 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 388 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: 3.702A pdb=" N GLU F 420 " --> pdb=" O MET F 417 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N GLN F 421 " --> pdb=" O ALA F 418 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N THR F 423 " --> pdb=" O GLU F 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 432 through 443 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 59 Proline residue: G 45 - end of helix 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: 4.187A 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 48 removed outlier: 3.977A pdb=" N VAL b 34 " --> pdb=" O PHE b 31 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE b 36 " --> pdb=" O ALA b 33 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ILE b 45 " --> pdb=" O LEU b 42 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS b 47 " --> pdb=" O VAL b 44 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N TRP b 48 " --> pdb=" O ILE b 45 " (cutoff:3.500A) Processing helix chain 'b' and resid 50 through 159 removed outlier: 3.673A pdb=" N SER b 142 " --> pdb=" O ASP b 138 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLY b 143 " --> pdb=" O GLN b 139 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ASP b 149 " --> pdb=" O GLU b 145 " (cutoff:3.500A) removed outlier: 4.398A 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 removed outlier: 3.701A pdb=" N GLU d 75 " --> pdb=" O LYS d 71 " (cutoff:3.500A) Processing helix chain 'd' and resid 140 through 156 Processing helix chain 'd' and resid 174 through 191 Processing helix chain 'd' and resid 196 through 215 Processing helix chain 'd' and resid 217 through 224 Processing helix chain 'd' and resid 231 through 241 Processing helix chain 'd' and resid 247 through 258 removed outlier: 3.613A pdb=" N ASP d 251 " --> pdb=" O ALA d 247 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU d 252 " --> pdb=" O THR d 248 " (cutoff:3.500A) Processing helix chain 'd' and resid 264 through 286 removed outlier: 4.047A pdb=" N ILE d 268 " --> pdb=" O GLU d 264 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU d 279 " --> pdb=" O ALA d 275 " (cutoff:3.500A) Processing helix chain 'd' and resid 289 through 305 Processing helix chain 'd' and resid 307 through 312 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 371 Processing helix chain 'd' and resid 386 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 442 Processing helix chain '2' and resid 6 through 45 Processing helix chain '2' and resid 47 through 80 removed outlier: 4.039A pdb=" N LEU 2 53 " --> pdb=" O GLN 2 50 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N PHE 2 54 " --> pdb=" O GLY 2 51 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR 2 55 " --> pdb=" O ARG 2 52 " (cutoff:3.500A) Proline residue: 2 56 - end of helix removed outlier: 3.825A pdb=" N VAL 2 61 " --> pdb=" O PHE 2 58 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLU 2 65 " --> pdb=" O GLY 2 62 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA 2 66 " --> pdb=" O LEU 2 63 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA 2 67 " --> pdb=" O VAL 2 64 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ILE 2 70 " --> pdb=" O ALA 2 67 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU 2 77 " --> pdb=" O PHE 2 74 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N PHE 2 80 " --> pdb=" O LEU 2 77 " (cutoff:3.500A) Processing helix chain '3' and resid 6 through 45 Processing helix chain '3' and resid 47 through 80 removed outlier: 3.537A pdb=" N GLN 3 50 " --> pdb=" O PRO 3 47 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLY 3 51 " --> pdb=" O GLU 3 48 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE 3 54 " --> pdb=" O GLY 3 51 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR 3 55 " --> pdb=" O ARG 3 52 " (cutoff:3.500A) Proline residue: 3 56 - end of helix removed outlier: 3.757A pdb=" N ILE 3 59 " --> pdb=" O PRO 3 56 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL 3 61 " --> pdb=" O PHE 3 58 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLU 3 65 " --> pdb=" O GLY 3 62 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE 3 70 " --> pdb=" O ALA 3 67 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N MET 3 75 " --> pdb=" O LEU 3 72 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU 3 77 " --> pdb=" O PHE 3 74 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL 3 79 " --> pdb=" O ALA 3 76 " (cutoff:3.500A) removed outlier: 4.146A 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 79 removed outlier: 3.924A pdb=" N GLN 4 50 " --> pdb=" O PRO 4 47 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLY 4 51 " --> pdb=" O GLU 4 48 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N PHE 4 54 " --> pdb=" O GLY 4 51 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N THR 4 55 " --> pdb=" O ARG 4 52 " (cutoff:3.500A) Proline residue: 4 56 - end of helix removed outlier: 3.539A pdb=" N ILE 4 59 " --> pdb=" O PRO 4 56 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL 4 61 " --> pdb=" O PHE 4 58 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLU 4 65 " --> pdb=" O GLY 4 62 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE 4 70 " --> pdb=" O ALA 4 67 " (cutoff:3.500A) Processing helix chain '5' and resid 6 through 45 Processing helix chain '5' and resid 47 through 80 removed outlier: 3.835A pdb=" N GLN 5 50 " --> pdb=" O PRO 5 47 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N GLY 5 51 " --> pdb=" O GLU 5 48 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU 5 53 " --> pdb=" O GLN 5 50 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE 5 54 " --> pdb=" O GLY 5 51 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR 5 55 " --> pdb=" O ARG 5 52 " (cutoff:3.500A) Proline residue: 5 56 - end of helix removed outlier: 3.665A pdb=" N MET 5 75 " --> pdb=" O LEU 5 72 " (cutoff:3.500A) removed outlier: 4.055A 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: 3.817A pdb=" N GLN 6 50 " --> pdb=" O PRO 6 47 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N GLY 6 51 " --> pdb=" O GLU 6 48 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE 6 54 " --> pdb=" O GLY 6 51 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N THR 6 55 " --> pdb=" O ARG 6 52 " (cutoff:3.500A) Proline residue: 6 56 - end of helix removed outlier: 3.754A pdb=" N VAL 6 61 " --> pdb=" O PHE 6 58 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N GLU 6 65 " --> pdb=" O GLY 6 62 " (cutoff:3.500A) removed outlier: 3.796A 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: 3.579A pdb=" N GLN 7 50 " --> pdb=" O PRO 7 47 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY 7 51 " --> pdb=" O GLU 7 48 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N PHE 7 54 " --> pdb=" O GLY 7 51 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N THR 7 55 " --> pdb=" O ARG 7 52 " (cutoff:3.500A) Proline residue: 7 56 - end of helix removed outlier: 3.676A pdb=" N ILE 7 59 " --> pdb=" O PRO 7 56 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL 7 61 " --> pdb=" O PHE 7 58 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLU 7 65 " --> pdb=" O GLY 7 62 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE 7 70 " --> pdb=" O ALA 7 67 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE 7 74 " --> pdb=" O ASN 7 71 " (cutoff:3.500A) Processing helix chain '8' and resid 6 through 45 Processing helix chain '8' and resid 48 through 79 removed outlier: 3.830A pdb=" N LEU 8 53 " --> pdb=" O GLN 8 50 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE 8 54 " --> pdb=" O GLY 8 51 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR 8 55 " --> pdb=" O ARG 8 52 " (cutoff:3.500A) Proline residue: 8 56 - end of helix removed outlier: 3.585A pdb=" N ILE 8 59 " --> pdb=" O PRO 8 56 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL 8 61 " --> pdb=" O PHE 8 58 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU 8 65 " --> pdb=" O GLY 8 62 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA 8 67 " --> pdb=" O VAL 8 64 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE 8 70 " --> pdb=" O ALA 8 67 " (cutoff:3.500A) Processing helix chain '9' and resid 6 through 45 Processing helix chain '9' and resid 47 through 79 removed outlier: 3.506A pdb=" N GLN 9 50 " --> pdb=" O PRO 9 47 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N GLY 9 51 " --> pdb=" O GLU 9 48 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N THR 9 55 " --> pdb=" O ARG 9 52 " (cutoff:3.500A) Proline residue: 9 56 - end of helix removed outlier: 3.658A pdb=" N ILE 9 59 " --> pdb=" O PRO 9 56 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL 9 61 " --> pdb=" O PHE 9 58 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU 9 65 " --> pdb=" O GLY 9 62 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE 9 70 " --> pdb=" O ALA 9 67 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA 9 76 " --> pdb=" O ALA 9 73 " (cutoff:3.500A) Processing helix chain 'a' and resid 29 through 52 Processing helix chain 'a' and resid 61 through 80 Processing helix chain 'a' and resid 88 through 108 removed outlier: 3.576A pdb=" N LEU a 92 " --> pdb=" O PHE a 88 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR a 95 " --> pdb=" O PRO a 91 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA a 107 " --> pdb=" O SER a 103 " (cutoff:3.500A) removed outlier: 3.919A 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 171 through 205 removed outlier: 3.634A pdb=" N VAL a 176 " --> pdb=" O PRO a 172 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU a 177 " --> pdb=" O ILE a 173 " (cutoff:3.500A) Proline residue: a 182 - end of helix removed outlier: 3.828A pdb=" N LEU a 189 " --> pdb=" O LEU a 185 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY a 196 " --> pdb=" O ASN a 192 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N MET a 205 " --> pdb=" O ALA a 201 " (cutoff:3.500A) Processing helix chain 'a' and resid 208 through 244 removed outlier: 5.561A pdb=" N PHE a 213 " --> pdb=" O TYR a 209 " (cutoff:3.500A) Proline residue: a 214 - end of helix Processing helix chain '1' and resid 6 through 45 Processing helix chain '1' and resid 47 through 79 removed outlier: 4.098A pdb=" N LEU 1 53 " --> pdb=" O GLN 1 50 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N PHE 1 54 " --> pdb=" O GLY 1 51 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR 1 55 " --> pdb=" O ARG 1 52 " (cutoff:3.500A) Proline residue: 1 56 - end of helix removed outlier: 3.569A pdb=" N ILE 1 59 " --> pdb=" O PRO 1 56 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL 1 61 " --> pdb=" O PHE 1 58 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA 1 67 " --> pdb=" O VAL 1 64 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE 1 70 " --> pdb=" O ALA 1 67 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN 1 71 " --> pdb=" O TYR 1 68 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N VAL 1 79 " --> pdb=" O ALA 1 76 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 31 through 33 removed outlier: 3.892A pdb=" N GLU A 54 " --> pdb=" O ALA A 66 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N GLY A 75 " --> pdb=" O LEU A 67 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP A 36 " --> pdb=" O HIS A 43 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N GLU A 45 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N VAL A 34 " --> pdb=" O GLU A 45 " (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: 8.639A pdb=" N THR A 233 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N CYS A 204 " --> pdb=" O THR A 233 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N VAL A 235 " --> pdb=" O CYS A 204 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N TYR A 206 " --> pdb=" O VAL A 235 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ALA A 237 " --> pdb=" O TYR A 206 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ALA A 208 " --> pdb=" O ALA A 237 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N HIS A 266 " --> pdb=" O ARG A 203 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N VAL A 205 " --> pdb=" O HIS A 266 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU A 268 " --> pdb=" O VAL A 205 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N VAL A 207 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL A 270 " --> pdb=" O VAL A 207 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ILE A 209 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ASP A 272 " --> pdb=" O ILE A 209 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N SER A 323 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N ILE A 269 " --> pdb=" O SER A 323 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N THR A 325 " --> pdb=" O ILE A 269 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N PHE A 271 " --> pdb=" O THR A 325 " (cutoff:3.500A) removed outlier: 7.106A 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 31 through 33 removed outlier: 4.044A pdb=" N GLU B 54 " --> pdb=" O ALA B 66 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU B 63 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N GLY B 75 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N LEU B 69 " --> pdb=" O SER B 73 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N SER B 73 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASP B 36 " --> pdb=" O HIS B 43 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N GLU B 45 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N VAL B 34 " --> pdb=" O GLU B 45 " (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: 6.648A pdb=" N LEU B 169 " --> pdb=" O CYS B 353 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU B 355 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 6.488A 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: 6.601A pdb=" N CYS B 204 " --> pdb=" O THR B 233 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N VAL B 235 " --> pdb=" O CYS B 204 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N TYR B 206 " --> pdb=" O VAL B 235 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ALA B 237 " --> pdb=" O TYR B 206 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ALA B 208 " --> pdb=" O ALA B 237 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N SER B 323 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N ILE B 269 " --> pdb=" O SER B 323 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N THR B 325 " --> pdb=" O ILE B 269 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N PHE B 271 " --> pdb=" O THR B 325 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU B 327 " --> pdb=" O PHE B 271 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 90 through 92 removed outlier: 6.623A pdb=" N HIS C 43 " --> pdb=" O ILE C 35 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ALA C 37 " --> pdb=" O ILE C 41 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE C 41 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N VAL C 77 " --> pdb=" O ALA C 66 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N ALA C 66 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N LEU C 79 " --> pdb=" O GLY C 64 " (cutoff:3.500A) removed outlier: 5.429A 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 170 through 172 removed outlier: 3.503A pdb=" N ILE C 330 " --> pdb=" O ILE C 170 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 232 through 237 removed outlier: 8.484A pdb=" N THR C 233 " --> pdb=" O VAL C 202 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N CYS C 204 " --> pdb=" O THR C 233 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N VAL C 235 " --> pdb=" O CYS C 204 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N TYR C 206 " --> pdb=" O VAL C 235 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ALA C 237 " --> pdb=" O TYR C 206 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ALA C 208 " --> pdb=" O ALA C 237 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N HIS C 266 " --> pdb=" O ARG C 203 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N VAL C 205 " --> pdb=" O HIS C 266 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N LEU C 268 " --> pdb=" O VAL C 205 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N VAL C 207 " --> pdb=" O LEU C 268 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N VAL C 270 " --> pdb=" O VAL C 207 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N ILE C 209 " --> pdb=" O VAL C 270 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ASP C 272 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N SER C 323 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N ILE C 269 " --> pdb=" O SER C 323 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N THR C 325 " --> pdb=" O ILE C 269 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N PHE C 271 " --> pdb=" O THR C 325 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N LEU C 327 " --> pdb=" O PHE C 271 " (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: 6.617A pdb=" N ASP D 21 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ILE D 15 " --> pdb=" O VAL D 19 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL D 19 " --> pdb=" O ILE D 15 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ILE D 65 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 5.800A 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 90 removed outlier: 4.091A pdb=" N GLU D 116 " --> pdb=" O VAL D 90 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 213 through 219 removed outlier: 6.827A pdb=" N SER D 185 " --> pdb=" O ALA D 214 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N VAL D 216 " --> pdb=" O SER D 185 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N PHE D 187 " --> pdb=" O VAL D 216 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N GLY D 218 " --> pdb=" O PHE D 187 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLY D 189 " --> pdb=" O GLY D 218 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N ALA D 157 " --> pdb=" O ASP D 328 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N THR D 330 " --> pdb=" O ALA D 157 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N PHE D 159 " --> pdb=" O THR D 330 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLU D 332 " --> pdb=" O PHE D 159 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 11 through 16 removed outlier: 6.641A pdb=" N ASP E 21 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILE E 15 " --> pdb=" O VAL E 19 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL E 19 " --> pdb=" O ILE E 15 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ILE E 65 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N VAL E 53 " --> pdb=" O ILE E 65 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 87 through 90 removed outlier: 3.918A pdb=" N GLU E 116 " --> pdb=" O VAL E 90 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 98 through 100 removed outlier: 8.535A pdb=" N PHE E 99 " --> pdb=" O THR E 213 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU E 215 " --> pdb=" O PHE E 99 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N SER E 185 " --> pdb=" O ALA E 214 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N VAL E 216 " --> pdb=" O SER E 185 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N PHE E 187 " --> pdb=" O VAL E 216 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N GLY E 218 " --> pdb=" O PHE E 187 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N GLY E 189 " --> pdb=" O GLY E 218 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ALA E 329 " --> pdb=" O ALA E 157 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N PHE E 159 " --> pdb=" O ALA E 329 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N THR E 331 " --> pdb=" O PHE E 159 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 11 through 16 removed outlier: 6.626A pdb=" N ASP F 21 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ILE F 15 " --> pdb=" O VAL F 19 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N VAL F 19 " --> pdb=" O ILE F 15 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ILE F 65 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N VAL F 53 " --> pdb=" O ILE F 65 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 87 through 90 removed outlier: 3.902A pdb=" N GLU F 116 " --> pdb=" O VAL F 90 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'F' and resid 135 through 137 removed outlier: 4.705A pdb=" N GLU F 135 " --> pdb=" O ARG F 152 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N TYR F 150 " --> pdb=" O LEU F 137 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 329 through 332 removed outlier: 7.287A pdb=" N ILE F 156 " --> pdb=" O ILE F 302 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N SER F 304 " --> pdb=" O ILE F 156 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N LEU F 158 " --> pdb=" O SER F 304 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N GLN F 306 " --> pdb=" O LEU F 158 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N GLY F 160 " --> pdb=" O GLN F 306 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL F 308 " --> pdb=" O GLY F 160 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL F 249 " --> pdb=" O THR F 303 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N MET F 305 " --> pdb=" O VAL F 249 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU F 251 " --> pdb=" O MET F 305 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ALA F 307 " --> pdb=" O LEU F 251 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ILE F 253 " --> pdb=" O ALA F 307 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N TYR F 309 " --> pdb=" O ILE F 253 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N THR F 184 " --> pdb=" O LEU F 250 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N PHE F 252 " --> pdb=" O THR F 184 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N VAL F 186 " --> pdb=" O PHE F 252 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'G' and resid 196 through 204 removed outlier: 6.681A pdb=" N LEU G 183 " --> pdb=" O ALA G 203 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N HIS G 184 " --> pdb=" O ARG G 76 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N GLY G 78 " --> pdb=" O HIS G 184 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N VAL G 186 " --> pdb=" O GLY G 78 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N LEU G 80 " --> pdb=" O VAL G 186 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N THR G 188 " --> pdb=" O LEU G 80 " (cutoff:3.500A) removed outlier: 9.087A pdb=" N VAL G 82 " --> pdb=" O THR G 188 " (cutoff:3.500A) removed outlier: 10.979A pdb=" N PHE G 190 " --> pdb=" O VAL G 82 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ASP G 113 " --> pdb=" O ALA G 77 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N VAL G 79 " --> pdb=" O ASP G 113 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N VAL G 115 " --> pdb=" O VAL G 79 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N VAL G 81 " --> pdb=" O VAL G 115 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N TYR G 117 " --> pdb=" O VAL G 81 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N VAL G 118 " --> pdb=" O VAL G 135 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N SER G 137 " --> pdb=" O VAL G 118 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'H' and resid 5 through 10 removed outlier: 3.582A pdb=" N VAL H 77 " --> pdb=" O ASN H 5 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'H' and resid 30 through 34 removed outlier: 3.868A pdb=" N ARG H 26 " --> pdb=" O MET H 50 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N MET H 50 " --> pdb=" O ARG H 26 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'd' and resid 405 through 409 removed outlier: 6.515A pdb=" N VAL d 375 " --> pdb=" O SER d 406 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N GLN d 408 " --> pdb=" O VAL d 375 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ALA d 377 " --> pdb=" O GLN d 408 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'a' and resid 20 through 22 Processing sheet with id= AB, first strand: chain 'a' and resid 112 through 114 2043 hydrogen bonds defined for protein. 5400 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: 13.04 Time building geometry restraints manager: 16.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 5950 1.28 - 1.41: 8401 1.41 - 1.54: 21620 1.54 - 1.68: 73 1.68 - 1.81: 186 Bond restraints: 36230 Sorted by residual: bond pdb=" CA ARG F 272 " pdb=" C ARG F 272 " ideal model delta sigma weight residual 1.523 1.428 0.095 1.18e-02 7.18e+03 6.53e+01 bond pdb=" CA ALA E 454 " pdb=" C ALA E 454 " ideal model delta sigma weight residual 1.523 1.409 0.113 1.41e-02 5.03e+03 6.46e+01 bond pdb=" C PHE a 221 " pdb=" O PHE a 221 " ideal model delta sigma weight residual 1.237 1.144 0.092 1.17e-02 7.31e+03 6.24e+01 bond pdb=" C ASN 6 6 " pdb=" O ASN 6 6 " ideal model delta sigma weight residual 1.237 1.146 0.091 1.17e-02 7.31e+03 5.98e+01 bond pdb=" CA TYR F 379 " pdb=" C TYR F 379 " ideal model delta sigma weight residual 1.523 1.419 0.104 1.41e-02 5.03e+03 5.44e+01 ... (remaining 36225 not shown) Histogram of bond angle deviations from ideal: 89.57 - 99.62: 8 99.62 - 109.66: 3817 109.66 - 119.70: 27906 119.70 - 129.74: 17334 129.74 - 139.79: 148 Bond angle restraints: 49213 Sorted by residual: angle pdb=" N GLY H 118 " pdb=" CA GLY H 118 " pdb=" C GLY H 118 " ideal model delta sigma weight residual 115.21 103.32 11.89 1.30e+00 5.92e-01 8.36e+01 angle pdb=" N ASP B 10 " pdb=" CA ASP B 10 " pdb=" C ASP B 10 " ideal model delta sigma weight residual 111.82 101.37 10.45 1.16e+00 7.43e-01 8.12e+01 angle pdb=" N LYS D 467 " pdb=" CA LYS D 467 " pdb=" C LYS D 467 " ideal model delta sigma weight residual 113.38 103.89 9.49 1.23e+00 6.61e-01 5.95e+01 angle pdb=" N ARG E 293 " pdb=" CA ARG E 293 " pdb=" C ARG E 293 " ideal model delta sigma weight residual 113.97 104.11 9.86 1.28e+00 6.10e-01 5.94e+01 angle pdb=" N ILE d 98 " pdb=" CA ILE d 98 " pdb=" C ILE d 98 " ideal model delta sigma weight residual 110.72 118.09 -7.37 1.01e+00 9.80e-01 5.33e+01 ... (remaining 49208 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 19799 17.97 - 35.95: 1305 35.95 - 53.92: 294 53.92 - 71.90: 78 71.90 - 89.87: 23 Dihedral angle restraints: 21499 sinusoidal: 7844 harmonic: 13655 Sorted by residual: dihedral pdb=" CA PHE D 343 " pdb=" C PHE D 343 " pdb=" N PRO D 344 " pdb=" CA PRO D 344 " ideal model delta harmonic sigma weight residual 0.00 25.17 -25.17 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA PHE F 343 " pdb=" C PHE F 343 " pdb=" N PRO F 344 " pdb=" CA PRO F 344 " ideal model delta harmonic sigma weight residual 0.00 22.76 -22.76 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" C ALA C 367 " pdb=" N ALA C 367 " pdb=" CA ALA C 367 " pdb=" CB ALA C 367 " ideal model delta harmonic sigma weight residual -122.60 -133.54 10.94 0 2.50e+00 1.60e-01 1.92e+01 ... (remaining 21496 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 5364 0.085 - 0.170: 416 0.170 - 0.255: 32 0.255 - 0.341: 13 0.341 - 0.426: 2 Chirality restraints: 5827 Sorted by residual: chirality pdb=" CA ALA C 367 " pdb=" N ALA C 367 " pdb=" C ALA C 367 " pdb=" CB ALA C 367 " both_signs ideal model delta sigma weight residual False 2.48 2.06 0.43 2.00e-01 2.50e+01 4.53e+00 chirality pdb=" CA PRO D 344 " pdb=" N PRO D 344 " pdb=" C PRO D 344 " pdb=" CB PRO D 344 " both_signs ideal model delta sigma weight residual False 2.72 2.38 0.34 2.00e-01 2.50e+01 2.93e+00 chirality pdb=" CA ALA F 345 " pdb=" N ALA F 345 " pdb=" C ALA F 345 " pdb=" CB ALA F 345 " both_signs ideal model delta sigma weight residual False 2.48 2.15 0.34 2.00e-01 2.50e+01 2.85e+00 ... (remaining 5824 not shown) Planarity restraints: 6370 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 271 " -0.072 2.00e-02 2.50e+03 4.53e-02 3.59e+01 pdb=" CG PHE C 271 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 PHE C 271 " 0.041 2.00e-02 2.50e+03 pdb=" CD2 PHE C 271 " 0.044 2.00e-02 2.50e+03 pdb=" CE1 PHE C 271 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE C 271 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE C 271 " -0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG H 115 " 0.023 2.00e-02 2.50e+03 4.65e-02 2.16e+01 pdb=" C ARG H 115 " -0.080 2.00e-02 2.50e+03 pdb=" O ARG H 115 " 0.029 2.00e-02 2.50e+03 pdb=" N ALA H 116 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 271 " -0.053 2.00e-02 2.50e+03 3.28e-02 1.88e+01 pdb=" CG PHE A 271 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 PHE A 271 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE A 271 " 0.030 2.00e-02 2.50e+03 pdb=" CE1 PHE A 271 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 271 " -0.012 2.00e-02 2.50e+03 pdb=" CZ PHE A 271 " -0.032 2.00e-02 2.50e+03 ... (remaining 6367 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.43: 91 2.43 - 3.05: 25500 3.05 - 3.67: 55562 3.67 - 4.28: 86334 4.28 - 4.90: 144491 Nonbonded interactions: 311978 Sorted by model distance: nonbonded pdb=" O2G ATP E 600 " pdb="MG MG E 601 " model vdw 1.816 2.170 nonbonded pdb=" OG1 THR B 179 " pdb="MG MG B 601 " model vdw 1.857 2.170 nonbonded pdb=" OG1 THR A 179 " pdb="MG MG A 601 " model vdw 1.874 2.170 nonbonded pdb=" O1G ATP A 600 " pdb="MG MG A 601 " model vdw 1.879 2.170 nonbonded pdb=" OD2 ASP A 272 " pdb="MG MG A 601 " model vdw 1.945 2.170 ... (remaining 311973 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 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 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 '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 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 '8' 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 '9' 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)) } 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 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 35 or (resid 36 through 37 and (name N or name CA or nam \ e C or name O or name CB )) or resid 38 or (resid 39 and (name N or name CA or n \ ame C or name O or name CB )) or resid 40 through 82 or (resid 83 and (name N or \ name CA or name C or name O or name CB )) or resid 84 through 294 or (resid 295 \ through 296 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 97 through 317 or (resid 318 and (name N or name CA or name C or name O or name \ CB )) or resid 319 through 357 or (resid 358 and (name N or name CA or name C or \ name O or name CB )) or resid 359 through 394 or (resid 395 through 396 and (na \ me N or name CA or name C or name O or name CB )) or resid 397 through 410 or (r \ esid 411 through 412 and (name N or name CA or name C or name O or name CB )) or \ resid 413 or (resid 414 through 416 and (name N or name CA or name C or name O \ or name CB )) or resid 417 or (resid 418 through 419 and (name N or name CA or n \ ame C or name O or name CB )) or resid 420 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 4 \ 72 or (resid 473 and (name N or name CA or name C or name O or name CB )) or res \ id 474 through 480 or (resid 481 and (name N or name CA or name C or name O or n \ ame 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 or (resid 494 through 496 and \ (name N or name CA or name C or name O or name CB )) or resid 497 through 505 o \ r (resid 506 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 07 through 511 or (resid 512 through 515 and (name N or name CA or name C or nam \ e O or name CB )) or resid 518 through 520 or resid 600 through 601)) selection = (chain 'B' and ((resid 9 through 29 and (name N or name CA or name C or name O o \ r name CB )) or resid 30 through 35 or (resid 36 through 37 and (name N or name \ CA or name C or name O or name CB )) or resid 38 or (resid 39 and (name N or nam \ e CA or name C or name O or name CB )) or resid 40 through 172 or (resid 173 and \ (name N or name CA or name C or name O or name CB )) or resid 174 through 183 o \ r (resid 184 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 85 through 190 or (resid 191 through 192 and (name N or name CA or name C or nam \ e O or name CB )) or resid 193 through 317 or (resid 318 and (name N or name CA \ or name C or name O or name CB )) or resid 319 through 395 or (resid 396 and (na \ me N or name CA or name C or name O or name CB )) or resid 397 through 403 or (r \ esid 404 through 405 and (name N or name CA or name C or name O or name CB )) or \ resid 406 through 480 or (resid 481 and (name N or name CA or name C or name O \ or name CB )) or resid 482 through 487 or (resid 488 and (name N or name CA or n \ ame C or name O or name CB )) or resid 489 through 497 or (resid 498 and (name N \ or name CA or name C or name O or name CB )) or resid 499 through 511 or (resid \ 512 through 515 and (name N or name CA or name C or name O or name CB )) or res \ id 518 through 520 or resid 600 through 601)) selection = (chain 'C' and ((resid 9 through 29 and (name N or name CA or name C or name O o \ r name CB )) or resid 30 through 183 or (resid 184 and (name N or name CA or nam \ e C or name O or name CB )) or resid 185 through 190 or (resid 191 through 192 a \ nd (name N or name CA or name C or name O or name CB )) or resid 193 through 294 \ or (resid 295 through 296 and (name N or name CA or name C or name O or name CB \ )) or resid 297 through 357 or (resid 358 and (name N or name CA or name C or n \ ame O or name CB )) or resid 359 through 394 or (resid 395 through 396 and (name \ N or name CA or name C or name O or name CB )) or resid 397 through 403 or (res \ id 404 through 405 and (name N or name CA or name C or name O or name CB )) or r \ esid 406 through 410 or (resid 411 through 412 and (name N or name CA or name C \ or name O or name CB )) or resid 413 or (resid 414 through 416 and (name N or na \ me CA or name C or name O or name CB )) or resid 417 or (resid 418 through 419 a \ nd (name N or name CA or name C or name O or name CB )) or resid 420 through 421 \ or (resid 422 and (name N or name CA or name C or name O or name CB )) or resid \ 423 through 483 or (resid 484 and (name N or name CA or name C or name O or nam \ e CB )) or resid 485 through 497 or (resid 498 and (name N or name CA or name C \ or name O or name CB )) or resid 499 through 505 or (resid 506 and (name N or na \ me CA or name C or name O or name CB )) or resid 507 through 515 or resid 537 th \ rough 538 or resid 540 or resid 600 through 601)) } ncs_group { reference = (chain 'D' and (resid 8 through 77 or (resid 78 and (name N or name CA or name C \ or name O or name CB )) or resid 79 through 113 or (resid 114 and (name N or na \ me CA or name C or name O or name CB )) or resid 115 through 191 or (resid 192 a \ nd (name N or name CA or name C or name O or name CB )) or resid 193 through 202 \ or (resid 203 and (name N or name CA or name C or name O or name CB )) or resid \ 204 through 220 or (resid 221 and (name N or name CA or name C or name O or nam \ e CB )) or resid 222 through 284 or (resid 285 through 286 and (name N or name C \ A or name C or name O or name CB )) or resid 287 through 363 or (resid 364 and ( \ name N or name CA or name C or name O or name CB )) or resid 365 through 383 or \ (resid 384 and (name N or name CA or name C or name O or name CB )) or resid 385 \ 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 471)) selection = (chain 'E' and (resid 8 through 134 or (resid 135 and (name N or name CA or name \ C or name O or name CB )) or resid 136 through 191 or (resid 192 and (name N or \ name CA or name C or name O or name CB )) or resid 193 through 253 or (resid 25 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 255 through \ 291 or (resid 292 and (name N or name CA or name C or name O or name CB )) or re \ sid 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 395 or (resid 396 and (name N or name CA or name \ C or name O or name CB )) or resid 397 or (resid 398 and (name N or name CA or \ name C or name O or name CB )) or 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 461 or (resi \ d 462 through 463 and (name N or name CA or name C or name O or name CB )) or re \ sid 464 through 468 or (resid 469 and (name N or name CA or name C or name O or \ name CB )) or resid 470 through 471)) selection = (chain 'F' and (resid 8 through 77 or (resid 78 and (name N or name CA or name C \ or name O or name CB )) or resid 79 through 113 or (resid 114 and (name N or na \ me CA or name C or name O or name CB )) or resid 115 through 134 or (resid 135 a \ nd (name N or name CA or name C or name O or name CB )) or resid 136 through 202 \ or (resid 203 and (name N or name CA or name C or name O or name CB )) or resid \ 204 through 220 or (resid 221 and (name N or name CA or name C or name O or nam \ e CB )) or resid 222 through 253 or (resid 254 and (name N or name CA or name C \ or name O or name CB )) or resid 255 through 285 or (resid 286 and (name N or na \ me CA or name C or name O or name CB )) or resid 287 through 288 or (resid 289 a \ nd (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 312 or (resid 313 and (name N or name CA or name C or name O or nam \ e CB )) or resid 314 through 331 or (resid 332 and (name N or name CA or name C \ or name O or name CB )) or resid 333 through 363 or (resid 364 and (name N or na \ me CA or name C or name O or name CB )) or resid 365 through 395 or (resid 396 a \ nd (name N or name CA or name C or name O or name CB )) or resid 397 or (resid 3 \ 98 and (name N or name CA or name C or name O or name CB )) or resid 399 through \ 447 or (resid 448 and (name N or name CA or name C or name O or name CB )) or r \ esid 449 through 462 or (resid 463 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: 1.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 8.680 Check model and map are aligned: 0.510 Set scattering table: 0.300 Process input model: 93.180 Find NCS groups from input model: 2.430 Set up NCS constraints: 0.180 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:12.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 118.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.113 36230 Z= 0.464 Angle : 0.776 16.633 49213 Z= 0.492 Chirality : 0.048 0.426 5827 Planarity : 0.005 0.122 6370 Dihedral : 13.531 89.869 12751 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.31 % Favored : 97.65 % Rotamer: Outliers : 1.12 % Allowed : 1.18 % Favored : 97.70 % Cbeta Deviations : 0.07 % 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: 0.37 (0.12), residues: 4807 helix: 0.79 (0.10), residues: 2629 sheet: -0.89 (0.21), residues: 534 loop : -0.03 (0.16), residues: 1644 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 975 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 936 time to evaluate : 4.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 8 residues processed: 957 average time/residue: 1.2783 time to fit residues: 1508.9014 Evaluate side-chains 582 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 574 time to evaluate : 4.060 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 7 residues processed: 3 average time/residue: 0.4725 time to fit residues: 8.1575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.1980 chunk 201 optimal weight: 5.9990 chunk 124 optimal weight: 0.8980 chunk 245 optimal weight: 0.8980 chunk 194 optimal weight: 0.9980 chunk 376 optimal weight: 9.9990 chunk 145 optimal weight: 7.9990 chunk 228 optimal weight: 4.9990 chunk 280 optimal weight: 0.8980 chunk 435 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN A 90 GLN A 188 ASN ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 335 ASN B 188 ASN B 361 ASN ** B 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 143 GLN C 211 GLN C 335 ASN C 399 GLN E 175 ASN F 400 GLN G 52 ASN G 93 ASN G 291 GLN H 44 GLN b 136 GLN d 34 GLN d 104 GLN d 408 GLN 2 37 ASN 5 6 ASN 6 6 ASN 6 37 ASN ** 7 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 72 GLN ** a 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 37 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.109 36230 Z= 0.278 Angle : 0.684 15.693 49213 Z= 0.343 Chirality : 0.045 0.313 5827 Planarity : 0.005 0.057 6370 Dihedral : 4.852 77.221 5185 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 3.75 % Allowed : 14.43 % Favored : 81.82 % 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: 0.71 (0.12), residues: 4807 helix: 1.04 (0.10), residues: 2617 sheet: -0.60 (0.22), residues: 537 loop : 0.15 (0.16), residues: 1653 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 790 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 660 time to evaluate : 3.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 130 outliers final: 30 residues processed: 724 average time/residue: 1.2076 time to fit residues: 1096.2929 Evaluate side-chains 601 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 571 time to evaluate : 4.029 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 17 residues processed: 16 average time/residue: 0.6972 time to fit residues: 21.2075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 242 optimal weight: 6.9990 chunk 135 optimal weight: 0.6980 chunk 362 optimal weight: 6.9990 chunk 296 optimal weight: 0.0170 chunk 120 optimal weight: 3.9990 chunk 436 optimal weight: 0.9990 chunk 471 optimal weight: 3.9990 chunk 388 optimal weight: 5.9990 chunk 433 optimal weight: 9.9990 chunk 148 optimal weight: 7.9990 chunk 350 optimal weight: 9.9990 overall best weight: 1.9424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 399 GLN B 305 HIS B 361 ASN B 444 GLN ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 335 ASN G 52 ASN G 65 HIS G 131 GLN G 291 GLN G 301 ASN H 44 GLN ** b 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 36230 Z= 0.316 Angle : 0.659 12.768 49213 Z= 0.329 Chirality : 0.044 0.235 5827 Planarity : 0.005 0.070 6370 Dihedral : 4.871 89.599 5185 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.51 % Allowed : 16.34 % Favored : 80.15 % 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: 0.92 (0.12), residues: 4807 helix: 1.21 (0.10), residues: 2588 sheet: -0.36 (0.22), residues: 533 loop : 0.19 (0.16), residues: 1686 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 732 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 610 time to evaluate : 3.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 122 outliers final: 49 residues processed: 674 average time/residue: 1.1944 time to fit residues: 1012.1511 Evaluate side-chains 603 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 554 time to evaluate : 4.323 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 31 residues processed: 22 average time/residue: 0.5926 time to fit residues: 25.0513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 431 optimal weight: 10.0000 chunk 328 optimal weight: 2.9990 chunk 226 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 208 optimal weight: 0.1980 chunk 293 optimal weight: 6.9990 chunk 438 optimal weight: 7.9990 chunk 463 optimal weight: 2.9990 chunk 228 optimal weight: 2.9990 chunk 415 optimal weight: 5.9990 chunk 125 optimal weight: 3.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 GLN B 361 ASN B 444 GLN ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 HIS E 117 HIS F 400 GLN G 37 GLN G 52 ASN G 93 ASN G 131 GLN G 291 GLN H 44 GLN 2 37 ASN ** 3 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 50 GLN ** 8 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 36230 Z= 0.363 Angle : 0.664 12.030 49213 Z= 0.335 Chirality : 0.045 0.275 5827 Planarity : 0.004 0.052 6370 Dihedral : 4.860 86.399 5185 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 4.03 % Allowed : 18.06 % Favored : 77.90 % 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: 0.99 (0.12), residues: 4807 helix: 1.22 (0.10), residues: 2600 sheet: -0.20 (0.22), residues: 543 loop : 0.25 (0.16), residues: 1664 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 726 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 586 time to evaluate : 3.993 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 outliers start: 140 outliers final: 52 residues processed: 667 average time/residue: 1.2242 time to fit residues: 1028.0542 Evaluate side-chains 578 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 526 time to evaluate : 4.285 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 34 residues processed: 21 average time/residue: 0.5066 time to fit residues: 22.1128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 386 optimal weight: 5.9990 chunk 263 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 345 optimal weight: 9.9990 chunk 191 optimal weight: 5.9990 chunk 395 optimal weight: 2.9990 chunk 320 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 236 optimal weight: 1.9990 chunk 416 optimal weight: 10.0000 chunk 117 optimal weight: 0.0980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 ASN ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 211 GLN C 335 ASN D 370 GLN F 400 GLN G 37 GLN G 131 GLN b 77 GLN ** b 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 37 ASN ** 3 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 50 GLN ** 8 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 215 ASN ** a 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 36230 Z= 0.294 Angle : 0.681 17.607 49213 Z= 0.337 Chirality : 0.046 0.613 5827 Planarity : 0.004 0.048 6370 Dihedral : 4.808 88.026 5185 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.06 % Favored : 97.92 % Rotamer: Outliers : 3.57 % Allowed : 19.71 % Favored : 76.72 % 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: 1.11 (0.12), residues: 4807 helix: 1.33 (0.10), residues: 2549 sheet: -0.12 (0.23), residues: 524 loop : 0.29 (0.16), residues: 1734 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 574 time to evaluate : 4.009 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 outliers start: 124 outliers final: 54 residues processed: 646 average time/residue: 1.2593 time to fit residues: 1022.1991 Evaluate side-chains 580 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 526 time to evaluate : 3.956 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 34 residues processed: 22 average time/residue: 0.5576 time to fit residues: 24.2373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 156 optimal weight: 5.9990 chunk 417 optimal weight: 10.0000 chunk 91 optimal weight: 3.9990 chunk 272 optimal weight: 4.9990 chunk 114 optimal weight: 5.9990 chunk 464 optimal weight: 5.9990 chunk 385 optimal weight: 7.9990 chunk 215 optimal weight: 0.6980 chunk 38 optimal weight: 7.9990 chunk 153 optimal weight: 4.9990 chunk 243 optimal weight: 6.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 GLN B 53 GLN ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 335 ASN D 121 HIS G 37 GLN G 52 ASN G 131 GLN ** b 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 37 ASN 3 37 ASN ** 4 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 6 ASN ** 7 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 50 GLN ** 8 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.097 36230 Z= 0.508 Angle : 0.740 22.344 49213 Z= 0.370 Chirality : 0.047 0.270 5827 Planarity : 0.004 0.049 6370 Dihedral : 4.799 69.267 5185 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.46 % Allowed : 20.71 % Favored : 75.83 % 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: 1.08 (0.12), residues: 4807 helix: 1.38 (0.10), residues: 2521 sheet: -0.22 (0.22), residues: 559 loop : 0.22 (0.16), residues: 1727 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 667 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 547 time to evaluate : 4.228 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 outliers start: 120 outliers final: 62 residues processed: 619 average time/residue: 1.1675 time to fit residues: 912.8203 Evaluate side-chains 571 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 509 time to evaluate : 4.387 Switching outliers to nearest non-outliers outliers start: 62 outliers final: 40 residues processed: 24 average time/residue: 0.6891 time to fit residues: 29.3024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 447 optimal weight: 9.9990 chunk 52 optimal weight: 9.9990 chunk 264 optimal weight: 4.9990 chunk 339 optimal weight: 5.9990 chunk 262 optimal weight: 1.9990 chunk 390 optimal weight: 8.9990 chunk 259 optimal weight: 0.8980 chunk 462 optimal weight: 5.9990 chunk 289 optimal weight: 2.9990 chunk 282 optimal weight: 0.4980 chunk 213 optimal weight: 0.7980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 GLN ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 335 ASN G 37 GLN G 131 GLN H 83 ASN ** b 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 37 ASN 6 71 ASN ** 7 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 50 GLN ** 8 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.121 36230 Z= 0.275 Angle : 0.715 22.457 49213 Z= 0.352 Chirality : 0.045 0.385 5827 Planarity : 0.004 0.050 6370 Dihedral : 4.711 61.447 5185 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.26 % Allowed : 22.04 % Favored : 74.70 % 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: 1.16 (0.13), residues: 4807 helix: 1.44 (0.10), residues: 2520 sheet: -0.17 (0.22), residues: 546 loop : 0.25 (0.16), residues: 1741 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 676 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 563 time to evaluate : 4.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 113 outliers final: 50 residues processed: 633 average time/residue: 1.2099 time to fit residues: 970.1385 Evaluate side-chains 573 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 523 time to evaluate : 4.262 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 37 residues processed: 14 average time/residue: 0.5624 time to fit residues: 17.5930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 286 optimal weight: 1.9990 chunk 184 optimal weight: 9.9990 chunk 276 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 90 optimal weight: 9.9990 chunk 89 optimal weight: 4.9990 chunk 294 optimal weight: 4.9990 chunk 315 optimal weight: 6.9990 chunk 228 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 363 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 GLN B 43 HIS B 53 GLN B 361 ASN ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 335 ASN G 37 GLN G 52 ASN G 93 ASN G 131 GLN ** b 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 37 ASN 3 37 ASN 7 50 GLN ** 8 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.3881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.104 36230 Z= 0.371 Angle : 0.759 20.685 49213 Z= 0.374 Chirality : 0.046 0.384 5827 Planarity : 0.005 0.089 6370 Dihedral : 4.752 60.990 5185 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.85 % Allowed : 22.88 % Favored : 74.27 % 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: 4807 helix: 1.39 (0.10), residues: 2527 sheet: -0.16 (0.22), residues: 555 loop : 0.27 (0.16), residues: 1725 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 645 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 546 time to evaluate : 4.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 99 outliers final: 55 residues processed: 606 average time/residue: 1.2061 time to fit residues: 920.6090 Evaluate side-chains 572 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 517 time to evaluate : 3.855 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 36 residues processed: 20 average time/residue: 0.5100 time to fit residues: 21.4050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 420 optimal weight: 2.9990 chunk 443 optimal weight: 20.0000 chunk 404 optimal weight: 5.9990 chunk 431 optimal weight: 8.9990 chunk 259 optimal weight: 0.8980 chunk 187 optimal weight: 0.4980 chunk 338 optimal weight: 40.0000 chunk 132 optimal weight: 3.9990 chunk 389 optimal weight: 2.9990 chunk 407 optimal weight: 5.9990 chunk 429 optimal weight: 8.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 GLN B 53 GLN B 361 ASN ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 335 ASN D 219 GLN G 131 GLN ** b 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 50 GLN ** 8 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.4003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 36230 Z= 0.345 Angle : 0.777 19.736 49213 Z= 0.379 Chirality : 0.047 0.541 5827 Planarity : 0.004 0.052 6370 Dihedral : 4.745 60.263 5185 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.54 % Allowed : 23.71 % Favored : 73.75 % 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: 1.09 (0.12), residues: 4807 helix: 1.37 (0.10), residues: 2525 sheet: -0.19 (0.22), residues: 555 loop : 0.25 (0.16), residues: 1727 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 625 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 537 time to evaluate : 4.396 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 outliers start: 88 outliers final: 50 residues processed: 591 average time/residue: 1.2126 time to fit residues: 909.7970 Evaluate side-chains 566 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 516 time to evaluate : 4.000 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 38 residues processed: 13 average time/residue: 0.4377 time to fit residues: 15.4718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 283 optimal weight: 3.9990 chunk 455 optimal weight: 5.9990 chunk 278 optimal weight: 4.9990 chunk 216 optimal weight: 0.1980 chunk 316 optimal weight: 3.9990 chunk 478 optimal weight: 3.9990 chunk 440 optimal weight: 4.9990 chunk 380 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 294 optimal weight: 1.9990 chunk 233 optimal weight: 0.9980 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 GLN B 53 GLN B 361 ASN ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 335 ASN G 52 ASN G 131 GLN ** b 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 37 ASN ** 4 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.4125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.106 36230 Z= 0.343 Angle : 0.798 19.929 49213 Z= 0.391 Chirality : 0.047 0.376 5827 Planarity : 0.005 0.064 6370 Dihedral : 4.743 59.127 5185 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 16.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.05 % Allowed : 24.66 % Favored : 73.29 % 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: 1.10 (0.13), residues: 4807 helix: 1.34 (0.10), residues: 2544 sheet: -0.21 (0.22), residues: 555 loop : 0.31 (0.16), residues: 1708 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 533 time to evaluate : 4.019 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 outliers start: 71 outliers final: 46 residues processed: 586 average time/residue: 1.1960 time to fit residues: 886.7700 Evaluate side-chains 564 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 518 time to evaluate : 4.059 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 38 residues processed: 12 average time/residue: 0.4921 time to fit residues: 15.7148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 302 optimal weight: 0.6980 chunk 405 optimal weight: 0.0970 chunk 116 optimal weight: 4.9990 chunk 351 optimal weight: 5.9990 chunk 56 optimal weight: 0.8980 chunk 105 optimal weight: 0.8980 chunk 381 optimal weight: 5.9990 chunk 159 optimal weight: 0.8980 chunk 391 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 70 optimal weight: 0.4980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 GLN ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 GLN B 361 ASN ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 131 GLN ** b 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.095456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.060966 restraints weight = 90318.184| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 2.82 r_work: 0.2699 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.4274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 36230 Z= 0.250 Angle : 0.789 21.744 49213 Z= 0.385 Chirality : 0.046 0.486 5827 Planarity : 0.005 0.065 6370 Dihedral : 4.684 57.649 5185 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.79 % Allowed : 25.27 % Favored : 72.95 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 4.12 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 1.13 (0.13), residues: 4807 helix: 1.33 (0.10), residues: 2584 sheet: -0.11 (0.22), residues: 565 loop : 0.33 (0.17), residues: 1658 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14751.02 seconds wall clock time: 262 minutes 18.18 seconds (15738.18 seconds total)