Starting phenix.real_space_refine on Fri Dec 15 07:46:51 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ybd_10769/12_2023/6ybd_10769.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ybd_10769/12_2023/6ybd_10769.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ybd_10769/12_2023/6ybd_10769.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ybd_10769/12_2023/6ybd_10769.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ybd_10769/12_2023/6ybd_10769.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ybd_10769/12_2023/6ybd_10769.pdb" } resolution = 3.3 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= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 130 5.16 5 C 19177 2.51 5 N 5699 2.21 5 O 5736 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "6 ARG 317": "NH1" <-> "NH2" Residue "6 ARG 330": "NH1" <-> "NH2" Residue "6 PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u GLU 9": "OE1" <-> "OE2" Residue "u ARG 14": "NH1" <-> "NH2" Residue "u ARG 14": "NH1" <-> "NH2" Residue "u ASP 33": "OD1" <-> "OD2" Residue "u ASP 60": "OD1" <-> "OD2" Residue "u ARG 62": "NH1" <-> "NH2" Residue "u TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u GLU 98": "OE1" <-> "OE2" Residue "u ARG 140": "NH1" <-> "NH2" Residue "u ARG 143": "NH1" <-> "NH2" Residue "u ASP 162": "OD1" <-> "OD2" Residue "u ARG 169": "NH1" <-> "NH2" Residue "u PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 195": "NH1" <-> "NH2" Residue "u ARG 298": "NH1" <-> "NH2" Residue "u ARG 304": "NH1" <-> "NH2" Residue "u GLU 305": "OE1" <-> "OE2" Residue "u ARG 307": "NH1" <-> "NH2" Residue "u ARG 317": "NH1" <-> "NH2" Residue "u ARG 321": "NH1" <-> "NH2" Residue "u GLU 334": "OE1" <-> "OE2" Residue "u ASP 343": "OD1" <-> "OD2" Residue "u ARG 376": "NH1" <-> "NH2" Residue "u PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u GLU 386": "OE1" <-> "OE2" Residue "u TYR 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 406": "NH1" <-> "NH2" Residue "u ARG 415": "NH1" <-> "NH2" Residue "u ARG 438": "NH1" <-> "NH2" Residue "u TYR 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u GLU 451": "OE1" <-> "OE2" Residue "u ARG 454": "NH1" <-> "NH2" Residue "u ASP 463": "OD1" <-> "OD2" Residue "u GLU 468": "OE1" <-> "OE2" Residue "u ASP 473": "OD1" <-> "OD2" Residue "u ARG 483": "NH1" <-> "NH2" Residue "u ARG 489": "NH1" <-> "NH2" Residue "u PHE 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u TYR 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 502": "NH1" <-> "NH2" Residue "u GLU 517": "OE1" <-> "OE2" Residue "u GLU 548": "OE1" <-> "OE2" Residue "v PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v ASP 230": "OD1" <-> "OD2" Residue "v PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v ASP 276": "OD1" <-> "OD2" Residue "v TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v TYR 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v ASP 331": "OD1" <-> "OD2" Residue "v PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v TYR 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y ASP 452": "OD1" <-> "OD2" Residue "y GLU 468": "OE1" <-> "OE2" Residue "y TYR 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y TYR 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y ARG 521": "NH1" <-> "NH2" Residue "y GLU 542": "OE1" <-> "OE2" Residue "y GLU 549": "OE1" <-> "OE2" Residue "y TYR 554": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y ARG 560": "NH1" <-> "NH2" Residue "y ASP 562": "OD1" <-> "OD2" Residue "y ARG 565": "NH1" <-> "NH2" Residue "y ARG 581": "NH1" <-> "NH2" Residue "y ARG 586": "NH1" <-> "NH2" Residue "y ARG 622": "NH1" <-> "NH2" Residue "y ASP 628": "OD1" <-> "OD2" Residue "y ARG 641": "NH1" <-> "NH2" Residue "y ARG 658": "NH1" <-> "NH2" Residue "y GLU 666": "OE1" <-> "OE2" Residue "y ARG 668": "NH1" <-> "NH2" Residue "y ARG 669": "NH1" <-> "NH2" Residue "y ASP 704": "OD1" <-> "OD2" Residue "y ARG 706": "NH1" <-> "NH2" Residue "y ARG 707": "NH1" <-> "NH2" Residue "y ARG 708": "NH1" <-> "NH2" Residue "y ARG 719": "NH1" <-> "NH2" Residue "y ARG 723": "NH1" <-> "NH2" Residue "y ARG 776": "NH1" <-> "NH2" Residue "y ARG 781": "NH1" <-> "NH2" Residue "y GLU 785": "OE1" <-> "OE2" Residue "y GLU 786": "OE1" <-> "OE2" Residue "y ARG 789": "NH1" <-> "NH2" Residue "y TYR 795": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y ASP 809": "OD1" <-> "OD2" Residue "y GLU 829": "OE1" <-> "OE2" Residue "y GLU 848": "OE1" <-> "OE2" Residue "G ASP 17": "OD1" <-> "OD2" Residue "G GLU 18": "OE1" <-> "OE2" Residue "G GLU 29": "OE1" <-> "OE2" Residue "G ARG 57": "NH1" <-> "NH2" Residue "G PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 78": "NH1" <-> "NH2" Residue "G ARG 81": "NH1" <-> "NH2" Residue "G PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 99": "NH1" <-> "NH2" Residue "G ARG 106": "NH1" <-> "NH2" Residue "G ARG 143": "NH1" <-> "NH2" Residue "G ASP 159": "OD1" <-> "OD2" Residue "G PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 6": "OD1" <-> "OD2" Residue "H GLU 13": "OE1" <-> "OE2" Residue "H GLU 15": "OE1" <-> "OE2" Residue "H PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 75": "OE1" <-> "OE2" Residue "K ASP 4": "OD1" <-> "OD2" Residue "K PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 28": "OD1" <-> "OD2" Residue "M ARG 81": "NH1" <-> "NH2" Residue "M GLU 94": "OE1" <-> "OE2" Residue "M ASP 101": "OD1" <-> "OD2" Residue "L ASP 57": "OD1" <-> "OD2" Residue "L GLU 59": "OE1" <-> "OE2" Residue "L GLU 79": "OE1" <-> "OE2" Residue "L GLU 90": "OE1" <-> "OE2" Residue "L PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 105": "OE1" <-> "OE2" Residue "L ARG 123": "NH1" <-> "NH2" Residue "L PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 166": "NH1" <-> "NH2" Residue "L ARG 167": "NH1" <-> "NH2" Residue "L ARG 200": "NH1" <-> "NH2" Residue "L ASP 220": "OD1" <-> "OD2" Residue "L ASP 221": "OD1" <-> "OD2" Residue "L ARG 227": "NH1" <-> "NH2" Residue "L GLU 268": "OE1" <-> "OE2" Residue "O TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 32": "OD1" <-> "OD2" Residue "O PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 68": "OE1" <-> "OE2" Residue "O ASP 73": "OD1" <-> "OD2" Residue "O ASP 77": "OD1" <-> "OD2" Residue "O ARG 82": "NH1" <-> "NH2" Residue "O GLU 89": "OE1" <-> "OE2" Residue "O ASP 108": "OD1" <-> "OD2" Residue "O PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 151": "NH1" <-> "NH2" Residue "O ARG 162": "NH1" <-> "NH2" Residue "O ARG 165": "NH1" <-> "NH2" Residue "O GLU 198": "OE1" <-> "OE2" Residue "O TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 213": "NH1" <-> "NH2" Residue "O PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 13": "OE1" <-> "OE2" Residue "N PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 126": "OD1" <-> "OD2" Residue "N ASP 151": "OD1" <-> "OD2" Residue "N GLU 196": "OE1" <-> "OE2" Residue "Q ARG 10": "NH1" <-> "NH2" Residue "Q ASP 33": "OD1" <-> "OD2" Residue "Q GLU 55": "OE1" <-> "OE2" Residue "Q ASP 60": "OD1" <-> "OD2" Residue "Q TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 85": "NH1" <-> "NH2" Residue "Q ARG 87": "NH1" <-> "NH2" Residue "Q ARG 89": "NH1" <-> "NH2" Residue "P GLU 23": "OE1" <-> "OE2" Residue "P PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 80": "OD1" <-> "OD2" Residue "P ARG 117": "NH1" <-> "NH2" Residue "P GLU 130": "OE1" <-> "OE2" Residue "P ARG 141": "NH1" <-> "NH2" Residue "P ARG 150": "NH1" <-> "NH2" Residue "I ASP 31": "OD1" <-> "OD2" Residue "I TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 104": "NH1" <-> "NH2" Residue "I ARG 114": "NH1" <-> "NH2" Residue "I ARG 121": "NH1" <-> "NH2" Residue "I TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 142": "OE1" <-> "OE2" Residue "x ARG 26": "NH1" <-> "NH2" Residue "x PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x ASP 84": "OD1" <-> "OD2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 30742 Number of models: 1 Model: "" Number of chains: 19 Chain: "6" Number of atoms: 1917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 1917 Classifications: {'peptide': 350} Incomplete info: {'truncation_to_alanine': 263} Link IDs: {'PTRANS': 6, 'TRANS': 343} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 914 Unresolved non-hydrogen angles: 1159 Unresolved non-hydrogen dihedrals: 747 Unresolved non-hydrogen chiralities: 90 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 7, 'TYR:plan': 8, 'ASN:plan1': 11, 'TRP:plan': 2, 'ASP:plan': 20, 'PHE:plan': 10, 'GLU:plan': 27, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 473 Chain: "4" Number of atoms: 1272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1272 Classifications: {'peptide': 257} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 226} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain breaks: 2 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 767 Unresolved non-hydrogen angles: 993 Unresolved non-hydrogen dihedrals: 618 Unresolved non-hydrogen chiralities: 87 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 8, 'TYR:plan': 11, 'ASN:plan1': 16, 'TRP:plan': 1, 'ASP:plan': 14, 'PHE:plan': 6, 'GLU:plan': 15, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 399 Chain: "u" Number of atoms: 4708 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 572, 4700 Classifications: {'peptide': 572} Link IDs: {'PTRANS': 24, 'TRANS': 547} Conformer: "B" Number of residues, atoms: 572, 4700 Classifications: {'peptide': 572} Link IDs: {'PTRANS': 24, 'TRANS': 547} bond proxies already assigned to first conformer: 4780 Chain: "v" Number of atoms: 2635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2635 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 145} Link IDs: {'PTRANS': 10, 'TRANS': 373} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 559 Unresolved non-hydrogen angles: 715 Unresolved non-hydrogen dihedrals: 468 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'GLN:plan1': 9, 'ARG:plan': 9, 'TYR:plan': 10, 'ASN:plan1': 8, 'TRP:plan': 2, 'ASP:plan': 15, 'PHE:plan': 7, 'GLU:plan': 13, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 342 Chain: "y" Number of atoms: 4325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 4325 Classifications: {'peptide': 535} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 17, 'TRANS': 517} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "8" Number of atoms: 1571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 1571 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 285} Link IDs: {'PTRANS': 12, 'TRANS': 304} Chain breaks: 1 Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 1046 Unresolved non-hydrogen angles: 1332 Unresolved non-hydrogen dihedrals: 868 Unresolved non-hydrogen chiralities: 84 Planarities with less than four sites: {'GLN:plan1': 31, 'ASP:plan': 16, 'TYR:plan': 14, 'ASN:plan1': 14, 'TRP:plan': 2, 'HIS:plan': 10, 'ASN%COO:plan1': 1, 'PHE:plan': 10, 'GLU:plan': 24, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 599 Chain: "G" Number of atoms: 1430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1430 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 9, 'TRANS': 167} Chain breaks: 2 Chain: "H" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 631 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 5, 'TRANS': 75} Chain: "K" Number of atoms: 617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 617 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "M" Number of atoms: 432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 432 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "L" Number of atoms: 1707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1707 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 12, 'TRANS': 207} Chain: "O" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1715 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 5, 'TRANS': 205} Chain: "N" Number of atoms: 1633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1633 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 12, 'TRANS': 194} Chain: "Q" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 792 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 6, 'TRANS': 92} Chain: "P" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 997 Classifications: {'peptide': 133} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 127} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "I" Number of atoms: 1208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1208 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 141} Chain: "x" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 514 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 3, 'TRANS': 57} Chain breaks: 1 Chain: "3" Number of atoms: 1057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1057 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 189} Link IDs: {'PTRANS': 5, 'TRANS': 207} Chain breaks: 1 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 704 Unresolved non-hydrogen angles: 904 Unresolved non-hydrogen dihedrals: 590 Unresolved non-hydrogen chiralities: 61 Planarities with less than four sites: {'GLN:plan1': 14, 'HIS:plan': 5, 'TYR:plan': 7, 'ASN:plan1': 9, 'TRP:plan': 4, 'ASP:plan': 14, 'PHE:plan': 11, 'GLU:plan': 17, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 404 Chain: "5" Number of atoms: 1581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 1581 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 289} Link IDs: {'PTRANS': 5, 'TRANS': 313} Chain breaks: 5 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 1124 Unresolved non-hydrogen angles: 1435 Unresolved non-hydrogen dihedrals: 958 Unresolved non-hydrogen chiralities: 88 Planarities with less than four sites: {'GLN:plan1': 20, 'HIS:plan': 10, 'TYR:plan': 21, 'ASN:plan1': 11, 'TRP:plan': 3, 'ASP:plan': 18, 'PHE:plan': 18, 'GLU:plan': 21, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 653 Time building chain proxies: 18.00, per 1000 atoms: 0.59 Number of scatterers: 30742 At special positions: 0 Unit cell: (213.726, 214.8, 187.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 130 16.00 O 5736 8.00 N 5699 7.00 C 19177 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: 11.60 Conformation dependent library (CDL) restraints added in 7.0 seconds 8712 Ramachandran restraints generated. 4356 Oldfield, 0 Emsley, 4356 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8454 Finding SS restraints... Secondary structure from input PDB file: 198 helices and 36 sheets defined 49.4% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.03 Creating SS restraints... Processing helix chain '6' and resid 17 through 25 Processing helix chain '6' and resid 30 through 35 Processing helix chain '6' and resid 63 through 68 removed outlier: 4.147A pdb=" N VAL 6 68 " --> pdb=" O MET 6 64 " (cutoff:3.500A) Processing helix chain '6' and resid 87 through 92 removed outlier: 3.777A pdb=" N LEU 6 90 " --> pdb=" O CYS 6 87 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS 6 92 " --> pdb=" O LYS 6 89 " (cutoff:3.500A) Processing helix chain '6' and resid 98 through 106 removed outlier: 3.604A pdb=" N ARG 6 102 " --> pdb=" O ARG 6 98 " (cutoff:3.500A) Processing helix chain '6' and resid 107 through 109 No H-bonds generated for 'chain '6' and resid 107 through 109' Processing helix chain '6' and resid 116 through 128 Processing helix chain '6' and resid 154 through 168 Processing helix chain '6' and resid 174 through 193 Processing helix chain '6' and resid 198 through 212 removed outlier: 3.881A pdb=" N VAL 6 202 " --> pdb=" O SER 6 198 " (cutoff:3.500A) Processing helix chain '6' and resid 262 through 267 removed outlier: 3.532A pdb=" N LEU 6 266 " --> pdb=" O PHE 6 262 " (cutoff:3.500A) Processing helix chain '6' and resid 268 through 278 Processing helix chain '6' and resid 280 through 285 Processing helix chain '6' and resid 296 through 301 Processing helix chain '6' and resid 307 through 318 removed outlier: 4.841A pdb=" N ILE 6 313 " --> pdb=" O GLU 6 309 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP 6 314 " --> pdb=" O ALA 6 310 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR 6 318 " --> pdb=" O ASP 6 314 " (cutoff:3.500A) Processing helix chain '6' and resid 341 through 346 Processing helix chain '6' and resid 347 through 355 removed outlier: 3.763A pdb=" N TYR 6 351 " --> pdb=" O TRP 6 347 " (cutoff:3.500A) Processing helix chain '4' and resid 96 through 106 Processing helix chain '4' and resid 152 through 163 Processing helix chain '4' and resid 183 through 192 Processing helix chain '4' and resid 245 through 254 Processing helix chain '4' and resid 266 through 290 Processing helix chain '4' and resid 295 through 298 No H-bonds generated for 'chain '4' and resid 295 through 298' Processing helix chain '4' and resid 304 through 314 removed outlier: 4.269A pdb=" N LEU 4 308 " --> pdb=" O VAL 4 304 " (cutoff:3.500A) Processing helix chain '4' and resid 320 through 352 Processing helix chain 'u' and resid 8 through 16 removed outlier: 4.124A pdb=" N LEU u 12 " --> pdb=" O PRO u 8 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS u 13 " --> pdb=" O GLU u 9 " (cutoff:3.500A) Processing helix chain 'u' and resid 23 through 36 removed outlier: 3.780A pdb=" N LEU u 31 " --> pdb=" O ALA u 27 " (cutoff:3.500A) Processing helix chain 'u' and resid 46 through 61 Processing helix chain 'u' and resid 64 through 77 Processing helix chain 'u' and resid 83 through 103 Processing helix chain 'u' and resid 105 through 116 removed outlier: 3.615A pdb=" N MET u 111 " --> pdb=" O GLU u 107 " (cutoff:3.500A) Processing helix chain 'u' and resid 128 through 132 Processing helix chain 'u' and resid 139 through 144 removed outlier: 3.993A pdb=" N ARG u 143 " --> pdb=" O ASP u 139 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU u 144 " --> pdb=" O ARG u 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 139 through 144' Processing helix chain 'u' and resid 146 through 163 removed outlier: 3.569A pdb=" N LEU u 161 " --> pdb=" O TYR u 157 " (cutoff:3.500A) Processing helix chain 'u' and resid 170 through 188 removed outlier: 3.656A pdb=" N HIS u 175 " --> pdb=" O GLU u 171 " (cutoff:3.500A) Processing helix chain 'u' and resid 191 through 204 removed outlier: 4.432A pdb=" N ARG u 195 " --> pdb=" O LYS u 191 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LYS u 196 " --> pdb=" O ALA u 192 " (cutoff:3.500A) Processing helix chain 'u' and resid 207 through 211 Processing helix chain 'u' and resid 222 through 242 removed outlier: 3.713A pdb=" N GLU u 231 " --> pdb=" O SER u 227 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N THR u 232 " --> pdb=" O MET u 228 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG u 233 " --> pdb=" O HIS u 229 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER u 242 " --> pdb=" O ASP u 238 " (cutoff:3.500A) Processing helix chain 'u' and resid 247 through 260 Processing helix chain 'u' and resid 271 through 286 removed outlier: 3.648A pdb=" N ASN u 277 " --> pdb=" O ALA u 273 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N SER u 280 " --> pdb=" O TYR u 276 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR u 281 " --> pdb=" O ASN u 277 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N TRP u 284 " --> pdb=" O SER u 280 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LYS u 285 " --> pdb=" O THR u 281 " (cutoff:3.500A) Processing helix chain 'u' and resid 288 through 307 removed outlier: 4.094A pdb=" N HIS u 292 " --> pdb=" O ASN u 288 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA u 293 " --> pdb=" O ALA u 289 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU u 305 " --> pdb=" O HIS u 301 " (cutoff:3.500A) Processing helix chain 'u' and resid 311 through 327 Processing helix chain 'u' and resid 338 through 345 Processing helix chain 'u' and resid 351 through 359 Processing helix chain 'u' and resid 370 through 376 removed outlier: 3.578A pdb=" N MET u 374 " --> pdb=" O LEU u 370 " (cutoff:3.500A) Processing helix chain 'u' and resid 378 through 382 Processing helix chain 'u' and resid 389 through 396 Processing helix chain 'u' and resid 399 through 401 No H-bonds generated for 'chain 'u' and resid 399 through 401' Processing helix chain 'u' and resid 402 through 416 removed outlier: 4.477A pdb=" N VAL u 410 " --> pdb=" O ARG u 406 " (cutoff:3.500A) Processing helix chain 'u' and resid 421 through 427 removed outlier: 3.597A pdb=" N GLN u 426 " --> pdb=" O GLU u 423 " (cutoff:3.500A) Processing helix chain 'u' and resid 428 through 444 Processing helix chain 'u' and resid 451 through 459 removed outlier: 3.673A pdb=" N LEU u 455 " --> pdb=" O GLU u 451 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N SER u 457 " --> pdb=" O SER u 453 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL u 459 " --> pdb=" O LEU u 455 " (cutoff:3.500A) Processing helix chain 'u' and resid 463 through 476 Processing helix chain 'u' and resid 518 through 523 removed outlier: 3.779A pdb=" N GLN u 522 " --> pdb=" O GLN u 518 " (cutoff:3.500A) Processing helix chain 'u' and resid 525 through 536 removed outlier: 4.030A pdb=" N VAL u 529 " --> pdb=" O ALA u 525 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA u 533 " --> pdb=" O VAL u 529 " (cutoff:3.500A) Processing helix chain 'u' and resid 539 through 560 removed outlier: 3.909A pdb=" N LEU u 543 " --> pdb=" O PRO u 539 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N HIS u 550 " --> pdb=" O LYS u 546 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ALA u 553 " --> pdb=" O GLN u 549 " (cutoff:3.500A) Processing helix chain 'u' and resid 561 through 563 No H-bonds generated for 'chain 'u' and resid 561 through 563' Processing helix chain 'u' and resid 564 through 572 removed outlier: 3.731A pdb=" N ALA u 570 " --> pdb=" O GLN u 566 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ARG u 572 " --> pdb=" O ILE u 568 " (cutoff:3.500A) Processing helix chain 'v' and resid 37 through 42 removed outlier: 3.747A pdb=" N GLY v 40 " --> pdb=" O LEU v 37 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS v 41 " --> pdb=" O LEU v 38 " (cutoff:3.500A) Processing helix chain 'v' and resid 49 through 55 Processing helix chain 'v' and resid 61 through 66 removed outlier: 3.756A pdb=" N ASP v 65 " --> pdb=" O LEU v 61 " (cutoff:3.500A) Processing helix chain 'v' and resid 67 through 70 removed outlier: 3.576A pdb=" N LEU v 70 " --> pdb=" O PRO v 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'v' and resid 67 through 70' Processing helix chain 'v' and resid 76 through 83 Processing helix chain 'v' and resid 96 through 106 removed outlier: 3.907A pdb=" N THR v 101 " --> pdb=" O ASP v 97 " (cutoff:3.500A) Processing helix chain 'v' and resid 107 through 109 No H-bonds generated for 'chain 'v' and resid 107 through 109' Processing helix chain 'v' and resid 128 through 138 removed outlier: 4.337A pdb=" N LYS v 136 " --> pdb=" O TYR v 132 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N PHE v 137 " --> pdb=" O ARG v 133 " (cutoff:3.500A) Processing helix chain 'v' and resid 164 through 177 removed outlier: 4.582A pdb=" N TRP v 170 " --> pdb=" O LEU v 166 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N SER v 175 " --> pdb=" O GLY v 171 " (cutoff:3.500A) Processing helix chain 'v' and resid 181 through 195 Processing helix chain 'v' and resid 203 through 218 Processing helix chain 'v' and resid 224 through 229 Processing helix chain 'v' and resid 230 through 232 No H-bonds generated for 'chain 'v' and resid 230 through 232' Processing helix chain 'v' and resid 237 through 245 Processing helix chain 'v' and resid 250 through 264 removed outlier: 3.653A pdb=" N ILE v 262 " --> pdb=" O THR v 258 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ASN v 264 " --> pdb=" O ALA v 260 " (cutoff:3.500A) Processing helix chain 'v' and resid 275 through 280 removed outlier: 4.094A pdb=" N LYS v 279 " --> pdb=" O LYS v 275 " (cutoff:3.500A) Processing helix chain 'v' and resid 304 through 308 removed outlier: 3.602A pdb=" N GLY v 307 " --> pdb=" O ASP v 304 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA v 308 " --> pdb=" O PHE v 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'v' and resid 304 through 308' Processing helix chain 'v' and resid 314 through 321 removed outlier: 4.201A pdb=" N VAL v 318 " --> pdb=" O GLU v 314 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASN v 321 " --> pdb=" O SER v 317 " (cutoff:3.500A) Processing helix chain 'v' and resid 329 through 347 removed outlier: 3.526A pdb=" N ILE v 333 " --> pdb=" O LEU v 329 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N PHE v 341 " --> pdb=" O ARG v 337 " (cutoff:3.500A) Processing helix chain 'v' and resid 352 through 357 removed outlier: 3.867A pdb=" N ALA v 357 " --> pdb=" O ILE v 353 " (cutoff:3.500A) Processing helix chain 'v' and resid 363 through 377 removed outlier: 4.074A pdb=" N GLU v 368 " --> pdb=" O PRO v 364 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ARG v 369 " --> pdb=" O GLU v 365 " (cutoff:3.500A) Processing helix chain 'v' and resid 402 through 420 removed outlier: 3.715A pdb=" N MET v 420 " --> pdb=" O GLN v 416 " (cutoff:3.500A) Processing helix chain 'y' and resid 327 through 338 removed outlier: 4.205A pdb=" N LYS y 331 " --> pdb=" O ALA y 327 " (cutoff:3.500A) Processing helix chain 'y' and resid 346 through 364 removed outlier: 3.777A pdb=" N ILE y 351 " --> pdb=" O ARG y 347 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU y 352 " --> pdb=" O ALA y 348 " (cutoff:3.500A) Processing helix chain 'y' and resid 367 through 384 removed outlier: 4.124A pdb=" N ILE y 371 " --> pdb=" O GLY y 367 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE y 379 " --> pdb=" O LYS y 375 " (cutoff:3.500A) Processing helix chain 'y' and resid 394 through 415 removed outlier: 3.568A pdb=" N ALA y 414 " --> pdb=" O ASP y 410 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASN y 415 " --> pdb=" O ILE y 411 " (cutoff:3.500A) Processing helix chain 'y' and resid 443 through 461 removed outlier: 3.574A pdb=" N ASN y 461 " --> pdb=" O LYS y 457 " (cutoff:3.500A) Processing helix chain 'y' and resid 466 through 474 removed outlier: 3.998A pdb=" N VAL y 470 " --> pdb=" O SER y 466 " (cutoff:3.500A) Processing helix chain 'y' and resid 475 through 493 removed outlier: 3.505A pdb=" N VAL y 479 " --> pdb=" O ASP y 475 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU y 491 " --> pdb=" O GLN y 487 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLU y 492 " --> pdb=" O ARG y 488 " (cutoff:3.500A) Processing helix chain 'y' and resid 495 through 508 removed outlier: 3.592A pdb=" N CYS y 500 " --> pdb=" O THR y 496 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ARG y 501 " --> pdb=" O GLU y 497 " (cutoff:3.500A) Processing helix chain 'y' and resid 515 through 520 removed outlier: 3.679A pdb=" N ALA y 518 " --> pdb=" O ASP y 515 " (cutoff:3.500A) Processing helix chain 'y' and resid 543 through 558 removed outlier: 3.746A pdb=" N LEU y 547 " --> pdb=" O ASP y 543 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N MET y 548 " --> pdb=" O SER y 544 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU y 549 " --> pdb=" O ALA y 545 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ILE y 555 " --> pdb=" O LEU y 551 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ALA y 557 " --> pdb=" O LYS y 553 " (cutoff:3.500A) Processing helix chain 'y' and resid 563 through 579 removed outlier: 3.758A pdb=" N HIS y 579 " --> pdb=" O HIS y 575 " (cutoff:3.500A) Processing helix chain 'y' and resid 585 through 593 removed outlier: 3.675A pdb=" N SER y 592 " --> pdb=" O LEU y 588 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N HIS y 593 " --> pdb=" O MET y 589 " (cutoff:3.500A) Processing helix chain 'y' and resid 597 through 601 Processing helix chain 'y' and resid 602 through 622 removed outlier: 3.655A pdb=" N ILE y 607 " --> pdb=" O PRO y 603 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N LEU y 608 " --> pdb=" O PRO y 604 " (cutoff:3.500A) Processing helix chain 'y' and resid 626 through 633 removed outlier: 3.633A pdb=" N LEU y 633 " --> pdb=" O ALA y 629 " (cutoff:3.500A) Processing helix chain 'y' and resid 633 through 638 Processing helix chain 'y' and resid 641 through 646 Processing helix chain 'y' and resid 651 through 655 Processing helix chain 'y' and resid 660 through 667 Processing helix chain 'y' and resid 678 through 700 Proline residue: y 696 - end of helix removed outlier: 3.600A pdb=" N ALA y 699 " --> pdb=" O ILE y 695 " (cutoff:3.500A) Processing helix chain 'y' and resid 712 through 723 Processing helix chain 'y' and resid 732 through 743 removed outlier: 3.511A pdb=" N ALA y 743 " --> pdb=" O ALA y 739 " (cutoff:3.500A) Processing helix chain 'y' and resid 749 through 757 Processing helix chain 'y' and resid 758 through 765 removed outlier: 3.698A pdb=" N GLY y 763 " --> pdb=" O GLU y 759 " (cutoff:3.500A) Processing helix chain 'y' and resid 766 through 769 Processing helix chain 'y' and resid 771 through 795 removed outlier: 4.450A pdb=" N VAL y 775 " --> pdb=" O GLU y 771 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG y 776 " --> pdb=" O ALA y 772 " (cutoff:3.500A) Processing helix chain 'y' and resid 814 through 825 removed outlier: 3.683A pdb=" N MET y 825 " --> pdb=" O ILE y 821 " (cutoff:3.500A) Processing helix chain 'y' and resid 851 through 860 Processing helix chain '8' and resid 43 through 54 removed outlier: 3.634A pdb=" N LYS 8 51 " --> pdb=" O LEU 8 47 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N HIS 8 52 " --> pdb=" O LYS 8 48 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLN 8 54 " --> pdb=" O ILE 8 50 " (cutoff:3.500A) Processing helix chain '8' and resid 97 through 104 removed outlier: 3.904A pdb=" N MET 8 101 " --> pdb=" O VAL 8 97 " (cutoff:3.500A) Processing helix chain '8' and resid 132 through 142 Processing helix chain '8' and resid 173 through 176 No H-bonds generated for 'chain '8' and resid 173 through 176' Processing helix chain '8' and resid 211 through 220 Processing helix chain '8' and resid 232 through 239 Processing helix chain '8' and resid 248 through 278 removed outlier: 3.744A pdb=" N GLN 8 278 " --> pdb=" O LYS 8 274 " (cutoff:3.500A) Processing helix chain '8' and resid 282 through 285 No H-bonds generated for 'chain '8' and resid 282 through 285' Processing helix chain '8' and resid 316 through 350 Processing helix chain 'G' and resid 17 through 31 removed outlier: 3.730A pdb=" N ALA G 26 " --> pdb=" O GLY G 22 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU G 29 " --> pdb=" O GLN G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 66 through 70 removed outlier: 4.417A pdb=" N LYS G 70 " --> pdb=" O VAL G 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 66 through 70' Processing helix chain 'G' and resid 77 through 87 removed outlier: 4.474A pdb=" N ARG G 81 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLU G 82 " --> pdb=" O ARG G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 129 through 134 removed outlier: 4.451A pdb=" N VAL G 134 " --> pdb=" O LEU G 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 169 through 182 removed outlier: 4.177A pdb=" N SER G 174 " --> pdb=" O VAL G 170 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLY G 175 " --> pdb=" O GLU G 171 " (cutoff:3.500A) Processing helix chain 'H' and resid 11 through 15 Processing helix chain 'K' and resid 56 through 62 Processing helix chain 'K' and resid 65 through 76 Processing helix chain 'M' and resid 99 through 109 removed outlier: 4.492A pdb=" N MET M 105 " --> pdb=" O ASP M 101 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU M 106 " --> pdb=" O THR M 102 " (cutoff:3.500A) Processing helix chain 'L' and resid 64 through 72 removed outlier: 3.742A pdb=" N LEU L 69 " --> pdb=" O LYS L 65 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 83 Processing helix chain 'L' and resid 92 through 98 Processing helix chain 'L' and resid 147 through 159 removed outlier: 3.966A pdb=" N ILE L 151 " --> pdb=" O VAL L 147 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ARG L 152 " --> pdb=" O ALA L 148 " (cutoff:3.500A) Processing helix chain 'L' and resid 160 through 162 No H-bonds generated for 'chain 'L' and resid 160 through 162' Processing helix chain 'L' and resid 207 through 215 removed outlier: 3.677A pdb=" N LYS L 212 " --> pdb=" O PRO L 208 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU L 213 " --> pdb=" O VAL L 209 " (cutoff:3.500A) Processing helix chain 'L' and resid 234 through 245 removed outlier: 3.904A pdb=" N THR L 240 " --> pdb=" O PHE L 236 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE L 244 " --> pdb=" O THR L 240 " (cutoff:3.500A) Processing helix chain 'L' and resid 252 through 257 removed outlier: 3.876A pdb=" N LYS L 257 " --> pdb=" O ASP L 254 " (cutoff:3.500A) Processing helix chain 'L' and resid 264 through 269 removed outlier: 3.690A pdb=" N PHE L 269 " --> pdb=" O PRO L 265 " (cutoff:3.500A) Processing helix chain 'L' and resid 271 through 275 removed outlier: 3.846A pdb=" N VAL L 274 " --> pdb=" O ASP L 271 " (cutoff:3.500A) Processing helix chain 'O' and resid 23 through 26 removed outlier: 3.944A pdb=" N SER O 26 " --> pdb=" O ASP O 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 23 through 26' Processing helix chain 'O' and resid 71 through 76 removed outlier: 3.668A pdb=" N ASN O 76 " --> pdb=" O ALA O 72 " (cutoff:3.500A) Processing helix chain 'O' and resid 106 through 111 Processing helix chain 'O' and resid 159 through 175 removed outlier: 3.754A pdb=" N LYS O 166 " --> pdb=" O ARG O 162 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N THR O 173 " --> pdb=" O MET O 169 " (cutoff:3.500A) Processing helix chain 'O' and resid 180 through 189 Processing helix chain 'O' and resid 193 through 201 removed outlier: 3.575A pdb=" N LYS O 199 " --> pdb=" O LYS O 195 " (cutoff:3.500A) Processing helix chain 'O' and resid 226 through 231 Processing helix chain 'N' and resid 11 through 22 removed outlier: 3.768A pdb=" N ALA N 20 " --> pdb=" O LEU N 16 " (cutoff:3.500A) Processing helix chain 'N' and resid 52 through 67 removed outlier: 3.923A pdb=" N LEU N 58 " --> pdb=" O THR N 54 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU N 60 " --> pdb=" O GLU N 56 " (cutoff:3.500A) Processing helix chain 'N' and resid 70 through 72 No H-bonds generated for 'chain 'N' and resid 70 through 72' Processing helix chain 'N' and resid 85 through 90 Processing helix chain 'N' and resid 90 through 95 Processing helix chain 'N' and resid 130 through 138 Processing helix chain 'N' and resid 168 through 187 removed outlier: 3.883A pdb=" N GLY N 172 " --> pdb=" O ALA N 168 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N MET N 174 " --> pdb=" O SER N 170 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU N 183 " --> pdb=" O ALA N 179 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N MET N 185 " --> pdb=" O GLU N 181 " (cutoff:3.500A) Processing helix chain 'N' and resid 198 through 202 removed outlier: 3.587A pdb=" N LEU N 201 " --> pdb=" O MET N 198 " (cutoff:3.500A) Processing helix chain 'Q' and resid 46 through 49 Processing helix chain 'Q' and resid 50 through 56 removed outlier: 3.818A pdb=" N ALA Q 56 " --> pdb=" O ASP Q 52 " (cutoff:3.500A) Processing helix chain 'P' and resid 65 through 69 removed outlier: 3.601A pdb=" N GLU P 68 " --> pdb=" O ASP P 65 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N SER P 69 " --> pdb=" O ARG P 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 65 through 69' Processing helix chain 'P' and resid 70 through 86 removed outlier: 4.280A pdb=" N ASP P 80 " --> pdb=" O LEU P 76 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL P 81 " --> pdb=" O ALA P 77 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN P 83 " --> pdb=" O GLN P 79 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ARG P 84 " --> pdb=" O ASP P 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 111 through 122 removed outlier: 4.406A pdb=" N LEU P 116 " --> pdb=" O ALA P 112 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ARG P 117 " --> pdb=" O GLN P 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 31 through 41 Processing helix chain 'I' and resid 48 through 57 Processing helix chain 'I' and resid 62 through 68 removed outlier: 3.543A pdb=" N VAL I 66 " --> pdb=" O GLN I 62 " (cutoff:3.500A) Processing helix chain 'I' and resid 71 through 76 Processing helix chain 'I' and resid 85 through 90 Processing helix chain 'I' and resid 90 through 95 Processing helix chain 'I' and resid 96 through 103 removed outlier: 3.672A pdb=" N GLU I 103 " --> pdb=" O ARG I 99 " (cutoff:3.500A) Processing helix chain 'I' and resid 110 through 115 Processing helix chain 'I' and resid 122 through 130 removed outlier: 4.819A pdb=" N TYR I 128 " --> pdb=" O ARG I 124 " (cutoff:3.500A) Processing helix chain 'I' and resid 145 through 150 Processing helix chain '3' and resid 3 through 17 removed outlier: 3.700A pdb=" N ALA 3 9 " --> pdb=" O GLU 3 5 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLY 3 17 " --> pdb=" O LYS 3 13 " (cutoff:3.500A) Processing helix chain '3' and resid 18 through 24 Proline residue: 3 23 - end of helix Processing helix chain '3' and resid 25 through 39 removed outlier: 4.042A pdb=" N LEU 3 29 " --> pdb=" O ASN 3 25 " (cutoff:3.500A) Processing helix chain '3' and resid 44 through 57 removed outlier: 3.913A pdb=" N LEU 3 48 " --> pdb=" O LEU 3 44 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU 3 53 " --> pdb=" O ALA 3 49 " (cutoff:3.500A) Processing helix chain '3' and resid 58 through 61 Processing helix chain '3' and resid 62 through 75 removed outlier: 3.942A pdb=" N THR 3 66 " --> pdb=" O GLN 3 62 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS 3 72 " --> pdb=" O GLN 3 68 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR 3 75 " --> pdb=" O LEU 3 71 " (cutoff:3.500A) Processing helix chain '3' and resid 80 through 88 removed outlier: 3.570A pdb=" N LEU 3 84 " --> pdb=" O THR 3 80 " (cutoff:3.500A) Processing helix chain '3' and resid 92 through 95 Processing helix chain '3' and resid 96 through 111 removed outlier: 4.234A pdb=" N LEU 3 108 " --> pdb=" O TYR 3 104 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU 3 109 " --> pdb=" O LEU 3 105 " (cutoff:3.500A) Processing helix chain '3' and resid 113 through 121 Processing helix chain '3' and resid 125 through 130 removed outlier: 3.772A pdb=" N GLY 3 130 " --> pdb=" O ASP 3 126 " (cutoff:3.500A) Processing helix chain '3' and resid 137 through 150 removed outlier: 3.617A pdb=" N PHE 3 141 " --> pdb=" O SER 3 137 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLY 3 147 " --> pdb=" O CYS 3 143 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE 3 148 " --> pdb=" O HIS 3 144 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR 3 150 " --> pdb=" O VAL 3 146 " (cutoff:3.500A) Processing helix chain '3' and resid 154 through 162 Processing helix chain '3' and resid 166 through 178 removed outlier: 3.924A pdb=" N LYS 3 176 " --> pdb=" O VAL 3 172 " (cutoff:3.500A) Processing helix chain '3' and resid 191 through 196 removed outlier: 3.923A pdb=" N ILE 3 196 " --> pdb=" O GLN 3 192 " (cutoff:3.500A) Processing helix chain '3' and resid 206 through 216 Processing helix chain '5' and resid 184 through 207 removed outlier: 4.083A pdb=" N CYS 5 202 " --> pdb=" O SER 5 198 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N LYS 5 203 " --> pdb=" O GLN 5 199 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N THR 5 204 " --> pdb=" O TYR 5 200 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS 5 207 " --> pdb=" O LYS 5 203 " (cutoff:3.500A) Processing helix chain '5' and resid 208 through 218 removed outlier: 3.700A pdb=" N ASN 5 218 " --> pdb=" O PHE 5 214 " (cutoff:3.500A) Processing helix chain '5' and resid 223 through 247 removed outlier: 4.021A pdb=" N VAL 5 227 " --> pdb=" O ASN 5 223 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL 5 230 " --> pdb=" O SER 5 226 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ARG 5 242 " --> pdb=" O SER 5 238 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLN 5 243 " --> pdb=" O ASN 5 239 " (cutoff:3.500A) Processing helix chain '5' and resid 252 through 268 removed outlier: 4.145A pdb=" N HIS 5 263 " --> pdb=" O GLU 5 259 " (cutoff:3.500A) Processing helix chain '5' and resid 274 through 290 removed outlier: 3.677A pdb=" N ARG 5 279 " --> pdb=" O VAL 5 275 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU 5 284 " --> pdb=" O LEU 5 280 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY 5 285 " --> pdb=" O HIS 5 281 " (cutoff:3.500A) Processing helix chain '5' and resid 297 through 303 Processing helix chain '5' and resid 312 through 326 removed outlier: 3.616A pdb=" N VAL 5 319 " --> pdb=" O THR 5 315 " (cutoff:3.500A) Processing helix chain '5' and resid 328 through 335 removed outlier: 3.899A pdb=" N ILE 5 333 " --> pdb=" O TYR 5 329 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ARG 5 334 " --> pdb=" O GLN 5 330 " (cutoff:3.500A) Processing helix chain '5' and resid 335 through 342 removed outlier: 4.341A pdb=" N ILE 5 339 " --> pdb=" O VAL 5 335 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU 5 340 " --> pdb=" O PHE 5 336 " (cutoff:3.500A) Processing helix chain '5' and resid 358 through 375 removed outlier: 4.015A pdb=" N LYS 5 362 " --> pdb=" O GLU 5 358 " (cutoff:3.500A) Processing helix chain '5' and resid 387 through 401 removed outlier: 3.879A pdb=" N LYS 5 393 " --> pdb=" O GLN 5 389 " (cutoff:3.500A) Processing helix chain '5' and resid 405 through 417 removed outlier: 3.758A pdb=" N TYR 5 409 " --> pdb=" O ASP 5 405 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N SER 5 414 " --> pdb=" O GLU 5 410 " (cutoff:3.500A) Processing helix chain '5' and resid 438 through 462 removed outlier: 3.576A pdb=" N LEU 5 457 " --> pdb=" O GLN 5 453 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ILE 5 460 " --> pdb=" O GLN 5 456 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG 5 461 " --> pdb=" O LEU 5 457 " (cutoff:3.500A) Processing helix chain '5' and resid 471 through 481 Processing helix chain '5' and resid 491 through 497 Processing helix chain '5' and resid 526 through 549 removed outlier: 3.780A pdb=" N ALA 5 531 " --> pdb=" O MET 5 527 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG 5 545 " --> pdb=" O ASP 5 541 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLN 5 546 " --> pdb=" O PHE 5 542 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE 5 547 " --> pdb=" O PHE 5 543 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'u' and resid 490 through 493 removed outlier: 7.257A pdb=" N ASP y 800 " --> pdb=" O VAL u 482 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ILE u 484 " --> pdb=" O ASP y 800 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N ILE y 802 " --> pdb=" O ILE u 484 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ASP y 800 " --> pdb=" O VAL y 843 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE y 802 " --> pdb=" O THR y 841 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 51 through 52 removed outlier: 3.983A pdb=" N ILE G 51 " --> pdb=" O ALA G 59 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA G 59 " --> pdb=" O ILE G 51 " (cutoff:3.500A) removed outlier: 8.767A pdb=" N VAL G 93 " --> pdb=" O LYS G 58 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ILE G 60 " --> pdb=" O VAL G 93 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N ILE G 95 " --> pdb=" O ILE G 60 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ILE G 62 " --> pdb=" O ILE G 95 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLN G 97 " --> pdb=" O ILE G 62 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N VAL G 64 " --> pdb=" O GLN G 97 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'G' and resid 142 through 146 removed outlier: 3.812A pdb=" N ARG G 145 " --> pdb=" O LEU G 153 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 32 through 36 Processing sheet with id=AA8, first strand: chain 'H' and resid 64 through 65 Processing sheet with id=AA9, first strand: chain 'K' and resid 35 through 37 Processing sheet with id=AB1, first strand: chain 'M' and resid 96 through 98 Processing sheet with id=AB2, first strand: chain 'L' and resid 105 through 106 removed outlier: 3.616A pdb=" N GLU L 105 " --> pdb=" O ALA L 129 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N MET L 110 " --> pdb=" O LYS L 125 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 105 through 106 removed outlier: 3.616A pdb=" N GLU L 105 " --> pdb=" O ALA L 129 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL L 128 " --> pdb=" O GLY L 140 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLY L 140 " --> pdb=" O VAL L 128 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 184 through 188 removed outlier: 3.600A pdb=" N VAL L 184 " --> pdb=" O LEU L 195 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N CYS L 222 " --> pdb=" O VAL L 205 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'O' and resid 45 through 50 removed outlier: 4.134A pdb=" N GLY O 45 " --> pdb=" O VAL O 33 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL O 49 " --> pdb=" O ASP O 29 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N CYS O 96 " --> pdb=" O TRP O 30 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ASP O 32 " --> pdb=" O CYS O 96 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N THR O 98 " --> pdb=" O ASP O 32 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ASN O 95 " --> pdb=" O VAL O 91 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N VAL O 91 " --> pdb=" O ASN O 95 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N LEU O 97 " --> pdb=" O GLU O 89 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'O' and resid 102 through 103 removed outlier: 4.090A pdb=" N VAL O 215 " --> pdb=" O MET O 103 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA O 123 " --> pdb=" O CYS O 139 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'O' and resid 102 through 103 removed outlier: 4.090A pdb=" N VAL O 215 " --> pdb=" O MET O 103 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N VAL O 140 " --> pdb=" O VAL O 210 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL O 210 " --> pdb=" O VAL O 140 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 38 through 41 removed outlier: 6.815A pdb=" N ILE N 48 " --> pdb=" O TYR N 39 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 97 through 100 removed outlier: 3.999A pdb=" N SER N 75 " --> pdb=" O LEU N 121 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL N 123 " --> pdb=" O SER N 75 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU N 122 " --> pdb=" O ILE N 145 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N LEU N 147 " --> pdb=" O LEU N 122 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N VAL N 124 " --> pdb=" O LEU N 147 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N THR N 144 " --> pdb=" O ILE N 159 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ILE N 161 " --> pdb=" O THR N 144 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ALA N 146 " --> pdb=" O ILE N 161 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'Q' and resid 20 through 22 Processing sheet with id=AC2, first strand: chain 'Q' and resid 36 through 43 Processing sheet with id=AC3, first strand: chain 'P' and resid 54 through 57 removed outlier: 3.522A pdb=" N VAL P 56 " --> pdb=" O VAL P 42 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL P 42 " --> pdb=" O VAL P 56 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N HIS P 43 " --> pdb=" O HIS P 32 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N GLY P 29 " --> pdb=" O HIS P 94 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N LYS P 96 " --> pdb=" O GLY P 29 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N CYS P 31 " --> pdb=" O LYS P 96 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N ARG P 98 " --> pdb=" O CYS P 31 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ILE P 33 " --> pdb=" O ARG P 98 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N LEU P 93 " --> pdb=" O GLY P 127 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE P 129 " --> pdb=" O LEU P 93 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE P 95 " --> pdb=" O ILE P 129 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N ASP P 131 " --> pdb=" O ILE P 95 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N LEU P 97 " --> pdb=" O ASP P 131 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain '3' and resid 180 through 181 removed outlier: 4.126A pdb=" N SER 3 180 " --> pdb=" O PHE 3 188 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain '5' and resid 469 through 470 removed outlier: 3.593A pdb=" N MET 5 470 " --> pdb=" O PHE 5 513 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain '4' and resid 91 through 94 No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain '4' and resid 117 through 125 No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain '4' and resid 128 through 136 No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain '4' and resid 139 through 142 No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain '4' and resid 145 through 148 No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain '4' and resid 168 through 175 No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain '4' and resid 198 through 202 No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain '4' and resid 213 through 218 No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain '4' and resid 231 through 239 No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain '8' and resid 38 through 41 No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain '8' and resid 65 through 71 No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain '8' and resid 75 through 83 No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain '8' and resid 116 through 121 No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain '8' and resid 148 through 152 No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain '8' and resid 164 through 169 No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain '8' and resid 198 through 200 No H-bonds generated for sheet with id=AE3 1325 hydrogen bonds defined for protein. 3845 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: 9.34 Time building geometry restraints manager: 12.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8775 1.33 - 1.46: 6389 1.46 - 1.58: 15777 1.58 - 1.71: 1 1.71 - 1.83: 208 Bond restraints: 31150 Sorted by residual: bond pdb=" C CYS H 64 " pdb=" N GLN H 65 " ideal model delta sigma weight residual 1.332 1.245 0.087 3.60e-02 7.72e+02 5.88e+00 bond pdb=" CB VAL y 358 " pdb=" CG2 VAL y 358 " ideal model delta sigma weight residual 1.521 1.442 0.079 3.30e-02 9.18e+02 5.80e+00 bond pdb=" CB GLN v 241 " pdb=" CG GLN v 241 " ideal model delta sigma weight residual 1.520 1.452 0.068 3.00e-02 1.11e+03 5.19e+00 bond pdb=" CB VAL u 34 " pdb=" CG2 VAL u 34 " ideal model delta sigma weight residual 1.521 1.451 0.070 3.30e-02 9.18e+02 4.51e+00 bond pdb=" C SER v 399 " pdb=" N PRO v 400 " ideal model delta sigma weight residual 1.334 1.382 -0.049 2.34e-02 1.83e+03 4.31e+00 ... (remaining 31145 not shown) Histogram of bond angle deviations from ideal: 97.23 - 104.66: 461 104.66 - 112.09: 14883 112.09 - 119.51: 11576 119.51 - 126.94: 15117 126.94 - 134.36: 301 Bond angle restraints: 42338 Sorted by residual: angle pdb=" N ASN y 423 " pdb=" CA ASN y 423 " pdb=" C ASN y 423 " ideal model delta sigma weight residual 110.42 118.77 -8.35 1.46e+00 4.69e-01 3.27e+01 angle pdb=" C PRO u 333 " pdb=" N GLU u 334 " pdb=" CA GLU u 334 " ideal model delta sigma weight residual 121.54 131.80 -10.26 1.91e+00 2.74e-01 2.89e+01 angle pdb=" N VAL N 7 " pdb=" CA VAL N 7 " pdb=" C VAL N 7 " ideal model delta sigma weight residual 108.80 101.04 7.76 1.46e+00 4.69e-01 2.82e+01 angle pdb=" C ILE 8 211 " pdb=" N ASN 8 212 " pdb=" CA ASN 8 212 " ideal model delta sigma weight residual 120.82 128.69 -7.87 1.50e+00 4.44e-01 2.75e+01 angle pdb=" N PRO y 603 " pdb=" CA PRO y 603 " pdb=" C PRO y 603 " ideal model delta sigma weight residual 110.70 116.81 -6.11 1.22e+00 6.72e-01 2.50e+01 ... (remaining 42333 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.86: 18613 35.86 - 71.73: 375 71.73 - 107.59: 18 107.59 - 143.46: 0 143.46 - 179.32: 1 Dihedral angle restraints: 19007 sinusoidal: 6077 harmonic: 12930 Sorted by residual: dihedral pdb=" CD BARG u 14 " pdb=" NE BARG u 14 " pdb=" CZ BARG u 14 " pdb=" NH1BARG u 14 " ideal model delta sinusoidal sigma weight residual 0.00 -179.32 179.32 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" CA GLY y 421 " pdb=" C GLY y 421 " pdb=" N GLU y 422 " pdb=" CA GLU y 422 " ideal model delta harmonic sigma weight residual 180.00 151.96 28.04 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" CA ALA 4 194 " pdb=" C ALA 4 194 " pdb=" N PRO 4 195 " pdb=" CA PRO 4 195 " ideal model delta harmonic sigma weight residual 180.00 152.97 27.03 0 5.00e+00 4.00e-02 2.92e+01 ... (remaining 19004 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 4149 0.078 - 0.156: 802 0.156 - 0.234: 82 0.234 - 0.311: 7 0.311 - 0.389: 3 Chirality restraints: 5043 Sorted by residual: chirality pdb=" CB VAL N 140 " pdb=" CA VAL N 140 " pdb=" CG1 VAL N 140 " pdb=" CG2 VAL N 140 " both_signs ideal model delta sigma weight residual False -2.63 -2.24 -0.39 2.00e-01 2.50e+01 3.79e+00 chirality pdb=" CB VAL P 132 " pdb=" CA VAL P 132 " pdb=" CG1 VAL P 132 " pdb=" CG2 VAL P 132 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" CB ILE v 233 " pdb=" CA ILE v 233 " pdb=" CG1 ILE v 233 " pdb=" CG2 ILE v 233 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.70e+00 ... (remaining 5040 not shown) Planarity restraints: 5595 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE u 331 " 0.023 2.00e-02 2.50e+03 4.82e-02 2.32e+01 pdb=" C ILE u 331 " -0.083 2.00e-02 2.50e+03 pdb=" O ILE u 331 " 0.032 2.00e-02 2.50e+03 pdb=" N THR u 332 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE 4 307 " 0.021 2.00e-02 2.50e+03 4.14e-02 1.71e+01 pdb=" C PHE 4 307 " -0.072 2.00e-02 2.50e+03 pdb=" O PHE 4 307 " 0.027 2.00e-02 2.50e+03 pdb=" N LEU 4 308 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY 5 258 " 0.019 2.00e-02 2.50e+03 3.82e-02 1.46e+01 pdb=" C GLY 5 258 " -0.066 2.00e-02 2.50e+03 pdb=" O GLY 5 258 " 0.025 2.00e-02 2.50e+03 pdb=" N GLU 5 259 " 0.022 2.00e-02 2.50e+03 ... (remaining 5592 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 7805 2.79 - 3.32: 28667 3.32 - 3.84: 48832 3.84 - 4.37: 52850 4.37 - 4.90: 90666 Nonbonded interactions: 228820 Sorted by model distance: nonbonded pdb=" NE2 GLN v 241 " pdb=" O PHE x 33 " model vdw 2.262 2.520 nonbonded pdb=" O SER y 703 " pdb=" OG SER y 703 " model vdw 2.268 2.440 nonbonded pdb=" OH TYR L 82 " pdb=" O ILE L 162 " model vdw 2.295 2.440 nonbonded pdb=" O HIS y 819 " pdb=" OG SER y 823 " model vdw 2.297 2.440 nonbonded pdb=" O LEU O 62 " pdb=" OG1 THR O 88 " model vdw 2.298 2.440 ... (remaining 228815 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.50 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: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.380 Check model and map are aligned: 0.440 Set scattering table: 0.260 Process input model: 79.000 Find NCS groups from input model: 1.120 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 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 : 0.009 0.087 31150 Z= 0.578 Angle : 1.082 12.746 42338 Z= 0.613 Chirality : 0.061 0.389 5043 Planarity : 0.007 0.088 5595 Dihedral : 15.554 179.320 10553 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.25 % Favored : 90.59 % Rotamer: Outliers : 0.55 % Allowed : 8.43 % Favored : 91.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.02 (0.11), residues: 4356 helix: -2.29 (0.09), residues: 2106 sheet: -2.55 (0.26), residues: 296 loop : -3.07 (0.12), residues: 1954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP u 284 HIS 0.015 0.002 HIS y 674 PHE 0.036 0.003 PHE H 47 TYR 0.034 0.003 TYR x 59 ARG 0.011 0.001 ARG Q 5 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8712 Ramachandran restraints generated. 4356 Oldfield, 0 Emsley, 4356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8712 Ramachandran restraints generated. 4356 Oldfield, 0 Emsley, 4356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 730 residues out of total 3931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 716 time to evaluate : 3.307 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: 14 outliers final: 6 residues processed: 724 average time/residue: 0.4388 time to fit residues: 492.6174 Evaluate side-chains 574 residues out of total 3931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 568 time to evaluate : 3.355 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2522 time to fit residues: 7.5426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 367 optimal weight: 2.9990 chunk 329 optimal weight: 5.9990 chunk 182 optimal weight: 7.9990 chunk 112 optimal weight: 4.9990 chunk 222 optimal weight: 0.0770 chunk 176 optimal weight: 5.9990 chunk 340 optimal weight: 2.9990 chunk 131 optimal weight: 30.0000 chunk 207 optimal weight: 5.9990 chunk 253 optimal weight: 4.9990 chunk 395 optimal weight: 40.0000 overall best weight: 3.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 6 345 GLN 6 355 ASN u 44 GLN u 109 GLN u 110 GLN u 175 HIS u 221 ASN u 222 ASN u 229 HIS u 236 GLN u 392 ASN u 466 GLN u 522 GLN v 231 ASN v 244 ASN v 252 HIS ** v 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 421 ASN y 364 ASN y 432 HIS y 460 GLN y 784 GLN ** y 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 852 GLN G 25 GLN G 33 ASN ** G 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 165 ASN G 186 ASN H 51 GLN M 93 GLN L 136 HIS L 272 HIS O 186 ASN O 208 HIS N 29 ASN ** N 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 50 ASN ** N 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 132 GLN ** N 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 86 ASN P 94 HIS ** I 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 36 GLN I 101 HIS I 105 ASN ** x 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7022 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 31150 Z= 0.297 Angle : 0.685 10.760 42338 Z= 0.369 Chirality : 0.044 0.171 5043 Planarity : 0.005 0.065 5595 Dihedral : 6.912 177.855 4683 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.90 % Favored : 92.03 % Rotamer: Outliers : 2.97 % Allowed : 18.52 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.04 (0.12), residues: 4356 helix: -1.28 (0.10), residues: 2136 sheet: -2.27 (0.29), residues: 268 loop : -2.82 (0.13), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP u 284 HIS 0.012 0.001 HIS L 272 PHE 0.028 0.002 PHE N 203 TYR 0.026 0.002 TYR I 38 ARG 0.009 0.001 ARG y 563 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8712 Ramachandran restraints generated. 4356 Oldfield, 0 Emsley, 4356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8712 Ramachandran restraints generated. 4356 Oldfield, 0 Emsley, 4356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 697 residues out of total 3931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 622 time to evaluate : 2.952 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 outliers start: 75 outliers final: 52 residues processed: 657 average time/residue: 0.4198 time to fit residues: 440.5649 Evaluate side-chains 623 residues out of total 3931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 571 time to evaluate : 2.785 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 0 residues processed: 52 average time/residue: 0.2871 time to fit residues: 32.5158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 219 optimal weight: 50.0000 chunk 122 optimal weight: 30.0000 chunk 328 optimal weight: 5.9990 chunk 268 optimal weight: 3.9990 chunk 108 optimal weight: 10.0000 chunk 395 optimal weight: 0.6980 chunk 427 optimal weight: 40.0000 chunk 352 optimal weight: 7.9990 chunk 392 optimal weight: 40.0000 chunk 134 optimal weight: 10.0000 chunk 317 optimal weight: 0.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: