Starting phenix.real_space_refine on Thu Dec 26 07:34:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dze_47327/12_2024/9dze_47327.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dze_47327/12_2024/9dze_47327.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dze_47327/12_2024/9dze_47327.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dze_47327/12_2024/9dze_47327.map" model { file = "/net/cci-nas-00/data/ceres_data/9dze_47327/12_2024/9dze_47327.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dze_47327/12_2024/9dze_47327.cif" } resolution = 4.3 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= 0.019 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: 3 Type Number sf(0) Gaussians C 26810 2.51 5 N 9060 2.21 5 O 9060 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 44930 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 1568 Classifications: {'peptide': 316} Incomplete info: {'truncation_to_alanine': 221} Link IDs: {'TRANS': 315} Unresolved non-hydrogen bonds: 807 Unresolved non-hydrogen angles: 1014 Unresolved non-hydrogen dihedrals: 618 Unresolved non-hydrogen chiralities: 81 Planarities with less than four sites: {'GLN:plan1': 21, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 12, 'TRP:plan': 1, 'ASP:plan': 15, 'GLU:plan': 39, 'ARG:plan': 23} Unresolved non-hydrogen planarities: 471 Chain: "B" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 1568 Classifications: {'peptide': 316} Incomplete info: {'truncation_to_alanine': 221} Link IDs: {'TRANS': 315} Unresolved non-hydrogen bonds: 807 Unresolved non-hydrogen angles: 1014 Unresolved non-hydrogen dihedrals: 618 Unresolved non-hydrogen chiralities: 81 Planarities with less than four sites: {'GLN:plan1': 21, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 12, 'TRP:plan': 1, 'ASP:plan': 15, 'GLU:plan': 39, 'ARG:plan': 23} Unresolved non-hydrogen planarities: 471 Chain: "C" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 1568 Classifications: {'peptide': 316} Incomplete info: {'truncation_to_alanine': 221} Link IDs: {'TRANS': 315} Unresolved non-hydrogen bonds: 807 Unresolved non-hydrogen angles: 1014 Unresolved non-hydrogen dihedrals: 618 Unresolved non-hydrogen chiralities: 81 Planarities with less than four sites: {'GLN:plan1': 21, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 12, 'TRP:plan': 1, 'ASP:plan': 15, 'GLU:plan': 39, 'ARG:plan': 23} Unresolved non-hydrogen planarities: 471 Chain: "D" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 1568 Classifications: {'peptide': 316} Incomplete info: {'truncation_to_alanine': 221} Link IDs: {'TRANS': 315} Unresolved non-hydrogen bonds: 807 Unresolved non-hydrogen angles: 1014 Unresolved non-hydrogen dihedrals: 618 Unresolved non-hydrogen chiralities: 81 Planarities with less than four sites: {'GLN:plan1': 21, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 12, 'TRP:plan': 1, 'ASP:plan': 15, 'GLU:plan': 39, 'ARG:plan': 23} Unresolved non-hydrogen planarities: 471 Chain: "E" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 1568 Classifications: {'peptide': 316} Incomplete info: {'truncation_to_alanine': 221} Link IDs: {'TRANS': 315} Unresolved non-hydrogen bonds: 807 Unresolved non-hydrogen angles: 1014 Unresolved non-hydrogen dihedrals: 618 Unresolved non-hydrogen chiralities: 81 Planarities with less than four sites: {'GLN:plan1': 21, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 12, 'TRP:plan': 1, 'ASP:plan': 15, 'GLU:plan': 39, 'ARG:plan': 23} Unresolved non-hydrogen planarities: 471 Chain: "F" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 1568 Classifications: {'peptide': 316} Incomplete info: {'truncation_to_alanine': 221} Link IDs: {'TRANS': 315} Unresolved non-hydrogen bonds: 807 Unresolved non-hydrogen angles: 1014 Unresolved non-hydrogen dihedrals: 618 Unresolved non-hydrogen chiralities: 81 Planarities with less than four sites: {'GLN:plan1': 21, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 12, 'TRP:plan': 1, 'ASP:plan': 15, 'GLU:plan': 39, 'ARG:plan': 23} Unresolved non-hydrogen planarities: 471 Chain: "G" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 1568 Classifications: {'peptide': 316} Incomplete info: {'truncation_to_alanine': 221} Link IDs: {'TRANS': 315} Unresolved non-hydrogen bonds: 807 Unresolved non-hydrogen angles: 1014 Unresolved non-hydrogen dihedrals: 618 Unresolved non-hydrogen chiralities: 81 Planarities with less than four sites: {'GLN:plan1': 21, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 12, 'TRP:plan': 1, 'ASP:plan': 15, 'GLU:plan': 39, 'ARG:plan': 23} Unresolved non-hydrogen planarities: 471 Chain: "H" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 1568 Classifications: {'peptide': 316} Incomplete info: {'truncation_to_alanine': 221} Link IDs: {'TRANS': 315} Unresolved non-hydrogen bonds: 807 Unresolved non-hydrogen angles: 1014 Unresolved non-hydrogen dihedrals: 618 Unresolved non-hydrogen chiralities: 81 Planarities with less than four sites: {'GLN:plan1': 21, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 12, 'TRP:plan': 1, 'ASP:plan': 15, 'GLU:plan': 39, 'ARG:plan': 23} Unresolved non-hydrogen planarities: 471 Chain: "I" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 1568 Classifications: {'peptide': 316} Incomplete info: {'truncation_to_alanine': 221} Link IDs: {'TRANS': 315} Unresolved non-hydrogen bonds: 807 Unresolved non-hydrogen angles: 1014 Unresolved non-hydrogen dihedrals: 618 Unresolved non-hydrogen chiralities: 81 Planarities with less than four sites: {'GLN:plan1': 21, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 12, 'TRP:plan': 1, 'ASP:plan': 15, 'GLU:plan': 39, 'ARG:plan': 23} Unresolved non-hydrogen planarities: 471 Chain: "J" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 1568 Classifications: {'peptide': 316} Incomplete info: {'truncation_to_alanine': 221} Link IDs: {'TRANS': 315} Unresolved non-hydrogen bonds: 807 Unresolved non-hydrogen angles: 1014 Unresolved non-hydrogen dihedrals: 618 Unresolved non-hydrogen chiralities: 81 Planarities with less than four sites: {'GLN:plan1': 21, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 12, 'TRP:plan': 1, 'ASP:plan': 15, 'GLU:plan': 39, 'ARG:plan': 23} Unresolved non-hydrogen planarities: 471 Chain: "K" Number of atoms: 1566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 1566 Classifications: {'peptide': 316} Incomplete info: {'truncation_to_alanine': 217} Link IDs: {'TRANS': 315} Unresolved non-hydrogen bonds: 802 Unresolved non-hydrogen angles: 1004 Unresolved non-hydrogen dihedrals: 619 Unresolved non-hydrogen chiralities: 75 Planarities with less than four sites: {'GLN:plan1': 14, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 14, 'TRP:plan': 1, 'ASP:plan': 12, 'GLU:plan': 44, 'ARG:plan': 26} Unresolved non-hydrogen planarities: 475 Chain: "L" Number of atoms: 1566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 1566 Classifications: {'peptide': 316} Incomplete info: {'truncation_to_alanine': 217} Link IDs: {'TRANS': 315} Unresolved non-hydrogen bonds: 802 Unresolved non-hydrogen angles: 1004 Unresolved non-hydrogen dihedrals: 619 Unresolved non-hydrogen chiralities: 75 Planarities with less than four sites: {'GLN:plan1': 14, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 14, 'TRP:plan': 1, 'ASP:plan': 12, 'GLU:plan': 44, 'ARG:plan': 26} Unresolved non-hydrogen planarities: 475 Chain: "M" Number of atoms: 1566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 1566 Classifications: {'peptide': 316} Incomplete info: {'truncation_to_alanine': 217} Link IDs: {'TRANS': 315} Unresolved non-hydrogen bonds: 802 Unresolved non-hydrogen angles: 1004 Unresolved non-hydrogen dihedrals: 619 Unresolved non-hydrogen chiralities: 75 Planarities with less than four sites: {'GLN:plan1': 14, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 14, 'TRP:plan': 1, 'ASP:plan': 12, 'GLU:plan': 44, 'ARG:plan': 26} Unresolved non-hydrogen planarities: 475 Chain: "N" Number of atoms: 1566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 1566 Classifications: {'peptide': 316} Incomplete info: {'truncation_to_alanine': 217} Link IDs: {'TRANS': 315} Unresolved non-hydrogen bonds: 802 Unresolved non-hydrogen angles: 1004 Unresolved non-hydrogen dihedrals: 619 Unresolved non-hydrogen chiralities: 75 Planarities with less than four sites: {'GLN:plan1': 14, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 14, 'TRP:plan': 1, 'ASP:plan': 12, 'GLU:plan': 44, 'ARG:plan': 26} Unresolved non-hydrogen planarities: 475 Chain: "O" Number of atoms: 1566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 1566 Classifications: {'peptide': 316} Incomplete info: {'truncation_to_alanine': 217} Link IDs: {'TRANS': 315} Unresolved non-hydrogen bonds: 802 Unresolved non-hydrogen angles: 1004 Unresolved non-hydrogen dihedrals: 619 Unresolved non-hydrogen chiralities: 75 Planarities with less than four sites: {'GLN:plan1': 14, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 14, 'TRP:plan': 1, 'ASP:plan': 12, 'GLU:plan': 44, 'ARG:plan': 26} Unresolved non-hydrogen planarities: 475 Chain: "P" Number of atoms: 1566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 1566 Classifications: {'peptide': 316} Incomplete info: {'truncation_to_alanine': 217} Link IDs: {'TRANS': 315} Unresolved non-hydrogen bonds: 802 Unresolved non-hydrogen angles: 1004 Unresolved non-hydrogen dihedrals: 619 Unresolved non-hydrogen chiralities: 75 Planarities with less than four sites: {'GLN:plan1': 14, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 14, 'TRP:plan': 1, 'ASP:plan': 12, 'GLU:plan': 44, 'ARG:plan': 26} Unresolved non-hydrogen planarities: 475 Chain: "Q" Number of atoms: 1566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 1566 Classifications: {'peptide': 316} Incomplete info: {'truncation_to_alanine': 217} Link IDs: {'TRANS': 315} Unresolved non-hydrogen bonds: 802 Unresolved non-hydrogen angles: 1004 Unresolved non-hydrogen dihedrals: 619 Unresolved non-hydrogen chiralities: 75 Planarities with less than four sites: {'GLN:plan1': 14, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 14, 'TRP:plan': 1, 'ASP:plan': 12, 'GLU:plan': 44, 'ARG:plan': 26} Unresolved non-hydrogen planarities: 475 Chain: "R" Number of atoms: 1566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 1566 Classifications: {'peptide': 316} Incomplete info: {'truncation_to_alanine': 217} Link IDs: {'TRANS': 315} Unresolved non-hydrogen bonds: 802 Unresolved non-hydrogen angles: 1004 Unresolved non-hydrogen dihedrals: 619 Unresolved non-hydrogen chiralities: 75 Planarities with less than four sites: {'GLN:plan1': 14, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 14, 'TRP:plan': 1, 'ASP:plan': 12, 'GLU:plan': 44, 'ARG:plan': 26} Unresolved non-hydrogen planarities: 475 Chain: "S" Number of atoms: 1566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 1566 Classifications: {'peptide': 316} Incomplete info: {'truncation_to_alanine': 217} Link IDs: {'TRANS': 315} Unresolved non-hydrogen bonds: 802 Unresolved non-hydrogen angles: 1004 Unresolved non-hydrogen dihedrals: 619 Unresolved non-hydrogen chiralities: 75 Planarities with less than four sites: {'GLN:plan1': 14, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 14, 'TRP:plan': 1, 'ASP:plan': 12, 'GLU:plan': 44, 'ARG:plan': 26} Unresolved non-hydrogen planarities: 475 Chain: "T" Number of atoms: 1566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 1566 Classifications: {'peptide': 316} Incomplete info: {'truncation_to_alanine': 217} Link IDs: {'TRANS': 315} Unresolved non-hydrogen bonds: 802 Unresolved non-hydrogen angles: 1004 Unresolved non-hydrogen dihedrals: 619 Unresolved non-hydrogen chiralities: 75 Planarities with less than four sites: {'GLN:plan1': 14, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 14, 'TRP:plan': 1, 'ASP:plan': 12, 'GLU:plan': 44, 'ARG:plan': 26} Unresolved non-hydrogen planarities: 475 Chain: "a" Number of atoms: 1359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 1359 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 194} Link IDs: {'TRANS': 273} Unresolved non-hydrogen bonds: 732 Unresolved non-hydrogen angles: 917 Unresolved non-hydrogen dihedrals: 576 Unresolved non-hydrogen chiralities: 64 Planarities with less than four sites: {'GLN:plan1': 14, 'ASP:plan': 8, 'TYR:plan': 3, 'ASN:plan1': 11, 'TRP:plan': 1, 'HIS:plan': 4, 'PHE:plan': 2, 'GLU:plan': 35, 'ARG:plan': 26} Unresolved non-hydrogen planarities: 445 Chain: "b" Number of atoms: 1359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 1359 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 194} Link IDs: {'TRANS': 273} Unresolved non-hydrogen bonds: 732 Unresolved non-hydrogen angles: 917 Unresolved non-hydrogen dihedrals: 576 Unresolved non-hydrogen chiralities: 64 Planarities with less than four sites: {'GLN:plan1': 14, 'ASP:plan': 8, 'TYR:plan': 3, 'ASN:plan1': 11, 'TRP:plan': 1, 'HIS:plan': 4, 'PHE:plan': 2, 'GLU:plan': 35, 'ARG:plan': 26} Unresolved non-hydrogen planarities: 445 Chain: "c" Number of atoms: 1359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 1359 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 194} Link IDs: {'TRANS': 273} Unresolved non-hydrogen bonds: 732 Unresolved non-hydrogen angles: 917 Unresolved non-hydrogen dihedrals: 576 Unresolved non-hydrogen chiralities: 64 Planarities with less than four sites: {'GLN:plan1': 14, 'ASP:plan': 8, 'TYR:plan': 3, 'ASN:plan1': 11, 'TRP:plan': 1, 'HIS:plan': 4, 'PHE:plan': 2, 'GLU:plan': 35, 'ARG:plan': 26} Unresolved non-hydrogen planarities: 445 Chain: "d" Number of atoms: 1359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 1359 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 194} Link IDs: {'TRANS': 273} Unresolved non-hydrogen bonds: 732 Unresolved non-hydrogen angles: 917 Unresolved non-hydrogen dihedrals: 576 Unresolved non-hydrogen chiralities: 64 Planarities with less than four sites: {'GLN:plan1': 14, 'ASP:plan': 8, 'TYR:plan': 3, 'ASN:plan1': 11, 'TRP:plan': 1, 'HIS:plan': 4, 'PHE:plan': 2, 'GLU:plan': 35, 'ARG:plan': 26} Unresolved non-hydrogen planarities: 445 Chain: "e" Number of atoms: 1359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 1359 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 194} Link IDs: {'TRANS': 273} Unresolved non-hydrogen bonds: 732 Unresolved non-hydrogen angles: 917 Unresolved non-hydrogen dihedrals: 576 Unresolved non-hydrogen chiralities: 64 Planarities with less than four sites: {'GLN:plan1': 14, 'ASP:plan': 8, 'TYR:plan': 3, 'ASN:plan1': 11, 'TRP:plan': 1, 'HIS:plan': 4, 'PHE:plan': 2, 'GLU:plan': 35, 'ARG:plan': 26} Unresolved non-hydrogen planarities: 445 Chain: "f" Number of atoms: 1359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 1359 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 195} Link IDs: {'TRANS': 273} Unresolved non-hydrogen bonds: 728 Unresolved non-hydrogen angles: 912 Unresolved non-hydrogen dihedrals: 570 Unresolved non-hydrogen chiralities: 65 Planarities with less than four sites: {'GLN:plan1': 14, 'ASP:plan': 8, 'TYR:plan': 2, 'ASN:plan1': 10, 'TRP:plan': 1, 'HIS:plan': 4, 'PHE:plan': 2, 'GLU:plan': 38, 'ARG:plan': 25} Unresolved non-hydrogen planarities: 442 Chain: "g" Number of atoms: 1359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 1359 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 195} Link IDs: {'TRANS': 273} Unresolved non-hydrogen bonds: 728 Unresolved non-hydrogen angles: 912 Unresolved non-hydrogen dihedrals: 570 Unresolved non-hydrogen chiralities: 65 Planarities with less than four sites: {'GLN:plan1': 14, 'ASP:plan': 8, 'TYR:plan': 2, 'ASN:plan1': 10, 'TRP:plan': 1, 'HIS:plan': 4, 'PHE:plan': 2, 'GLU:plan': 38, 'ARG:plan': 25} Unresolved non-hydrogen planarities: 442 Chain: "h" Number of atoms: 1359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 1359 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 195} Link IDs: {'TRANS': 273} Unresolved non-hydrogen bonds: 728 Unresolved non-hydrogen angles: 912 Unresolved non-hydrogen dihedrals: 570 Unresolved non-hydrogen chiralities: 65 Planarities with less than four sites: {'GLN:plan1': 14, 'ASP:plan': 8, 'TYR:plan': 2, 'ASN:plan1': 10, 'TRP:plan': 1, 'HIS:plan': 4, 'PHE:plan': 2, 'GLU:plan': 38, 'ARG:plan': 25} Unresolved non-hydrogen planarities: 442 Chain: "i" Number of atoms: 1359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 1359 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 195} Link IDs: {'TRANS': 273} Unresolved non-hydrogen bonds: 728 Unresolved non-hydrogen angles: 912 Unresolved non-hydrogen dihedrals: 570 Unresolved non-hydrogen chiralities: 65 Planarities with less than four sites: {'GLN:plan1': 14, 'ASP:plan': 8, 'TYR:plan': 2, 'ASN:plan1': 10, 'TRP:plan': 1, 'HIS:plan': 4, 'PHE:plan': 2, 'GLU:plan': 38, 'ARG:plan': 25} Unresolved non-hydrogen planarities: 442 Chain: "j" Number of atoms: 1359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 1359 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 195} Link IDs: {'TRANS': 273} Unresolved non-hydrogen bonds: 728 Unresolved non-hydrogen angles: 912 Unresolved non-hydrogen dihedrals: 570 Unresolved non-hydrogen chiralities: 65 Planarities with less than four sites: {'GLN:plan1': 14, 'ASP:plan': 8, 'TYR:plan': 2, 'ASN:plan1': 10, 'TRP:plan': 1, 'HIS:plan': 4, 'PHE:plan': 2, 'GLU:plan': 38, 'ARG:plan': 25} Unresolved non-hydrogen planarities: 442 Time building chain proxies: 28.50, per 1000 atoms: 0.63 Number of scatterers: 44930 At special positions: 0 Unit cell: (292.32, 280.56, 162.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 9060 8.00 N 9060 7.00 C 26810 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 - 3.00 Amino acid : True - 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: 14.96 Conformation dependent library (CDL) restraints added in 9.3 seconds 18000 Ramachandran restraints generated. 9000 Oldfield, 0 Emsley, 9000 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17380 Finding SS restraints... Secondary structure from input PDB file: 382 helices and 0 sheets defined 98.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.66 Creating SS restraints... Processing helix chain 'A' and resid 1 through 26 removed outlier: 3.767A pdb=" N LEU A 5 " --> pdb=" O LEU A 1 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LYS A 6 " --> pdb=" O GLU A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 56 Processing helix chain 'A' and resid 57 through 83 removed outlier: 3.856A pdb=" N ASP A 81 " --> pdb=" O GLU A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 113 removed outlier: 3.779A pdb=" N LEU A 88 " --> pdb=" O ASN A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 140 removed outlier: 3.805A pdb=" N ASP A 138 " --> pdb=" O GLU A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 168 removed outlier: 3.917A pdb=" N LEU A 145 " --> pdb=" O ASN A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 188 removed outlier: 3.741A pdb=" N ALA A 173 " --> pdb=" O ASP A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 210 removed outlier: 3.724A pdb=" N ALA A 195 " --> pdb=" O ASP A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 231 removed outlier: 4.129A pdb=" N GLN A 229 " --> pdb=" O GLU A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 253 Processing helix chain 'A' and resid 255 through 274 removed outlier: 3.774A pdb=" N GLN A 272 " --> pdb=" O GLU A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 297 Processing helix chain 'A' and resid 298 through 315 Processing helix chain 'B' and resid 2 through 24 removed outlier: 3.832A pdb=" N LYS B 6 " --> pdb=" O GLU B 2 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ASP B 24 " --> pdb=" O GLU B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 56 Processing helix chain 'B' and resid 57 through 83 removed outlier: 4.006A pdb=" N ASP B 81 " --> pdb=" O GLU B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 113 removed outlier: 3.929A pdb=" N LEU B 88 " --> pdb=" O ASN B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 140 removed outlier: 4.404A pdb=" N ASP B 138 " --> pdb=" O GLU B 134 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG B 139 " --> pdb=" O ILE B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 168 Processing helix chain 'B' and resid 169 through 188 removed outlier: 3.552A pdb=" N GLU B 179 " --> pdb=" O ARG B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 211 removed outlier: 3.600A pdb=" N LEU B 201 " --> pdb=" O ALA B 197 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG B 202 " --> pdb=" O ILE B 198 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS B 209 " --> pdb=" O LYS B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 231 removed outlier: 3.761A pdb=" N VAL B 222 " --> pdb=" O LYS B 218 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLN B 229 " --> pdb=" O GLU B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 253 Processing helix chain 'B' and resid 255 through 274 removed outlier: 3.505A pdb=" N VAL B 265 " --> pdb=" O LYS B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 297 Processing helix chain 'B' and resid 298 through 316 Processing helix chain 'C' and resid 2 through 26 removed outlier: 4.324A pdb=" N LYS C 6 " --> pdb=" O GLU C 2 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASP C 24 " --> pdb=" O GLU C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 56 removed outlier: 3.629A pdb=" N LEU C 31 " --> pdb=" O ASN C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 83 removed outlier: 4.025A pdb=" N ASP C 81 " --> pdb=" O GLU C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 113 Processing helix chain 'C' and resid 114 through 140 removed outlier: 4.177A pdb=" N ASP C 138 " --> pdb=" O GLU C 134 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ARG C 139 " --> pdb=" O ILE C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 168 Processing helix chain 'C' and resid 169 through 188 removed outlier: 3.732A pdb=" N GLU C 179 " --> pdb=" O ARG C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 211 removed outlier: 3.541A pdb=" N LEU C 201 " --> pdb=" O ALA C 197 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG C 202 " --> pdb=" O ILE C 198 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS C 209 " --> pdb=" O LYS C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 231 removed outlier: 4.588A pdb=" N VAL C 222 " --> pdb=" O LYS C 218 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ALA C 223 " --> pdb=" O ALA C 219 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL C 224 " --> pdb=" O ALA C 220 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLU C 225 " --> pdb=" O ARG C 221 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLN C 229 " --> pdb=" O GLU C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 253 Processing helix chain 'C' and resid 255 through 274 Processing helix chain 'C' and resid 275 through 297 Processing helix chain 'C' and resid 298 through 314 Processing helix chain 'C' and resid 315 through 316 No H-bonds generated for 'chain 'C' and resid 315 through 316' Processing helix chain 'D' and resid 1 through 1 No H-bonds generated for 'chain 'D' and resid 1 through 1' Processing helix chain 'D' and resid 2 through 24 removed outlier: 3.798A pdb=" N LYS D 6 " --> pdb=" O GLU D 2 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ASP D 24 " --> pdb=" O GLU D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 56 removed outlier: 3.610A pdb=" N LEU D 31 " --> pdb=" O ASN D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 83 removed outlier: 4.565A pdb=" N ASP D 81 " --> pdb=" O GLU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 113 removed outlier: 4.258A pdb=" N LEU D 88 " --> pdb=" O ASN D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 140 removed outlier: 3.942A pdb=" N LYS D 120 " --> pdb=" O GLN D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 168 removed outlier: 3.518A pdb=" N LEU D 145 " --> pdb=" O ASN D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 188 removed outlier: 3.540A pdb=" N GLU D 179 " --> pdb=" O ARG D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 211 removed outlier: 3.669A pdb=" N LYS D 209 " --> pdb=" O LYS D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 231 removed outlier: 3.954A pdb=" N LYS D 218 " --> pdb=" O GLU D 214 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLN D 229 " --> pdb=" O GLU D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 253 Processing helix chain 'D' and resid 255 through 274 removed outlier: 3.936A pdb=" N GLN D 272 " --> pdb=" O GLU D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 297 Processing helix chain 'D' and resid 298 through 314 Processing helix chain 'D' and resid 315 through 316 No H-bonds generated for 'chain 'D' and resid 315 through 316' Processing helix chain 'E' and resid 1 through 1 No H-bonds generated for 'chain 'E' and resid 1 through 1' Processing helix chain 'E' and resid 2 through 26 removed outlier: 3.593A pdb=" N LYS E 6 " --> pdb=" O GLU E 2 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 56 Processing helix chain 'E' and resid 57 through 83 removed outlier: 3.911A pdb=" N ASP E 81 " --> pdb=" O GLU E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 113 Processing helix chain 'E' and resid 114 through 140 removed outlier: 3.516A pdb=" N HIS E 123 " --> pdb=" O THR E 119 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE E 124 " --> pdb=" O LYS E 120 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASP E 138 " --> pdb=" O GLU E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 141 through 168 Processing helix chain 'E' and resid 169 through 188 Processing helix chain 'E' and resid 189 through 211 removed outlier: 3.772A pdb=" N ARG E 202 " --> pdb=" O ILE E 198 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS E 209 " --> pdb=" O LYS E 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 212 through 221 Processing helix chain 'E' and resid 222 through 231 removed outlier: 4.017A pdb=" N GLN E 229 " --> pdb=" O GLU E 225 " (cutoff:3.500A) Processing helix chain 'E' and resid 232 through 253 Processing helix chain 'E' and resid 255 through 274 removed outlier: 3.613A pdb=" N ALA E 263 " --> pdb=" O ALA E 259 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ARG E 264 " --> pdb=" O VAL E 260 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N VAL E 265 " --> pdb=" O LYS E 261 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA E 266 " --> pdb=" O ALA E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 297 Processing helix chain 'E' and resid 298 through 314 Processing helix chain 'F' and resid 2 through 26 removed outlier: 3.689A pdb=" N LYS F 6 " --> pdb=" O GLU F 2 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 56 removed outlier: 3.724A pdb=" N LYS F 54 " --> pdb=" O ARG F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 83 removed outlier: 4.346A pdb=" N ASP F 81 " --> pdb=" O GLU F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 84 through 113 Processing helix chain 'F' and resid 114 through 137 removed outlier: 4.167A pdb=" N LYS F 120 " --> pdb=" O GLN F 116 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU F 133 " --> pdb=" O ALA F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 168 removed outlier: 4.613A pdb=" N LEU F 151 " --> pdb=" O LYS F 147 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL F 152 " --> pdb=" O ALA F 148 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASP F 153 " --> pdb=" O ALA F 149 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ALA F 154 " --> pdb=" O SER F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 178 Processing helix chain 'F' and resid 179 through 188 removed outlier: 4.341A pdb=" N ALA F 183 " --> pdb=" O GLU F 179 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ALA F 184 " --> pdb=" O ALA F 180 " (cutoff:3.500A) Processing helix chain 'F' and resid 189 through 210 removed outlier: 3.558A pdb=" N ALA F 195 " --> pdb=" O ASP F 191 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS F 209 " --> pdb=" O LYS F 205 " (cutoff:3.500A) Processing helix chain 'F' and resid 212 through 231 removed outlier: 3.980A pdb=" N VAL F 222 " --> pdb=" O LYS F 218 " (cutoff:3.500A) Processing helix chain 'F' and resid 232 through 253 Processing helix chain 'F' and resid 255 through 274 removed outlier: 3.909A pdb=" N GLN F 272 " --> pdb=" O GLU F 268 " (cutoff:3.500A) Processing helix chain 'F' and resid 275 through 297 Processing helix chain 'F' and resid 298 through 314 Processing helix chain 'F' and resid 315 through 316 No H-bonds generated for 'chain 'F' and resid 315 through 316' Processing helix chain 'G' and resid 1 through 2 No H-bonds generated for 'chain 'G' and resid 1 through 2' Processing helix chain 'G' and resid 3 through 26 removed outlier: 4.134A pdb=" N ALA G 7 " --> pdb=" O LEU G 3 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LEU G 8 " --> pdb=" O ALA G 4 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLN G 9 " --> pdb=" O LEU G 5 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL G 17 " --> pdb=" O ASN G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 56 removed outlier: 3.728A pdb=" N ARG G 47 " --> pdb=" O ARG G 43 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE G 48 " --> pdb=" O GLN G 44 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS G 54 " --> pdb=" O ARG G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 83 removed outlier: 3.664A pdb=" N ALA G 61 " --> pdb=" O ASN G 57 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL G 74 " --> pdb=" O ASN G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 84 through 113 removed outlier: 3.626A pdb=" N GLU G 104 " --> pdb=" O ARG G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 114 through 140 removed outlier: 3.788A pdb=" N ARG G 118 " --> pdb=" O ASN G 114 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LYS G 120 " --> pdb=" O GLN G 116 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ASP G 138 " --> pdb=" O GLU G 134 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ARG G 139 " --> pdb=" O ILE G 135 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY G 140 " --> pdb=" O ALA G 136 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 168 Processing helix chain 'G' and resid 169 through 188 removed outlier: 4.222A pdb=" N GLU G 179 " --> pdb=" O ARG G 175 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL G 181 " --> pdb=" O ALA G 177 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N LYS G 182 " --> pdb=" O GLN G 178 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA G 183 " --> pdb=" O GLU G 179 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA G 184 " --> pdb=" O ALA G 180 " (cutoff:3.500A) Processing helix chain 'G' and resid 191 through 210 removed outlier: 3.883A pdb=" N LYS G 209 " --> pdb=" O LYS G 205 " (cutoff:3.500A) Processing helix chain 'G' and resid 212 through 231 removed outlier: 3.970A pdb=" N ALA G 216 " --> pdb=" O ASN G 212 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N VAL G 222 " --> pdb=" O LYS G 218 " (cutoff:3.500A) Processing helix chain 'G' and resid 234 through 253 removed outlier: 3.959A pdb=" N LYS G 238 " --> pdb=" O ASP G 234 " (cutoff:3.500A) Processing helix chain 'G' and resid 255 through 274 removed outlier: 3.948A pdb=" N GLN G 272 " --> pdb=" O GLU G 268 " (cutoff:3.500A) Processing helix chain 'G' and resid 275 through 297 Processing helix chain 'G' and resid 298 through 314 Processing helix chain 'G' and resid 315 through 316 No H-bonds generated for 'chain 'G' and resid 315 through 316' Processing helix chain 'H' and resid 1 through 2 No H-bonds generated for 'chain 'H' and resid 1 through 2' Processing helix chain 'H' and resid 3 through 25 removed outlier: 3.861A pdb=" N ALA H 7 " --> pdb=" O LEU H 3 " (cutoff:3.500A) Processing helix chain 'H' and resid 27 through 56 removed outlier: 4.197A pdb=" N ARG H 47 " --> pdb=" O ARG H 43 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ILE H 48 " --> pdb=" O GLN H 44 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ARG H 53 " --> pdb=" O ALA H 49 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LYS H 54 " --> pdb=" O ARG H 50 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 83 removed outlier: 4.909A pdb=" N ASP H 81 " --> pdb=" O GLU H 77 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ARG H 82 " --> pdb=" O ILE H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 84 through 113 removed outlier: 4.248A pdb=" N GLU H 104 " --> pdb=" O ARG H 100 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ILE H 105 " --> pdb=" O GLN H 101 " (cutoff:3.500A) Processing helix chain 'H' and resid 114 through 140 removed outlier: 3.785A pdb=" N ARG H 118 " --> pdb=" O ASN H 114 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LYS H 120 " --> pdb=" O GLN H 116 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N ASP H 138 " --> pdb=" O GLU H 134 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ARG H 139 " --> pdb=" O ILE H 135 " (cutoff:3.500A) Processing helix chain 'H' and resid 141 through 168 removed outlier: 3.511A pdb=" N LYS H 147 " --> pdb=" O GLU H 143 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA H 148 " --> pdb=" O LEU H 144 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA H 149 " --> pdb=" O LEU H 145 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ALA H 154 " --> pdb=" O SER H 150 " (cutoff:3.500A) Processing helix chain 'H' and resid 169 through 188 removed outlier: 4.424A pdb=" N GLU H 179 " --> pdb=" O ARG H 175 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N VAL H 181 " --> pdb=" O ALA H 177 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N LYS H 182 " --> pdb=" O GLN H 178 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ALA H 183 " --> pdb=" O GLU H 179 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ALA H 184 " --> pdb=" O ALA H 180 " (cutoff:3.500A) Processing helix chain 'H' and resid 191 through 211 removed outlier: 4.051A pdb=" N ALA H 195 " --> pdb=" O ASP H 191 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LYS H 209 " --> pdb=" O LYS H 205 " (cutoff:3.500A) Processing helix chain 'H' and resid 212 through 231 removed outlier: 3.880A pdb=" N VAL H 222 " --> pdb=" O LYS H 218 " (cutoff:3.500A) Processing helix chain 'H' and resid 232 through 253 removed outlier: 4.339A pdb=" N ALA H 240 " --> pdb=" O LEU H 236 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N GLU H 241 " --> pdb=" O ARG H 237 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLN H 242 " --> pdb=" O LYS H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 255 through 274 removed outlier: 3.910A pdb=" N GLN H 272 " --> pdb=" O GLU H 268 " (cutoff:3.500A) Processing helix chain 'H' and resid 275 through 297 Processing helix chain 'H' and resid 298 through 314 removed outlier: 4.189A pdb=" N LYS H 304 " --> pdb=" O ASP H 300 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 26 removed outlier: 3.606A pdb=" N VAL I 12 " --> pdb=" O LEU I 8 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ASN I 13 " --> pdb=" O GLN I 9 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA I 14 " --> pdb=" O ILE I 10 " (cutoff:3.500A) Processing helix chain 'I' and resid 27 through 56 removed outlier: 4.020A pdb=" N ARG I 47 " --> pdb=" O ARG I 43 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ILE I 48 " --> pdb=" O GLN I 44 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG I 53 " --> pdb=" O ALA I 49 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LYS I 54 " --> pdb=" O ARG I 50 " (cutoff:3.500A) Processing helix chain 'I' and resid 57 through 83 removed outlier: 3.950A pdb=" N TYR I 73 " --> pdb=" O VAL I 69 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N VAL I 74 " --> pdb=" O ASN I 70 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU I 75 " --> pdb=" O ALA I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 84 through 113 removed outlier: 4.114A pdb=" N GLU I 104 " --> pdb=" O ARG I 100 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE I 105 " --> pdb=" O GLN I 101 " (cutoff:3.500A) Processing helix chain 'I' and resid 114 through 137 removed outlier: 3.959A pdb=" N ARG I 118 " --> pdb=" O ASN I 114 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LYS I 120 " --> pdb=" O GLN I 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 141 through 168 removed outlier: 4.196A pdb=" N LYS I 147 " --> pdb=" O GLU I 143 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA I 148 " --> pdb=" O LEU I 144 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU I 166 " --> pdb=" O ALA I 162 " (cutoff:3.500A) Processing helix chain 'I' and resid 169 through 188 removed outlier: 4.194A pdb=" N GLU I 179 " --> pdb=" O ARG I 175 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS I 182 " --> pdb=" O GLN I 178 " (cutoff:3.500A) Processing helix chain 'I' and resid 191 through 211 removed outlier: 3.952A pdb=" N ALA I 195 " --> pdb=" O ASP I 191 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ALA I 199 " --> pdb=" O ALA I 195 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA I 200 " --> pdb=" O VAL I 196 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU I 201 " --> pdb=" O ALA I 197 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU I 206 " --> pdb=" O ARG I 202 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS I 209 " --> pdb=" O LYS I 205 " (cutoff:3.500A) Processing helix chain 'I' and resid 212 through 231 removed outlier: 3.557A pdb=" N VAL I 222 " --> pdb=" O LYS I 218 " (cutoff:3.500A) Processing helix chain 'I' and resid 234 through 253 removed outlier: 3.848A pdb=" N LYS I 238 " --> pdb=" O ASP I 234 " (cutoff:3.500A) Processing helix chain 'I' and resid 255 through 274 removed outlier: 3.580A pdb=" N GLN I 272 " --> pdb=" O GLU I 268 " (cutoff:3.500A) Processing helix chain 'I' and resid 275 through 297 removed outlier: 3.649A pdb=" N GLU I 288 " --> pdb=" O ASP I 284 " (cutoff:3.500A) Processing helix chain 'I' and resid 298 through 314 Processing helix chain 'J' and resid 2 through 26 removed outlier: 3.919A pdb=" N ASN J 13 " --> pdb=" O GLN J 9 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 56 removed outlier: 3.822A pdb=" N LYS J 54 " --> pdb=" O ARG J 50 " (cutoff:3.500A) Processing helix chain 'J' and resid 57 through 83 removed outlier: 4.868A pdb=" N ASP J 81 " --> pdb=" O GLU J 77 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ARG J 82 " --> pdb=" O ILE J 78 " (cutoff:3.500A) Processing helix chain 'J' and resid 84 through 113 removed outlier: 4.306A pdb=" N GLU J 104 " --> pdb=" O ARG J 100 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ILE J 105 " --> pdb=" O GLN J 101 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TRP J 106 " --> pdb=" O ALA J 102 " (cutoff:3.500A) Processing helix chain 'J' and resid 114 through 137 removed outlier: 3.989A pdb=" N ARG J 118 " --> pdb=" O ASN J 114 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N LYS J 120 " --> pdb=" O GLN J 116 " (cutoff:3.500A) Processing helix chain 'J' and resid 141 through 168 removed outlier: 3.648A pdb=" N LYS J 147 " --> pdb=" O GLU J 143 " (cutoff:3.500A) Processing helix chain 'J' and resid 169 through 188 removed outlier: 4.083A pdb=" N GLU J 179 " --> pdb=" O ARG J 175 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS J 182 " --> pdb=" O GLN J 178 " (cutoff:3.500A) Processing helix chain 'J' and resid 191 through 211 removed outlier: 4.110A pdb=" N ALA J 195 " --> pdb=" O ASP J 191 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS J 209 " --> pdb=" O LYS J 205 " (cutoff:3.500A) Processing helix chain 'J' and resid 212 through 231 removed outlier: 4.137A pdb=" N VAL J 222 " --> pdb=" O LYS J 218 " (cutoff:3.500A) Processing helix chain 'J' and resid 232 through 253 Processing helix chain 'J' and resid 255 through 274 removed outlier: 4.250A pdb=" N GLN J 272 " --> pdb=" O GLU J 268 " (cutoff:3.500A) Processing helix chain 'J' and resid 275 through 297 Processing helix chain 'J' and resid 298 through 314 Processing helix chain 'K' and resid 2 through 26 removed outlier: 3.504A pdb=" N ASP K 24 " --> pdb=" O GLU K 20 " (cutoff:3.500A) Processing helix chain 'K' and resid 27 through 55 removed outlier: 3.754A pdb=" N LEU K 31 " --> pdb=" O ASN K 27 " (cutoff:3.500A) Processing helix chain 'K' and resid 57 through 83 removed outlier: 3.648A pdb=" N ASP K 81 " --> pdb=" O GLU K 77 " (cutoff:3.500A) Processing helix chain 'K' and resid 84 through 113 Processing helix chain 'K' and resid 114 through 140 removed outlier: 3.508A pdb=" N LYS K 120 " --> pdb=" O GLU K 116 " (cutoff:3.500A) Processing helix chain 'K' and resid 141 through 168 removed outlier: 3.707A pdb=" N LEU K 145 " --> pdb=" O ASN K 141 " (cutoff:3.500A) Processing helix chain 'K' and resid 169 through 188 Processing helix chain 'K' and resid 189 through 210 Processing helix chain 'K' and resid 212 through 231 removed outlier: 3.779A pdb=" N GLN K 229 " --> pdb=" O GLU K 225 " (cutoff:3.500A) Processing helix chain 'K' and resid 232 through 253 Processing helix chain 'K' and resid 255 through 274 Processing helix chain 'K' and resid 275 through 297 Processing helix chain 'K' and resid 298 through 314 Processing helix chain 'L' and resid 2 through 26 Processing helix chain 'L' and resid 27 through 55 removed outlier: 4.227A pdb=" N LEU L 31 " --> pdb=" O ASN L 27 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG L 47 " --> pdb=" O ARG L 43 " (cutoff:3.500A) Processing helix chain 'L' and resid 57 through 83 removed outlier: 3.723A pdb=" N ASP L 81 " --> pdb=" O GLU L 77 " (cutoff:3.500A) Processing helix chain 'L' and resid 84 through 113 Processing helix chain 'L' and resid 114 through 140 Processing helix chain 'L' and resid 141 through 168 Processing helix chain 'L' and resid 169 through 188 Processing helix chain 'L' and resid 189 through 210 Processing helix chain 'L' and resid 212 through 231 removed outlier: 3.712A pdb=" N GLN L 229 " --> pdb=" O GLU L 225 " (cutoff:3.500A) Processing helix chain 'L' and resid 232 through 253 Processing helix chain 'L' and resid 255 through 274 removed outlier: 3.801A pdb=" N GLN L 272 " --> pdb=" O GLU L 268 " (cutoff:3.500A) Processing helix chain 'L' and resid 275 through 297 Processing helix chain 'L' and resid 298 through 314 Processing helix chain 'M' and resid 2 through 24 Processing helix chain 'M' and resid 27 through 55 removed outlier: 3.891A pdb=" N LEU M 31 " --> pdb=" O ASN M 27 " (cutoff:3.500A) Processing helix chain 'M' and resid 57 through 83 removed outlier: 3.949A pdb=" N ASP M 81 " --> pdb=" O GLU M 77 " (cutoff:3.500A) Processing helix chain 'M' and resid 84 through 113 Processing helix chain 'M' and resid 114 through 140 removed outlier: 3.585A pdb=" N ASP M 138 " --> pdb=" O GLU M 134 " (cutoff:3.500A) Processing helix chain 'M' and resid 141 through 168 Processing helix chain 'M' and resid 169 through 188 Processing helix chain 'M' and resid 189 through 210 Processing helix chain 'M' and resid 212 through 231 removed outlier: 3.874A pdb=" N GLN M 229 " --> pdb=" O GLU M 225 " (cutoff:3.500A) Processing helix chain 'M' and resid 232 through 253 Processing helix chain 'M' and resid 255 through 274 Processing helix chain 'M' and resid 275 through 297 Processing helix chain 'M' and resid 298 through 314 Processing helix chain 'N' and resid 2 through 26 Processing helix chain 'N' and resid 28 through 55 Processing helix chain 'N' and resid 57 through 83 removed outlier: 3.621A pdb=" N ASP N 81 " --> pdb=" O GLU N 77 " (cutoff:3.500A) Processing helix chain 'N' and resid 84 through 113 Processing helix chain 'N' and resid 114 through 140 Processing helix chain 'N' and resid 141 through 168 Processing helix chain 'N' and resid 169 through 188 Processing helix chain 'N' and resid 189 through 210 Processing helix chain 'N' and resid 212 through 231 removed outlier: 3.864A pdb=" N GLN N 229 " --> pdb=" O GLU N 225 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA N 230 " --> pdb=" O ALA N 226 " (cutoff:3.500A) Processing helix chain 'N' and resid 232 through 253 Processing helix chain 'N' and resid 255 through 274 removed outlier: 3.670A pdb=" N GLN N 272 " --> pdb=" O GLU N 268 " (cutoff:3.500A) Processing helix chain 'N' and resid 275 through 297 Processing helix chain 'N' and resid 298 through 314 Processing helix chain 'O' and resid 2 through 26 Processing helix chain 'O' and resid 27 through 56 Processing helix chain 'O' and resid 57 through 83 removed outlier: 3.577A pdb=" N ASP O 81 " --> pdb=" O GLU O 77 " (cutoff:3.500A) Processing helix chain 'O' and resid 84 through 113 Processing helix chain 'O' and resid 114 through 140 Processing helix chain 'O' and resid 141 through 168 Processing helix chain 'O' and resid 169 through 188 Processing helix chain 'O' and resid 189 through 210 Processing helix chain 'O' and resid 212 through 231 removed outlier: 4.064A pdb=" N GLN O 229 " --> pdb=" O GLU O 225 " (cutoff:3.500A) Processing helix chain 'O' and resid 232 through 253 Processing helix chain 'O' and resid 255 through 274 removed outlier: 3.569A pdb=" N GLN O 272 " --> pdb=" O GLU O 268 " (cutoff:3.500A) Processing helix chain 'O' and resid 275 through 297 Processing helix chain 'O' and resid 298 through 316 Processing helix chain 'P' and resid 2 through 26 removed outlier: 3.660A pdb=" N ARG P 23 " --> pdb=" O ALA P 19 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASP P 24 " --> pdb=" O GLU P 20 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASN P 25 " --> pdb=" O ILE P 21 " (cutoff:3.500A) Processing helix chain 'P' and resid 27 through 56 removed outlier: 3.533A pdb=" N LYS P 54 " --> pdb=" O ARG P 50 " (cutoff:3.500A) Processing helix chain 'P' and resid 57 through 83 removed outlier: 3.722A pdb=" N ASP P 81 " --> pdb=" O GLU P 77 " (cutoff:3.500A) Processing helix chain 'P' and resid 85 through 113 Processing helix chain 'P' and resid 114 through 140 removed outlier: 3.563A pdb=" N ASP P 138 " --> pdb=" O GLU P 134 " (cutoff:3.500A) Processing helix chain 'P' and resid 141 through 168 Processing helix chain 'P' and resid 169 through 186 Processing helix chain 'P' and resid 189 through 211 removed outlier: 3.891A pdb=" N LEU P 193 " --> pdb=" O ASP P 189 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLU P 208 " --> pdb=" O ALA P 204 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N LYS P 209 " --> pdb=" O LYS P 205 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLN P 210 " --> pdb=" O GLU P 206 " (cutoff:3.500A) Processing helix chain 'P' and resid 212 through 231 removed outlier: 4.036A pdb=" N GLN P 229 " --> pdb=" O GLU P 225 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA P 230 " --> pdb=" O ALA P 226 " (cutoff:3.500A) Processing helix chain 'P' and resid 232 through 253 Processing helix chain 'P' and resid 255 through 274 removed outlier: 3.568A pdb=" N GLU P 268 " --> pdb=" O ARG P 264 " (cutoff:3.500A) Processing helix chain 'P' and resid 275 through 296 Processing helix chain 'P' and resid 298 through 315 Processing helix chain 'Q' and resid 2 through 24 removed outlier: 3.644A pdb=" N ASP Q 24 " --> pdb=" O GLU Q 20 " (cutoff:3.500A) Processing helix chain 'Q' and resid 27 through 56 removed outlier: 4.074A pdb=" N LEU Q 31 " --> pdb=" O ASN Q 27 " (cutoff:3.500A) Processing helix chain 'Q' and resid 57 through 83 removed outlier: 3.519A pdb=" N ASP Q 81 " --> pdb=" O GLU Q 77 " (cutoff:3.500A) Processing helix chain 'Q' and resid 85 through 113 Processing helix chain 'Q' and resid 114 through 140 Processing helix chain 'Q' and resid 141 through 168 Processing helix chain 'Q' and resid 169 through 188 removed outlier: 3.566A pdb=" N ALA Q 173 " --> pdb=" O ASP Q 169 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU Q 179 " --> pdb=" O ARG Q 175 " (cutoff:3.500A) Processing helix chain 'Q' and resid 189 through 208 Processing helix chain 'Q' and resid 212 through 231 removed outlier: 4.135A pdb=" N GLN Q 229 " --> pdb=" O GLU Q 225 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA Q 230 " --> pdb=" O ALA Q 226 " (cutoff:3.500A) Processing helix chain 'Q' and resid 232 through 253 Processing helix chain 'Q' and resid 255 through 274 Processing helix chain 'Q' and resid 275 through 297 Processing helix chain 'Q' and resid 298 through 314 Processing helix chain 'R' and resid 2 through 24 removed outlier: 3.614A pdb=" N ASP R 24 " --> pdb=" O GLU R 20 " (cutoff:3.500A) Processing helix chain 'R' and resid 27 through 56 removed outlier: 3.535A pdb=" N ARG R 47 " --> pdb=" O ARG R 43 " (cutoff:3.500A) Processing helix chain 'R' and resid 57 through 83 removed outlier: 3.663A pdb=" N ASP R 81 " --> pdb=" O GLU R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 85 through 113 Processing helix chain 'R' and resid 114 through 140 Processing helix chain 'R' and resid 142 through 168 removed outlier: 3.652A pdb=" N GLU R 146 " --> pdb=" O GLU R 142 " (cutoff:3.500A) Processing helix chain 'R' and resid 169 through 188 Processing helix chain 'R' and resid 189 through 208 Processing helix chain 'R' and resid 212 through 231 removed outlier: 4.152A pdb=" N GLN R 229 " --> pdb=" O GLU R 225 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA R 230 " --> pdb=" O ALA R 226 " (cutoff:3.500A) Processing helix chain 'R' and resid 232 through 253 Processing helix chain 'R' and resid 255 through 274 removed outlier: 3.933A pdb=" N GLN R 272 " --> pdb=" O GLU R 268 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA R 273 " --> pdb=" O ALA R 269 " (cutoff:3.500A) Processing helix chain 'R' and resid 275 through 296 Processing helix chain 'R' and resid 298 through 314 Processing helix chain 'S' and resid 2 through 24 removed outlier: 3.688A pdb=" N ASP S 24 " --> pdb=" O GLU S 20 " (cutoff:3.500A) Processing helix chain 'S' and resid 27 through 56 Processing helix chain 'S' and resid 57 through 83 removed outlier: 3.786A pdb=" N ASP S 81 " --> pdb=" O GLU S 77 " (cutoff:3.500A) Processing helix chain 'S' and resid 84 through 113 removed outlier: 3.754A pdb=" N LEU S 88 " --> pdb=" O ASN S 84 " (cutoff:3.500A) Processing helix chain 'S' and resid 114 through 140 removed outlier: 3.634A pdb=" N ASP S 138 " --> pdb=" O GLU S 134 " (cutoff:3.500A) Processing helix chain 'S' and resid 141 through 168 Processing helix chain 'S' and resid 169 through 188 removed outlier: 3.529A pdb=" N ALA S 187 " --> pdb=" O ALA S 183 " (cutoff:3.500A) Processing helix chain 'S' and resid 189 through 211 removed outlier: 4.258A pdb=" N LYS S 209 " --> pdb=" O LYS S 205 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN S 210 " --> pdb=" O GLU S 206 " (cutoff:3.500A) Processing helix chain 'S' and resid 212 through 231 removed outlier: 4.091A pdb=" N GLN S 229 " --> pdb=" O GLU S 225 " (cutoff:3.500A) Processing helix chain 'S' and resid 232 through 253 Processing helix chain 'S' and resid 255 through 274 removed outlier: 3.853A pdb=" N GLN S 272 " --> pdb=" O GLU S 268 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA S 273 " --> pdb=" O ALA S 269 " (cutoff:3.500A) Processing helix chain 'S' and resid 275 through 296 Processing helix chain 'S' and resid 298 through 314 Processing helix chain 'T' and resid 2 through 26 removed outlier: 4.653A pdb=" N ASP T 24 " --> pdb=" O GLU T 20 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASN T 25 " --> pdb=" O ILE T 21 " (cutoff:3.500A) Processing helix chain 'T' and resid 27 through 56 removed outlier: 3.505A pdb=" N LYS T 54 " --> pdb=" O ARG T 50 " (cutoff:3.500A) Processing helix chain 'T' and resid 57 through 83 removed outlier: 3.544A pdb=" N ALA T 61 " --> pdb=" O ASN T 57 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ASP T 81 " --> pdb=" O GLU T 77 " (cutoff:3.500A) Processing helix chain 'T' and resid 84 through 113 removed outlier: 3.820A pdb=" N LEU T 88 " --> pdb=" O ASN T 84 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ALA T 91 " --> pdb=" O GLU T 87 " (cutoff:3.500A) Processing helix chain 'T' and resid 114 through 140 Processing helix chain 'T' and resid 141 through 168 removed outlier: 3.534A pdb=" N LEU T 145 " --> pdb=" O ASN T 141 " (cutoff:3.500A) Processing helix chain 'T' and resid 169 through 186 Processing helix chain 'T' and resid 189 through 211 removed outlier: 4.278A pdb=" N LYS T 209 " --> pdb=" O LYS T 205 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN T 210 " --> pdb=" O GLU T 206 " (cutoff:3.500A) Processing helix chain 'T' and resid 212 through 231 removed outlier: 3.929A pdb=" N GLN T 229 " --> pdb=" O GLU T 225 " (cutoff:3.500A) Processing helix chain 'T' and resid 232 through 253 Processing helix chain 'T' and resid 255 through 274 removed outlier: 4.329A pdb=" N GLN T 272 " --> pdb=" O GLU T 268 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA T 273 " --> pdb=" O ALA T 269 " (cutoff:3.500A) Processing helix chain 'T' and resid 275 through 297 Processing helix chain 'T' and resid 298 through 314 Processing helix chain 'T' and resid 315 through 316 No H-bonds generated for 'chain 'T' and resid 315 through 316' Processing helix chain 'a' and resid 1 through 1 No H-bonds generated for 'chain 'a' and resid 1 through 1' Processing helix chain 'a' and resid 2 through 26 removed outlier: 3.574A pdb=" N GLN a 6 " --> pdb=" O GLU a 2 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN a 24 " --> pdb=" O ARG a 20 " (cutoff:3.500A) Processing helix chain 'a' and resid 27 through 56 removed outlier: 3.733A pdb=" N LYS a 54 " --> pdb=" O ARG a 50 " (cutoff:3.500A) Processing helix chain 'a' and resid 57 through 83 removed outlier: 3.761A pdb=" N ASP a 81 " --> pdb=" O GLU a 77 " (cutoff:3.500A) Processing helix chain 'a' and resid 84 through 113 Processing helix chain 'a' and resid 114 through 140 removed outlier: 3.935A pdb=" N HIS a 138 " --> pdb=" O ARG a 134 " (cutoff:3.500A) Processing helix chain 'a' and resid 141 through 168 Processing helix chain 'a' and resid 169 through 188 removed outlier: 3.545A pdb=" N LYS a 182 " --> pdb=" O GLN a 178 " (cutoff:3.500A) Processing helix chain 'a' and resid 189 through 211 Processing helix chain 'a' and resid 212 through 231 Processing helix chain 'a' and resid 232 through 253 Processing helix chain 'a' and resid 255 through 274 Processing helix chain 'b' and resid 2 through 26 removed outlier: 3.743A pdb=" N GLN b 6 " --> pdb=" O GLU b 2 " (cutoff:3.500A) Processing helix chain 'b' and resid 27 through 56 removed outlier: 3.716A pdb=" N LEU b 48 " --> pdb=" O GLN b 44 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ARG b 53 " --> pdb=" O ALA b 49 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LYS b 54 " --> pdb=" O ARG b 50 " (cutoff:3.500A) Processing helix chain 'b' and resid 57 through 83 removed outlier: 3.658A pdb=" N ASP b 81 " --> pdb=" O GLU b 77 " (cutoff:3.500A) Processing helix chain 'b' and resid 84 through 113 Processing helix chain 'b' and resid 114 through 140 removed outlier: 3.539A pdb=" N ALA b 118 " --> pdb=" O ASN b 114 " (cutoff:3.500A) Processing helix chain 'b' and resid 141 through 168 Processing helix chain 'b' and resid 169 through 188 removed outlier: 3.556A pdb=" N LYS b 182 " --> pdb=" O GLN b 178 " (cutoff:3.500A) Processing helix chain 'b' and resid 189 through 211 Processing helix chain 'b' and resid 212 through 231 Processing helix chain 'b' and resid 232 through 253 Processing helix chain 'b' and resid 255 through 274 Processing helix chain 'c' and resid 2 through 26 removed outlier: 3.563A pdb=" N GLN c 6 " --> pdb=" O GLU c 2 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN c 24 " --> pdb=" O ARG c 20 " (cutoff:3.500A) Processing helix chain 'c' and resid 27 through 56 removed outlier: 3.616A pdb=" N LEU c 31 " --> pdb=" O ASP c 27 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS c 54 " --> pdb=" O ARG c 50 " (cutoff:3.500A) Processing helix chain 'c' and resid 57 through 83 Processing helix chain 'c' and resid 84 through 113 removed outlier: 3.732A pdb=" N LEU c 88 " --> pdb=" O ASN c 84 " (cutoff:3.500A) Processing helix chain 'c' and resid 114 through 140 removed outlier: 3.637A pdb=" N HIS c 138 " --> pdb=" O ARG c 134 " (cutoff:3.500A) Processing helix chain 'c' and resid 141 through 168 removed outlier: 3.666A pdb=" N LEU c 145 " --> pdb=" O ASN c 141 " (cutoff:3.500A) Processing helix chain 'c' and resid 169 through 188 removed outlier: 3.697A pdb=" N GLU c 179 " --> pdb=" O ARG c 175 " (cutoff:3.500A) Processing helix chain 'c' and resid 189 through 211 Processing helix chain 'c' and resid 212 through 231 Processing helix chain 'c' and resid 232 through 253 Processing helix chain 'c' and resid 255 through 274 Processing helix chain 'd' and resid 2 through 25 removed outlier: 3.626A pdb=" N GLN d 6 " --> pdb=" O GLU d 2 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN d 24 " --> pdb=" O ARG d 20 " (cutoff:3.500A) Processing helix chain 'd' and resid 27 through 56 removed outlier: 3.631A pdb=" N ARG d 53 " --> pdb=" O ALA d 49 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS d 54 " --> pdb=" O ARG d 50 " (cutoff:3.500A) Processing helix chain 'd' and resid 57 through 83 Processing helix chain 'd' and resid 84 through 113 Processing helix chain 'd' and resid 114 through 140 removed outlier: 3.529A pdb=" N ALA d 118 " --> pdb=" O ASN d 114 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N HIS d 138 " --> pdb=" O ARG d 134 " (cutoff:3.500A) Processing helix chain 'd' and resid 141 through 168 Processing helix chain 'd' and resid 169 through 188 removed outlier: 3.581A pdb=" N LYS d 182 " --> pdb=" O GLN d 178 " (cutoff:3.500A) Processing helix chain 'd' and resid 189 through 211 Processing helix chain 'd' and resid 212 through 231 Processing helix chain 'd' and resid 232 through 253 Processing helix chain 'd' and resid 255 through 274 Processing helix chain 'e' and resid 2 through 25 removed outlier: 3.624A pdb=" N GLN e 24 " --> pdb=" O ARG e 20 " (cutoff:3.500A) Processing helix chain 'e' and resid 27 through 56 removed outlier: 3.696A pdb=" N LEU e 48 " --> pdb=" O GLN e 44 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ARG e 53 " --> pdb=" O ALA e 49 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LYS e 54 " --> pdb=" O ARG e 50 " (cutoff:3.500A) Processing helix chain 'e' and resid 57 through 83 removed outlier: 3.599A pdb=" N VAL e 74 " --> pdb=" O ASN e 70 " (cutoff:3.500A) Processing helix chain 'e' and resid 84 through 113 Processing helix chain 'e' and resid 114 through 140 removed outlier: 3.688A pdb=" N ALA e 118 " --> pdb=" O ASN e 114 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N HIS e 138 " --> pdb=" O ARG e 134 " (cutoff:3.500A) Processing helix chain 'e' and resid 141 through 168 Processing helix chain 'e' and resid 169 through 188 removed outlier: 3.579A pdb=" N LYS e 182 " --> pdb=" O GLN e 178 " (cutoff:3.500A) Processing helix chain 'e' and resid 189 through 211 Processing helix chain 'e' and resid 212 through 231 Processing helix chain 'e' and resid 232 through 253 Processing helix chain 'e' and resid 255 through 274 Processing helix chain 'f' and resid 2 through 25 removed outlier: 3.536A pdb=" N GLN f 6 " --> pdb=" O GLU f 2 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN f 24 " --> pdb=" O ARG f 20 " (cutoff:3.500A) Processing helix chain 'f' and resid 28 through 56 removed outlier: 3.703A pdb=" N GLN f 44 " --> pdb=" O GLN f 40 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG f 47 " --> pdb=" O ARG f 43 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LYS f 54 " --> pdb=" O ARG f 50 " (cutoff:3.500A) Processing helix chain 'f' and resid 57 through 83 removed outlier: 4.320A pdb=" N ASP f 81 " --> pdb=" O GLU f 77 " (cutoff:3.500A) Processing helix chain 'f' and resid 84 through 112 removed outlier: 4.232A pdb=" N LEU f 88 " --> pdb=" O ASN f 84 " (cutoff:3.500A) Processing helix chain 'f' and resid 114 through 140 removed outlier: 3.659A pdb=" N GLU f 120 " --> pdb=" O GLU f 116 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N HIS f 138 " --> pdb=" O ARG f 134 " (cutoff:3.500A) Processing helix chain 'f' and resid 141 through 168 Processing helix chain 'f' and resid 169 through 188 removed outlier: 3.534A pdb=" N LYS f 182 " --> pdb=" O GLN f 178 " (cutoff:3.500A) Processing helix chain 'f' and resid 189 through 211 Processing helix chain 'f' and resid 212 through 230 Processing helix chain 'f' and resid 232 through 253 Processing helix chain 'f' and resid 255 through 274 Processing helix chain 'g' and resid 2 through 25 Processing helix chain 'g' and resid 28 through 56 removed outlier: 4.238A pdb=" N LYS g 54 " --> pdb=" O ARG g 50 " (cutoff:3.500A) Processing helix chain 'g' and resid 57 through 83 removed outlier: 4.692A pdb=" N ASP g 81 " --> pdb=" O GLU g 77 " (cutoff:3.500A) Processing helix chain 'g' and resid 84 through 113 removed outlier: 3.531A pdb=" N LEU g 88 " --> pdb=" O ASN g 84 " (cutoff:3.500A) Processing helix chain 'g' and resid 114 through 140 removed outlier: 4.199A pdb=" N ARG g 130 " --> pdb=" O ASN g 126 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL g 131 " --> pdb=" O GLU g 127 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N HIS g 138 " --> pdb=" O ARG g 134 " (cutoff:3.500A) Processing helix chain 'g' and resid 141 through 168 removed outlier: 3.511A pdb=" N LEU g 145 " --> pdb=" O ASN g 141 " (cutoff:3.500A) Processing helix chain 'g' and resid 169 through 188 Processing helix chain 'g' and resid 189 through 210 Processing helix chain 'g' and resid 212 through 230 Processing helix chain 'g' and resid 232 through 253 Processing helix chain 'g' and resid 255 through 274 Processing helix chain 'h' and resid 2 through 26 removed outlier: 3.795A pdb=" N GLN h 6 " --> pdb=" O GLU h 2 " (cutoff:3.500A) Processing helix chain 'h' and resid 27 through 56 removed outlier: 3.583A pdb=" N ALA h 41 " --> pdb=" O TRP h 37 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS h 54 " --> pdb=" O ARG h 50 " (cutoff:3.500A) Processing helix chain 'h' and resid 57 through 80 Processing helix chain 'h' and resid 84 through 112 Processing helix chain 'h' and resid 114 through 140 removed outlier: 3.514A pdb=" N HIS h 138 " --> pdb=" O ARG h 134 " (cutoff:3.500A) Processing helix chain 'h' and resid 141 through 168 Processing helix chain 'h' and resid 169 through 188 Processing helix chain 'h' and resid 189 through 211 Processing helix chain 'h' and resid 212 through 230 Processing helix chain 'h' and resid 232 through 253 Processing helix chain 'h' and resid 255 through 274 Processing helix chain 'i' and resid 2 through 25 removed outlier: 4.138A pdb=" N GLN i 6 " --> pdb=" O GLU i 2 " (cutoff:3.500A) Processing helix chain 'i' and resid 27 through 56 removed outlier: 3.634A pdb=" N ARG i 53 " --> pdb=" O ALA i 49 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LYS i 54 " --> pdb=" O ARG i 50 " (cutoff:3.500A) Processing helix chain 'i' and resid 57 through 83 removed outlier: 3.700A pdb=" N ILE i 67 " --> pdb=" O LYS i 63 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU i 68 " --> pdb=" O ALA i 64 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ASP i 81 " --> pdb=" O GLU i 77 " (cutoff:3.500A) Processing helix chain 'i' and resid 84 through 113 removed outlier: 3.959A pdb=" N LEU i 88 " --> pdb=" O ASN i 84 " (cutoff:3.500A) Processing helix chain 'i' and resid 114 through 140 removed outlier: 3.667A pdb=" N ALA i 129 " --> pdb=" O ILE i 125 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ARG i 130 " --> pdb=" O ASN i 126 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL i 131 " --> pdb=" O GLU i 127 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N HIS i 138 " --> pdb=" O ARG i 134 " (cutoff:3.500A) Processing helix chain 'i' and resid 141 through 168 removed outlier: 3.789A pdb=" N LEU i 145 " --> pdb=" O ASN i 141 " (cutoff:3.500A) Processing helix chain 'i' and resid 169 through 188 Processing helix chain 'i' and resid 189 through 210 Processing helix chain 'i' and resid 212 through 231 Processing helix chain 'i' and resid 232 through 253 Processing helix chain 'i' and resid 255 through 274 Processing helix chain 'j' and resid 2 through 26 removed outlier: 3.798A pdb=" N GLN j 24 " --> pdb=" O ARG j 20 " (cutoff:3.500A) Processing helix chain 'j' and resid 27 through 56 removed outlier: 3.888A pdb=" N LEU j 31 " --> pdb=" O ASP j 27 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLN j 44 " --> pdb=" O GLN j 40 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ARG j 53 " --> pdb=" O ALA j 49 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N LYS j 54 " --> pdb=" O ARG j 50 " (cutoff:3.500A) Processing helix chain 'j' and resid 57 through 83 removed outlier: 4.302A pdb=" N ASP j 81 " --> pdb=" O GLU j 77 " (cutoff:3.500A) Processing helix chain 'j' and resid 84 through 112 Processing helix chain 'j' and resid 114 through 140 removed outlier: 3.618A pdb=" N ALA j 129 " --> pdb=" O ILE j 125 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ARG j 130 " --> pdb=" O ASN j 126 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N VAL j 131 " --> pdb=" O GLU j 127 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU j 132 " --> pdb=" O ALA j 128 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N HIS j 138 " --> pdb=" O ARG j 134 " (cutoff:3.500A) Processing helix chain 'j' and resid 141 through 168 removed outlier: 3.540A pdb=" N ALA j 164 " --> pdb=" O ARG j 160 " (cutoff:3.500A) Processing helix chain 'j' and resid 169 through 188 removed outlier: 3.517A pdb=" N LYS j 182 " --> pdb=" O GLN j 178 " (cutoff:3.500A) Processing helix chain 'j' and resid 189 through 210 Processing helix chain 'j' and resid 212 through 230 Processing helix chain 'j' and resid 232 through 253 Processing helix chain 'j' and resid 255 through 274 7056 hydrogen bonds defined for protein. 21168 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: 27.32 Time building geometry restraints manager: 16.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 9060 1.29 - 1.35: 9030 1.35 - 1.42: 0 1.42 - 1.49: 9055 1.49 - 1.56: 17755 Bond restraints: 44900 Sorted by residual: bond pdb=" CA GLY i 26 " pdb=" C GLY i 26 " ideal model delta sigma weight residual 1.511 1.542 -0.031 1.25e-02 6.40e+03 6.15e+00 bond pdb=" CA GLY i 231 " pdb=" C GLY i 231 " ideal model delta sigma weight residual 1.510 1.541 -0.031 1.36e-02 5.41e+03 5.05e+00 bond pdb=" CA GLY a 168 " pdb=" C GLY a 168 " ideal model delta sigma weight residual 1.511 1.541 -0.030 1.34e-02 5.57e+03 4.99e+00 bond pdb=" CA GLY e 211 " pdb=" C GLY e 211 " ideal model delta sigma weight residual 1.511 1.541 -0.030 1.34e-02 5.57e+03 4.96e+00 bond pdb=" CA GLY b 211 " pdb=" C GLY b 211 " ideal model delta sigma weight residual 1.511 1.541 -0.030 1.34e-02 5.57e+03 4.95e+00 ... (remaining 44895 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 49244 1.51 - 3.02: 11809 3.02 - 4.52: 1393 4.52 - 6.03: 126 6.03 - 7.54: 18 Bond angle restraints: 62590 Sorted by residual: angle pdb=" C PRO j 1 " pdb=" N GLU j 2 " pdb=" CA GLU j 2 " ideal model delta sigma weight residual 120.38 127.79 -7.41 1.37e+00 5.33e-01 2.93e+01 angle pdb=" C PRO c 1 " pdb=" N GLU c 2 " pdb=" CA GLU c 2 " ideal model delta sigma weight residual 120.38 127.71 -7.33 1.37e+00 5.33e-01 2.86e+01 angle pdb=" C PRO d 1 " pdb=" N GLU d 2 " pdb=" CA GLU d 2 " ideal model delta sigma weight residual 120.38 127.70 -7.32 1.37e+00 5.33e-01 2.85e+01 angle pdb=" C PRO e 1 " pdb=" N GLU e 2 " pdb=" CA GLU e 2 " ideal model delta sigma weight residual 120.38 127.56 -7.18 1.37e+00 5.33e-01 2.75e+01 angle pdb=" C LEU B 1 " pdb=" N GLU B 2 " pdb=" CA GLU B 2 " ideal model delta sigma weight residual 120.54 127.57 -7.03 1.35e+00 5.49e-01 2.71e+01 ... (remaining 62585 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 5.79: 23913 5.79 - 11.58: 2174 11.58 - 17.37: 273 17.37 - 23.17: 37 23.17 - 28.96: 13 Dihedral angle restraints: 26410 sinusoidal: 0 harmonic: 26410 Sorted by residual: dihedral pdb=" CA ALA I 230 " pdb=" C ALA I 230 " pdb=" N GLY I 231 " pdb=" CA GLY I 231 " ideal model delta harmonic sigma weight residual -180.00 -151.04 -28.96 0 5.00e+00 4.00e-02 3.35e+01 dihedral pdb=" CA ALA J 187 " pdb=" C ALA J 187 " pdb=" N GLY J 188 " pdb=" CA GLY J 188 " ideal model delta harmonic sigma weight residual -180.00 -151.16 -28.84 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA LEU F 151 " pdb=" C LEU F 151 " pdb=" N VAL F 152 " pdb=" CA VAL F 152 " ideal model delta harmonic sigma weight residual -180.00 -151.22 -28.78 0 5.00e+00 4.00e-02 3.31e+01 ... (remaining 26407 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 7762 0.076 - 0.151: 814 0.151 - 0.227: 87 0.227 - 0.303: 26 0.303 - 0.378: 1 Chirality restraints: 8690 Sorted by residual: chirality pdb=" CA LEU O 62 " pdb=" N LEU O 62 " pdb=" C LEU O 62 " pdb=" CB LEU O 62 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.58e+00 chirality pdb=" CA LEU b 62 " pdb=" N LEU b 62 " pdb=" C LEU b 62 " pdb=" CB LEU b 62 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" CA LEU K 62 " pdb=" N LEU K 62 " pdb=" C LEU K 62 " pdb=" CB LEU K 62 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.02e+00 ... (remaining 8687 not shown) Planarity restraints: 9030 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET I 192 " 0.017 2.00e-02 2.50e+03 3.29e-02 1.09e+01 pdb=" C MET I 192 " -0.057 2.00e-02 2.50e+03 pdb=" O MET I 192 " 0.021 2.00e-02 2.50e+03 pdb=" N LEU I 193 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET J 192 " 0.016 2.00e-02 2.50e+03 3.10e-02 9.61e+00 pdb=" C MET J 192 " -0.054 2.00e-02 2.50e+03 pdb=" O MET J 192 " 0.020 2.00e-02 2.50e+03 pdb=" N LEU J 193 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU E 171 " 0.013 2.00e-02 2.50e+03 2.59e-02 6.69e+00 pdb=" C GLU E 171 " -0.045 2.00e-02 2.50e+03 pdb=" O GLU E 171 " 0.017 2.00e-02 2.50e+03 pdb=" N LYS E 172 " 0.015 2.00e-02 2.50e+03 ... (remaining 9027 not shown) Histogram of nonbonded interaction distances: 2.65 - 3.10: 36730 3.10 - 3.55: 65332 3.55 - 4.00: 55381 4.00 - 4.45: 79162 4.45 - 4.90: 100356 Nonbonded interactions: 336961 Sorted by model distance: nonbonded pdb=" O VAL J 152 " pdb=" CA ASP J 153 " model vdw 2.654 2.776 nonbonded pdb=" O VAL Q 170 " pdb=" CA GLU Q 171 " model vdw 2.666 2.776 nonbonded pdb=" O VAL F 131 " pdb=" CA LEU F 132 " model vdw 2.671 2.776 nonbonded pdb=" O VAL J 131 " pdb=" CA LEU J 132 " model vdw 2.674 2.776 nonbonded pdb=" O VAL H 152 " pdb=" CA ASP H 153 " model vdw 2.675 2.776 ... (remaining 336956 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 or resid 5 or resid 7 through 8 or resid 12 or resid 14 \ through 15 or resid 18 through 24 or resid 26 through 29 or resid 31 through 32 \ or resid 34 through 40 or resid 42 through 43 or resid 45 through 47 or resid 49 \ through 50 or resid 52 through 86 or resid 88 through 105 or resid 107 through \ 114 or resid 117 or resid 120 through 121 or resid 124 through 125 or resid 128 \ through 129 or resid 131 through 132 or resid 134 through 141 or resid 143 throu \ gh 151 or resid 154 or resid 156 through 158 or resid 161 or resid 163 through 2 \ 83 or resid 285 through 291 or resid 293 or resid 295 through 298 or resid 301 o \ r resid 303 through 309 or resid 312 or resid 315 through 316)) selection = (chain 'B' and (resid 3 or resid 5 or resid 7 through 8 or resid 12 or resid 14 \ through 15 or resid 18 through 24 or resid 26 through 29 or resid 31 through 32 \ or resid 34 through 40 or resid 42 through 43 or resid 45 through 47 or resid 49 \ through 50 or resid 52 through 86 or resid 88 through 105 or resid 107 through \ 114 or resid 117 or resid 120 through 121 or resid 124 through 125 or resid 128 \ through 129 or resid 131 through 132 or resid 134 through 141 or resid 143 throu \ gh 151 or resid 154 or resid 156 through 158 or resid 161 or resid 163 through 2 \ 83 or resid 285 through 291 or resid 293 or resid 295 through 298 or resid 301 o \ r resid 303 through 309 or resid 312 or resid 315 through 316)) selection = (chain 'C' and (resid 3 or resid 5 or resid 7 through 8 or resid 12 or resid 14 \ through 15 or resid 18 through 24 or resid 26 through 29 or resid 31 through 32 \ or resid 34 through 40 or resid 42 through 43 or resid 45 through 47 or resid 49 \ through 50 or resid 52 through 86 or resid 88 through 105 or resid 107 through \ 114 or resid 117 or resid 120 through 121 or resid 124 through 125 or resid 128 \ through 129 or resid 131 through 132 or resid 134 through 141 or resid 143 throu \ gh 151 or resid 154 or resid 156 through 158 or resid 161 or resid 163 through 2 \ 83 or resid 285 through 291 or resid 293 or resid 295 through 298 or resid 301 o \ r resid 303 through 309 or resid 312 or resid 315 through 316)) selection = (chain 'D' and (resid 3 or resid 5 or resid 7 through 8 or resid 12 or resid 14 \ through 15 or resid 18 through 24 or resid 26 through 29 or resid 31 through 32 \ or resid 34 through 40 or resid 42 through 43 or resid 45 through 47 or resid 49 \ through 50 or resid 52 through 86 or resid 88 through 105 or resid 107 through \ 114 or resid 117 or resid 120 through 121 or resid 124 through 125 or resid 128 \ through 129 or resid 131 through 132 or resid 134 through 141 or resid 143 throu \ gh 151 or resid 154 or resid 156 through 158 or resid 161 or resid 163 through 2 \ 83 or resid 285 through 291 or resid 293 or resid 295 through 298 or resid 301 o \ r resid 303 through 309 or resid 312 or resid 315 through 316)) selection = (chain 'E' and (resid 3 or resid 5 or resid 7 through 8 or resid 12 or resid 14 \ through 15 or resid 18 through 24 or resid 26 through 29 or resid 31 through 32 \ or resid 34 through 40 or resid 42 through 43 or resid 45 through 47 or resid 49 \ through 50 or resid 52 through 86 or resid 88 through 105 or resid 107 through \ 114 or resid 117 or resid 120 through 121 or resid 124 through 125 or resid 128 \ through 129 or resid 131 through 132 or resid 134 through 141 or resid 143 throu \ gh 151 or resid 154 or resid 156 through 158 or resid 161 or resid 163 through 2 \ 83 or resid 285 through 291 or resid 293 or resid 295 through 298 or resid 301 o \ r resid 303 through 309 or resid 312 or resid 315 through 316)) selection = (chain 'F' and (resid 3 or resid 5 or resid 7 through 8 or resid 12 or resid 14 \ through 15 or resid 18 through 24 or resid 26 through 29 or resid 31 through 32 \ or resid 34 through 40 or resid 42 through 43 or resid 45 through 47 or resid 49 \ through 50 or resid 52 through 86 or resid 88 through 105 or resid 107 through \ 114 or resid 117 or resid 120 through 121 or resid 124 through 125 or resid 128 \ through 129 or resid 131 through 132 or resid 134 through 141 or resid 143 throu \ gh 151 or resid 154 or resid 156 through 158 or resid 161 or resid 163 through 2 \ 83 or resid 285 through 291 or resid 293 or resid 295 through 298 or resid 301 o \ r resid 303 through 309 or resid 312 or resid 315 through 316)) selection = (chain 'G' and (resid 3 or resid 5 or resid 7 through 8 or resid 12 or resid 14 \ through 15 or resid 18 through 24 or resid 26 through 29 or resid 31 through 32 \ or resid 34 through 40 or resid 42 through 43 or resid 45 through 47 or resid 49 \ through 50 or resid 52 through 86 or resid 88 through 105 or resid 107 through \ 114 or resid 117 or resid 120 through 121 or resid 124 through 125 or resid 128 \ through 129 or resid 131 through 132 or resid 134 through 141 or resid 143 throu \ gh 151 or resid 154 or resid 156 through 158 or resid 161 or resid 163 through 2 \ 83 or resid 285 through 291 or resid 293 or resid 295 through 298 or resid 301 o \ r resid 303 through 309 or resid 312 or resid 315 through 316)) selection = (chain 'H' and (resid 3 or resid 5 or resid 7 through 8 or resid 12 or resid 14 \ through 15 or resid 18 through 24 or resid 26 through 29 or resid 31 through 32 \ or resid 34 through 40 or resid 42 through 43 or resid 45 through 47 or resid 49 \ through 50 or resid 52 through 86 or resid 88 through 105 or resid 107 through \ 114 or resid 117 or resid 120 through 121 or resid 124 through 125 or resid 128 \ through 129 or resid 131 through 132 or resid 134 through 141 or resid 143 throu \ gh 151 or resid 154 or resid 156 through 158 or resid 161 or resid 163 through 2 \ 83 or resid 285 through 291 or resid 293 or resid 295 through 298 or resid 301 o \ r resid 303 through 309 or resid 312 or resid 315 through 316)) selection = (chain 'I' and (resid 3 or resid 5 or resid 7 through 8 or resid 12 or resid 14 \ through 15 or resid 18 through 24 or resid 26 through 29 or resid 31 through 32 \ or resid 34 through 40 or resid 42 through 43 or resid 45 through 47 or resid 49 \ through 50 or resid 52 through 86 or resid 88 through 105 or resid 107 through \ 114 or resid 117 or resid 120 through 121 or resid 124 through 125 or resid 128 \ through 129 or resid 131 through 132 or resid 134 through 141 or resid 143 throu \ gh 151 or resid 154 or resid 156 through 158 or resid 161 or resid 163 through 2 \ 83 or resid 285 through 291 or resid 293 or resid 295 through 298 or resid 301 o \ r resid 303 through 309 or resid 312 or resid 315 through 316)) selection = (chain 'J' and (resid 3 or resid 5 or resid 7 through 8 or resid 12 or resid 14 \ through 15 or resid 18 through 24 or resid 26 through 29 or resid 31 through 32 \ or resid 34 through 40 or resid 42 through 43 or resid 45 through 47 or resid 49 \ through 50 or resid 52 through 86 or resid 88 through 105 or resid 107 through \ 114 or resid 117 or resid 120 through 121 or resid 124 through 125 or resid 128 \ through 129 or resid 131 through 132 or resid 134 through 141 or resid 143 throu \ gh 151 or resid 154 or resid 156 through 158 or resid 161 or resid 163 through 2 \ 83 or resid 285 through 291 or resid 293 or resid 295 through 298 or resid 301 o \ r resid 303 through 309 or resid 312 or resid 315 through 316)) selection = (chain 'K' and (resid 3 or resid 5 or resid 7 through 8 or resid 12 or resid 14 \ through 15 or resid 18 through 24 or resid 26 through 29 or resid 31 through 32 \ or resid 34 through 40 or resid 42 through 43 or resid 45 through 47 or resid 49 \ through 50 or resid 52 through 86 or resid 88 through 105 or resid 107 through \ 114 or resid 117 or resid 120 through 121 or resid 124 through 125 or resid 128 \ through 129 or resid 131 through 132 or resid 134 through 141 or resid 143 throu \ gh 151 or resid 154 or resid 156 through 158 or resid 161 or resid 163 through 2 \ 83 or resid 285 through 291 or resid 293 or resid 295 through 298 or resid 301 o \ r resid 303 through 309 or resid 312 or resid 315 through 316)) selection = (chain 'L' and (resid 3 or resid 5 or resid 7 through 8 or resid 12 or resid 14 \ through 15 or resid 18 through 24 or resid 26 through 29 or resid 31 through 32 \ or resid 34 through 40 or resid 42 through 43 or resid 45 through 47 or resid 49 \ through 50 or resid 52 through 86 or resid 88 through 105 or resid 107 through \ 114 or resid 117 or resid 120 through 121 or resid 124 through 125 or resid 128 \ through 129 or resid 131 through 132 or resid 134 through 141 or resid 143 throu \ gh 151 or resid 154 or resid 156 through 158 or resid 161 or resid 163 through 2 \ 83 or resid 285 through 291 or resid 293 or resid 295 through 298 or resid 301 o \ r resid 303 through 309 or resid 312 or resid 315 through 316)) selection = (chain 'M' and (resid 3 or resid 5 or resid 7 through 8 or resid 12 or resid 14 \ through 15 or resid 18 through 24 or resid 26 through 29 or resid 31 through 32 \ or resid 34 through 40 or resid 42 through 43 or resid 45 through 47 or resid 49 \ through 50 or resid 52 through 86 or resid 88 through 105 or resid 107 through \ 114 or resid 117 or resid 120 through 121 or resid 124 through 125 or resid 128 \ through 129 or resid 131 through 132 or resid 134 through 141 or resid 143 throu \ gh 151 or resid 154 or resid 156 through 158 or resid 161 or resid 163 through 2 \ 83 or resid 285 through 291 or resid 293 or resid 295 through 298 or resid 301 o \ r resid 303 through 309 or resid 312 or resid 315 through 316)) selection = (chain 'N' and (resid 3 or resid 5 or resid 7 through 8 or resid 12 or resid 14 \ through 15 or resid 18 through 24 or resid 26 through 29 or resid 31 through 32 \ or resid 34 through 40 or resid 42 through 43 or resid 45 through 47 or resid 49 \ through 50 or resid 52 through 86 or resid 88 through 105 or resid 107 through \ 114 or resid 117 or resid 120 through 121 or resid 124 through 125 or resid 128 \ through 129 or resid 131 through 132 or resid 134 through 141 or resid 143 throu \ gh 151 or resid 154 or resid 156 through 158 or resid 161 or resid 163 through 2 \ 83 or resid 285 through 291 or resid 293 or resid 295 through 298 or resid 301 o \ r resid 303 through 309 or resid 312 or resid 315 through 316)) selection = (chain 'O' and (resid 3 or resid 5 or resid 7 through 8 or resid 12 or resid 14 \ through 15 or resid 18 through 24 or resid 26 through 29 or resid 31 through 32 \ or resid 34 through 40 or resid 42 through 43 or resid 45 through 47 or resid 49 \ through 50 or resid 52 through 86 or resid 88 through 105 or resid 107 through \ 114 or resid 117 or resid 120 through 121 or resid 124 through 125 or resid 128 \ through 129 or resid 131 through 132 or resid 134 through 141 or resid 143 throu \ gh 151 or resid 154 or resid 156 through 158 or resid 161 or resid 163 through 2 \ 83 or resid 285 through 291 or resid 293 or resid 295 through 298 or resid 301 o \ r resid 303 through 309 or resid 312 or resid 315 through 316)) selection = (chain 'P' and (resid 3 or resid 5 or resid 7 through 8 or resid 12 or resid 14 \ through 15 or resid 18 through 24 or resid 26 through 29 or resid 31 through 32 \ or resid 34 through 40 or resid 42 through 43 or resid 45 through 47 or resid 49 \ through 50 or resid 52 through 86 or resid 88 through 105 or resid 107 through \ 114 or resid 117 or resid 120 through 121 or resid 124 through 125 or resid 128 \ through 129 or resid 131 through 132 or resid 134 through 141 or resid 143 throu \ gh 151 or resid 154 or resid 156 through 158 or resid 161 or resid 163 through 2 \ 83 or resid 285 through 291 or resid 293 or resid 295 through 298 or resid 301 o \ r resid 303 through 309 or resid 312 or resid 315 through 316)) selection = (chain 'Q' and (resid 3 or resid 5 or resid 7 through 8 or resid 12 or resid 14 \ through 15 or resid 18 through 24 or resid 26 through 29 or resid 31 through 32 \ or resid 34 through 40 or resid 42 through 43 or resid 45 through 47 or resid 49 \ through 50 or resid 52 through 86 or resid 88 through 105 or resid 107 through \ 114 or resid 117 or resid 120 through 121 or resid 124 through 125 or resid 128 \ through 129 or resid 131 through 132 or resid 134 through 141 or resid 143 throu \ gh 151 or resid 154 or resid 156 through 158 or resid 161 or resid 163 through 2 \ 83 or resid 285 through 291 or resid 293 or resid 295 through 298 or resid 301 o \ r resid 303 through 309 or resid 312 or resid 315 through 316)) selection = (chain 'R' and (resid 3 or resid 5 or resid 7 through 8 or resid 12 or resid 14 \ through 15 or resid 18 through 24 or resid 26 through 29 or resid 31 through 32 \ or resid 34 through 40 or resid 42 through 43 or resid 45 through 47 or resid 49 \ through 50 or resid 52 through 86 or resid 88 through 105 or resid 107 through \ 114 or resid 117 or resid 120 through 121 or resid 124 through 125 or resid 128 \ through 129 or resid 131 through 132 or resid 134 through 141 or resid 143 throu \ gh 151 or resid 154 or resid 156 through 158 or resid 161 or resid 163 through 2 \ 83 or resid 285 through 291 or resid 293 or resid 295 through 298 or resid 301 o \ r resid 303 through 309 or resid 312 or resid 315 through 316)) selection = (chain 'S' and (resid 3 or resid 5 or resid 7 through 8 or resid 12 or resid 14 \ through 15 or resid 18 through 24 or resid 26 through 29 or resid 31 through 32 \ or resid 34 through 40 or resid 42 through 43 or resid 45 through 47 or resid 49 \ through 50 or resid 52 through 86 or resid 88 through 105 or resid 107 through \ 114 or resid 117 or resid 120 through 121 or resid 124 through 125 or resid 128 \ through 129 or resid 131 through 132 or resid 134 through 141 or resid 143 throu \ gh 151 or resid 154 or resid 156 through 158 or resid 161 or resid 163 through 2 \ 83 or resid 285 through 291 or resid 293 or resid 295 through 298 or resid 301 o \ r resid 303 through 309 or resid 312 or resid 315 through 316)) selection = (chain 'T' and (resid 3 or resid 5 or resid 7 through 8 or resid 12 or resid 14 \ through 15 or resid 18 through 24 or resid 26 through 29 or resid 31 through 32 \ or resid 34 through 40 or resid 42 through 43 or resid 45 through 47 or resid 49 \ through 50 or resid 52 through 86 or resid 88 through 105 or resid 107 through \ 114 or resid 117 or resid 120 through 121 or resid 124 through 125 or resid 128 \ through 129 or resid 131 through 132 or resid 134 through 141 or resid 143 throu \ gh 151 or resid 154 or resid 156 through 158 or resid 161 or resid 163 through 2 \ 83 or resid 285 through 291 or resid 293 or resid 295 through 298 or resid 301 o \ r resid 303 through 309 or resid 312 or resid 315 through 316)) } ncs_group { reference = (chain 'a' and (resid 1 through 236 or resid 239 through 241 or resid 244 throug \ h 248 or resid 252 through 255 or resid 257 through 258 or resid 260 through 265 \ or resid 268 through 269 or resid 271 through 274)) selection = (chain 'b' and (resid 1 through 236 or resid 239 through 241 or resid 244 throug \ h 248 or resid 252 through 255 or resid 257 through 258 or resid 260 through 265 \ or resid 268 through 269 or resid 271 through 274)) selection = (chain 'c' and (resid 1 through 236 or resid 239 through 241 or resid 244 throug \ h 248 or resid 252 through 255 or resid 257 through 258 or resid 260 through 265 \ or resid 268 through 269 or resid 271 through 274)) selection = (chain 'd' and (resid 1 through 236 or resid 239 through 241 or resid 244 throug \ h 248 or resid 252 through 255 or resid 257 through 258 or resid 260 through 265 \ or resid 268 through 269 or resid 271 through 274)) selection = (chain 'e' and (resid 1 through 236 or resid 239 through 241 or resid 244 throug \ h 248 or resid 252 through 255 or resid 257 through 258 or resid 260 through 265 \ or resid 268 through 269 or resid 271 through 274)) selection = (chain 'f' and (resid 1 through 236 or resid 239 through 241 or resid 244 throug \ h 248 or resid 252 through 255 or resid 257 through 258 or resid 260 through 265 \ or resid 268 through 269 or resid 271 through 274)) selection = (chain 'g' and (resid 1 through 236 or resid 239 through 241 or resid 244 throug \ h 248 or resid 252 through 255 or resid 257 through 258 or resid 260 through 265 \ or resid 268 through 269 or resid 271 through 274)) selection = (chain 'h' and (resid 1 through 236 or resid 239 through 241 or resid 244 throug \ h 248 or resid 252 through 255 or resid 257 through 258 or resid 260 through 265 \ or resid 268 through 269 or resid 271 through 274)) selection = (chain 'i' and (resid 1 through 236 or resid 239 through 241 or resid 244 throug \ h 248 or resid 252 through 255 or resid 257 through 258 or resid 260 through 265 \ or resid 268 through 269 or resid 271 through 274)) selection = (chain 'j' and (resid 1 through 236 or resid 239 through 241 or resid 244 throug \ h 248 or resid 252 through 255 or resid 257 through 258 or resid 260 through 265 \ or resid 268 through 269 or resid 271 through 274)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.170 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: 0.070 Extract box with map and model: 1.920 Check model and map are aligned: 0.330 Set scattering table: 0.460 Process input model: 118.240 Find NCS groups from input model: 3.270 Set up NCS constraints: 0.310 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: 0.020 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 131.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.037 44900 Z= 0.566 Angle : 1.268 7.540 62590 Z= 0.936 Chirality : 0.050 0.378 8690 Planarity : 0.011 0.033 9030 Dihedral : 5.485 28.957 9030 Min Nonbonded Distance : 2.654 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.01 % 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: 0.34 (0.07), residues: 9000 helix: 0.38 (0.05), residues: 8586 sheet: None (None), residues: 0 loop : -0.22 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 106 PHE 0.000 0.000 PHE a 4 TYR 0.000 0.000 TYR A 16 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18000 Ramachandran restraints generated. 9000 Oldfield, 0 Emsley, 9000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18000 Ramachandran restraints generated. 9000 Oldfield, 0 Emsley, 9000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 6325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 4.812 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.4140 time to fit residues: 88.9728 Evaluate side-chains 105 residues out of total 6325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 4.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 890 random chunks: chunk 751 optimal weight: 0.0980 chunk 674 optimal weight: 3.9990 chunk 374 optimal weight: 2.9990 chunk 230 optimal weight: 0.6980 chunk 455 optimal weight: 0.8980 chunk 360 optimal weight: 2.9990 chunk 697 optimal weight: 0.5980 chunk 269 optimal weight: 4.9990 chunk 424 optimal weight: 0.4980 chunk 519 optimal weight: 0.1980 chunk 808 optimal weight: 6.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.016 44900 Z= 0.097 Angle : 0.264 4.960 62590 Z= 0.196 Chirality : 0.027 0.080 8690 Planarity : 0.002 0.011 9030 Dihedral : 3.099 16.187 9030 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 0.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: 5.62 (0.08), residues: 9000 helix: 3.73 (0.05), residues: 8601 sheet: None (None), residues: 0 loop : 1.31 (0.33), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 106 PHE 0.000 0.000 PHE a 4 TYR 0.000 0.000 TYR A 16 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18000 Ramachandran restraints generated. 9000 Oldfield, 0 Emsley, 9000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18000 Ramachandran restraints generated. 9000 Oldfield, 0 Emsley, 9000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 6325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 4.608 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.4237 time to fit residues: 90.5311 Evaluate side-chains 105 residues out of total 6325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 4.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 890 random chunks: chunk 449 optimal weight: 0.9980 chunk 250 optimal weight: 1.9990 chunk 672 optimal weight: 7.9990 chunk 550 optimal weight: 7.9990 chunk 222 optimal weight: 5.9990 chunk 809 optimal weight: 0.9990 chunk 874 optimal weight: 6.9990 chunk 721 optimal weight: 5.9990 chunk 802 optimal weight: 5.9990 chunk 276 optimal weight: 5.9990 chunk 649 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 44900 Z= 0.363 Angle : 0.506 6.948 62590 Z= 0.409 Chirality : 0.028 0.119 8690 Planarity : 0.003 0.017 9030 Dihedral : 3.964 21.972 9030 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 0.38 Ramachandran Plot: Outliers : 0.02 % Allowed : 0.77 % Favored : 99.21 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: 3.89 (0.08), residues: 9000 helix: 2.70 (0.05), residues: 8461 sheet: None (None), residues: 0 loop : 0.01 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 106 PHE 0.000 0.000 PHE a 4 TYR 0.000 0.000 TYR A 16 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18000 Ramachandran restraints generated. 9000 Oldfield, 0 Emsley, 9000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18000 Ramachandran restraints generated. 9000 Oldfield, 0 Emsley, 9000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 6325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 4.526 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.4132 time to fit residues: 89.2465 Evaluate side-chains 105 residues out of total 6325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 5.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 890 random chunks: chunk 799 optimal weight: 4.9990 chunk 608 optimal weight: 3.9990 chunk 420 optimal weight: 0.5980 chunk 89 optimal weight: 6.9990 chunk 386 optimal weight: 2.9990 chunk 543 optimal weight: 3.9990 chunk 812 optimal weight: 6.9990 chunk 860 optimal weight: 5.9990 chunk 424 optimal weight: 0.7980 chunk 770 optimal weight: 4.9990 chunk 231 optimal weight: 0.5980 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.4359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.015 44900 Z= 0.277 Angle : 0.392 6.328 62590 Z= 0.319 Chirality : 0.027 0.089 8690 Planarity : 0.002 0.014 9030 Dihedral : 3.482 21.875 9030 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 0.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: 4.36 (0.08), residues: 9000 helix: 3.04 (0.05), residues: 8448 sheet: None (None), residues: 0 loop : -0.41 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 106 PHE 0.000 0.000 PHE a 4 TYR 0.000 0.000 TYR A 16 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18000 Ramachandran restraints generated. 9000 Oldfield, 0 Emsley, 9000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18000 Ramachandran restraints generated. 9000 Oldfield, 0 Emsley, 9000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 6325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 5.067 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.4460 time to fit residues: 96.2720 Evaluate side-chains 105 residues out of total 6325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 4.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 890 random chunks: chunk 716 optimal weight: 4.9990 chunk 488 optimal weight: 7.9990 chunk 12 optimal weight: 6.9990 chunk 640 optimal weight: 3.9990 chunk 354 optimal weight: 5.9990 chunk 734 optimal weight: 4.9990 chunk 594 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 439 optimal weight: 5.9990 chunk 772 optimal weight: 4.9990 chunk 217 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.5357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.029 44900 Z= 0.609 Angle : 0.777 10.639 62590 Z= 0.632 Chirality : 0.029 0.101 8690 Planarity : 0.006 0.031 9030 Dihedral : 5.513 34.819 9030 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.86 % Favored : 95.93 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -1.21 (0.08), residues: 9000 helix: -0.59 (0.05), residues: 8335 sheet: None (None), residues: 0 loop : -1.10 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 106 PHE 0.000 0.000 PHE a 4 TYR 0.000 0.000 TYR A 16 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18000 Ramachandran restraints generated. 9000 Oldfield, 0 Emsley, 9000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18000 Ramachandran restraints generated. 9000 Oldfield, 0 Emsley, 9000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 6325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 4.780 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.3931 time to fit residues: 85.2398 Evaluate side-chains 105 residues out of total 6325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 4.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 890 random chunks: chunk 289 optimal weight: 4.9990 chunk 774 optimal weight: 2.9990 chunk 170 optimal weight: 0.6980 chunk 505 optimal weight: 5.9990 chunk 212 optimal weight: 0.0970 chunk 861 optimal weight: 4.9990 chunk 714 optimal weight: 2.9990 chunk 398 optimal weight: 0.5980 chunk 71 optimal weight: 0.5980 chunk 284 optimal weight: 5.9990 chunk 452 optimal weight: 2.9990 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.5113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.010 44900 Z= 0.156 Angle : 0.297 6.764 62590 Z= 0.231 Chirality : 0.027 0.085 8690 Planarity : 0.002 0.010 9030 Dihedral : 3.495 20.176 9030 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 0.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: 3.45 (0.08), residues: 9000 helix: 2.49 (0.05), residues: 8390 sheet: None (None), residues: 0 loop : -0.95 (0.23), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 106 PHE 0.000 0.000 PHE a 4 TYR 0.000 0.000 TYR A 16 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18000 Ramachandran restraints generated. 9000 Oldfield, 0 Emsley, 9000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18000 Ramachandran restraints generated. 9000 Oldfield, 0 Emsley, 9000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 6325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 4.911 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.4364 time to fit residues: 93.5539 Evaluate side-chains 105 residues out of total 6325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 4.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 890 random chunks: chunk 830 optimal weight: 5.9990 chunk 97 optimal weight: 7.9990 chunk 490 optimal weight: 10.0000 chunk 628 optimal weight: 8.9990 chunk 487 optimal weight: 0.2980 chunk 724 optimal weight: 6.9990 chunk 480 optimal weight: 0.6980 chunk 857 optimal weight: 7.9990 chunk 536 optimal weight: 4.9990 chunk 522 optimal weight: 4.9990 chunk 396 optimal weight: 5.9990 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.5619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.025 44900 Z= 0.504 Angle : 0.651 9.236 62590 Z= 0.532 Chirality : 0.028 0.095 8690 Planarity : 0.005 0.024 9030 Dihedral : 4.840 33.601 9030 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 1.08 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.97 % Favored : 95.83 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 0.02 (0.08), residues: 9000 helix: 0.25 (0.05), residues: 8295 sheet: None (None), residues: 0 loop : -1.22 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 106 PHE 0.000 0.000 PHE a 4 TYR 0.000 0.000 TYR A 16 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18000 Ramachandran restraints generated. 9000 Oldfield, 0 Emsley, 9000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18000 Ramachandran restraints generated. 9000 Oldfield, 0 Emsley, 9000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 6325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 4.436 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.3819 time to fit residues: 82.1628 Evaluate side-chains 105 residues out of total 6325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 4.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 890 random chunks: chunk 530 optimal weight: 5.9990 chunk 342 optimal weight: 4.9990 chunk 512 optimal weight: 0.9980 chunk 258 optimal weight: 5.9990 chunk 168 optimal weight: 0.9990 chunk 166 optimal weight: 8.9990 chunk 545 optimal weight: 0.9990 chunk 584 optimal weight: 0.5980 chunk 424 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 674 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.5509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.012 44900 Z= 0.201 Angle : 0.329 6.753 62590 Z= 0.262 Chirality : 0.027 0.085 8690 Planarity : 0.002 0.011 9030 Dihedral : 3.538 23.031 9030 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 0.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: 3.19 (0.08), residues: 9000 helix: 2.31 (0.05), residues: 8415 sheet: None (None), residues: 0 loop : -1.05 (0.24), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 106 PHE 0.000 0.000 PHE a 4 TYR 0.000 0.000 TYR A 16 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18000 Ramachandran restraints generated. 9000 Oldfield, 0 Emsley, 9000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18000 Ramachandran restraints generated. 9000 Oldfield, 0 Emsley, 9000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 6325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 5.153 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.4222 time to fit residues: 90.0284 Evaluate side-chains 105 residues out of total 6325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 4.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 890 random chunks: chunk 780 optimal weight: 7.9990 chunk 821 optimal weight: 6.9990 chunk 749 optimal weight: 4.9990 chunk 799 optimal weight: 4.9990 chunk 481 optimal weight: 4.9990 chunk 348 optimal weight: 4.9990 chunk 627 optimal weight: 5.9990 chunk 245 optimal weight: 6.9990 chunk 722 optimal weight: 5.9990 chunk 756 optimal weight: 7.9990 chunk 796 optimal weight: 0.1980 overall best weight: 4.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.6084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.029 44900 Z= 0.593 Angle : 0.749 10.232 62590 Z= 0.612 Chirality : 0.029 0.095 8690 Planarity : 0.006 0.030 9030 Dihedral : 5.277 34.925 9030 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.71 % Favored : 94.88 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -1.14 (0.08), residues: 9000 helix: -0.52 (0.05), residues: 8275 sheet: None (None), residues: 0 loop : -1.46 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 106 PHE 0.000 0.000 PHE a 4 TYR 0.000 0.000 TYR A 16 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18000 Ramachandran restraints generated. 9000 Oldfield, 0 Emsley, 9000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18000 Ramachandran restraints generated. 9000 Oldfield, 0 Emsley, 9000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 6325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 4.915 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.4410 time to fit residues: 94.6006 Evaluate side-chains 105 residues out of total 6325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 4.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 890 random chunks: chunk 524 optimal weight: 6.9990 chunk 845 optimal weight: 5.9990 chunk 515 optimal weight: 2.9990 chunk 401 optimal weight: 6.9990 chunk 587 optimal weight: 10.0000 chunk 886 optimal weight: 5.9990 chunk 816 optimal weight: 2.9990 chunk 706 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 545 optimal weight: 2.9990 chunk 432 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.6317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.025 44900 Z= 0.502 Angle : 0.639 9.541 62590 Z= 0.523 Chirality : 0.028 0.095 8690 Planarity : 0.005 0.025 9030 Dihedral : 4.962 34.552 9030 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 1.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.08), residues: 9000 helix: -0.82 (0.05), residues: 8350 sheet: None (None), residues: 0 loop : -1.66 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 106 PHE 0.000 0.000 PHE a 4 TYR 0.000 0.000 TYR A 16 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18000 Ramachandran restraints generated. 9000 Oldfield, 0 Emsley, 9000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18000 Ramachandran restraints generated. 9000 Oldfield, 0 Emsley, 9000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 6325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 5.455 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.4386 time to fit residues: 93.8308 Evaluate side-chains 105 residues out of total 6325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 5.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 890 random chunks: chunk 560 optimal weight: 9.9990 chunk 752 optimal weight: 4.9990 chunk 216 optimal weight: 3.9990 chunk 651 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 196 optimal weight: 4.9990 chunk 707 optimal weight: 0.9990 chunk 295 optimal weight: 2.9990 chunk 726 optimal weight: 0.5980 chunk 89 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.059024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.044497 restraints weight = 254124.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.045176 restraints weight = 211981.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.045711 restraints weight = 181884.048| |-----------------------------------------------------------------------------| r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.6331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.017 44900 Z= 0.343 Angle : 0.471 8.453 62590 Z= 0.383 Chirality : 0.028 0.088 8690 Planarity : 0.003 0.021 9030 Dihedral : 4.343 31.318 9030 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 0.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.08), residues: 9000 helix: 0.19 (0.05), residues: 8375 sheet: None (None), residues: 0 loop : -1.54 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 106 PHE 0.000 0.000 PHE a 4 TYR 0.000 0.000 TYR A 16 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5241.52 seconds wall clock time: 98 minutes 3.78 seconds (5883.78 seconds total)