Starting phenix.real_space_refine on Wed Aug 27 00:05:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dze_47327/08_2025/9dze_47327.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dze_47327/08_2025/9dze_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_47327/08_2025/9dze_47327.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dze_47327/08_2025/9dze_47327.map" model { file = "/net/cci-nas-00/data/ceres_data/9dze_47327/08_2025/9dze_47327.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dze_47327/08_2025/9dze_47327.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'GLU:plan': 39, 'GLN:plan1': 21, 'ASN:plan1': 12, 'TYR:plan': 3, 'ARG:plan': 23, 'ASP:plan': 15, 'TRP:plan': 1, 'HIS:plan': 1} 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: {'GLU:plan': 39, 'GLN:plan1': 21, 'ASN:plan1': 12, 'TYR:plan': 3, 'ARG:plan': 23, 'ASP:plan': 15, 'TRP:plan': 1, 'HIS:plan': 1} 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: {'GLU:plan': 39, 'GLN:plan1': 21, 'ASN:plan1': 12, 'TYR:plan': 3, 'ARG:plan': 23, 'ASP:plan': 15, 'TRP:plan': 1, 'HIS:plan': 1} 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: {'GLU:plan': 39, 'GLN:plan1': 21, 'ASN:plan1': 12, 'TYR:plan': 3, 'ARG:plan': 23, 'ASP:plan': 15, 'TRP:plan': 1, 'HIS:plan': 1} 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: {'GLU:plan': 39, 'GLN:plan1': 21, 'ASN:plan1': 12, 'TYR:plan': 3, 'ARG:plan': 23, 'ASP:plan': 15, 'TRP:plan': 1, 'HIS:plan': 1} 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: {'GLU:plan': 39, 'GLN:plan1': 21, 'ASN:plan1': 12, 'TYR:plan': 3, 'ARG:plan': 23, 'ASP:plan': 15, 'TRP:plan': 1, 'HIS:plan': 1} 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: {'GLU:plan': 39, 'GLN:plan1': 21, 'ASN:plan1': 12, 'TYR:plan': 3, 'ARG:plan': 23, 'ASP:plan': 15, 'TRP:plan': 1, 'HIS:plan': 1} 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: {'GLU:plan': 39, 'GLN:plan1': 21, 'ASN:plan1': 12, 'TYR:plan': 3, 'ARG:plan': 23, 'ASP:plan': 15, 'TRP:plan': 1, 'HIS:plan': 1} 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: {'GLU:plan': 39, 'GLN:plan1': 21, 'ASN:plan1': 12, 'TYR:plan': 3, 'ARG:plan': 23, 'ASP:plan': 15, 'TRP:plan': 1, 'HIS:plan': 1} 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: {'GLU:plan': 39, 'GLN:plan1': 21, 'ASN:plan1': 12, 'TYR:plan': 3, 'ARG:plan': 23, 'ASP:plan': 15, 'TRP:plan': 1, 'HIS:plan': 1} 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: {'ARG:plan': 26, 'GLU:plan': 44, 'ASN:plan1': 14, 'HIS:plan': 1, 'ASP:plan': 12, 'TRP:plan': 1, 'GLN:plan1': 14, 'TYR:plan': 3} 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: {'ARG:plan': 26, 'GLU:plan': 44, 'ASN:plan1': 14, 'HIS:plan': 1, 'ASP:plan': 12, 'TRP:plan': 1, 'GLN:plan1': 14, 'TYR:plan': 3} 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: {'ARG:plan': 26, 'GLU:plan': 44, 'ASN:plan1': 14, 'HIS:plan': 1, 'ASP:plan': 12, 'TRP:plan': 1, 'GLN:plan1': 14, 'TYR:plan': 3} 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: {'ARG:plan': 26, 'GLU:plan': 44, 'ASN:plan1': 14, 'HIS:plan': 1, 'ASP:plan': 12, 'TRP:plan': 1, 'GLN:plan1': 14, 'TYR:plan': 3} 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: {'ARG:plan': 26, 'GLU:plan': 44, 'ASN:plan1': 14, 'HIS:plan': 1, 'ASP:plan': 12, 'TRP:plan': 1, 'GLN:plan1': 14, 'TYR:plan': 3} 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: {'ARG:plan': 26, 'GLU:plan': 44, 'ASN:plan1': 14, 'HIS:plan': 1, 'ASP:plan': 12, 'TRP:plan': 1, 'GLN:plan1': 14, 'TYR:plan': 3} 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: {'ARG:plan': 26, 'GLU:plan': 44, 'ASN:plan1': 14, 'HIS:plan': 1, 'ASP:plan': 12, 'TRP:plan': 1, 'GLN:plan1': 14, 'TYR:plan': 3} 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: {'ARG:plan': 26, 'GLU:plan': 44, 'ASN:plan1': 14, 'HIS:plan': 1, 'ASP:plan': 12, 'TRP:plan': 1, 'GLN:plan1': 14, 'TYR:plan': 3} 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: {'ARG:plan': 26, 'GLU:plan': 44, 'ASN:plan1': 14, 'HIS:plan': 1, 'ASP:plan': 12, 'TRP:plan': 1, 'GLN:plan1': 14, 'TYR:plan': 3} 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: {'ARG:plan': 26, 'GLU:plan': 44, 'ASN:plan1': 14, 'HIS:plan': 1, 'ASP:plan': 12, 'TRP:plan': 1, 'GLN:plan1': 14, 'TYR:plan': 3} 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: {'GLU:plan': 35, 'PHE:plan': 2, 'GLN:plan1': 14, 'ASP:plan': 8, 'ARG:plan': 26, 'HIS:plan': 4, 'TRP:plan': 1, 'ASN:plan1': 11, 'TYR:plan': 3} 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: {'GLU:plan': 35, 'PHE:plan': 2, 'GLN:plan1': 14, 'ASP:plan': 8, 'ARG:plan': 26, 'HIS:plan': 4, 'TRP:plan': 1, 'ASN:plan1': 11, 'TYR:plan': 3} 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: {'GLU:plan': 35, 'PHE:plan': 2, 'GLN:plan1': 14, 'ASP:plan': 8, 'ARG:plan': 26, 'HIS:plan': 4, 'TRP:plan': 1, 'ASN:plan1': 11, 'TYR:plan': 3} 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: {'GLU:plan': 35, 'PHE:plan': 2, 'GLN:plan1': 14, 'ASP:plan': 8, 'ARG:plan': 26, 'HIS:plan': 4, 'TRP:plan': 1, 'ASN:plan1': 11, 'TYR:plan': 3} 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: {'GLU:plan': 35, 'PHE:plan': 2, 'GLN:plan1': 14, 'ASP:plan': 8, 'ARG:plan': 26, 'HIS:plan': 4, 'TRP:plan': 1, 'ASN:plan1': 11, 'TYR:plan': 3} 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: {'GLU:plan': 38, 'PHE:plan': 2, 'GLN:plan1': 14, 'ASP:plan': 8, 'ARG:plan': 25, 'HIS:plan': 4, 'TRP:plan': 1, 'ASN:plan1': 10, 'TYR:plan': 2} 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: {'GLU:plan': 38, 'PHE:plan': 2, 'GLN:plan1': 14, 'ASP:plan': 8, 'ARG:plan': 25, 'HIS:plan': 4, 'TRP:plan': 1, 'ASN:plan1': 10, 'TYR:plan': 2} 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: {'GLU:plan': 38, 'PHE:plan': 2, 'GLN:plan1': 14, 'ASP:plan': 8, 'ARG:plan': 25, 'HIS:plan': 4, 'TRP:plan': 1, 'ASN:plan1': 10, 'TYR:plan': 2} 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: {'GLU:plan': 38, 'PHE:plan': 2, 'GLN:plan1': 14, 'ASP:plan': 8, 'ARG:plan': 25, 'HIS:plan': 4, 'TRP:plan': 1, 'ASN:plan1': 10, 'TYR:plan': 2} 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: {'GLU:plan': 38, 'PHE:plan': 2, 'GLN:plan1': 14, 'ASP:plan': 8, 'ARG:plan': 25, 'HIS:plan': 4, 'TRP:plan': 1, 'ASN:plan1': 10, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 442 Time building chain proxies: 11.23, per 1000 atoms: 0.25 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: 4.52 Conformation dependent library (CDL) restraints added in 2.2 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.00 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: 11.42 Time building geometry restraints manager: 5.69 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: 0.01 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: 5.330 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: 0.030 Extract box with map and model: 0.470 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 43.030 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.500 ------------------------------------------------------------------------------- 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= 0.599 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 TYR 0.000 0.000 TYR A 16 PHE 0.000 0.000 PHE a 4 TRP 0.000 0.000 TRP A 106 Details of bonding type rmsd covalent geometry : bond 0.00782 (44900) covalent geometry : angle 1.26818 (62590) hydrogen bonds : bond 0.12498 ( 7056) hydrogen bonds : angle 6.19801 (21168) *********************** 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 : 1.161 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.1715 time to fit residues: 35.8205 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 : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 890 random chunks: chunk 864 optimal weight: 0.5980 chunk 394 optimal weight: 2.9990 chunk 776 optimal weight: 0.3980 chunk 430 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 265 optimal weight: 0.9980 chunk 523 optimal weight: 5.9990 chunk 497 optimal weight: 4.9990 chunk 414 optimal weight: 3.9990 chunk 802 optimal weight: 3.9990 chunk 849 optimal weight: 6.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- 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 = 0.3138 r_free = 0.3138 target = 0.064026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.048307 restraints weight = 244875.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.048886 restraints weight = 211224.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.048890 restraints weight = 187207.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.049465 restraints weight = 187057.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.049465 restraints weight = 168541.462| |-----------------------------------------------------------------------------| r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.2653 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= 0.302 Angle : 0.423 7.343 62590 Z= 0.339 Chirality : 0.027 0.085 8690 Planarity : 0.003 0.017 9030 Dihedral : 3.833 21.309 9030 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 0.27 Ramachandran Plot: Outliers : 0.01 % Allowed : 0.61 % Favored : 99.38 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.43 (0.08), residues: 9000 helix: 2.35 (0.05), residues: 8546 sheet: None (None), residues: 0 loop : 0.51 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 16 PHE 0.000 0.000 PHE a 4 TRP 0.000 0.000 TRP A 106 Details of bonding type rmsd covalent geometry : bond 0.00385 (44900) covalent geometry : angle 0.42254 (62590) hydrogen bonds : bond 0.04543 ( 7056) hydrogen bonds : angle 4.04992 (21168) *********************** 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 : 1.396 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.1867 time to fit residues: 39.2348 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 : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 890 random chunks: chunk 17 optimal weight: 6.9990 chunk 390 optimal weight: 1.9990 chunk 112 optimal weight: 0.5980 chunk 847 optimal weight: 3.9990 chunk 719 optimal weight: 0.6980 chunk 76 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 868 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 144 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- 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 = 0.3115 r_free = 0.3115 target = 0.062833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.047629 restraints weight = 247900.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.048135 restraints weight = 208627.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.048780 restraints weight = 185811.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.049217 restraints weight = 165019.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.049225 restraints weight = 151696.043| |-----------------------------------------------------------------------------| r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.4146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 44900 Z= 0.273 Angle : 0.381 7.273 62590 Z= 0.305 Chirality : 0.027 0.090 8690 Planarity : 0.002 0.014 9030 Dihedral : 3.506 20.154 9030 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 0.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.47 (0.08), residues: 9000 helix: 3.10 (0.05), residues: 8457 sheet: None (None), residues: 0 loop : -0.26 (0.25), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 16 PHE 0.000 0.000 PHE a 4 TRP 0.000 0.000 TRP A 106 Details of bonding type rmsd covalent geometry : bond 0.00349 (44900) covalent geometry : angle 0.38069 (62590) hydrogen bonds : bond 0.04081 ( 7056) hydrogen bonds : angle 3.77449 (21168) *********************** 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 : 1.263 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.1769 time to fit residues: 36.8096 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 : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 890 random chunks: chunk 867 optimal weight: 6.9990 chunk 83 optimal weight: 0.7980 chunk 82 optimal weight: 4.9990 chunk 436 optimal weight: 6.9990 chunk 526 optimal weight: 3.9990 chunk 712 optimal weight: 5.9990 chunk 418 optimal weight: 3.9990 chunk 419 optimal weight: 0.7980 chunk 563 optimal weight: 0.9990 chunk 241 optimal weight: 9.9990 chunk 401 optimal weight: 9.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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 = 0.3075 r_free = 0.3075 target = 0.060949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.046291 restraints weight = 252280.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.046857 restraints weight = 215989.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 16)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.047320 restraints weight = 190871.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 15)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.047737 restraints weight = 173296.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.047746 restraints weight = 159359.814| |-----------------------------------------------------------------------------| r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.4794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.016 44900 Z= 0.347 Angle : 0.456 7.326 62590 Z= 0.368 Chirality : 0.028 0.089 8690 Planarity : 0.003 0.020 9030 Dihedral : 4.024 27.557 9030 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 0.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.27 (0.08), residues: 9000 helix: 2.34 (0.05), residues: 8425 sheet: None (None), residues: 0 loop : -0.59 (0.24), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 16 PHE 0.000 0.000 PHE a 4 TRP 0.000 0.000 TRP A 106 Details of bonding type rmsd covalent geometry : bond 0.00443 (44900) covalent geometry : angle 0.45583 (62590) hydrogen bonds : bond 0.04330 ( 7056) hydrogen bonds : angle 4.40960 (21168) *********************** 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 : 1.520 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.1766 time to fit residues: 37.0040 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 : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 890 random chunks: chunk 847 optimal weight: 4.9990 chunk 753 optimal weight: 0.2980 chunk 410 optimal weight: 4.9990 chunk 643 optimal weight: 0.9990 chunk 541 optimal weight: 4.9990 chunk 645 optimal weight: 5.9990 chunk 323 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 279 optimal weight: 4.9990 chunk 232 optimal weight: 3.9990 chunk 883 optimal weight: 3.9990 overall best weight: 2.6588 ------------------------------------------------------------------------------- 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 = 0.3037 r_free = 0.3037 target = 0.059328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.044820 restraints weight = 252575.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.045405 restraints weight = 213607.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.045941 restraints weight = 186977.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.046287 restraints weight = 168412.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.046644 restraints weight = 155803.263| |-----------------------------------------------------------------------------| r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.5389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.019 44900 Z= 0.430 Angle : 0.539 8.950 62590 Z= 0.438 Chirality : 0.028 0.094 8690 Planarity : 0.004 0.019 9030 Dihedral : 4.424 29.833 9030 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 0.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.56 % Favored : 97.41 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.49 (0.08), residues: 9000 helix: 1.20 (0.05), residues: 8315 sheet: None (None), residues: 0 loop : -0.79 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 16 PHE 0.000 0.000 PHE a 4 TRP 0.000 0.000 TRP A 106 Details of bonding type rmsd covalent geometry : bond 0.00550 (44900) covalent geometry : angle 0.53907 (62590) hydrogen bonds : bond 0.04859 ( 7056) hydrogen bonds : angle 5.05798 (21168) *********************** 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 : 1.009 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.1863 time to fit residues: 38.9996 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 : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 890 random chunks: chunk 577 optimal weight: 0.1980 chunk 489 optimal weight: 8.9990 chunk 266 optimal weight: 3.9990 chunk 879 optimal weight: 2.9990 chunk 257 optimal weight: 4.9990 chunk 139 optimal weight: 5.9990 chunk 128 optimal weight: 7.9990 chunk 234 optimal weight: 4.9990 chunk 379 optimal weight: 1.9990 chunk 374 optimal weight: 2.9990 chunk 595 optimal weight: 4.9990 overall best weight: 2.4388 ------------------------------------------------------------------------------- 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 = 0.3046 r_free = 0.3046 target = 0.059680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.044997 restraints weight = 252492.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.045595 restraints weight = 212696.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.046100 restraints weight = 185959.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.046595 restraints weight = 166933.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 15)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.046600 restraints weight = 151665.230| |-----------------------------------------------------------------------------| r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.5675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.018 44900 Z= 0.397 Angle : 0.495 7.729 62590 Z= 0.404 Chirality : 0.028 0.090 8690 Planarity : 0.003 0.017 9030 Dihedral : 4.183 29.702 9030 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 0.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.50 (0.08), residues: 9000 helix: 1.21 (0.05), residues: 8340 sheet: None (None), residues: 0 loop : -1.01 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 16 PHE 0.000 0.000 PHE a 4 TRP 0.000 0.000 TRP A 106 Details of bonding type rmsd covalent geometry : bond 0.00507 (44900) covalent geometry : angle 0.49451 (62590) hydrogen bonds : bond 0.04624 ( 7056) hydrogen bonds : angle 4.83792 (21168) *********************** 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 : 1.448 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.1636 time to fit residues: 34.5778 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 : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 890 random chunks: chunk 736 optimal weight: 0.2980 chunk 569 optimal weight: 3.9990 chunk 240 optimal weight: 6.9990 chunk 699 optimal weight: 0.7980 chunk 50 optimal weight: 5.9990 chunk 437 optimal weight: 4.9990 chunk 370 optimal weight: 2.9990 chunk 863 optimal weight: 0.0670 chunk 748 optimal weight: 3.9990 chunk 669 optimal weight: 4.9990 chunk 193 optimal weight: 0.5980 overall best weight: 0.9520 ------------------------------------------------------------------------------- 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 = 0.3125 r_free = 0.3125 target = 0.063234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.048120 restraints weight = 248028.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.048774 restraints weight = 206197.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.049445 restraints weight = 179212.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.049872 restraints weight = 160201.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.050208 restraints weight = 147366.342| |-----------------------------------------------------------------------------| r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.5621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.008 44900 Z= 0.157 Angle : 0.278 6.267 62590 Z= 0.216 Chirality : 0.027 0.084 8690 Planarity : 0.002 0.009 9030 Dihedral : 3.241 19.441 9030 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 0.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.60 (0.08), residues: 9000 helix: 3.22 (0.05), residues: 8435 sheet: None (None), residues: 0 loop : -0.79 (0.24), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 16 PHE 0.000 0.000 PHE a 4 TRP 0.000 0.000 TRP A 106 Details of bonding type rmsd covalent geometry : bond 0.00199 (44900) covalent geometry : angle 0.27777 (62590) hydrogen bonds : bond 0.03436 ( 7056) hydrogen bonds : angle 3.28653 (21168) *********************** 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 : 1.424 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.1805 time to fit residues: 37.9223 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 : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 890 random chunks: chunk 583 optimal weight: 7.9990 chunk 862 optimal weight: 6.9990 chunk 857 optimal weight: 7.9990 chunk 402 optimal weight: 0.7980 chunk 455 optimal weight: 5.9990 chunk 423 optimal weight: 4.9990 chunk 470 optimal weight: 5.9990 chunk 446 optimal weight: 3.9990 chunk 242 optimal weight: 5.9990 chunk 213 optimal weight: 4.9990 chunk 728 optimal weight: 4.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- 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 = 0.2972 r_free = 0.2972 target = 0.056608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.042164 restraints weight = 260102.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.042787 restraints weight = 218644.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.043306 restraints weight = 190300.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.043702 restraints weight = 172328.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.043958 restraints weight = 157773.933| |-----------------------------------------------------------------------------| r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.6138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.028 44900 Z= 0.628 Angle : 0.737 9.679 62590 Z= 0.603 Chirality : 0.029 0.095 8690 Planarity : 0.006 0.027 9030 Dihedral : 5.093 35.359 9030 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 1.32 Ramachandran Plot: Outliers : 0.41 % Allowed : 3.79 % Favored : 95.80 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.08), residues: 9000 helix: -0.04 (0.05), residues: 8275 sheet: None (None), residues: 0 loop : -1.23 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 16 PHE 0.000 0.000 PHE a 4 TRP 0.000 0.000 TRP A 106 Details of bonding type rmsd covalent geometry : bond 0.00803 (44900) covalent geometry : angle 0.73661 (62590) hydrogen bonds : bond 0.05880 ( 7056) hydrogen bonds : angle 6.21958 (21168) *********************** 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 : 1.053 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.1712 time to fit residues: 35.9385 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 : 1.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 890 random chunks: chunk 391 optimal weight: 1.9990 chunk 271 optimal weight: 0.1980 chunk 26 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 619 optimal weight: 0.5980 chunk 873 optimal weight: 4.9990 chunk 485 optimal weight: 0.0170 chunk 853 optimal weight: 4.9990 chunk 411 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 overall best weight: 0.5018 ------------------------------------------------------------------------------- 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 = 0.3139 r_free = 0.3139 target = 0.063827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.048723 restraints weight = 247367.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.049383 restraints weight = 204873.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.050102 restraints weight = 177918.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.050504 restraints weight = 157241.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.050839 restraints weight = 145586.105| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.5906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.011 44900 Z= 0.106 Angle : 0.252 6.002 62590 Z= 0.188 Chirality : 0.027 0.081 8690 Planarity : 0.002 0.010 9030 Dihedral : 3.216 17.978 9030 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 0.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.73 (0.08), residues: 9000 helix: 3.32 (0.05), residues: 8430 sheet: None (None), residues: 0 loop : -1.00 (0.24), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 16 PHE 0.000 0.000 PHE a 4 TRP 0.000 0.000 TRP A 106 Details of bonding type rmsd covalent geometry : bond 0.00133 (44900) covalent geometry : angle 0.25185 (62590) hydrogen bonds : bond 0.03341 ( 7056) hydrogen bonds : angle 3.10763 (21168) *********************** 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 : 1.338 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.1709 time to fit residues: 36.1518 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 : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 890 random chunks: chunk 474 optimal weight: 4.9990 chunk 240 optimal weight: 7.9990 chunk 274 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 403 optimal weight: 4.9990 chunk 484 optimal weight: 4.9990 chunk 653 optimal weight: 5.9990 chunk 889 optimal weight: 7.9990 chunk 839 optimal weight: 6.9990 chunk 778 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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 = 0.2905 r_free = 0.2905 target = 0.053906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2582 r_free = 0.2582 target = 0.040393 restraints weight = 265911.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2593 r_free = 0.2593 target = 0.040723 restraints weight = 226414.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2607 r_free = 0.2607 target = 0.041218 restraints weight = 205439.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.041603 restraints weight = 185147.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.041879 restraints weight = 170662.081| |-----------------------------------------------------------------------------| r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 moved from start: 0.6674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.037 44900 Z= 0.801 Angle : 0.921 11.710 62590 Z= 0.749 Chirality : 0.030 0.127 8690 Planarity : 0.008 0.039 9030 Dihedral : 6.118 37.410 9030 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.60 % Allowed : 6.11 % Favored : 93.29 % 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 : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.71 (0.07), residues: 9000 helix: -1.54 (0.05), residues: 8255 sheet: None (None), residues: 0 loop : -1.86 (0.22), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 16 PHE 0.000 0.000 PHE a 4 TRP 0.000 0.000 TRP A 106 Details of bonding type rmsd covalent geometry : bond 0.01027 (44900) covalent geometry : angle 0.92052 (62590) hydrogen bonds : bond 0.07259 ( 7056) hydrogen bonds : angle 7.43629 (21168) ********************** 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 : 1.123 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.1764 time to fit residues: 37.4069 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 : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 890 random chunks: chunk 59 optimal weight: 8.9990 chunk 416 optimal weight: 2.9990 chunk 283 optimal weight: 5.9990 chunk 752 optimal weight: 0.5980 chunk 391 optimal weight: 0.5980 chunk 506 optimal weight: 6.9990 chunk 784 optimal weight: 4.9990 chunk 204 optimal weight: 1.9990 chunk 757 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 428 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- 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 = 0.3070 r_free = 0.3070 target = 0.060756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.045893 restraints weight = 250062.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.046631 restraints weight = 206954.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.047147 restraints weight = 176770.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.047518 restraints weight = 158845.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.047518 restraints weight = 146058.585| |-----------------------------------------------------------------------------| r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.6355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.011 44900 Z= 0.235 Angle : 0.355 7.371 62590 Z= 0.281 Chirality : 0.027 0.088 8690 Planarity : 0.002 0.022 9030 Dihedral : 3.885 25.328 9030 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 0.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.40 (0.08), residues: 9000 helix: 1.15 (0.05), residues: 8360 sheet: None (None), residues: 0 loop : -1.25 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 16 PHE 0.000 0.000 PHE a 4 TRP 0.000 0.000 TRP A 106 Details of bonding type rmsd covalent geometry : bond 0.00299 (44900) covalent geometry : angle 0.35455 (62590) hydrogen bonds : bond 0.04102 ( 7056) hydrogen bonds : angle 4.20613 (21168) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5166.19 seconds wall clock time: 89 minutes 18.54 seconds (5358.54 seconds total)