Starting phenix.real_space_refine (version: 1.21rc1) on Mon Apr 24 00:17:28 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tdj_25831/04_2023/7tdj_25831_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tdj_25831/04_2023/7tdj_25831.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tdj_25831/04_2023/7tdj_25831.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tdj_25831/04_2023/7tdj_25831.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tdj_25831/04_2023/7tdj_25831_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tdj_25831/04_2023/7tdj_25831_neut_updated.pdb" } resolution = 3.7 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 ------------------------------------------------------------------------------- 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= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 8 9.91 5 Zn 4 6.06 5 P 12 5.49 5 S 628 5.16 5 C 74080 2.51 5 N 20744 2.21 5 O 21636 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 139": "OE1" <-> "OE2" Residue "A TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 396": "OE1" <-> "OE2" Residue "A GLU 439": "OE1" <-> "OE2" Residue "A GLU 453": "OE1" <-> "OE2" Residue "A GLU 457": "OE1" <-> "OE2" Residue "A GLU 462": "OE1" <-> "OE2" Residue "A GLU 463": "OE1" <-> "OE2" Residue "A PHE 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 509": "OE1" <-> "OE2" Residue "A GLU 562": "OE1" <-> "OE2" Residue "A GLU 630": "OE1" <-> "OE2" Residue "A TYR 663": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 791": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 910": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1051": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1181": "OE1" <-> "OE2" Residue "A GLU 1183": "OE1" <-> "OE2" Residue "A GLU 1655": "OE1" <-> "OE2" Residue "A GLU 1733": "OE1" <-> "OE2" Residue "A GLU 2115": "OE1" <-> "OE2" Residue "A PHE 2754": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2882": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 3657": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 3665": "OE1" <-> "OE2" Residue "A ASP 3696": "OD1" <-> "OD2" Residue "A GLU 3811": "OE1" <-> "OE2" Residue "A ASP 3941": "OD1" <-> "OD2" Residue "A GLU 3944": "OE1" <-> "OE2" Residue "A GLU 4011": "OE1" <-> "OE2" Residue "A GLU 4056": "OE1" <-> "OE2" Residue "A PHE 4103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 4138": "OD1" <-> "OD2" Residue "A GLU 4168": "OE1" <-> "OE2" Residue "A GLU 4199": "OE1" <-> "OE2" Residue "A GLU 4212": "OE1" <-> "OE2" Residue "A TYR 4580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 4631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 4633": "OE1" <-> "OE2" Residue "A GLU 4634": "OE1" <-> "OE2" Residue "A ASP 4694": "OD1" <-> "OD2" Residue "A ASP 4696": "OD1" <-> "OD2" Residue "A ASP 4786": "OD1" <-> "OD2" Residue "A ASP 4868": "OD1" <-> "OD2" Residue "A GLU 4869": "OE1" <-> "OE2" Residue "A ASP 4877": "OD1" <-> "OD2" Residue "A GLU 4900": "OE1" <-> "OE2" Residue "A PHE 4920": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 4923": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 5007": "OE1" <-> "OE2" Residue "B GLU 139": "OE1" <-> "OE2" Residue "B TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 396": "OE1" <-> "OE2" Residue "B GLU 439": "OE1" <-> "OE2" Residue "B GLU 453": "OE1" <-> "OE2" Residue "B GLU 457": "OE1" <-> "OE2" Residue "B GLU 462": "OE1" <-> "OE2" Residue "B GLU 463": "OE1" <-> "OE2" Residue "B PHE 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 509": "OE1" <-> "OE2" Residue "B GLU 562": "OE1" <-> "OE2" Residue "B GLU 630": "OE1" <-> "OE2" Residue "B TYR 663": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 791": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 910": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1051": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1181": "OE1" <-> "OE2" Residue "B GLU 1183": "OE1" <-> "OE2" Residue "B GLU 1655": "OE1" <-> "OE2" Residue "B GLU 1733": "OE1" <-> "OE2" Residue "B GLU 2115": "OE1" <-> "OE2" Residue "B PHE 2754": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 2882": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 3657": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 3665": "OE1" <-> "OE2" Residue "B ASP 3696": "OD1" <-> "OD2" Residue "B GLU 3811": "OE1" <-> "OE2" Residue "B ASP 3941": "OD1" <-> "OD2" Residue "B GLU 3944": "OE1" <-> "OE2" Residue "B GLU 4011": "OE1" <-> "OE2" Residue "B GLU 4056": "OE1" <-> "OE2" Residue "B PHE 4103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 4138": "OD1" <-> "OD2" Residue "B GLU 4168": "OE1" <-> "OE2" Residue "B GLU 4199": "OE1" <-> "OE2" Residue "B GLU 4212": "OE1" <-> "OE2" Residue "B TYR 4580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 4631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 4633": "OE1" <-> "OE2" Residue "B GLU 4634": "OE1" <-> "OE2" Residue "B ASP 4694": "OD1" <-> "OD2" Residue "B ASP 4696": "OD1" <-> "OD2" Residue "B ASP 4786": "OD1" <-> "OD2" Residue "B ASP 4868": "OD1" <-> "OD2" Residue "B GLU 4869": "OE1" <-> "OE2" Residue "B ASP 4877": "OD1" <-> "OD2" Residue "B GLU 4900": "OE1" <-> "OE2" Residue "B PHE 4920": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 4923": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 5007": "OE1" <-> "OE2" Residue "C GLU 139": "OE1" <-> "OE2" Residue "C TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 396": "OE1" <-> "OE2" Residue "C GLU 439": "OE1" <-> "OE2" Residue "C GLU 453": "OE1" <-> "OE2" Residue "C GLU 457": "OE1" <-> "OE2" Residue "C GLU 462": "OE1" <-> "OE2" Residue "C GLU 463": "OE1" <-> "OE2" Residue "C PHE 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 509": "OE1" <-> "OE2" Residue "C GLU 562": "OE1" <-> "OE2" Residue "C GLU 630": "OE1" <-> "OE2" Residue "C TYR 663": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 791": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 910": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1051": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1181": "OE1" <-> "OE2" Residue "C GLU 1183": "OE1" <-> "OE2" Residue "C GLU 1655": "OE1" <-> "OE2" Residue "C GLU 1733": "OE1" <-> "OE2" Residue "C GLU 2115": "OE1" <-> "OE2" Residue "C TYR 2142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2754": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 2882": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 3657": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 3665": "OE1" <-> "OE2" Residue "C ASP 3696": "OD1" <-> "OD2" Residue "C GLU 3811": "OE1" <-> "OE2" Residue "C ASP 3941": "OD1" <-> "OD2" Residue "C GLU 3944": "OE1" <-> "OE2" Residue "C GLU 4011": "OE1" <-> "OE2" Residue "C GLU 4056": "OE1" <-> "OE2" Residue "C PHE 4103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 4138": "OD1" <-> "OD2" Residue "C GLU 4168": "OE1" <-> "OE2" Residue "C GLU 4199": "OE1" <-> "OE2" Residue "C GLU 4212": "OE1" <-> "OE2" Residue "C TYR 4580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 4631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 4633": "OE1" <-> "OE2" Residue "C GLU 4634": "OE1" <-> "OE2" Residue "C ASP 4694": "OD1" <-> "OD2" Residue "C ASP 4696": "OD1" <-> "OD2" Residue "C ASP 4786": "OD1" <-> "OD2" Residue "C ASP 4868": "OD1" <-> "OD2" Residue "C GLU 4869": "OE1" <-> "OE2" Residue "C ASP 4877": "OD1" <-> "OD2" Residue "C GLU 4900": "OE1" <-> "OE2" Residue "C PHE 4920": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 4923": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 5007": "OE1" <-> "OE2" Residue "D GLU 139": "OE1" <-> "OE2" Residue "D TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 396": "OE1" <-> "OE2" Residue "D GLU 439": "OE1" <-> "OE2" Residue "D GLU 453": "OE1" <-> "OE2" Residue "D GLU 457": "OE1" <-> "OE2" Residue "D GLU 462": "OE1" <-> "OE2" Residue "D GLU 463": "OE1" <-> "OE2" Residue "D PHE 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 509": "OE1" <-> "OE2" Residue "D GLU 562": "OE1" <-> "OE2" Residue "D GLU 630": "OE1" <-> "OE2" Residue "D TYR 663": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 791": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 910": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1051": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1181": "OE1" <-> "OE2" Residue "D GLU 1183": "OE1" <-> "OE2" Residue "D GLU 1655": "OE1" <-> "OE2" Residue "D GLU 1733": "OE1" <-> "OE2" Residue "D PHE 1748": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 2115": "OE1" <-> "OE2" Residue "D PHE 2754": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 2882": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 3657": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 3665": "OE1" <-> "OE2" Residue "D ASP 3696": "OD1" <-> "OD2" Residue "D GLU 3811": "OE1" <-> "OE2" Residue "D ASP 3941": "OD1" <-> "OD2" Residue "D GLU 3944": "OE1" <-> "OE2" Residue "D GLU 4011": "OE1" <-> "OE2" Residue "D GLU 4056": "OE1" <-> "OE2" Residue "D PHE 4103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 4138": "OD1" <-> "OD2" Residue "D GLU 4168": "OE1" <-> "OE2" Residue "D GLU 4199": "OE1" <-> "OE2" Residue "D GLU 4212": "OE1" <-> "OE2" Residue "D TYR 4580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 4631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 4633": "OE1" <-> "OE2" Residue "D GLU 4634": "OE1" <-> "OE2" Residue "D ASP 4694": "OD1" <-> "OD2" Residue "D ASP 4696": "OD1" <-> "OD2" Residue "D ASP 4786": "OD1" <-> "OD2" Residue "D ASP 4868": "OD1" <-> "OD2" Residue "D GLU 4869": "OE1" <-> "OE2" Residue "D ASP 4877": "OD1" <-> "OD2" Residue "D GLU 4900": "OE1" <-> "OE2" Residue "D PHE 4920": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 4923": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 5007": "OE1" <-> "OE2" Time to flip residues: 0.26s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 117112 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 29242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4133, 29242 Classifications: {'peptide': 4133} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1198} Link IDs: {'PTRANS': 152, 'TRANS': 3980} Chain breaks: 24 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2877 Unresolved non-hydrogen angles: 4040 Unresolved non-hydrogen dihedrals: 1771 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'GLN:plan1': 16, 'UNK:plan-1': 900, 'ASP:plan': 37, 'TYR:plan': 3, 'ASN:plan1': 13, 'TRP:plan': 4, 'HIS:plan': 5, 'PHE:plan': 4, 'GLU:plan': 76, 'ARG:plan': 28} Unresolved non-hydrogen planarities: 1664 Chain: "B" Number of atoms: 29242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4133, 29242 Classifications: {'peptide': 4133} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1198} Link IDs: {'PTRANS': 152, 'TRANS': 3980} Chain breaks: 24 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2877 Unresolved non-hydrogen angles: 4040 Unresolved non-hydrogen dihedrals: 1771 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'GLN:plan1': 16, 'UNK:plan-1': 900, 'ASP:plan': 37, 'TYR:plan': 3, 'ASN:plan1': 13, 'TRP:plan': 4, 'HIS:plan': 5, 'PHE:plan': 4, 'GLU:plan': 76, 'ARG:plan': 28} Unresolved non-hydrogen planarities: 1664 Chain: "C" Number of atoms: 29242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4133, 29242 Classifications: {'peptide': 4133} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1198} Link IDs: {'PTRANS': 152, 'TRANS': 3980} Chain breaks: 24 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2877 Unresolved non-hydrogen angles: 4040 Unresolved non-hydrogen dihedrals: 1771 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'GLN:plan1': 16, 'UNK:plan-1': 900, 'ASP:plan': 37, 'TYR:plan': 3, 'ASN:plan1': 13, 'TRP:plan': 4, 'HIS:plan': 5, 'PHE:plan': 4, 'GLU:plan': 76, 'ARG:plan': 28} Unresolved non-hydrogen planarities: 1664 Chain: "D" Number of atoms: 29242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4133, 29242 Classifications: {'peptide': 4133} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1198} Link IDs: {'PTRANS': 152, 'TRANS': 3980} Chain breaks: 24 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2877 Unresolved non-hydrogen angles: 4040 Unresolved non-hydrogen dihedrals: 1771 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'GLN:plan1': 16, 'UNK:plan-1': 900, 'ASP:plan': 37, 'TYR:plan': 3, 'ASN:plan1': 13, 'TRP:plan': 4, 'HIS:plan': 5, 'PHE:plan': 4, 'GLU:plan': 76, 'ARG:plan': 28} Unresolved non-hydrogen planarities: 1664 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' CA': 2, ' ZN': 1, 'ACP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' CA': 2, ' ZN': 1, 'ACP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' CA': 2, ' ZN': 1, 'ACP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' CA': 2, ' ZN': 1, 'ACP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 28592 SG CYS A4961 179.579 204.249 99.531 1.00 59.80 S ATOM 29149 SG CYS A5027 181.006 206.361 95.617 1.00 69.40 S ATOM 57834 SG CYS B4961 182.487 179.594 99.521 1.00 59.80 S ATOM 87076 SG CYS C4961 207.166 182.488 99.513 1.00 59.80 S ATOM A0CLA SG CYS D4961 204.275 207.152 99.515 1.00 59.80 S Time building chain proxies: 44.51, per 1000 atoms: 0.38 Number of scatterers: 117112 At special positions: 0 Unit cell: (387.855, 387.855, 192.27, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 Ca 8 19.99 S 628 16.00 P 12 15.00 O 21636 8.00 N 20744 7.00 C 74080 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A4876 " - pdb=" SG CYS A4882 " distance=2.03 Simple disulfide: pdb=" SG CYS B4876 " - pdb=" SG CYS B4882 " distance=2.03 Simple disulfide: pdb=" SG CYS C4876 " - pdb=" SG CYS C4882 " distance=2.03 Simple disulfide: pdb=" SG CYS D4876 " - pdb=" SG CYS D4882 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 35.32 Conformation dependent library (CDL) restraints added in 11.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A5102 " pdb="ZN ZN A5102 " - pdb=" ND1 HIS A4983 " pdb="ZN ZN A5102 " - pdb=" SG CYS A4961 " pdb="ZN ZN A5102 " - pdb=" SG CYS A5027 " pdb=" ZN B5102 " pdb="ZN ZN B5102 " - pdb=" NE2 HIS B4978 " pdb="ZN ZN B5102 " - pdb=" ND1 HIS B4983 " pdb="ZN ZN B5102 " - pdb=" SG CYS B4961 " pdb=" ZN C5102 " pdb="ZN ZN C5102 " - pdb=" SG CYS C4961 " pdb="ZN ZN C5102 " - pdb=" NE2 HIS C4978 " pdb="ZN ZN C5102 " - pdb=" ND1 HIS C4983 " pdb=" ZN D5102 " pdb="ZN ZN D5102 " - pdb=" SG CYS D4961 " pdb="ZN ZN D5102 " - pdb=" NE2 HIS D4978 " pdb="ZN ZN D5102 " - pdb=" ND1 HIS D4983 " 25608 Ramachandran restraints generated. 12804 Oldfield, 0 Emsley, 12804 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 31352 Finding SS restraints... Warning!!! ksdssp method is not applicable forstructures with more than 99999 atoms! Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 480 helices and 64 sheets defined 54.4% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 17.19 Creating SS restraints... Processing helix chain 'A' and resid 61 through 66 removed outlier: 4.488A pdb=" N CYS A 65 " --> pdb=" O ASP A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 84 Processing helix chain 'A' and resid 249 through 256 removed outlier: 4.815A pdb=" N CYS A 253 " --> pdb=" O GLY A 249 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N THR A 254 " --> pdb=" O GLY A 250 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N HIS A 255 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ALA A 256 " --> pdb=" O VAL A 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 249 through 256' Processing helix chain 'A' and resid 364 through 371 removed outlier: 5.502A pdb=" N VAL A 371 " --> pdb=" O LEU A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 423 removed outlier: 3.691A pdb=" N SER A 420 " --> pdb=" O LYS A 416 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N PHE A 421 " --> pdb=" O GLY A 417 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N SER A 422 " --> pdb=" O LEU A 418 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N GLY A 423 " --> pdb=" O ASP A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 453 removed outlier: 4.147A pdb=" N VAL A 441 " --> pdb=" O PRO A 437 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE A 442 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU A 443 " --> pdb=" O GLU A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 482 removed outlier: 3.652A pdb=" N GLN A 479 " --> pdb=" O GLN A 475 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLU A 480 " --> pdb=" O SER A 476 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLU A 481 " --> pdb=" O LEU A 477 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N GLY A 482 " --> pdb=" O PHE A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 496 removed outlier: 4.641A pdb=" N VAL A 487 " --> pdb=" O MET A 483 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL A 496 " --> pdb=" O ASP A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 531 removed outlier: 4.267A pdb=" N LYS A 516 " --> pdb=" O ALA A 512 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N GLU A 517 " --> pdb=" O GLU A 513 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR A 523 " --> pdb=" O VAL A 519 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU A 524 " --> pdb=" O ASN A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 541 removed outlier: 3.751A pdb=" N CYS A 537 " --> pdb=" O ASN A 533 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA A 538 " --> pdb=" O ARG A 534 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU A 539 " --> pdb=" O ALA A 535 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N PHE A 540 " --> pdb=" O ASN A 536 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N SER A 541 " --> pdb=" O CYS A 537 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 533 through 541' Processing helix chain 'A' and resid 543 through 551 removed outlier: 3.693A pdb=" N LYS A 550 " --> pdb=" O TRP A 546 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N LEU A 551 " --> pdb=" O VAL A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 571 removed outlier: 3.803A pdb=" N VAL A 567 " --> pdb=" O VAL A 563 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU A 568 " --> pdb=" O LEU A 564 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ILE A 569 " --> pdb=" O TYR A 565 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLU A 570 " --> pdb=" O CYS A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 578 removed outlier: 4.412A pdb=" N ASN A 576 " --> pdb=" O PRO A 572 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ILE A 577 " --> pdb=" O GLU A 573 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE A 578 " --> pdb=" O VAL A 574 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 572 through 578' Processing helix chain 'A' and resid 579 through 594 removed outlier: 3.563A pdb=" N LEU A 590 " --> pdb=" O ILE A 586 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP A 591 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 609 removed outlier: 3.863A pdb=" N LEU A 600 " --> pdb=" O ASN A 596 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N CYS A 607 " --> pdb=" O LEU A 603 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N VAL A 608 " --> pdb=" O CYS A 604 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N CYS A 609 " --> pdb=" O SER A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 626 removed outlier: 4.306A pdb=" N GLN A 618 " --> pdb=" O VAL A 614 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N LEU A 626 " --> pdb=" O THR A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 890 removed outlier: 3.853A pdb=" N GLU A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N LYS A 873 " --> pdb=" O ARG A 869 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N TRP A 882 " --> pdb=" O ILE A 878 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA A 883 " --> pdb=" O HIS A 879 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N GLU A 888 " --> pdb=" O LEU A 884 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N GLN A 889 " --> pdb=" O THR A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 935 removed outlier: 5.399A pdb=" N LEU A 935 " --> pdb=" O THR A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 948 removed outlier: 6.694A pdb=" N GLU A 947 " --> pdb=" O ASP A 943 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ASP A 948 " --> pdb=" O GLU A 944 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 943 through 948' Processing helix chain 'A' and resid 956 through 961 Processing helix chain 'A' and resid 978 through 1001 removed outlier: 4.452A pdb=" N THR A 982 " --> pdb=" O THR A 978 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ASP A 999 " --> pdb=" O VAL A 995 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ARG A1000 " --> pdb=" O TRP A 996 " (cutoff:3.500A) Processing helix chain 'A' and resid 1030 through 1045 removed outlier: 3.535A pdb=" N ASP A1037 " --> pdb=" O ARG A1033 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N SER A1038 " --> pdb=" O SER A1034 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU A1039 " --> pdb=" O ASN A1035 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N THR A1045 " --> pdb=" O GLN A1041 " (cutoff:3.500A) Processing helix chain 'A' and resid 1207 through 1212 removed outlier: 3.857A pdb=" N LEU A1211 " --> pdb=" O ASP A1207 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N ARG A1212 " --> pdb=" O VAL A1208 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1207 through 1212' Processing helix chain 'A' and resid 1574 through 1581 removed outlier: 4.282A pdb=" N ALA A1578 " --> pdb=" O PRO A1574 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N MET A1579 " --> pdb=" O LEU A1575 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE A1580 " --> pdb=" O SER A1576 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU A1581 " --> pdb=" O ALA A1577 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1574 through 1581' Processing helix chain 'A' and resid 1649 through 1657 removed outlier: 4.001A pdb=" N LEU A1653 " --> pdb=" O ASP A1649 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N SER A1654 " --> pdb=" O ILE A1650 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N GLU A1655 " --> pdb=" O LEU A1651 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ARG A1656 " --> pdb=" O GLU A1652 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU A1657 " --> pdb=" O LEU A1653 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1649 through 1657' Processing helix chain 'A' and resid 1658 through 1675 Processing helix chain 'A' and resid 1678 through 1690 removed outlier: 4.417A pdb=" N ALA A1682 " --> pdb=" O ASN A1678 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N HIS A1683 " --> pdb=" O ASN A1679 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA A1684 " --> pdb=" O ARG A1680 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ASP A1690 " --> pdb=" O CYS A1686 " (cutoff:3.500A) Processing helix chain 'A' and resid 1691 through 1700 removed outlier: 3.804A pdb=" N LEU A1698 " --> pdb=" O LEU A1694 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLU A1699 " --> pdb=" O LEU A1695 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ASP A1700 " --> pdb=" O HIS A1696 " (cutoff:3.500A) Processing helix chain 'A' and resid 1704 through 1719 removed outlier: 6.825A pdb=" N ARG A1708 " --> pdb=" O PRO A1704 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA A1709 " --> pdb=" O GLY A1705 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N HIS A1719 " --> pdb=" O LEU A1715 " (cutoff:3.500A) Processing helix chain 'A' and resid 1720 through 1732 removed outlier: 4.422A pdb=" N SER A1732 " --> pdb=" O ARG A1728 " (cutoff:3.500A) Processing helix chain 'A' and resid 1739 through 1746 removed outlier: 4.069A pdb=" N ILE A1745 " --> pdb=" O GLU A1741 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N THR A1746 " --> pdb=" O THR A1742 " (cutoff:3.500A) Processing helix chain 'A' and resid 1754 through 1759 removed outlier: 4.272A pdb=" N ARG A1759 " --> pdb=" O GLY A1755 " (cutoff:3.500A) Processing helix chain 'A' and resid 1803 through 1825 removed outlier: 3.747A pdb=" N VAL A1819 " --> pdb=" O LEU A1815 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG A1820 " --> pdb=" O GLY A1816 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLN A1824 " --> pdb=" O ARG A1820 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N HIS A1825 " --> pdb=" O ASP A1821 " (cutoff:3.500A) Processing helix chain 'A' and resid 1833 through 1852 Proline residue: A1840 - end of helix removed outlier: 3.847A pdb=" N MET A1851 " --> pdb=" O THR A1847 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLY A1852 " --> pdb=" O LEU A1848 " (cutoff:3.500A) Processing helix chain 'A' and resid 1855 through 1865 removed outlier: 4.221A pdb=" N MET A1865 " --> pdb=" O GLN A1861 " (cutoff:3.500A) Processing helix chain 'A' and resid 1866 through 1871 Processing helix chain 'A' and resid 1934 through 1984 removed outlier: 4.148A pdb=" N GLN A1938 " --> pdb=" O SER A1934 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N TYR A1945 " --> pdb=" O ASN A1941 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N PHE A1946 " --> pdb=" O LEU A1942 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU A1950 " --> pdb=" O PHE A1946 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU A1951 " --> pdb=" O CYS A1947 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU A1963 " --> pdb=" O ALA A1959 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ARG A1964 " --> pdb=" O ALA A1960 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N PHE A1984 " --> pdb=" O LEU A1980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1987 through 1999 removed outlier: 4.207A pdb=" N ARG A1996 " --> pdb=" O ALA A1992 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N GLU A1997 " --> pdb=" O ARG A1993 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE A1998 " --> pdb=" O ARG A1994 " (cutoff:3.500A) Processing helix chain 'A' and resid 2001 through 2015 removed outlier: 3.624A pdb=" N LEU A2009 " --> pdb=" O GLN A2005 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU A2010 " --> pdb=" O ILE A2006 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLU A2015 " --> pdb=" O HIS A2011 " (cutoff:3.500A) Processing helix chain 'A' and resid 2027 through 2043 removed outlier: 4.717A pdb=" N LEU A2031 " --> pdb=" O ILE A2027 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN A2032 " --> pdb=" O ARG A2028 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N GLY A2043 " --> pdb=" O LEU A2039 " (cutoff:3.500A) Processing helix chain 'A' and resid 2093 through 2109 removed outlier: 4.229A pdb=" N ASP A2109 " --> pdb=" O TRP A2105 " (cutoff:3.500A) Processing helix chain 'A' and resid 2113 through 2130 removed outlier: 3.594A pdb=" N VAL A2117 " --> pdb=" O SER A2113 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLY A2130 " --> pdb=" O ARG A2126 " (cutoff:3.500A) Processing helix chain 'A' and resid 2131 through 2139 Proline residue: A2139 - end of helix Processing helix chain 'A' and resid 2148 through 2169 removed outlier: 4.044A pdb=" N SER A2154 " --> pdb=" O GLU A2150 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU A2155 " --> pdb=" O ASP A2151 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ILE A2167 " --> pdb=" O ARG A2163 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N VAL A2168 " --> pdb=" O SER A2164 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N GLN A2169 " --> pdb=" O LEU A2165 " (cutoff:3.500A) Processing helix chain 'A' and resid 2171 through 2188 removed outlier: 3.816A pdb=" N ASN A2176 " --> pdb=" O PRO A2172 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU A2177 " --> pdb=" O GLN A2173 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ASN A2187 " --> pdb=" O GLY A2183 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ASN A2188 " --> pdb=" O ASN A2184 " (cutoff:3.500A) Processing helix chain 'A' and resid 2189 through 2195 removed outlier: 4.658A pdb=" N GLN A2193 " --> pdb=" O LYS A2189 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N HIS A2194 " --> pdb=" O VAL A2190 " (cutoff:3.500A) Proline residue: A2195 - end of helix No H-bonds generated for 'chain 'A' and resid 2189 through 2195' Processing helix chain 'A' and resid 2196 through 2202 Processing helix chain 'A' and resid 2203 through 2216 removed outlier: 4.177A pdb=" N ASN A2213 " --> pdb=" O GLU A2209 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N VAL A2214 " --> pdb=" O VAL A2210 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU A2215 " --> pdb=" O MET A2211 " (cutoff:3.500A) Processing helix chain 'A' and resid 2226 through 2244 removed outlier: 6.776A pdb=" N THR A2230 " --> pdb=" O PRO A2226 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N SER A2231 " --> pdb=" O LYS A2227 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N SER A2243 " --> pdb=" O PHE A2239 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N ARG A2244 " --> pdb=" O CYS A2240 " (cutoff:3.500A) Processing helix chain 'A' and resid 2245 through 2255 removed outlier: 3.906A pdb=" N SER A2249 " --> pdb=" O GLN A2245 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASP A2252 " --> pdb=" O ARG A2248 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N HIS A2253 " --> pdb=" O SER A2249 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LEU A2254 " --> pdb=" O MET A2250 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N SER A2255 " --> pdb=" O PHE A2251 " (cutoff:3.500A) Processing helix chain 'A' and resid 2256 through 2265 removed outlier: 3.569A pdb=" N ASN A2260 " --> pdb=" O TYR A2256 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLY A2262 " --> pdb=" O LEU A2258 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ILE A2263 " --> pdb=" O GLU A2259 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLY A2264 " --> pdb=" O ASN A2260 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N LEU A2265 " --> pdb=" O SER A2261 " (cutoff:3.500A) Processing helix chain 'A' and resid 2271 through 2282 removed outlier: 3.553A pdb=" N VAL A2275 " --> pdb=" O THR A2271 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA A2276 " --> pdb=" O PRO A2272 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL A2280 " --> pdb=" O ALA A2276 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ILE A2281 " --> pdb=" O ALA A2277 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N ASP A2282 " --> pdb=" O ALA A2278 " (cutoff:3.500A) Processing helix chain 'A' and resid 2286 through 2291 removed outlier: 3.747A pdb=" N LEU A2290 " --> pdb=" O LEU A2286 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N GLN A2291 " --> pdb=" O ALA A2287 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2286 through 2291' Processing helix chain 'A' and resid 2294 through 2308 removed outlier: 3.642A pdb=" N SER A2300 " --> pdb=" O GLU A2296 " (cutoff:3.500A) Processing helix chain 'A' and resid 2310 through 2315 removed outlier: 3.605A pdb=" N LEU A2314 " --> pdb=" O CYS A2310 " (cutoff:3.500A) Processing helix chain 'A' and resid 2324 through 2341 removed outlier: 4.111A pdb=" N GLY A2328 " --> pdb=" O ASN A2324 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LEU A2332 " --> pdb=" O GLY A2328 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N ASP A2333 " --> pdb=" O GLU A2329 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N PHE A2334 " --> pdb=" O ARG A2330 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LEU A2335 " --> pdb=" O TYR A2331 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N VAL A2341 " --> pdb=" O PHE A2337 " (cutoff:3.500A) Processing helix chain 'A' and resid 2346 through 2361 removed outlier: 4.300A pdb=" N VAL A2352 " --> pdb=" O GLU A2348 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG A2359 " --> pdb=" O ARG A2355 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N LYS A2360 " --> pdb=" O LEU A2356 " (cutoff:3.500A) Proline residue: A2361 - end of helix Processing helix chain 'A' and resid 2365 through 2370 Processing helix chain 'A' and resid 2375 through 2390 Proline residue: A2390 - end of helix Processing helix chain 'A' and resid 2417 through 2438 Proline residue: A2438 - end of helix Processing helix chain 'A' and resid 2440 through 2447 Processing helix chain 'A' and resid 2448 through 2462 removed outlier: 4.651A pdb=" N ARG A2452 " --> pdb=" O GLY A2448 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE A2453 " --> pdb=" O GLU A2449 " (cutoff:3.500A) Proline residue: A2462 - end of helix Processing helix chain 'A' and resid 2464 through 2473 removed outlier: 3.999A pdb=" N GLY A2468 " --> pdb=" O ASP A2464 " (cutoff:3.500A) Proline residue: A2473 - end of helix Processing helix chain 'A' and resid 2751 through 2774 removed outlier: 4.815A pdb=" N ILE A2755 " --> pdb=" O LEU A2751 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA A2759 " --> pdb=" O ILE A2755 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N THR A2762 " --> pdb=" O PHE A2758 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N HIS A2763 " --> pdb=" O ALA A2759 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N GLU A2764 " --> pdb=" O GLU A2760 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LYS A2765 " --> pdb=" O TYR A2761 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N TRP A2766 " --> pdb=" O THR A2762 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ALA A2767 " --> pdb=" O HIS A2763 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE A2768 " --> pdb=" O GLU A2764 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N ASP A2769 " --> pdb=" O LYS A2765 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N LYS A2770 " --> pdb=" O TRP A2766 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ILE A2771 " --> pdb=" O ALA A2767 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLN A2772 " --> pdb=" O PHE A2768 " (cutoff:3.500A) Processing helix chain 'A' and resid 2798 through 2804 removed outlier: 4.323A pdb=" N LYS A2802 " --> pdb=" O SER A2798 " (cutoff:3.500A) Processing helix chain 'A' and resid 2868 through 2879 removed outlier: 5.258A pdb=" N GLN A2872 " --> pdb=" O SER A2868 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ALA A2873 " --> pdb=" O ARG A2869 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N MET A2874 " --> pdb=" O GLU A2870 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ALA A2875 " --> pdb=" O LEU A2871 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N GLU A2876 " --> pdb=" O GLN A2872 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLN A2877 " --> pdb=" O ALA A2873 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ALA A2879 " --> pdb=" O ALA A2875 " (cutoff:3.500A) Processing helix chain 'A' and resid 2880 through 2892 removed outlier: 4.374A pdb=" N LYS A2891 " --> pdb=" O GLY A2887 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLN A2892 " --> pdb=" O ARG A2888 " (cutoff:3.500A) Processing helix chain 'A' and resid 2920 through 2930 removed outlier: 4.833A pdb=" N GLU A2925 " --> pdb=" O GLU A2921 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS A2928 " --> pdb=" O GLN A2924 " (cutoff:3.500A) Processing helix chain 'A' and resid 3645 through 3656 removed outlier: 3.636A pdb=" N LEU A3654 " --> pdb=" O CYS A3650 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLU A3655 " --> pdb=" O ASN A3651 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N SER A3656 " --> pdb=" O MET A3652 " (cutoff:3.500A) Processing helix chain 'A' and resid 3668 through 3679 removed outlier: 3.663A pdb=" N LYS A3679 " --> pdb=" O ASP A3675 " (cutoff:3.500A) Processing helix chain 'A' and resid 3696 through 3711 Processing helix chain 'A' and resid 3719 through 3735 removed outlier: 3.506A pdb=" N SER A3732 " --> pdb=" O ILE A3728 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N CYS A3733 " --> pdb=" O MET A3729 " (cutoff:3.500A) Processing helix chain 'A' and resid 3752 through 3771 removed outlier: 4.384A pdb=" N ARG A3762 " --> pdb=" O MET A3758 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LEU A3763 " --> pdb=" O GLU A3759 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU A3764 " --> pdb=" O LYS A3760 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N TYR A3765 " --> pdb=" O GLN A3761 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N GLN A3766 " --> pdb=" O ARG A3762 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N GLN A3767 " --> pdb=" O LEU A3763 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N SER A3768 " --> pdb=" O LEU A3764 " (cutoff:3.500A) Processing helix chain 'A' and resid 3774 through 3787 removed outlier: 3.512A pdb=" N MET A3778 " --> pdb=" O GLY A3774 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N LYS A3787 " --> pdb=" O ILE A3783 " (cutoff:3.500A) Processing helix chain 'A' and resid 3791 through 3806 Processing helix chain 'A' and resid 3809 through 3824 Processing helix chain 'A' and resid 3826 through 3839 removed outlier: 6.618A pdb=" N GLN A3830 " --> pdb=" O VAL A3826 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N CYS A3839 " --> pdb=" O LEU A3835 " (cutoff:3.500A) Processing helix chain 'A' and resid 3844 through 3858 removed outlier: 7.386A pdb=" N GLU A3848 " --> pdb=" O LEU A3844 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ARG A3849 " --> pdb=" O ASN A3845 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY A3855 " --> pdb=" O ASN A3851 " (cutoff:3.500A) Processing helix chain 'A' and resid 3877 through 3893 Processing helix chain 'A' and resid 3896 through 3905 removed outlier: 6.594A pdb=" N GLN A3900 " --> pdb=" O ASN A3896 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ASN A3901 " --> pdb=" O ASN A3897 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG A3904 " --> pdb=" O GLN A3900 " (cutoff:3.500A) Processing helix chain 'A' and resid 3914 through 3938 Processing helix chain 'A' and resid 3944 through 3970 Processing helix chain 'A' and resid 3973 through 3984 removed outlier: 5.111A pdb=" N ARG A3984 " --> pdb=" O LEU A3980 " (cutoff:3.500A) Processing helix chain 'A' and resid 3985 through 4004 removed outlier: 3.619A pdb=" N GLY A3991 " --> pdb=" O ASP A3987 " (cutoff:3.500A) Processing helix chain 'A' and resid 4009 through 4032 Processing helix chain 'A' and resid 4038 through 4052 removed outlier: 6.843A pdb=" N ARG A4042 " --> pdb=" O GLY A4038 " (cutoff:3.500A) Processing helix chain 'A' and resid 4053 through 4072 removed outlier: 4.001A pdb=" N PHE A4065 " --> pdb=" O PHE A4061 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASP A4070 " --> pdb=" O LEU A4066 " (cutoff:3.500A) Processing helix chain 'A' and resid 4074 through 4082 removed outlier: 4.932A pdb=" N THR A4082 " --> pdb=" O GLN A4078 " (cutoff:3.500A) Processing helix chain 'A' and resid 4089 through 4101 removed outlier: 5.144A pdb=" N LYS A4101 " --> pdb=" O MET A4097 " (cutoff:3.500A) Processing helix chain 'A' and resid 4104 through 4116 removed outlier: 5.086A pdb=" N GLU A4116 " --> pdb=" O LEU A4112 " (cutoff:3.500A) Processing helix chain 'A' and resid 4124 through 4138 removed outlier: 5.694A pdb=" N PHE A4132 " --> pdb=" O PHE A4128 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N GLN A4133 " --> pdb=" O ALA A4129 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N GLU A4134 " --> pdb=" O ASN A4130 " (cutoff:3.500A) Proline residue: A4135 - end of helix removed outlier: 5.060A pdb=" N ASP A4138 " --> pdb=" O GLU A4134 " (cutoff:3.500A) Processing helix chain 'A' and resid 4139 through 4155 Proline residue: A4155 - end of helix Processing helix chain 'A' and resid 4157 through 4168 removed outlier: 4.068A pdb=" N PHE A4163 " --> pdb=" O ARG A4159 " (cutoff:3.500A) Processing helix chain 'A' and resid 4169 through 4179 removed outlier: 4.186A pdb=" N ARG A4175 " --> pdb=" O LEU A4171 " (cutoff:3.500A) Proline residue: A4176 - end of helix removed outlier: 5.557A pdb=" N GLY A4179 " --> pdb=" O ARG A4175 " (cutoff:3.500A) Processing helix chain 'A' and resid 4198 through 4208 Proline residue: A4208 - end of helix Processing helix chain 'A' and resid 4209 through 4224 removed outlier: 3.536A pdb=" N GLU A4224 " --> pdb=" O ASP A4220 " (cutoff:3.500A) Processing helix chain 'A' and resid 4226 through 4252 removed outlier: 4.694A pdb=" N MET A4231 " --> pdb=" O GLU A4227 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N GLU A4232 " --> pdb=" O ALA A4228 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE A4243 " --> pdb=" O GLU A4239 " (cutoff:3.500A) Processing helix chain 'A' and resid 4540 through 4559 removed outlier: 4.490A pdb=" N ARG A4557 " --> pdb=" O ASN A4553 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASN A4558 " --> pdb=" O TYR A4554 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N PHE A4559 " --> pdb=" O LEU A4555 " (cutoff:3.500A) Processing helix chain 'A' and resid 4560 through 4579 removed outlier: 4.590A pdb=" N PHE A4579 " --> pdb=" O PHE A4575 " (cutoff:3.500A) Processing helix chain 'A' and resid 4642 through 4683 removed outlier: 4.287A pdb=" N LEU A4648 " --> pdb=" O TRP A4644 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU A4649 " --> pdb=" O CYS A4645 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU A4652 " --> pdb=" O LEU A4648 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N VAL A4666 " --> pdb=" O ASN A4662 " (cutoff:3.500A) Proline residue: A4667 - end of helix Processing helix chain 'A' and resid 4696 through 4709 removed outlier: 5.341A pdb=" N GLN A4700 " --> pdb=" O ASP A4696 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N TRP A4701 " --> pdb=" O VAL A4697 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ARG A4703 " --> pdb=" O GLY A4699 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N LEU A4704 " --> pdb=" O GLN A4700 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N VAL A4705 " --> pdb=" O TRP A4701 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LEU A4706 " --> pdb=" O ASP A4702 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ASN A4707 " --> pdb=" O ARG A4703 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N THR A4708 " --> pdb=" O LEU A4704 " (cutoff:3.500A) Proline residue: A4709 - end of helix Processing helix chain 'A' and resid 4719 through 4729 removed outlier: 3.741A pdb=" N LEU A4725 " --> pdb=" O LYS A4721 " (cutoff:3.500A) Processing helix chain 'A' and resid 4733 through 4742 removed outlier: 3.561A pdb=" N GLY A4742 " --> pdb=" O ALA A4738 " (cutoff:3.500A) Processing helix chain 'A' and resid 4748 through 4756 removed outlier: 3.934A pdb=" N ALA A4752 " --> pdb=" O LEU A4748 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU A4755 " --> pdb=" O THR A4751 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ARG A4756 " --> pdb=" O ALA A4752 " (cutoff:3.500A) Processing helix chain 'A' and resid 4766 through 4771 Processing helix chain 'A' and resid 4772 through 4786 removed outlier: 4.297A pdb=" N GLN A4776 " --> pdb=" O ASP A4772 " (cutoff:3.500A) Processing helix chain 'A' and resid 4787 through 4805 removed outlier: 4.052A pdb=" N TYR A4804 " --> pdb=" O LEU A4800 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ASN A4805 " --> pdb=" O LEU A4801 " (cutoff:3.500A) Processing helix chain 'A' and resid 4808 through 4820 removed outlier: 4.395A pdb=" N HIS A4812 " --> pdb=" O PHE A4808 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LEU A4813 " --> pdb=" O PHE A4809 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LEU A4814 " --> pdb=" O ALA A4810 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ASP A4815 " --> pdb=" O ALA A4811 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLY A4819 " --> pdb=" O ASP A4815 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N VAL A4820 " --> pdb=" O ILE A4816 " (cutoff:3.500A) Processing helix chain 'A' and resid 4821 through 4833 removed outlier: 4.158A pdb=" N THR A4825 " --> pdb=" O LYS A4821 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ILE A4826 " --> pdb=" O THR A4822 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL A4830 " --> pdb=" O ILE A4826 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ASN A4833 " --> pdb=" O SER A4829 " (cutoff:3.500A) Processing helix chain 'A' and resid 4834 through 4858 removed outlier: 3.930A pdb=" N VAL A4838 " --> pdb=" O GLY A4834 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL A4854 " --> pdb=" O LEU A4850 " (cutoff:3.500A) Processing helix chain 'A' and resid 4859 through 4864 removed outlier: 3.749A pdb=" N ASN A4864 " --> pdb=" O ARG A4860 " (cutoff:3.500A) Processing helix chain 'A' and resid 4878 through 4893 removed outlier: 3.749A pdb=" N ARG A4892 " --> pdb=" O TYR A4888 " (cutoff:3.500A) Processing helix chain 'A' and resid 4896 through 4902 removed outlier: 4.789A pdb=" N GLU A4900 " --> pdb=" O GLY A4896 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N GLU A4902 " --> pdb=" O GLY A4898 " (cutoff:3.500A) Processing helix chain 'A' and resid 4909 through 4924 Processing helix chain 'A' and resid 4928 through 4957 Processing helix chain 'A' and resid 4964 through 4970 removed outlier: 4.272A pdb=" N PHE A4968 " --> pdb=" O GLY A4964 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR A4970 " --> pdb=" O ASP A4966 " (cutoff:3.500A) Processing helix chain 'A' and resid 4973 through 4982 Processing helix chain 'A' and resid 4984 through 4998 removed outlier: 3.798A pdb=" N TYR A4988 " --> pdb=" O ASN A4984 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N MET A4989 " --> pdb=" O LEU A4985 " (cutoff:3.500A) Processing helix chain 'A' and resid 5004 through 5017 Processing helix chain 'A' and resid 5027 through 5033 removed outlier: 6.208A pdb=" N GLN A5031 " --> pdb=" O CYS A5027 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 66 removed outlier: 4.489A pdb=" N CYS B 65 " --> pdb=" O ASP B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 84 Processing helix chain 'B' and resid 249 through 256 removed outlier: 4.816A pdb=" N CYS B 253 " --> pdb=" O GLY B 249 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N THR B 254 " --> pdb=" O GLY B 250 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N HIS B 255 " --> pdb=" O ALA B 251 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N ALA B 256 " --> pdb=" O VAL B 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 249 through 256' Processing helix chain 'B' and resid 364 through 371 removed outlier: 5.502A pdb=" N VAL B 371 " --> pdb=" O LEU B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 423 removed outlier: 3.691A pdb=" N SER B 420 " --> pdb=" O LYS B 416 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N PHE B 421 " --> pdb=" O GLY B 417 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N SER B 422 " --> pdb=" O LEU B 418 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N GLY B 423 " --> pdb=" O ASP B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 453 removed outlier: 4.148A pdb=" N VAL B 441 " --> pdb=" O PRO B 437 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE B 442 " --> pdb=" O ILE B 438 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU B 443 " --> pdb=" O GLU B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 482 removed outlier: 3.652A pdb=" N GLN B 479 " --> pdb=" O GLN B 475 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLU B 480 " --> pdb=" O SER B 476 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLU B 481 " --> pdb=" O LEU B 477 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N GLY B 482 " --> pdb=" O PHE B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 496 removed outlier: 4.641A pdb=" N VAL B 487 " --> pdb=" O MET B 483 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL B 496 " --> pdb=" O ASP B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 531 removed outlier: 4.267A pdb=" N LYS B 516 " --> pdb=" O ALA B 512 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N GLU B 517 " --> pdb=" O GLU B 513 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N TYR B 523 " --> pdb=" O VAL B 519 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU B 524 " --> pdb=" O ASN B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 541 removed outlier: 3.752A pdb=" N CYS B 537 " --> pdb=" O ASN B 533 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA B 538 " --> pdb=" O ARG B 534 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU B 539 " --> pdb=" O ALA B 535 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N PHE B 540 " --> pdb=" O ASN B 536 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N SER B 541 " --> pdb=" O CYS B 537 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 533 through 541' Processing helix chain 'B' and resid 543 through 551 removed outlier: 3.693A pdb=" N LYS B 550 " --> pdb=" O TRP B 546 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N LEU B 551 " --> pdb=" O VAL B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 571 removed outlier: 3.804A pdb=" N VAL B 567 " --> pdb=" O VAL B 563 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU B 568 " --> pdb=" O LEU B 564 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ILE B 569 " --> pdb=" O TYR B 565 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLU B 570 " --> pdb=" O CYS B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 578 removed outlier: 4.412A pdb=" N ASN B 576 " --> pdb=" O PRO B 572 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ILE B 577 " --> pdb=" O GLU B 573 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE B 578 " --> pdb=" O VAL B 574 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 572 through 578' Processing helix chain 'B' and resid 579 through 594 removed outlier: 3.563A pdb=" N LEU B 590 " --> pdb=" O ILE B 586 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP B 591 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 609 removed outlier: 3.863A pdb=" N LEU B 600 " --> pdb=" O ASN B 596 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N CYS B 607 " --> pdb=" O LEU B 603 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N VAL B 608 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N CYS B 609 " --> pdb=" O SER B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 626 removed outlier: 4.306A pdb=" N GLN B 618 " --> pdb=" O VAL B 614 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N LEU B 626 " --> pdb=" O THR B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 868 through 890 removed outlier: 3.852A pdb=" N GLU B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N LYS B 873 " --> pdb=" O ARG B 869 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TRP B 882 " --> pdb=" O ILE B 878 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA B 883 " --> pdb=" O HIS B 879 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N GLU B 888 " --> pdb=" O LEU B 884 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N GLN B 889 " --> pdb=" O THR B 885 " (cutoff:3.500A) Processing helix chain 'B' and resid 914 through 935 removed outlier: 5.399A pdb=" N LEU B 935 " --> pdb=" O THR B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 943 through 948 removed outlier: 6.694A pdb=" N GLU B 947 " --> pdb=" O ASP B 943 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ASP B 948 " --> pdb=" O GLU B 944 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 943 through 948' Processing helix chain 'B' and resid 956 through 961 Processing helix chain 'B' and resid 978 through 1001 removed outlier: 4.453A pdb=" N THR B 982 " --> pdb=" O THR B 978 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ASP B 999 " --> pdb=" O VAL B 995 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ARG B1000 " --> pdb=" O TRP B 996 " (cutoff:3.500A) Processing helix chain 'B' and resid 1030 through 1045 removed outlier: 3.535A pdb=" N ASP B1037 " --> pdb=" O ARG B1033 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N SER B1038 " --> pdb=" O SER B1034 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU B1039 " --> pdb=" O ASN B1035 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N THR B1045 " --> pdb=" O GLN B1041 " (cutoff:3.500A) Processing helix chain 'B' and resid 1207 through 1212 removed outlier: 3.858A pdb=" N LEU B1211 " --> pdb=" O ASP B1207 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N ARG B1212 " --> pdb=" O VAL B1208 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1207 through 1212' Processing helix chain 'B' and resid 1574 through 1581 removed outlier: 4.283A pdb=" N ALA B1578 " --> pdb=" O PRO B1574 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N MET B1579 " --> pdb=" O LEU B1575 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE B1580 " --> pdb=" O SER B1576 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU B1581 " --> pdb=" O ALA B1577 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1574 through 1581' Processing helix chain 'B' and resid 1649 through 1657 removed outlier: 4.000A pdb=" N LEU B1653 " --> pdb=" O ASP B1649 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N SER B1654 " --> pdb=" O ILE B1650 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N GLU B1655 " --> pdb=" O LEU B1651 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ARG B1656 " --> pdb=" O GLU B1652 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU B1657 " --> pdb=" O LEU B1653 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1649 through 1657' Processing helix chain 'B' and resid 1658 through 1675 Processing helix chain 'B' and resid 1678 through 1690 removed outlier: 4.417A pdb=" N ALA B1682 " --> pdb=" O ASN B1678 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N HIS B1683 " --> pdb=" O ASN B1679 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA B1684 " --> pdb=" O ARG B1680 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASP B1690 " --> pdb=" O CYS B1686 " (cutoff:3.500A) Processing helix chain 'B' and resid 1691 through 1700 removed outlier: 3.804A pdb=" N LEU B1698 " --> pdb=" O LEU B1694 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLU B1699 " --> pdb=" O LEU B1695 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ASP B1700 " --> pdb=" O HIS B1696 " (cutoff:3.500A) Processing helix chain 'B' and resid 1704 through 1719 removed outlier: 6.825A pdb=" N ARG B1708 " --> pdb=" O PRO B1704 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA B1709 " --> pdb=" O GLY B1705 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N HIS B1719 " --> pdb=" O LEU B1715 " (cutoff:3.500A) Processing helix chain 'B' and resid 1720 through 1732 removed outlier: 4.422A pdb=" N SER B1732 " --> pdb=" O ARG B1728 " (cutoff:3.500A) Processing helix chain 'B' and resid 1739 through 1746 removed outlier: 4.069A pdb=" N ILE B1745 " --> pdb=" O GLU B1741 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N THR B1746 " --> pdb=" O THR B1742 " (cutoff:3.500A) Processing helix chain 'B' and resid 1754 through 1759 removed outlier: 4.271A pdb=" N ARG B1759 " --> pdb=" O GLY B1755 " (cutoff:3.500A) Processing helix chain 'B' and resid 1803 through 1825 removed outlier: 3.747A pdb=" N VAL B1819 " --> pdb=" O LEU B1815 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG B1820 " --> pdb=" O GLY B1816 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLN B1824 " --> pdb=" O ARG B1820 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N HIS B1825 " --> pdb=" O ASP B1821 " (cutoff:3.500A) Processing helix chain 'B' and resid 1833 through 1852 Proline residue: B1840 - end of helix removed outlier: 3.847A pdb=" N MET B1851 " --> pdb=" O THR B1847 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLY B1852 " --> pdb=" O LEU B1848 " (cutoff:3.500A) Processing helix chain 'B' and resid 1855 through 1865 removed outlier: 4.221A pdb=" N MET B1865 " --> pdb=" O GLN B1861 " (cutoff:3.500A) Processing helix chain 'B' and resid 1866 through 1871 Processing helix chain 'B' and resid 1934 through 1984 removed outlier: 4.147A pdb=" N GLN B1938 " --> pdb=" O SER B1934 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N TYR B1945 " --> pdb=" O ASN B1941 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N PHE B1946 " --> pdb=" O LEU B1942 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU B1950 " --> pdb=" O PHE B1946 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU B1951 " --> pdb=" O CYS B1947 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU B1963 " --> pdb=" O ALA B1959 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ARG B1964 " --> pdb=" O ALA B1960 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N PHE B1984 " --> pdb=" O LEU B1980 " (cutoff:3.500A) Processing helix chain 'B' and resid 1987 through 1999 removed outlier: 4.207A pdb=" N ARG B1996 " --> pdb=" O ALA B1992 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N GLU B1997 " --> pdb=" O ARG B1993 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE B1998 " --> pdb=" O ARG B1994 " (cutoff:3.500A) Processing helix chain 'B' and resid 2001 through 2015 removed outlier: 3.623A pdb=" N LEU B2009 " --> pdb=" O GLN B2005 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU B2010 " --> pdb=" O ILE B2006 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLU B2015 " --> pdb=" O HIS B2011 " (cutoff:3.500A) Processing helix chain 'B' and resid 2027 through 2043 removed outlier: 4.718A pdb=" N LEU B2031 " --> pdb=" O ILE B2027 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLN B2032 " --> pdb=" O ARG B2028 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N GLY B2043 " --> pdb=" O LEU B2039 " (cutoff:3.500A) Processing helix chain 'B' and resid 2093 through 2109 removed outlier: 4.229A pdb=" N ASP B2109 " --> pdb=" O TRP B2105 " (cutoff:3.500A) Processing helix chain 'B' and resid 2113 through 2130 removed outlier: 3.594A pdb=" N VAL B2117 " --> pdb=" O SER B2113 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLY B2130 " --> pdb=" O ARG B2126 " (cutoff:3.500A) Processing helix chain 'B' and resid 2131 through 2139 Proline residue: B2139 - end of helix Processing helix chain 'B' and resid 2148 through 2169 removed outlier: 4.044A pdb=" N SER B2154 " --> pdb=" O GLU B2150 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU B2155 " --> pdb=" O ASP B2151 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ILE B2167 " --> pdb=" O ARG B2163 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N VAL B2168 " --> pdb=" O SER B2164 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N GLN B2169 " --> pdb=" O LEU B2165 " (cutoff:3.500A) Processing helix chain 'B' and resid 2171 through 2188 removed outlier: 3.816A pdb=" N ASN B2176 " --> pdb=" O PRO B2172 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU B2177 " --> pdb=" O GLN B2173 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ASN B2187 " --> pdb=" O GLY B2183 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ASN B2188 " --> pdb=" O ASN B2184 " (cutoff:3.500A) Processing helix chain 'B' and resid 2189 through 2195 removed outlier: 4.658A pdb=" N GLN B2193 " --> pdb=" O LYS B2189 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N HIS B2194 " --> pdb=" O VAL B2190 " (cutoff:3.500A) Proline residue: B2195 - end of helix No H-bonds generated for 'chain 'B' and resid 2189 through 2195' Processing helix chain 'B' and resid 2196 through 2202 Processing helix chain 'B' and resid 2203 through 2216 removed outlier: 4.177A pdb=" N ASN B2213 " --> pdb=" O GLU B2209 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N VAL B2214 " --> pdb=" O VAL B2210 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU B2215 " --> pdb=" O MET B2211 " (cutoff:3.500A) Processing helix chain 'B' and resid 2226 through 2244 removed outlier: 6.777A pdb=" N THR B2230 " --> pdb=" O PRO B2226 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N SER B2231 " --> pdb=" O LYS B2227 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N SER B2243 " --> pdb=" O PHE B2239 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N ARG B2244 " --> pdb=" O CYS B2240 " (cutoff:3.500A) Processing helix chain 'B' and resid 2245 through 2255 removed outlier: 3.907A pdb=" N SER B2249 " --> pdb=" O GLN B2245 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASP B2252 " --> pdb=" O ARG B2248 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N HIS B2253 " --> pdb=" O SER B2249 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LEU B2254 " --> pdb=" O MET B2250 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N SER B2255 " --> pdb=" O PHE B2251 " (cutoff:3.500A) Processing helix chain 'B' and resid 2256 through 2265 removed outlier: 3.569A pdb=" N ASN B2260 " --> pdb=" O TYR B2256 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N GLY B2262 " --> pdb=" O LEU B2258 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N ILE B2263 " --> pdb=" O GLU B2259 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLY B2264 " --> pdb=" O ASN B2260 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N LEU B2265 " --> pdb=" O SER B2261 " (cutoff:3.500A) Processing helix chain 'B' and resid 2271 through 2282 removed outlier: 3.554A pdb=" N VAL B2275 " --> pdb=" O THR B2271 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA B2276 " --> pdb=" O PRO B2272 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL B2280 " --> pdb=" O ALA B2276 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE B2281 " --> pdb=" O ALA B2277 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N ASP B2282 " --> pdb=" O ALA B2278 " (cutoff:3.500A) Processing helix chain 'B' and resid 2286 through 2291 removed outlier: 3.746A pdb=" N LEU B2290 " --> pdb=" O LEU B2286 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N GLN B2291 " --> pdb=" O ALA B2287 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2286 through 2291' Processing helix chain 'B' and resid 2294 through 2308 removed outlier: 3.642A pdb=" N SER B2300 " --> pdb=" O GLU B2296 " (cutoff:3.500A) Processing helix chain 'B' and resid 2310 through 2315 removed outlier: 3.605A pdb=" N LEU B2314 " --> pdb=" O CYS B2310 " (cutoff:3.500A) Processing helix chain 'B' and resid 2324 through 2341 removed outlier: 4.111A pdb=" N GLY B2328 " --> pdb=" O ASN B2324 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LEU B2332 " --> pdb=" O GLY B2328 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N ASP B2333 " --> pdb=" O GLU B2329 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N PHE B2334 " --> pdb=" O ARG B2330 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LEU B2335 " --> pdb=" O TYR B2331 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N VAL B2341 " --> pdb=" O PHE B2337 " (cutoff:3.500A) Processing helix chain 'B' and resid 2346 through 2361 removed outlier: 4.298A pdb=" N VAL B2352 " --> pdb=" O GLU B2348 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG B2359 " --> pdb=" O ARG B2355 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N LYS B2360 " --> pdb=" O LEU B2356 " (cutoff:3.500A) Proline residue: B2361 - end of helix Processing helix chain 'B' and resid 2365 through 2370 Processing helix chain 'B' and resid 2375 through 2390 Proline residue: B2390 - end of helix Processing helix chain 'B' and resid 2417 through 2438 Proline residue: B2438 - end of helix Processing helix chain 'B' and resid 2440 through 2447 Processing helix chain 'B' and resid 2448 through 2462 removed outlier: 4.652A pdb=" N ARG B2452 " --> pdb=" O GLY B2448 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE B2453 " --> pdb=" O GLU B2449 " (cutoff:3.500A) Proline residue: B2462 - end of helix Processing helix chain 'B' and resid 2464 through 2473 removed outlier: 3.999A pdb=" N GLY B2468 " --> pdb=" O ASP B2464 " (cutoff:3.500A) Proline residue: B2473 - end of helix Processing helix chain 'B' and resid 2751 through 2774 removed outlier: 4.814A pdb=" N ILE B2755 " --> pdb=" O LEU B2751 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA B2759 " --> pdb=" O ILE B2755 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N THR B2762 " --> pdb=" O PHE B2758 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N HIS B2763 " --> pdb=" O ALA B2759 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N GLU B2764 " --> pdb=" O GLU B2760 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N LYS B2765 " --> pdb=" O TYR B2761 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N TRP B2766 " --> pdb=" O THR B2762 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ALA B2767 " --> pdb=" O HIS B2763 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE B2768 " --> pdb=" O GLU B2764 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N ASP B2769 " --> pdb=" O LYS B2765 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N LYS B2770 " --> pdb=" O TRP B2766 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ILE B2771 " --> pdb=" O ALA B2767 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLN B2772 " --> pdb=" O PHE B2768 " (cutoff:3.500A) Processing helix chain 'B' and resid 2798 through 2804 removed outlier: 4.323A pdb=" N LYS B2802 " --> pdb=" O SER B2798 " (cutoff:3.500A) Processing helix chain 'B' and resid 2868 through 2879 removed outlier: 5.258A pdb=" N GLN B2872 " --> pdb=" O SER B2868 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ALA B2873 " --> pdb=" O ARG B2869 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N MET B2874 " --> pdb=" O GLU B2870 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA B2875 " --> pdb=" O LEU B2871 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N GLU B2876 " --> pdb=" O GLN B2872 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLN B2877 " --> pdb=" O ALA B2873 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ALA B2879 " --> pdb=" O ALA B2875 " (cutoff:3.500A) Processing helix chain 'B' and resid 2880 through 2892 removed outlier: 4.374A pdb=" N LYS B2891 " --> pdb=" O GLY B2887 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLN B2892 " --> pdb=" O ARG B2888 " (cutoff:3.500A) Processing helix chain 'B' and resid 2920 through 2930 removed outlier: 4.833A pdb=" N GLU B2925 " --> pdb=" O GLU B2921 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS B2928 " --> pdb=" O GLN B2924 " (cutoff:3.500A) Processing helix chain 'B' and resid 3645 through 3656 removed outlier: 3.635A pdb=" N LEU B3654 " --> pdb=" O CYS B3650 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N GLU B3655 " --> pdb=" O ASN B3651 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N SER B3656 " --> pdb=" O MET B3652 " (cutoff:3.500A) Processing helix chain 'B' and resid 3668 through 3679 removed outlier: 3.663A pdb=" N LYS B3679 " --> pdb=" O ASP B3675 " (cutoff:3.500A) Processing helix chain 'B' and resid 3696 through 3711 Processing helix chain 'B' and resid 3719 through 3735 removed outlier: 3.506A pdb=" N SER B3732 " --> pdb=" O ILE B3728 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N CYS B3733 " --> pdb=" O MET B3729 " (cutoff:3.500A) Processing helix chain 'B' and resid 3752 through 3771 removed outlier: 4.383A pdb=" N ARG B3762 " --> pdb=" O MET B3758 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU B3763 " --> pdb=" O GLU B3759 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU B3764 " --> pdb=" O LYS B3760 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N TYR B3765 " --> pdb=" O GLN B3761 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N GLN B3766 " --> pdb=" O ARG B3762 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N GLN B3767 " --> pdb=" O LEU B3763 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N SER B3768 " --> pdb=" O LEU B3764 " (cutoff:3.500A) Processing helix chain 'B' and resid 3774 through 3787 removed outlier: 3.513A pdb=" N MET B3778 " --> pdb=" O GLY B3774 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N LYS B3787 " --> pdb=" O ILE B3783 " (cutoff:3.500A) Processing helix chain 'B' and resid 3791 through 3806 Processing helix chain 'B' and resid 3809 through 3824 Processing helix chain 'B' and resid 3826 through 3839 removed outlier: 6.618A pdb=" N GLN B3830 " --> pdb=" O VAL B3826 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N CYS B3839 " --> pdb=" O LEU B3835 " (cutoff:3.500A) Processing helix chain 'B' and resid 3844 through 3858 removed outlier: 7.387A pdb=" N GLU B3848 " --> pdb=" O LEU B3844 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ARG B3849 " --> pdb=" O ASN B3845 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY B3855 " --> pdb=" O ASN B3851 " (cutoff:3.500A) Processing helix chain 'B' and resid 3877 through 3893 Processing helix chain 'B' and resid 3896 through 3905 removed outlier: 6.595A pdb=" N GLN B3900 " --> pdb=" O ASN B3896 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ASN B3901 " --> pdb=" O ASN B3897 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG B3904 " --> pdb=" O GLN B3900 " (cutoff:3.500A) Processing helix chain 'B' and resid 3914 through 3938 Processing helix chain 'B' and resid 3944 through 3970 Processing helix chain 'B' and resid 3973 through 3984 removed outlier: 5.112A pdb=" N ARG B3984 " --> pdb=" O LEU B3980 " (cutoff:3.500A) Processing helix chain 'B' and resid 3985 through 4004 removed outlier: 3.619A pdb=" N GLY B3991 " --> pdb=" O ASP B3987 " (cutoff:3.500A) Processing helix chain 'B' and resid 4009 through 4032 Processing helix chain 'B' and resid 4038 through 4052 removed outlier: 6.841A pdb=" N ARG B4042 " --> pdb=" O GLY B4038 " (cutoff:3.500A) Processing helix chain 'B' and resid 4053 through 4072 removed outlier: 4.001A pdb=" N PHE B4065 " --> pdb=" O PHE B4061 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASP B4070 " --> pdb=" O LEU B4066 " (cutoff:3.500A) Processing helix chain 'B' and resid 4074 through 4082 removed outlier: 4.932A pdb=" N THR B4082 " --> pdb=" O GLN B4078 " (cutoff:3.500A) Processing helix chain 'B' and resid 4089 through 4101 removed outlier: 5.145A pdb=" N LYS B4101 " --> pdb=" O MET B4097 " (cutoff:3.500A) Processing helix chain 'B' and resid 4104 through 4116 removed outlier: 5.085A pdb=" N GLU B4116 " --> pdb=" O LEU B4112 " (cutoff:3.500A) Processing helix chain 'B' and resid 4124 through 4138 removed outlier: 5.694A pdb=" N PHE B4132 " --> pdb=" O PHE B4128 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N GLN B4133 " --> pdb=" O ALA B4129 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N GLU B4134 " --> pdb=" O ASN B4130 " (cutoff:3.500A) Proline residue: B4135 - end of helix removed outlier: 5.060A pdb=" N ASP B4138 " --> pdb=" O GLU B4134 " (cutoff:3.500A) Processing helix chain 'B' and resid 4139 through 4155 Proline residue: B4155 - end of helix Processing helix chain 'B' and resid 4157 through 4168 removed outlier: 4.067A pdb=" N PHE B4163 " --> pdb=" O ARG B4159 " (cutoff:3.500A) Processing helix chain 'B' and resid 4169 through 4179 removed outlier: 4.185A pdb=" N ARG B4175 " --> pdb=" O LEU B4171 " (cutoff:3.500A) Proline residue: B4176 - end of helix removed outlier: 5.557A pdb=" N GLY B4179 " --> pdb=" O ARG B4175 " (cutoff:3.500A) Processing helix chain 'B' and resid 4198 through 4208 Proline residue: B4208 - end of helix Processing helix chain 'B' and resid 4209 through 4224 removed outlier: 3.535A pdb=" N GLU B4224 " --> pdb=" O ASP B4220 " (cutoff:3.500A) Processing helix chain 'B' and resid 4226 through 4252 removed outlier: 4.693A pdb=" N MET B4231 " --> pdb=" O GLU B4227 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N GLU B4232 " --> pdb=" O ALA B4228 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE B4243 " --> pdb=" O GLU B4239 " (cutoff:3.500A) Processing helix chain 'B' and resid 4540 through 4559 removed outlier: 4.489A pdb=" N ARG B4557 " --> pdb=" O ASN B4553 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ASN B4558 " --> pdb=" O TYR B4554 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N PHE B4559 " --> pdb=" O LEU B4555 " (cutoff:3.500A) Processing helix chain 'B' and resid 4560 through 4579 removed outlier: 4.591A pdb=" N PHE B4579 " --> pdb=" O PHE B4575 " (cutoff:3.500A) Processing helix chain 'B' and resid 4642 through 4683 removed outlier: 4.288A pdb=" N LEU B4648 " --> pdb=" O TRP B4644 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU B4649 " --> pdb=" O CYS B4645 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU B4652 " --> pdb=" O LEU B4648 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N VAL B4666 " --> pdb=" O ASN B4662 " (cutoff:3.500A) Proline residue: B4667 - end of helix Processing helix chain 'B' and resid 4696 through 4709 removed outlier: 5.341A pdb=" N GLN B4700 " --> pdb=" O ASP B4696 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N TRP B4701 " --> pdb=" O VAL B4697 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ARG B4703 " --> pdb=" O GLY B4699 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N LEU B4704 " --> pdb=" O GLN B4700 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N VAL B4705 " --> pdb=" O TRP B4701 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LEU B4706 " --> pdb=" O ASP B4702 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ASN B4707 " --> pdb=" O ARG B4703 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N THR B4708 " --> pdb=" O LEU B4704 " (cutoff:3.500A) Proline residue: B4709 - end of helix Processing helix chain 'B' and resid 4719 through 4729 removed outlier: 3.740A pdb=" N LEU B4725 " --> pdb=" O LYS B4721 " (cutoff:3.500A) Processing helix chain 'B' and resid 4733 through 4742 removed outlier: 3.562A pdb=" N GLY B4742 " --> pdb=" O ALA B4738 " (cutoff:3.500A) Processing helix chain 'B' and resid 4748 through 4756 removed outlier: 3.934A pdb=" N ALA B4752 " --> pdb=" O LEU B4748 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU B4755 " --> pdb=" O THR B4751 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ARG B4756 " --> pdb=" O ALA B4752 " (cutoff:3.500A) Processing helix chain 'B' and resid 4766 through 4771 Processing helix chain 'B' and resid 4772 through 4786 removed outlier: 4.297A pdb=" N GLN B4776 " --> pdb=" O ASP B4772 " (cutoff:3.500A) Processing helix chain 'B' and resid 4787 through 4805 removed outlier: 4.053A pdb=" N TYR B4804 " --> pdb=" O LEU B4800 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ASN B4805 " --> pdb=" O LEU B4801 " (cutoff:3.500A) Processing helix chain 'B' and resid 4808 through 4820 removed outlier: 4.394A pdb=" N HIS B4812 " --> pdb=" O PHE B4808 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LEU B4813 " --> pdb=" O PHE B4809 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LEU B4814 " --> pdb=" O ALA B4810 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ASP B4815 " --> pdb=" O ALA B4811 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLY B4819 " --> pdb=" O ASP B4815 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N VAL B4820 " --> pdb=" O ILE B4816 " (cutoff:3.500A) Processing helix chain 'B' and resid 4821 through 4833 removed outlier: 4.159A pdb=" N THR B4825 " --> pdb=" O LYS B4821 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ILE B4826 " --> pdb=" O THR B4822 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL B4830 " --> pdb=" O ILE B4826 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ASN B4833 " --> pdb=" O SER B4829 " (cutoff:3.500A) Processing helix chain 'B' and resid 4834 through 4858 removed outlier: 3.932A pdb=" N VAL B4838 " --> pdb=" O GLY B4834 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL B4854 " --> pdb=" O LEU B4850 " (cutoff:3.500A) Processing helix chain 'B' and resid 4859 through 4864 removed outlier: 3.748A pdb=" N ASN B4864 " --> pdb=" O ARG B4860 " (cutoff:3.500A) Processing helix chain 'B' and resid 4878 through 4893 removed outlier: 3.749A pdb=" N ARG B4892 " --> pdb=" O TYR B4888 " (cutoff:3.500A) Processing helix chain 'B' and resid 4896 through 4902 removed outlier: 4.789A pdb=" N GLU B4900 " --> pdb=" O GLY B4896 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N GLU B4902 " --> pdb=" O GLY B4898 " (cutoff:3.500A) Processing helix chain 'B' and resid 4909 through 4924 Processing helix chain 'B' and resid 4928 through 4957 Processing helix chain 'B' and resid 4964 through 4970 removed outlier: 4.272A pdb=" N PHE B4968 " --> pdb=" O GLY B4964 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N THR B4970 " --> pdb=" O ASP B4966 " (cutoff:3.500A) Processing helix chain 'B' and resid 4973 through 4982 Processing helix chain 'B' and resid 4984 through 4998 removed outlier: 3.798A pdb=" N TYR B4988 " --> pdb=" O ASN B4984 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N MET B4989 " --> pdb=" O LEU B4985 " (cutoff:3.500A) Processing helix chain 'B' and resid 5004 through 5017 Processing helix chain 'B' and resid 5027 through 5033 removed outlier: 6.208A pdb=" N GLN B5031 " --> pdb=" O CYS B5027 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 66 removed outlier: 4.489A pdb=" N CYS C 65 " --> pdb=" O ASP C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 84 Processing helix chain 'C' and resid 249 through 256 removed outlier: 4.816A pdb=" N CYS C 253 " --> pdb=" O GLY C 249 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N THR C 254 " --> pdb=" O GLY C 250 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N HIS C 255 " --> pdb=" O ALA C 251 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N ALA C 256 " --> pdb=" O VAL C 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 249 through 256' Processing helix chain 'C' and resid 364 through 371 removed outlier: 5.502A pdb=" N VAL C 371 " --> pdb=" O LEU C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 423 removed outlier: 3.691A pdb=" N SER C 420 " --> pdb=" O LYS C 416 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N PHE C 421 " --> pdb=" O GLY C 417 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N SER C 422 " --> pdb=" O LEU C 418 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N GLY C 423 " --> pdb=" O ASP C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 453 removed outlier: 4.147A pdb=" N VAL C 441 " --> pdb=" O PRO C 437 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE C 442 " --> pdb=" O ILE C 438 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU C 443 " --> pdb=" O GLU C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 482 removed outlier: 3.653A pdb=" N GLN C 479 " --> pdb=" O GLN C 475 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLU C 480 " --> pdb=" O SER C 476 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLU C 481 " --> pdb=" O LEU C 477 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N GLY C 482 " --> pdb=" O PHE C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 496 removed outlier: 4.641A pdb=" N VAL C 487 " --> pdb=" O MET C 483 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL C 496 " --> pdb=" O ASP C 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 531 removed outlier: 4.266A pdb=" N LYS C 516 " --> pdb=" O ALA C 512 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N GLU C 517 " --> pdb=" O GLU C 513 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR C 523 " --> pdb=" O VAL C 519 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU C 524 " --> pdb=" O ASN C 520 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 541 removed outlier: 3.751A pdb=" N CYS C 537 " --> pdb=" O ASN C 533 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA C 538 " --> pdb=" O ARG C 534 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU C 539 " --> pdb=" O ALA C 535 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N PHE C 540 " --> pdb=" O ASN C 536 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N SER C 541 " --> pdb=" O CYS C 537 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 533 through 541' Processing helix chain 'C' and resid 543 through 551 removed outlier: 3.694A pdb=" N LYS C 550 " --> pdb=" O TRP C 546 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N LEU C 551 " --> pdb=" O VAL C 547 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 571 removed outlier: 3.804A pdb=" N VAL C 567 " --> pdb=" O VAL C 563 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU C 568 " --> pdb=" O LEU C 564 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ILE C 569 " --> pdb=" O TYR C 565 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLU C 570 " --> pdb=" O CYS C 566 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 578 removed outlier: 4.413A pdb=" N ASN C 576 " --> pdb=" O PRO C 572 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ILE C 577 " --> pdb=" O GLU C 573 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE C 578 " --> pdb=" O VAL C 574 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 572 through 578' Processing helix chain 'C' and resid 579 through 594 removed outlier: 3.563A pdb=" N LEU C 590 " --> pdb=" O ILE C 586 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP C 591 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 609 removed outlier: 3.864A pdb=" N LEU C 600 " --> pdb=" O ASN C 596 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N CYS C 607 " --> pdb=" O LEU C 603 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N VAL C 608 " --> pdb=" O CYS C 604 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N CYS C 609 " --> pdb=" O SER C 605 " (cutoff:3.500A) Processing helix chain 'C' and resid 614 through 626 removed outlier: 4.306A pdb=" N GLN C 618 " --> pdb=" O VAL C 614 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N LEU C 626 " --> pdb=" O THR C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 868 through 890 removed outlier: 3.852A pdb=" N GLU C 872 " --> pdb=" O GLU C 868 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N LYS C 873 " --> pdb=" O ARG C 869 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N TRP C 882 " --> pdb=" O ILE C 878 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA C 883 " --> pdb=" O HIS C 879 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N GLU C 888 " --> pdb=" O LEU C 884 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N GLN C 889 " --> pdb=" O THR C 885 " (cutoff:3.500A) Processing helix chain 'C' and resid 914 through 935 removed outlier: 5.399A pdb=" N LEU C 935 " --> pdb=" O THR C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 943 through 948 removed outlier: 6.694A pdb=" N GLU C 947 " --> pdb=" O ASP C 943 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ASP C 948 " --> pdb=" O GLU C 944 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 943 through 948' Processing helix chain 'C' and resid 956 through 961 Processing helix chain 'C' and resid 978 through 1001 removed outlier: 4.452A pdb=" N THR C 982 " --> pdb=" O THR C 978 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ASP C 999 " --> pdb=" O VAL C 995 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ARG C1000 " --> pdb=" O TRP C 996 " (cutoff:3.500A) Processing helix chain 'C' and resid 1030 through 1045 removed outlier: 3.536A pdb=" N ASP C1037 " --> pdb=" O ARG C1033 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N SER C1038 " --> pdb=" O SER C1034 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU C1039 " --> pdb=" O ASN C1035 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N THR C1045 " --> pdb=" O GLN C1041 " (cutoff:3.500A) Processing helix chain 'C' and resid 1207 through 1212 removed outlier: 3.857A pdb=" N LEU C1211 " --> pdb=" O ASP C1207 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N ARG C1212 " --> pdb=" O VAL C1208 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1207 through 1212' Processing helix chain 'C' and resid 1574 through 1581 removed outlier: 4.283A pdb=" N ALA C1578 " --> pdb=" O PRO C1574 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N MET C1579 " --> pdb=" O LEU C1575 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE C1580 " --> pdb=" O SER C1576 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU C1581 " --> pdb=" O ALA C1577 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1574 through 1581' Processing helix chain 'C' and resid 1649 through 1657 removed outlier: 3.999A pdb=" N LEU C1653 " --> pdb=" O ASP C1649 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N SER C1654 " --> pdb=" O ILE C1650 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N GLU C1655 " --> pdb=" O LEU C1651 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ARG C1656 " --> pdb=" O GLU C1652 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU C1657 " --> pdb=" O LEU C1653 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1649 through 1657' Processing helix chain 'C' and resid 1658 through 1675 Processing helix chain 'C' and resid 1678 through 1690 removed outlier: 4.418A pdb=" N ALA C1682 " --> pdb=" O ASN C1678 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N HIS C1683 " --> pdb=" O ASN C1679 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA C1684 " --> pdb=" O ARG C1680 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ASP C1690 " --> pdb=" O CYS C1686 " (cutoff:3.500A) Processing helix chain 'C' and resid 1691 through 1700 removed outlier: 3.804A pdb=" N LEU C1698 " --> pdb=" O LEU C1694 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLU C1699 " --> pdb=" O LEU C1695 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ASP C1700 " --> pdb=" O HIS C1696 " (cutoff:3.500A) Processing helix chain 'C' and resid 1704 through 1719 removed outlier: 6.825A pdb=" N ARG C1708 " --> pdb=" O PRO C1704 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA C1709 " --> pdb=" O GLY C1705 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N HIS C1719 " --> pdb=" O LEU C1715 " (cutoff:3.500A) Processing helix chain 'C' and resid 1720 through 1732 removed outlier: 4.422A pdb=" N SER C1732 " --> pdb=" O ARG C1728 " (cutoff:3.500A) Processing helix chain 'C' and resid 1739 through 1746 removed outlier: 4.069A pdb=" N ILE C1745 " --> pdb=" O GLU C1741 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N THR C1746 " --> pdb=" O THR C1742 " (cutoff:3.500A) Processing helix chain 'C' and resid 1754 through 1759 removed outlier: 4.272A pdb=" N ARG C1759 " --> pdb=" O GLY C1755 " (cutoff:3.500A) Processing helix chain 'C' and resid 1803 through 1825 removed outlier: 3.747A pdb=" N VAL C1819 " --> pdb=" O LEU C1815 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG C1820 " --> pdb=" O GLY C1816 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLN C1824 " --> pdb=" O ARG C1820 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N HIS C1825 " --> pdb=" O ASP C1821 " (cutoff:3.500A) Processing helix chain 'C' and resid 1833 through 1852 Proline residue: C1840 - end of helix removed outlier: 3.847A pdb=" N MET C1851 " --> pdb=" O THR C1847 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLY C1852 " --> pdb=" O LEU C1848 " (cutoff:3.500A) Processing helix chain 'C' and resid 1855 through 1865 removed outlier: 4.222A pdb=" N MET C1865 " --> pdb=" O GLN C1861 " (cutoff:3.500A) Processing helix chain 'C' and resid 1866 through 1871 Processing helix chain 'C' and resid 1934 through 1984 removed outlier: 4.148A pdb=" N GLN C1938 " --> pdb=" O SER C1934 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N TYR C1945 " --> pdb=" O ASN C1941 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N PHE C1946 " --> pdb=" O LEU C1942 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU C1950 " --> pdb=" O PHE C1946 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU C1951 " --> pdb=" O CYS C1947 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU C1963 " --> pdb=" O ALA C1959 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ARG C1964 " --> pdb=" O ALA C1960 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N PHE C1984 " --> pdb=" O LEU C1980 " (cutoff:3.500A) Processing helix chain 'C' and resid 1987 through 1999 removed outlier: 4.206A pdb=" N ARG C1996 " --> pdb=" O ALA C1992 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N GLU C1997 " --> pdb=" O ARG C1993 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N PHE C1998 " --> pdb=" O ARG C1994 " (cutoff:3.500A) Processing helix chain 'C' and resid 2001 through 2015 removed outlier: 3.624A pdb=" N LEU C2009 " --> pdb=" O GLN C2005 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU C2010 " --> pdb=" O ILE C2006 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLU C2015 " --> pdb=" O HIS C2011 " (cutoff:3.500A) Processing helix chain 'C' and resid 2027 through 2043 removed outlier: 4.717A pdb=" N LEU C2031 " --> pdb=" O ILE C2027 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN C2032 " --> pdb=" O ARG C2028 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N GLY C2043 " --> pdb=" O LEU C2039 " (cutoff:3.500A) Processing helix chain 'C' and resid 2093 through 2109 removed outlier: 4.228A pdb=" N ASP C2109 " --> pdb=" O TRP C2105 " (cutoff:3.500A) Processing helix chain 'C' and resid 2113 through 2130 removed outlier: 3.594A pdb=" N VAL C2117 " --> pdb=" O SER C2113 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLY C2130 " --> pdb=" O ARG C2126 " (cutoff:3.500A) Processing helix chain 'C' and resid 2131 through 2139 Proline residue: C2139 - end of helix Processing helix chain 'C' and resid 2148 through 2169 removed outlier: 4.043A pdb=" N SER C2154 " --> pdb=" O GLU C2150 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU C2155 " --> pdb=" O ASP C2151 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ILE C2167 " --> pdb=" O ARG C2163 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N VAL C2168 " --> pdb=" O SER C2164 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N GLN C2169 " --> pdb=" O LEU C2165 " (cutoff:3.500A) Processing helix chain 'C' and resid 2171 through 2188 removed outlier: 3.815A pdb=" N ASN C2176 " --> pdb=" O PRO C2172 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU C2177 " --> pdb=" O GLN C2173 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ASN C2187 " --> pdb=" O GLY C2183 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ASN C2188 " --> pdb=" O ASN C2184 " (cutoff:3.500A) Processing helix chain 'C' and resid 2189 through 2195 removed outlier: 4.657A pdb=" N GLN C2193 " --> pdb=" O LYS C2189 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N HIS C2194 " --> pdb=" O VAL C2190 " (cutoff:3.500A) Proline residue: C2195 - end of helix No H-bonds generated for 'chain 'C' and resid 2189 through 2195' Processing helix chain 'C' and resid 2196 through 2202 Processing helix chain 'C' and resid 2203 through 2216 removed outlier: 4.176A pdb=" N ASN C2213 " --> pdb=" O GLU C2209 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL C2214 " --> pdb=" O VAL C2210 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU C2215 " --> pdb=" O MET C2211 " (cutoff:3.500A) Processing helix chain 'C' and resid 2226 through 2244 removed outlier: 6.776A pdb=" N THR C2230 " --> pdb=" O PRO C2226 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N SER C2231 " --> pdb=" O LYS C2227 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N SER C2243 " --> pdb=" O PHE C2239 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N ARG C2244 " --> pdb=" O CYS C2240 " (cutoff:3.500A) Processing helix chain 'C' and resid 2245 through 2255 removed outlier: 3.906A pdb=" N SER C2249 " --> pdb=" O GLN C2245 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASP C2252 " --> pdb=" O ARG C2248 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N HIS C2253 " --> pdb=" O SER C2249 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LEU C2254 " --> pdb=" O MET C2250 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N SER C2255 " --> pdb=" O PHE C2251 " (cutoff:3.500A) Processing helix chain 'C' and resid 2256 through 2265 removed outlier: 3.569A pdb=" N ASN C2260 " --> pdb=" O TYR C2256 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLY C2262 " --> pdb=" O LEU C2258 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ILE C2263 " --> pdb=" O GLU C2259 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLY C2264 " --> pdb=" O ASN C2260 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N LEU C2265 " --> pdb=" O SER C2261 " (cutoff:3.500A) Processing helix chain 'C' and resid 2271 through 2282 removed outlier: 3.553A pdb=" N VAL C2275 " --> pdb=" O THR C2271 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA C2276 " --> pdb=" O PRO C2272 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL C2280 " --> pdb=" O ALA C2276 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ILE C2281 " --> pdb=" O ALA C2277 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N ASP C2282 " --> pdb=" O ALA C2278 " (cutoff:3.500A) Processing helix chain 'C' and resid 2286 through 2291 removed outlier: 3.747A pdb=" N LEU C2290 " --> pdb=" O LEU C2286 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N GLN C2291 " --> pdb=" O ALA C2287 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2286 through 2291' Processing helix chain 'C' and resid 2294 through 2308 removed outlier: 3.642A pdb=" N SER C2300 " --> pdb=" O GLU C2296 " (cutoff:3.500A) Processing helix chain 'C' and resid 2310 through 2315 removed outlier: 3.605A pdb=" N LEU C2314 " --> pdb=" O CYS C2310 " (cutoff:3.500A) Processing helix chain 'C' and resid 2324 through 2341 removed outlier: 4.111A pdb=" N GLY C2328 " --> pdb=" O ASN C2324 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LEU C2332 " --> pdb=" O GLY C2328 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N ASP C2333 " --> pdb=" O GLU C2329 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N PHE C2334 " --> pdb=" O ARG C2330 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LEU C2335 " --> pdb=" O TYR C2331 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N VAL C2341 " --> pdb=" O PHE C2337 " (cutoff:3.500A) Processing helix chain 'C' and resid 2346 through 2361 removed outlier: 4.299A pdb=" N VAL C2352 " --> pdb=" O GLU C2348 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG C2359 " --> pdb=" O ARG C2355 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N LYS C2360 " --> pdb=" O LEU C2356 " (cutoff:3.500A) Proline residue: C2361 - end of helix Processing helix chain 'C' and resid 2365 through 2370 Processing helix chain 'C' and resid 2375 through 2390 Proline residue: C2390 - end of helix Processing helix chain 'C' and resid 2417 through 2438 Proline residue: C2438 - end of helix Processing helix chain 'C' and resid 2440 through 2447 Processing helix chain 'C' and resid 2448 through 2462 removed outlier: 4.652A pdb=" N ARG C2452 " --> pdb=" O GLY C2448 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE C2453 " --> pdb=" O GLU C2449 " (cutoff:3.500A) Proline residue: C2462 - end of helix Processing helix chain 'C' and resid 2464 through 2473 removed outlier: 3.998A pdb=" N GLY C2468 " --> pdb=" O ASP C2464 " (cutoff:3.500A) Proline residue: C2473 - end of helix Processing helix chain 'C' and resid 2751 through 2774 removed outlier: 4.814A pdb=" N ILE C2755 " --> pdb=" O LEU C2751 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA C2759 " --> pdb=" O ILE C2755 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N THR C2762 " --> pdb=" O PHE C2758 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N HIS C2763 " --> pdb=" O ALA C2759 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N GLU C2764 " --> pdb=" O GLU C2760 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LYS C2765 " --> pdb=" O TYR C2761 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N TRP C2766 " --> pdb=" O THR C2762 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ALA C2767 " --> pdb=" O HIS C2763 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE C2768 " --> pdb=" O GLU C2764 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ASP C2769 " --> pdb=" O LYS C2765 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N LYS C2770 " --> pdb=" O TRP C2766 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ILE C2771 " --> pdb=" O ALA C2767 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLN C2772 " --> pdb=" O PHE C2768 " (cutoff:3.500A) Processing helix chain 'C' and resid 2798 through 2804 removed outlier: 4.323A pdb=" N LYS C2802 " --> pdb=" O SER C2798 " (cutoff:3.500A) Processing helix chain 'C' and resid 2868 through 2879 removed outlier: 5.259A pdb=" N GLN C2872 " --> pdb=" O SER C2868 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ALA C2873 " --> pdb=" O ARG C2869 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N MET C2874 " --> pdb=" O GLU C2870 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ALA C2875 " --> pdb=" O LEU C2871 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N GLU C2876 " --> pdb=" O GLN C2872 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLN C2877 " --> pdb=" O ALA C2873 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ALA C2879 " --> pdb=" O ALA C2875 " (cutoff:3.500A) Processing helix chain 'C' and resid 2880 through 2892 removed outlier: 4.374A pdb=" N LYS C2891 " --> pdb=" O GLY C2887 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLN C2892 " --> pdb=" O ARG C2888 " (cutoff:3.500A) Processing helix chain 'C' and resid 2920 through 2930 removed outlier: 4.833A pdb=" N GLU C2925 " --> pdb=" O GLU C2921 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS C2928 " --> pdb=" O GLN C2924 " (cutoff:3.500A) Processing helix chain 'C' and resid 3645 through 3656 removed outlier: 3.635A pdb=" N LEU C3654 " --> pdb=" O CYS C3650 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLU C3655 " --> pdb=" O ASN C3651 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N SER C3656 " --> pdb=" O MET C3652 " (cutoff:3.500A) Processing helix chain 'C' and resid 3668 through 3679 removed outlier: 3.663A pdb=" N LYS C3679 " --> pdb=" O ASP C3675 " (cutoff:3.500A) Processing helix chain 'C' and resid 3696 through 3711 Processing helix chain 'C' and resid 3719 through 3735 removed outlier: 3.506A pdb=" N SER C3732 " --> pdb=" O ILE C3728 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N CYS C3733 " --> pdb=" O MET C3729 " (cutoff:3.500A) Processing helix chain 'C' and resid 3752 through 3771 removed outlier: 4.384A pdb=" N ARG C3762 " --> pdb=" O MET C3758 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU C3763 " --> pdb=" O GLU C3759 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU C3764 " --> pdb=" O LYS C3760 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N TYR C3765 " --> pdb=" O GLN C3761 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N GLN C3766 " --> pdb=" O ARG C3762 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N GLN C3767 " --> pdb=" O LEU C3763 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N SER C3768 " --> pdb=" O LEU C3764 " (cutoff:3.500A) Processing helix chain 'C' and resid 3774 through 3787 removed outlier: 3.512A pdb=" N MET C3778 " --> pdb=" O GLY C3774 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N LYS C3787 " --> pdb=" O ILE C3783 " (cutoff:3.500A) Processing helix chain 'C' and resid 3791 through 3806 Processing helix chain 'C' and resid 3809 through 3824 Processing helix chain 'C' and resid 3826 through 3839 removed outlier: 6.618A pdb=" N GLN C3830 " --> pdb=" O VAL C3826 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N CYS C3839 " --> pdb=" O LEU C3835 " (cutoff:3.500A) Processing helix chain 'C' and resid 3844 through 3858 removed outlier: 7.386A pdb=" N GLU C3848 " --> pdb=" O LEU C3844 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ARG C3849 " --> pdb=" O ASN C3845 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY C3855 " --> pdb=" O ASN C3851 " (cutoff:3.500A) Processing helix chain 'C' and resid 3877 through 3893 Processing helix chain 'C' and resid 3896 through 3905 removed outlier: 6.594A pdb=" N GLN C3900 " --> pdb=" O ASN C3896 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ASN C3901 " --> pdb=" O ASN C3897 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG C3904 " --> pdb=" O GLN C3900 " (cutoff:3.500A) Processing helix chain 'C' and resid 3914 through 3938 Processing helix chain 'C' and resid 3944 through 3970 Processing helix chain 'C' and resid 3973 through 3984 removed outlier: 5.112A pdb=" N ARG C3984 " --> pdb=" O LEU C3980 " (cutoff:3.500A) Processing helix chain 'C' and resid 3985 through 4004 removed outlier: 3.620A pdb=" N GLY C3991 " --> pdb=" O ASP C3987 " (cutoff:3.500A) Processing helix chain 'C' and resid 4009 through 4032 Processing helix chain 'C' and resid 4038 through 4052 removed outlier: 6.842A pdb=" N ARG C4042 " --> pdb=" O GLY C4038 " (cutoff:3.500A) Processing helix chain 'C' and resid 4053 through 4072 removed outlier: 4.001A pdb=" N PHE C4065 " --> pdb=" O PHE C4061 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASP C4070 " --> pdb=" O LEU C4066 " (cutoff:3.500A) Processing helix chain 'C' and resid 4074 through 4082 removed outlier: 4.932A pdb=" N THR C4082 " --> pdb=" O GLN C4078 " (cutoff:3.500A) Processing helix chain 'C' and resid 4089 through 4101 removed outlier: 5.145A pdb=" N LYS C4101 " --> pdb=" O MET C4097 " (cutoff:3.500A) Processing helix chain 'C' and resid 4104 through 4116 removed outlier: 5.085A pdb=" N GLU C4116 " --> pdb=" O LEU C4112 " (cutoff:3.500A) Processing helix chain 'C' and resid 4124 through 4138 removed outlier: 5.693A pdb=" N PHE C4132 " --> pdb=" O PHE C4128 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N GLN C4133 " --> pdb=" O ALA C4129 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N GLU C4134 " --> pdb=" O ASN C4130 " (cutoff:3.500A) Proline residue: C4135 - end of helix removed outlier: 5.060A pdb=" N ASP C4138 " --> pdb=" O GLU C4134 " (cutoff:3.500A) Processing helix chain 'C' and resid 4139 through 4155 Proline residue: C4155 - end of helix Processing helix chain 'C' and resid 4157 through 4168 removed outlier: 4.068A pdb=" N PHE C4163 " --> pdb=" O ARG C4159 " (cutoff:3.500A) Processing helix chain 'C' and resid 4169 through 4179 removed outlier: 4.186A pdb=" N ARG C4175 " --> pdb=" O LEU C4171 " (cutoff:3.500A) Proline residue: C4176 - end of helix removed outlier: 5.556A pdb=" N GLY C4179 " --> pdb=" O ARG C4175 " (cutoff:3.500A) Processing helix chain 'C' and resid 4198 through 4208 Proline residue: C4208 - end of helix Processing helix chain 'C' and resid 4209 through 4224 removed outlier: 3.536A pdb=" N GLU C4224 " --> pdb=" O ASP C4220 " (cutoff:3.500A) Processing helix chain 'C' and resid 4226 through 4252 removed outlier: 4.693A pdb=" N MET C4231 " --> pdb=" O GLU C4227 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N GLU C4232 " --> pdb=" O ALA C4228 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE C4243 " --> pdb=" O GLU C4239 " (cutoff:3.500A) Processing helix chain 'C' and resid 4540 through 4559 removed outlier: 4.489A pdb=" N ARG C4557 " --> pdb=" O ASN C4553 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ASN C4558 " --> pdb=" O TYR C4554 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N PHE C4559 " --> pdb=" O LEU C4555 " (cutoff:3.500A) Processing helix chain 'C' and resid 4560 through 4579 removed outlier: 4.590A pdb=" N PHE C4579 " --> pdb=" O PHE C4575 " (cutoff:3.500A) Processing helix chain 'C' and resid 4642 through 4683 removed outlier: 4.287A pdb=" N LEU C4648 " --> pdb=" O TRP C4644 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU C4649 " --> pdb=" O CYS C4645 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU C4652 " --> pdb=" O LEU C4648 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N VAL C4666 " --> pdb=" O ASN C4662 " (cutoff:3.500A) Proline residue: C4667 - end of helix Processing helix chain 'C' and resid 4696 through 4709 removed outlier: 5.341A pdb=" N GLN C4700 " --> pdb=" O ASP C4696 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N TRP C4701 " --> pdb=" O VAL C4697 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ARG C4703 " --> pdb=" O GLY C4699 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N LEU C4704 " --> pdb=" O GLN C4700 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N VAL C4705 " --> pdb=" O TRP C4701 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LEU C4706 " --> pdb=" O ASP C4702 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ASN C4707 " --> pdb=" O ARG C4703 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N THR C4708 " --> pdb=" O LEU C4704 " (cutoff:3.500A) Proline residue: C4709 - end of helix Processing helix chain 'C' and resid 4719 through 4729 removed outlier: 3.740A pdb=" N LEU C4725 " --> pdb=" O LYS C4721 " (cutoff:3.500A) Processing helix chain 'C' and resid 4733 through 4742 removed outlier: 3.562A pdb=" N GLY C4742 " --> pdb=" O ALA C4738 " (cutoff:3.500A) Processing helix chain 'C' and resid 4748 through 4756 removed outlier: 3.933A pdb=" N ALA C4752 " --> pdb=" O LEU C4748 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU C4755 " --> pdb=" O THR C4751 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG C4756 " --> pdb=" O ALA C4752 " (cutoff:3.500A) Processing helix chain 'C' and resid 4766 through 4771 Processing helix chain 'C' and resid 4772 through 4786 removed outlier: 4.298A pdb=" N GLN C4776 " --> pdb=" O ASP C4772 " (cutoff:3.500A) Processing helix chain 'C' and resid 4787 through 4805 removed outlier: 4.053A pdb=" N TYR C4804 " --> pdb=" O LEU C4800 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ASN C4805 " --> pdb=" O LEU C4801 " (cutoff:3.500A) Processing helix chain 'C' and resid 4808 through 4820 removed outlier: 4.394A pdb=" N HIS C4812 " --> pdb=" O PHE C4808 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LEU C4813 " --> pdb=" O PHE C4809 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LEU C4814 " --> pdb=" O ALA C4810 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ASP C4815 " --> pdb=" O ALA C4811 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLY C4819 " --> pdb=" O ASP C4815 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N VAL C4820 " --> pdb=" O ILE C4816 " (cutoff:3.500A) Processing helix chain 'C' and resid 4821 through 4833 removed outlier: 4.158A pdb=" N THR C4825 " --> pdb=" O LYS C4821 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ILE C4826 " --> pdb=" O THR C4822 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL C4830 " --> pdb=" O ILE C4826 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ASN C4833 " --> pdb=" O SER C4829 " (cutoff:3.500A) Processing helix chain 'C' and resid 4834 through 4858 removed outlier: 3.932A pdb=" N VAL C4838 " --> pdb=" O GLY C4834 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL C4854 " --> pdb=" O LEU C4850 " (cutoff:3.500A) Processing helix chain 'C' and resid 4859 through 4864 removed outlier: 3.748A pdb=" N ASN C4864 " --> pdb=" O ARG C4860 " (cutoff:3.500A) Processing helix chain 'C' and resid 4878 through 4893 removed outlier: 3.749A pdb=" N ARG C4892 " --> pdb=" O TYR C4888 " (cutoff:3.500A) Processing helix chain 'C' and resid 4896 through 4902 removed outlier: 4.790A pdb=" N GLU C4900 " --> pdb=" O GLY C4896 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N GLU C4902 " --> pdb=" O GLY C4898 " (cutoff:3.500A) Processing helix chain 'C' and resid 4909 through 4924 Processing helix chain 'C' and resid 4928 through 4957 Processing helix chain 'C' and resid 4964 through 4970 removed outlier: 4.273A pdb=" N PHE C4968 " --> pdb=" O GLY C4964 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR C4970 " --> pdb=" O ASP C4966 " (cutoff:3.500A) Processing helix chain 'C' and resid 4973 through 4982 Processing helix chain 'C' and resid 4984 through 4998 removed outlier: 3.797A pdb=" N TYR C4988 " --> pdb=" O ASN C4984 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N MET C4989 " --> pdb=" O LEU C4985 " (cutoff:3.500A) Processing helix chain 'C' and resid 5004 through 5017 Processing helix chain 'C' and resid 5027 through 5033 removed outlier: 6.208A pdb=" N GLN C5031 " --> pdb=" O CYS C5027 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 66 removed outlier: 4.487A pdb=" N CYS D 65 " --> pdb=" O ASP D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 84 Processing helix chain 'D' and resid 249 through 256 removed outlier: 4.816A pdb=" N CYS D 253 " --> pdb=" O GLY D 249 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N THR D 254 " --> pdb=" O GLY D 250 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N HIS D 255 " --> pdb=" O ALA D 251 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N ALA D 256 " --> pdb=" O VAL D 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 249 through 256' Processing helix chain 'D' and resid 364 through 371 removed outlier: 5.502A pdb=" N VAL D 371 " --> pdb=" O LEU D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 423 removed outlier: 3.692A pdb=" N SER D 420 " --> pdb=" O LYS D 416 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N PHE D 421 " --> pdb=" O GLY D 417 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N SER D 422 " --> pdb=" O LEU D 418 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N GLY D 423 " --> pdb=" O ASP D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 453 removed outlier: 4.148A pdb=" N VAL D 441 " --> pdb=" O PRO D 437 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE D 442 " --> pdb=" O ILE D 438 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU D 443 " --> pdb=" O GLU D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 482 removed outlier: 3.652A pdb=" N GLN D 479 " --> pdb=" O GLN D 475 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLU D 480 " --> pdb=" O SER D 476 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLU D 481 " --> pdb=" O LEU D 477 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N GLY D 482 " --> pdb=" O PHE D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 483 through 496 removed outlier: 4.641A pdb=" N VAL D 487 " --> pdb=" O MET D 483 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL D 496 " --> pdb=" O ASP D 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 512 through 531 removed outlier: 4.267A pdb=" N LYS D 516 " --> pdb=" O ALA D 512 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N GLU D 517 " --> pdb=" O GLU D 513 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N TYR D 523 " --> pdb=" O VAL D 519 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU D 524 " --> pdb=" O ASN D 520 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 541 removed outlier: 3.751A pdb=" N CYS D 537 " --> pdb=" O ASN D 533 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA D 538 " --> pdb=" O ARG D 534 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU D 539 " --> pdb=" O ALA D 535 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N PHE D 540 " --> pdb=" O ASN D 536 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N SER D 541 " --> pdb=" O CYS D 537 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 533 through 541' Processing helix chain 'D' and resid 543 through 551 removed outlier: 3.693A pdb=" N LYS D 550 " --> pdb=" O TRP D 546 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N LEU D 551 " --> pdb=" O VAL D 547 " (cutoff:3.500A) Processing helix chain 'D' and resid 556 through 571 removed outlier: 3.803A pdb=" N VAL D 567 " --> pdb=" O VAL D 563 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU D 568 " --> pdb=" O LEU D 564 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ILE D 569 " --> pdb=" O TYR D 565 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLU D 570 " --> pdb=" O CYS D 566 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 578 removed outlier: 4.412A pdb=" N ASN D 576 " --> pdb=" O PRO D 572 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ILE D 577 " --> pdb=" O GLU D 573 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE D 578 " --> pdb=" O VAL D 574 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 572 through 578' Processing helix chain 'D' and resid 579 through 594 removed outlier: 3.563A pdb=" N LEU D 590 " --> pdb=" O ILE D 586 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP D 591 " --> pdb=" O ILE D 587 " (cutoff:3.500A) Processing helix chain 'D' and resid 596 through 609 removed outlier: 3.864A pdb=" N LEU D 600 " --> pdb=" O ASN D 596 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N CYS D 607 " --> pdb=" O LEU D 603 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N VAL D 608 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N CYS D 609 " --> pdb=" O SER D 605 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 626 removed outlier: 4.305A pdb=" N GLN D 618 " --> pdb=" O VAL D 614 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N LEU D 626 " --> pdb=" O THR D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 868 through 890 removed outlier: 3.853A pdb=" N GLU D 872 " --> pdb=" O GLU D 868 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N LYS D 873 " --> pdb=" O ARG D 869 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TRP D 882 " --> pdb=" O ILE D 878 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA D 883 " --> pdb=" O HIS D 879 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLU D 888 " --> pdb=" O LEU D 884 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N GLN D 889 " --> pdb=" O THR D 885 " (cutoff:3.500A) Processing helix chain 'D' and resid 914 through 935 removed outlier: 5.398A pdb=" N LEU D 935 " --> pdb=" O THR D 931 " (cutoff:3.500A) Processing helix chain 'D' and resid 943 through 948 removed outlier: 6.694A pdb=" N GLU D 947 " --> pdb=" O ASP D 943 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ASP D 948 " --> pdb=" O GLU D 944 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 943 through 948' Processing helix chain 'D' and resid 956 through 961 Processing helix chain 'D' and resid 978 through 1001 removed outlier: 4.453A pdb=" N THR D 982 " --> pdb=" O THR D 978 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ASP D 999 " --> pdb=" O VAL D 995 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ARG D1000 " --> pdb=" O TRP D 996 " (cutoff:3.500A) Processing helix chain 'D' and resid 1030 through 1045 removed outlier: 3.535A pdb=" N ASP D1037 " --> pdb=" O ARG D1033 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N SER D1038 " --> pdb=" O SER D1034 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU D1039 " --> pdb=" O ASN D1035 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N THR D1045 " --> pdb=" O GLN D1041 " (cutoff:3.500A) Processing helix chain 'D' and resid 1207 through 1212 removed outlier: 3.857A pdb=" N LEU D1211 " --> pdb=" O ASP D1207 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N ARG D1212 " --> pdb=" O VAL D1208 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1207 through 1212' Processing helix chain 'D' and resid 1574 through 1581 removed outlier: 4.283A pdb=" N ALA D1578 " --> pdb=" O PRO D1574 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N MET D1579 " --> pdb=" O LEU D1575 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE D1580 " --> pdb=" O SER D1576 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU D1581 " --> pdb=" O ALA D1577 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1574 through 1581' Processing helix chain 'D' and resid 1649 through 1657 removed outlier: 4.001A pdb=" N LEU D1653 " --> pdb=" O ASP D1649 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N SER D1654 " --> pdb=" O ILE D1650 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N GLU D1655 " --> pdb=" O LEU D1651 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ARG D1656 " --> pdb=" O GLU D1652 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU D1657 " --> pdb=" O LEU D1653 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1649 through 1657' Processing helix chain 'D' and resid 1658 through 1675 Processing helix chain 'D' and resid 1678 through 1690 removed outlier: 4.417A pdb=" N ALA D1682 " --> pdb=" O ASN D1678 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N HIS D1683 " --> pdb=" O ASN D1679 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA D1684 " --> pdb=" O ARG D1680 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ASP D1690 " --> pdb=" O CYS D1686 " (cutoff:3.500A) Processing helix chain 'D' and resid 1691 through 1700 removed outlier: 3.803A pdb=" N LEU D1698 " --> pdb=" O LEU D1694 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLU D1699 " --> pdb=" O LEU D1695 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ASP D1700 " --> pdb=" O HIS D1696 " (cutoff:3.500A) Processing helix chain 'D' and resid 1704 through 1719 removed outlier: 6.824A pdb=" N ARG D1708 " --> pdb=" O PRO D1704 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA D1709 " --> pdb=" O GLY D1705 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N HIS D1719 " --> pdb=" O LEU D1715 " (cutoff:3.500A) Processing helix chain 'D' and resid 1720 through 1732 removed outlier: 4.422A pdb=" N SER D1732 " --> pdb=" O ARG D1728 " (cutoff:3.500A) Processing helix chain 'D' and resid 1739 through 1746 removed outlier: 4.069A pdb=" N ILE D1745 " --> pdb=" O GLU D1741 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N THR D1746 " --> pdb=" O THR D1742 " (cutoff:3.500A) Processing helix chain 'D' and resid 1754 through 1759 removed outlier: 4.271A pdb=" N ARG D1759 " --> pdb=" O GLY D1755 " (cutoff:3.500A) Processing helix chain 'D' and resid 1803 through 1825 removed outlier: 3.748A pdb=" N VAL D1819 " --> pdb=" O LEU D1815 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG D1820 " --> pdb=" O GLY D1816 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLN D1824 " --> pdb=" O ARG D1820 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N HIS D1825 " --> pdb=" O ASP D1821 " (cutoff:3.500A) Processing helix chain 'D' and resid 1833 through 1852 Proline residue: D1840 - end of helix removed outlier: 3.847A pdb=" N MET D1851 " --> pdb=" O THR D1847 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLY D1852 " --> pdb=" O LEU D1848 " (cutoff:3.500A) Processing helix chain 'D' and resid 1855 through 1865 removed outlier: 4.221A pdb=" N MET D1865 " --> pdb=" O GLN D1861 " (cutoff:3.500A) Processing helix chain 'D' and resid 1866 through 1871 Processing helix chain 'D' and resid 1934 through 1984 removed outlier: 4.148A pdb=" N GLN D1938 " --> pdb=" O SER D1934 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N TYR D1945 " --> pdb=" O ASN D1941 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N PHE D1946 " --> pdb=" O LEU D1942 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU D1950 " --> pdb=" O PHE D1946 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU D1951 " --> pdb=" O CYS D1947 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU D1963 " --> pdb=" O ALA D1959 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ARG D1964 " --> pdb=" O ALA D1960 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N PHE D1984 " --> pdb=" O LEU D1980 " (cutoff:3.500A) Processing helix chain 'D' and resid 1987 through 1999 removed outlier: 4.206A pdb=" N ARG D1996 " --> pdb=" O ALA D1992 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N GLU D1997 " --> pdb=" O ARG D1993 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE D1998 " --> pdb=" O ARG D1994 " (cutoff:3.500A) Processing helix chain 'D' and resid 2001 through 2015 removed outlier: 3.623A pdb=" N LEU D2009 " --> pdb=" O GLN D2005 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU D2010 " --> pdb=" O ILE D2006 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLU D2015 " --> pdb=" O HIS D2011 " (cutoff:3.500A) Processing helix chain 'D' and resid 2027 through 2043 removed outlier: 4.717A pdb=" N LEU D2031 " --> pdb=" O ILE D2027 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLN D2032 " --> pdb=" O ARG D2028 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N GLY D2043 " --> pdb=" O LEU D2039 " (cutoff:3.500A) Processing helix chain 'D' and resid 2093 through 2109 removed outlier: 4.229A pdb=" N ASP D2109 " --> pdb=" O TRP D2105 " (cutoff:3.500A) Processing helix chain 'D' and resid 2113 through 2130 removed outlier: 3.594A pdb=" N VAL D2117 " --> pdb=" O SER D2113 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLY D2130 " --> pdb=" O ARG D2126 " (cutoff:3.500A) Processing helix chain 'D' and resid 2131 through 2139 Proline residue: D2139 - end of helix Processing helix chain 'D' and resid 2148 through 2169 removed outlier: 4.044A pdb=" N SER D2154 " --> pdb=" O GLU D2150 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU D2155 " --> pdb=" O ASP D2151 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ILE D2167 " --> pdb=" O ARG D2163 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N VAL D2168 " --> pdb=" O SER D2164 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N GLN D2169 " --> pdb=" O LEU D2165 " (cutoff:3.500A) Processing helix chain 'D' and resid 2171 through 2188 removed outlier: 3.816A pdb=" N ASN D2176 " --> pdb=" O PRO D2172 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU D2177 " --> pdb=" O GLN D2173 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ASN D2187 " --> pdb=" O GLY D2183 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ASN D2188 " --> pdb=" O ASN D2184 " (cutoff:3.500A) Processing helix chain 'D' and resid 2189 through 2195 removed outlier: 4.658A pdb=" N GLN D2193 " --> pdb=" O LYS D2189 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N HIS D2194 " --> pdb=" O VAL D2190 " (cutoff:3.500A) Proline residue: D2195 - end of helix No H-bonds generated for 'chain 'D' and resid 2189 through 2195' Processing helix chain 'D' and resid 2196 through 2202 Processing helix chain 'D' and resid 2203 through 2216 removed outlier: 4.176A pdb=" N ASN D2213 " --> pdb=" O GLU D2209 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL D2214 " --> pdb=" O VAL D2210 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU D2215 " --> pdb=" O MET D2211 " (cutoff:3.500A) Processing helix chain 'D' and resid 2226 through 2244 removed outlier: 6.777A pdb=" N THR D2230 " --> pdb=" O PRO D2226 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N SER D2231 " --> pdb=" O LYS D2227 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N SER D2243 " --> pdb=" O PHE D2239 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N ARG D2244 " --> pdb=" O CYS D2240 " (cutoff:3.500A) Processing helix chain 'D' and resid 2245 through 2255 removed outlier: 3.907A pdb=" N SER D2249 " --> pdb=" O GLN D2245 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASP D2252 " --> pdb=" O ARG D2248 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N HIS D2253 " --> pdb=" O SER D2249 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LEU D2254 " --> pdb=" O MET D2250 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N SER D2255 " --> pdb=" O PHE D2251 " (cutoff:3.500A) Processing helix chain 'D' and resid 2256 through 2265 removed outlier: 3.570A pdb=" N ASN D2260 " --> pdb=" O TYR D2256 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLY D2262 " --> pdb=" O LEU D2258 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ILE D2263 " --> pdb=" O GLU D2259 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLY D2264 " --> pdb=" O ASN D2260 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N LEU D2265 " --> pdb=" O SER D2261 " (cutoff:3.500A) Processing helix chain 'D' and resid 2271 through 2282 removed outlier: 3.553A pdb=" N VAL D2275 " --> pdb=" O THR D2271 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA D2276 " --> pdb=" O PRO D2272 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL D2280 " --> pdb=" O ALA D2276 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE D2281 " --> pdb=" O ALA D2277 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N ASP D2282 " --> pdb=" O ALA D2278 " (cutoff:3.500A) Processing helix chain 'D' and resid 2286 through 2291 removed outlier: 3.747A pdb=" N LEU D2290 " --> pdb=" O LEU D2286 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N GLN D2291 " --> pdb=" O ALA D2287 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2286 through 2291' Processing helix chain 'D' and resid 2294 through 2308 removed outlier: 3.642A pdb=" N SER D2300 " --> pdb=" O GLU D2296 " (cutoff:3.500A) Processing helix chain 'D' and resid 2310 through 2315 removed outlier: 3.605A pdb=" N LEU D2314 " --> pdb=" O CYS D2310 " (cutoff:3.500A) Processing helix chain 'D' and resid 2324 through 2341 removed outlier: 4.111A pdb=" N GLY D2328 " --> pdb=" O ASN D2324 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LEU D2332 " --> pdb=" O GLY D2328 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N ASP D2333 " --> pdb=" O GLU D2329 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N PHE D2334 " --> pdb=" O ARG D2330 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LEU D2335 " --> pdb=" O TYR D2331 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N VAL D2341 " --> pdb=" O PHE D2337 " (cutoff:3.500A) Processing helix chain 'D' and resid 2346 through 2361 removed outlier: 4.299A pdb=" N VAL D2352 " --> pdb=" O GLU D2348 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG D2359 " --> pdb=" O ARG D2355 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LYS D2360 " --> pdb=" O LEU D2356 " (cutoff:3.500A) Proline residue: D2361 - end of helix Processing helix chain 'D' and resid 2365 through 2370 Processing helix chain 'D' and resid 2375 through 2390 Proline residue: D2390 - end of helix Processing helix chain 'D' and resid 2417 through 2438 Proline residue: D2438 - end of helix Processing helix chain 'D' and resid 2440 through 2447 Processing helix chain 'D' and resid 2448 through 2462 removed outlier: 4.651A pdb=" N ARG D2452 " --> pdb=" O GLY D2448 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE D2453 " --> pdb=" O GLU D2449 " (cutoff:3.500A) Proline residue: D2462 - end of helix Processing helix chain 'D' and resid 2464 through 2473 removed outlier: 3.998A pdb=" N GLY D2468 " --> pdb=" O ASP D2464 " (cutoff:3.500A) Proline residue: D2473 - end of helix Processing helix chain 'D' and resid 2751 through 2774 removed outlier: 4.815A pdb=" N ILE D2755 " --> pdb=" O LEU D2751 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA D2759 " --> pdb=" O ILE D2755 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N THR D2762 " --> pdb=" O PHE D2758 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N HIS D2763 " --> pdb=" O ALA D2759 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N GLU D2764 " --> pdb=" O GLU D2760 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LYS D2765 " --> pdb=" O TYR D2761 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N TRP D2766 " --> pdb=" O THR D2762 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ALA D2767 " --> pdb=" O HIS D2763 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE D2768 " --> pdb=" O GLU D2764 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ASP D2769 " --> pdb=" O LYS D2765 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N LYS D2770 " --> pdb=" O TRP D2766 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ILE D2771 " --> pdb=" O ALA D2767 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLN D2772 " --> pdb=" O PHE D2768 " (cutoff:3.500A) Processing helix chain 'D' and resid 2798 through 2804 removed outlier: 4.323A pdb=" N LYS D2802 " --> pdb=" O SER D2798 " (cutoff:3.500A) Processing helix chain 'D' and resid 2868 through 2879 removed outlier: 5.259A pdb=" N GLN D2872 " --> pdb=" O SER D2868 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ALA D2873 " --> pdb=" O ARG D2869 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N MET D2874 " --> pdb=" O GLU D2870 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA D2875 " --> pdb=" O LEU D2871 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N GLU D2876 " --> pdb=" O GLN D2872 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLN D2877 " --> pdb=" O ALA D2873 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ALA D2879 " --> pdb=" O ALA D2875 " (cutoff:3.500A) Processing helix chain 'D' and resid 2880 through 2892 removed outlier: 4.374A pdb=" N LYS D2891 " --> pdb=" O GLY D2887 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLN D2892 " --> pdb=" O ARG D2888 " (cutoff:3.500A) Processing helix chain 'D' and resid 2920 through 2930 removed outlier: 4.833A pdb=" N GLU D2925 " --> pdb=" O GLU D2921 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS D2928 " --> pdb=" O GLN D2924 " (cutoff:3.500A) Processing helix chain 'D' and resid 3645 through 3656 removed outlier: 3.634A pdb=" N LEU D3654 " --> pdb=" O CYS D3650 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N GLU D3655 " --> pdb=" O ASN D3651 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N SER D3656 " --> pdb=" O MET D3652 " (cutoff:3.500A) Processing helix chain 'D' and resid 3668 through 3679 removed outlier: 3.663A pdb=" N LYS D3679 " --> pdb=" O ASP D3675 " (cutoff:3.500A) Processing helix chain 'D' and resid 3696 through 3711 Processing helix chain 'D' and resid 3719 through 3735 removed outlier: 3.506A pdb=" N SER D3732 " --> pdb=" O ILE D3728 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N CYS D3733 " --> pdb=" O MET D3729 " (cutoff:3.500A) Processing helix chain 'D' and resid 3752 through 3771 removed outlier: 4.383A pdb=" N ARG D3762 " --> pdb=" O MET D3758 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU D3763 " --> pdb=" O GLU D3759 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU D3764 " --> pdb=" O LYS D3760 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N TYR D3765 " --> pdb=" O GLN D3761 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N GLN D3766 " --> pdb=" O ARG D3762 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N GLN D3767 " --> pdb=" O LEU D3763 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N SER D3768 " --> pdb=" O LEU D3764 " (cutoff:3.500A) Processing helix chain 'D' and resid 3774 through 3787 removed outlier: 3.512A pdb=" N MET D3778 " --> pdb=" O GLY D3774 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N LYS D3787 " --> pdb=" O ILE D3783 " (cutoff:3.500A) Processing helix chain 'D' and resid 3791 through 3806 Processing helix chain 'D' and resid 3809 through 3824 Processing helix chain 'D' and resid 3826 through 3839 removed outlier: 6.618A pdb=" N GLN D3830 " --> pdb=" O VAL D3826 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N CYS D3839 " --> pdb=" O LEU D3835 " (cutoff:3.500A) Processing helix chain 'D' and resid 3844 through 3858 removed outlier: 7.386A pdb=" N GLU D3848 " --> pdb=" O LEU D3844 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ARG D3849 " --> pdb=" O ASN D3845 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY D3855 " --> pdb=" O ASN D3851 " (cutoff:3.500A) Processing helix chain 'D' and resid 3877 through 3893 Processing helix chain 'D' and resid 3896 through 3905 removed outlier: 6.594A pdb=" N GLN D3900 " --> pdb=" O ASN D3896 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ASN D3901 " --> pdb=" O ASN D3897 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG D3904 " --> pdb=" O GLN D3900 " (cutoff:3.500A) Processing helix chain 'D' and resid 3914 through 3938 Processing helix chain 'D' and resid 3944 through 3970 Processing helix chain 'D' and resid 3973 through 3984 removed outlier: 5.112A pdb=" N ARG D3984 " --> pdb=" O LEU D3980 " (cutoff:3.500A) Processing helix chain 'D' and resid 3985 through 4004 removed outlier: 3.619A pdb=" N GLY D3991 " --> pdb=" O ASP D3987 " (cutoff:3.500A) Processing helix chain 'D' and resid 4009 through 4032 Processing helix chain 'D' and resid 4038 through 4052 removed outlier: 6.842A pdb=" N ARG D4042 " --> pdb=" O GLY D4038 " (cutoff:3.500A) Processing helix chain 'D' and resid 4053 through 4072 removed outlier: 4.000A pdb=" N PHE D4065 " --> pdb=" O PHE D4061 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASP D4070 " --> pdb=" O LEU D4066 " (cutoff:3.500A) Processing helix chain 'D' and resid 4074 through 4082 removed outlier: 4.932A pdb=" N THR D4082 " --> pdb=" O GLN D4078 " (cutoff:3.500A) Processing helix chain 'D' and resid 4089 through 4101 removed outlier: 5.145A pdb=" N LYS D4101 " --> pdb=" O MET D4097 " (cutoff:3.500A) Processing helix chain 'D' and resid 4104 through 4116 removed outlier: 5.086A pdb=" N GLU D4116 " --> pdb=" O LEU D4112 " (cutoff:3.500A) Processing helix chain 'D' and resid 4124 through 4138 removed outlier: 5.693A pdb=" N PHE D4132 " --> pdb=" O PHE D4128 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N GLN D4133 " --> pdb=" O ALA D4129 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N GLU D4134 " --> pdb=" O ASN D4130 " (cutoff:3.500A) Proline residue: D4135 - end of helix removed outlier: 5.061A pdb=" N ASP D4138 " --> pdb=" O GLU D4134 " (cutoff:3.500A) Processing helix chain 'D' and resid 4139 through 4155 Proline residue: D4155 - end of helix Processing helix chain 'D' and resid 4157 through 4168 removed outlier: 4.068A pdb=" N PHE D4163 " --> pdb=" O ARG D4159 " (cutoff:3.500A) Processing helix chain 'D' and resid 4169 through 4179 removed outlier: 4.186A pdb=" N ARG D4175 " --> pdb=" O LEU D4171 " (cutoff:3.500A) Proline residue: D4176 - end of helix removed outlier: 5.557A pdb=" N GLY D4179 " --> pdb=" O ARG D4175 " (cutoff:3.500A) Processing helix chain 'D' and resid 4198 through 4208 Proline residue: D4208 - end of helix Processing helix chain 'D' and resid 4209 through 4224 removed outlier: 3.536A pdb=" N GLU D4224 " --> pdb=" O ASP D4220 " (cutoff:3.500A) Processing helix chain 'D' and resid 4226 through 4252 removed outlier: 4.694A pdb=" N MET D4231 " --> pdb=" O GLU D4227 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N GLU D4232 " --> pdb=" O ALA D4228 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE D4243 " --> pdb=" O GLU D4239 " (cutoff:3.500A) Processing helix chain 'D' and resid 4540 through 4559 removed outlier: 4.489A pdb=" N ARG D4557 " --> pdb=" O ASN D4553 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASN D4558 " --> pdb=" O TYR D4554 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N PHE D4559 " --> pdb=" O LEU D4555 " (cutoff:3.500A) Processing helix chain 'D' and resid 4560 through 4579 removed outlier: 4.590A pdb=" N PHE D4579 " --> pdb=" O PHE D4575 " (cutoff:3.500A) Processing helix chain 'D' and resid 4642 through 4683 removed outlier: 4.288A pdb=" N LEU D4648 " --> pdb=" O TRP D4644 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU D4649 " --> pdb=" O CYS D4645 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU D4652 " --> pdb=" O LEU D4648 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N VAL D4666 " --> pdb=" O ASN D4662 " (cutoff:3.500A) Proline residue: D4667 - end of helix Processing helix chain 'D' and resid 4696 through 4709 removed outlier: 5.341A pdb=" N GLN D4700 " --> pdb=" O ASP D4696 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N TRP D4701 " --> pdb=" O VAL D4697 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ARG D4703 " --> pdb=" O GLY D4699 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N LEU D4704 " --> pdb=" O GLN D4700 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N VAL D4705 " --> pdb=" O TRP D4701 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LEU D4706 " --> pdb=" O ASP D4702 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ASN D4707 " --> pdb=" O ARG D4703 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N THR D4708 " --> pdb=" O LEU D4704 " (cutoff:3.500A) Proline residue: D4709 - end of helix Processing helix chain 'D' and resid 4719 through 4729 removed outlier: 3.740A pdb=" N LEU D4725 " --> pdb=" O LYS D4721 " (cutoff:3.500A) Processing helix chain 'D' and resid 4733 through 4742 removed outlier: 3.562A pdb=" N GLY D4742 " --> pdb=" O ALA D4738 " (cutoff:3.500A) Processing helix chain 'D' and resid 4748 through 4756 removed outlier: 3.933A pdb=" N ALA D4752 " --> pdb=" O LEU D4748 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU D4755 " --> pdb=" O THR D4751 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ARG D4756 " --> pdb=" O ALA D4752 " (cutoff:3.500A) Processing helix chain 'D' and resid 4766 through 4771 Processing helix chain 'D' and resid 4772 through 4786 removed outlier: 4.297A pdb=" N GLN D4776 " --> pdb=" O ASP D4772 " (cutoff:3.500A) Processing helix chain 'D' and resid 4787 through 4805 removed outlier: 4.052A pdb=" N TYR D4804 " --> pdb=" O LEU D4800 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ASN D4805 " --> pdb=" O LEU D4801 " (cutoff:3.500A) Processing helix chain 'D' and resid 4808 through 4820 removed outlier: 4.394A pdb=" N HIS D4812 " --> pdb=" O PHE D4808 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LEU D4813 " --> pdb=" O PHE D4809 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LEU D4814 " --> pdb=" O ALA D4810 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ASP D4815 " --> pdb=" O ALA D4811 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLY D4819 " --> pdb=" O ASP D4815 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N VAL D4820 " --> pdb=" O ILE D4816 " (cutoff:3.500A) Processing helix chain 'D' and resid 4821 through 4833 removed outlier: 4.158A pdb=" N THR D4825 " --> pdb=" O LYS D4821 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ILE D4826 " --> pdb=" O THR D4822 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL D4830 " --> pdb=" O ILE D4826 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ASN D4833 " --> pdb=" O SER D4829 " (cutoff:3.500A) Processing helix chain 'D' and resid 4834 through 4858 removed outlier: 3.931A pdb=" N VAL D4838 " --> pdb=" O GLY D4834 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL D4854 " --> pdb=" O LEU D4850 " (cutoff:3.500A) Processing helix chain 'D' and resid 4859 through 4864 removed outlier: 3.749A pdb=" N ASN D4864 " --> pdb=" O ARG D4860 " (cutoff:3.500A) Processing helix chain 'D' and resid 4878 through 4893 removed outlier: 3.749A pdb=" N ARG D4892 " --> pdb=" O TYR D4888 " (cutoff:3.500A) Processing helix chain 'D' and resid 4896 through 4902 removed outlier: 4.790A pdb=" N GLU D4900 " --> pdb=" O GLY D4896 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N GLU D4902 " --> pdb=" O GLY D4898 " (cutoff:3.500A) Processing helix chain 'D' and resid 4909 through 4924 Processing helix chain 'D' and resid 4928 through 4957 Processing helix chain 'D' and resid 4964 through 4970 removed outlier: 4.273A pdb=" N PHE D4968 " --> pdb=" O GLY D4964 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR D4970 " --> pdb=" O ASP D4966 " (cutoff:3.500A) Processing helix chain 'D' and resid 4973 through 4982 Processing helix chain 'D' and resid 4984 through 4998 removed outlier: 3.798A pdb=" N TYR D4988 " --> pdb=" O ASN D4984 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N MET D4989 " --> pdb=" O LEU D4985 " (cutoff:3.500A) Processing helix chain 'D' and resid 5004 through 5017 Processing helix chain 'D' and resid 5027 through 5033 removed outlier: 6.208A pdb=" N GLN D5031 " --> pdb=" O CYS D5027 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'A' and resid 47 through 52 removed outlier: 6.179A pdb=" N LYS A 34 " --> pdb=" O THR A 52 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU A 33 " --> pdb=" O ALA A 26 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU A 37 " --> pdb=" O LEU A 22 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N LEU A 22 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 10.420A pdb=" N ALA A 39 " --> pdb=" O VAL A 20 " (cutoff:3.500A) removed outlier: 13.570A pdb=" N VAL A 20 " --> pdb=" O ALA A 39 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU A 19 " --> pdb=" O ILE A 205 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 67 through 70 removed outlier: 7.004A pdb=" N LEU A 108 " --> pdb=" O GLU A 70 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N LEU A 109 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N MET A 116 " --> pdb=" O HIS A 111 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 181 through 184 Processing sheet with id= 4, first strand: chain 'A' and resid 220 through 224 Processing sheet with id= 5, first strand: chain 'A' and resid 260 through 264 Processing sheet with id= 6, first strand: chain 'A' and resid 314 through 318 Processing sheet with id= 7, first strand: chain 'A' and resid 641 through 645 removed outlier: 3.588A pdb=" N GLY A 685 " --> pdb=" O VAL A 780 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER A 782 " --> pdb=" O ARG A 683 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N HIS A 681 " --> pdb=" O SER A 784 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N HIS A 720 " --> pdb=" O ASP A 717 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'A' and resid 753 through 759 removed outlier: 3.695A pdb=" N ASP A 742 " --> pdb=" O VAL A 668 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LEU A 750 " --> pdb=" O GLY A 660 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N GLY A 660 " --> pdb=" O LEU A 750 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'A' and resid 830 through 833 removed outlier: 4.407A pdb=" N GLY A 836 " --> pdb=" O GLY A 833 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N LEU A1202 " --> pdb=" O PRO A 837 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N GLN A1198 " --> pdb=" O GLY A 841 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL A1199 " --> pdb=" O VAL A1095 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'A' and resid 937 through 940 removed outlier: 3.816A pdb=" N GLY A 940 " --> pdb=" O GLY A1050 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N GLY A1050 " --> pdb=" O GLY A 940 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'A' and resid 1122 through 1125 removed outlier: 6.704A pdb=" N GLU A1099 " --> pdb=" O GLY A1195 " (cutoff:3.500A) removed outlier: 10.220A pdb=" N VAL A1072 " --> pdb=" O SER A1241 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N SER A1241 " --> pdb=" O VAL A1072 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N ILE A1074 " --> pdb=" O SER A1239 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'A' and resid 1243 through 1247 Processing sheet with id= 13, first strand: chain 'A' and resid 1734 through 1738 Processing sheet with id= 14, first strand: chain 'A' and resid 4180 through 4184 Processing sheet with id= 15, first strand: chain 'A' and resid 4580 through 4584 Processing sheet with id= 16, first strand: chain 'A' and resid 105 through 108 removed outlier: 4.273A pdb=" N HIS A 105 " --> pdb=" O MET A 150 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'B' and resid 47 through 52 removed outlier: 6.179A pdb=" N LYS B 34 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU B 33 " --> pdb=" O ALA B 26 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU B 37 " --> pdb=" O LEU B 22 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N LEU B 22 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 10.419A pdb=" N ALA B 39 " --> pdb=" O VAL B 20 " (cutoff:3.500A) removed outlier: 13.569A pdb=" N VAL B 20 " --> pdb=" O ALA B 39 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU B 19 " --> pdb=" O ILE B 205 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'B' and resid 67 through 70 removed outlier: 7.004A pdb=" N LEU B 108 " --> pdb=" O GLU B 70 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N LEU B 109 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N MET B 116 " --> pdb=" O HIS B 111 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'B' and resid 181 through 184 Processing sheet with id= 20, first strand: chain 'B' and resid 220 through 224 Processing sheet with id= 21, first strand: chain 'B' and resid 260 through 264 Processing sheet with id= 22, first strand: chain 'B' and resid 314 through 318 Processing sheet with id= 23, first strand: chain 'B' and resid 641 through 645 removed outlier: 3.587A pdb=" N GLY B 685 " --> pdb=" O VAL B 780 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER B 782 " --> pdb=" O ARG B 683 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N HIS B 681 " --> pdb=" O SER B 784 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N HIS B 720 " --> pdb=" O ASP B 717 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'B' and resid 753 through 759 removed outlier: 3.694A pdb=" N ASP B 742 " --> pdb=" O VAL B 668 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LEU B 750 " --> pdb=" O GLY B 660 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N GLY B 660 " --> pdb=" O LEU B 750 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'B' and resid 830 through 833 removed outlier: 4.407A pdb=" N GLY B 836 " --> pdb=" O GLY B 833 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N LEU B1202 " --> pdb=" O PRO B 837 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N GLN B1198 " --> pdb=" O GLY B 841 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL B1199 " --> pdb=" O VAL B1095 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'B' and resid 937 through 940 removed outlier: 3.817A pdb=" N GLY B 940 " --> pdb=" O GLY B1050 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N GLY B1050 " --> pdb=" O GLY B 940 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'B' and resid 1122 through 1125 removed outlier: 6.704A pdb=" N GLU B1099 " --> pdb=" O GLY B1195 " (cutoff:3.500A) removed outlier: 10.220A pdb=" N VAL B1072 " --> pdb=" O SER B1241 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N SER B1241 " --> pdb=" O VAL B1072 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N ILE B1074 " --> pdb=" O SER B1239 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'B' and resid 1243 through 1247 Processing sheet with id= 29, first strand: chain 'B' and resid 1734 through 1738 Processing sheet with id= 30, first strand: chain 'B' and resid 4180 through 4184 Processing sheet with id= 31, first strand: chain 'B' and resid 4580 through 4584 Processing sheet with id= 32, first strand: chain 'B' and resid 105 through 108 removed outlier: 4.273A pdb=" N HIS B 105 " --> pdb=" O MET B 150 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'C' and resid 47 through 52 removed outlier: 6.179A pdb=" N LYS C 34 " --> pdb=" O THR C 52 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU C 33 " --> pdb=" O ALA C 26 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU C 37 " --> pdb=" O LEU C 22 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N LEU C 22 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 10.420A pdb=" N ALA C 39 " --> pdb=" O VAL C 20 " (cutoff:3.500A) removed outlier: 13.569A pdb=" N VAL C 20 " --> pdb=" O ALA C 39 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU C 19 " --> pdb=" O ILE C 205 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'C' and resid 67 through 70 removed outlier: 7.005A pdb=" N LEU C 108 " --> pdb=" O GLU C 70 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N LEU C 109 " --> pdb=" O LEU C 118 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N MET C 116 " --> pdb=" O HIS C 111 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'C' and resid 181 through 184 Processing sheet with id= 36, first strand: chain 'C' and resid 220 through 224 Processing sheet with id= 37, first strand: chain 'C' and resid 260 through 264 Processing sheet with id= 38, first strand: chain 'C' and resid 314 through 318 Processing sheet with id= 39, first strand: chain 'C' and resid 641 through 645 removed outlier: 3.588A pdb=" N GLY C 685 " --> pdb=" O VAL C 780 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER C 782 " --> pdb=" O ARG C 683 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N HIS C 681 " --> pdb=" O SER C 784 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N HIS C 720 " --> pdb=" O ASP C 717 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'C' and resid 753 through 759 removed outlier: 3.694A pdb=" N ASP C 742 " --> pdb=" O VAL C 668 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LEU C 750 " --> pdb=" O GLY C 660 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N GLY C 660 " --> pdb=" O LEU C 750 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'C' and resid 830 through 833 removed outlier: 4.407A pdb=" N GLY C 836 " --> pdb=" O GLY C 833 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N LEU C1202 " --> pdb=" O PRO C 837 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N GLN C1198 " --> pdb=" O GLY C 841 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL C1199 " --> pdb=" O VAL C1095 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'C' and resid 937 through 940 removed outlier: 3.816A pdb=" N GLY C 940 " --> pdb=" O GLY C1050 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N GLY C1050 " --> pdb=" O GLY C 940 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'C' and resid 1122 through 1125 removed outlier: 6.703A pdb=" N GLU C1099 " --> pdb=" O GLY C1195 " (cutoff:3.500A) removed outlier: 10.220A pdb=" N VAL C1072 " --> pdb=" O SER C1241 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N SER C1241 " --> pdb=" O VAL C1072 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N ILE C1074 " --> pdb=" O SER C1239 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'C' and resid 1243 through 1247 Processing sheet with id= 45, first strand: chain 'C' and resid 1734 through 1738 Processing sheet with id= 46, first strand: chain 'C' and resid 4180 through 4184 Processing sheet with id= 47, first strand: chain 'C' and resid 4580 through 4584 Processing sheet with id= 48, first strand: chain 'C' and resid 105 through 108 removed outlier: 4.274A pdb=" N HIS C 105 " --> pdb=" O MET C 150 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'D' and resid 47 through 52 removed outlier: 6.179A pdb=" N LYS D 34 " --> pdb=" O THR D 52 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU D 33 " --> pdb=" O ALA D 26 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU D 37 " --> pdb=" O LEU D 22 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N LEU D 22 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 10.419A pdb=" N ALA D 39 " --> pdb=" O VAL D 20 " (cutoff:3.500A) removed outlier: 13.568A pdb=" N VAL D 20 " --> pdb=" O ALA D 39 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU D 19 " --> pdb=" O ILE D 205 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'D' and resid 67 through 70 removed outlier: 7.005A pdb=" N LEU D 108 " --> pdb=" O GLU D 70 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N LEU D 109 " --> pdb=" O LEU D 118 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N MET D 116 " --> pdb=" O HIS D 111 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'D' and resid 181 through 184 Processing sheet with id= 52, first strand: chain 'D' and resid 220 through 224 Processing sheet with id= 53, first strand: chain 'D' and resid 260 through 264 Processing sheet with id= 54, first strand: chain 'D' and resid 314 through 318 Processing sheet with id= 55, first strand: chain 'D' and resid 641 through 645 removed outlier: 3.588A pdb=" N GLY D 685 " --> pdb=" O VAL D 780 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER D 782 " --> pdb=" O ARG D 683 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N HIS D 681 " --> pdb=" O SER D 784 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N HIS D 720 " --> pdb=" O ASP D 717 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'D' and resid 753 through 759 removed outlier: 3.695A pdb=" N ASP D 742 " --> pdb=" O VAL D 668 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LEU D 750 " --> pdb=" O GLY D 660 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N GLY D 660 " --> pdb=" O LEU D 750 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'D' and resid 830 through 833 removed outlier: 4.406A pdb=" N GLY D 836 " --> pdb=" O GLY D 833 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N LEU D1202 " --> pdb=" O PRO D 837 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N GLN D1198 " --> pdb=" O GLY D 841 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL D1199 " --> pdb=" O VAL D1095 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'D' and resid 937 through 940 removed outlier: 3.816A pdb=" N GLY D 940 " --> pdb=" O GLY D1050 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N GLY D1050 " --> pdb=" O GLY D 940 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'D' and resid 1122 through 1125 removed outlier: 6.702A pdb=" N GLU D1099 " --> pdb=" O GLY D1195 " (cutoff:3.500A) removed outlier: 10.221A pdb=" N VAL D1072 " --> pdb=" O SER D1241 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N SER D1241 " --> pdb=" O VAL D1072 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N ILE D1074 " --> pdb=" O SER D1239 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'D' and resid 1243 through 1247 Processing sheet with id= 61, first strand: chain 'D' and resid 1734 through 1738 Processing sheet with id= 62, first strand: chain 'D' and resid 4180 through 4184 Processing sheet with id= 63, first strand: chain 'D' and resid 4580 through 4584 Processing sheet with id= 64, first strand: chain 'D' and resid 105 through 108 removed outlier: 4.273A pdb=" N HIS D 105 " --> pdb=" O MET D 150 " (cutoff:3.500A) 4452 hydrogen bonds defined for protein. 13308 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: 65.17 Time building geometry restraints manager: 38.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 40052 1.35 - 1.48: 28031 1.48 - 1.61: 50157 1.61 - 1.73: 28 1.73 - 1.86: 1004 Bond restraints: 119272 Sorted by residual: bond pdb=" C1' ACP C5101 " pdb=" O4' ACP C5101 " ideal model delta sigma weight residual 1.390 1.622 -0.232 2.00e-02 2.50e+03 1.35e+02 bond pdb=" C1' ACP D5101 " pdb=" O4' ACP D5101 " ideal model delta sigma weight residual 1.390 1.621 -0.231 2.00e-02 2.50e+03 1.34e+02 bond pdb=" C1' ACP B5101 " pdb=" O4' ACP B5101 " ideal model delta sigma weight residual 1.390 1.621 -0.231 2.00e-02 2.50e+03 1.34e+02 bond pdb=" C1' ACP A5101 " pdb=" O4' ACP A5101 " ideal model delta sigma weight residual 1.390 1.620 -0.230 2.00e-02 2.50e+03 1.33e+02 bond pdb=" C1' ACP B5101 " pdb=" C2' ACP B5101 " ideal model delta sigma weight residual 1.527 1.303 0.224 2.00e-02 2.50e+03 1.25e+02 ... (remaining 119267 not shown) Histogram of bond angle deviations from ideal: 92.20 - 100.58: 138 100.58 - 108.95: 6654 108.95 - 117.33: 79676 117.33 - 125.71: 74292 125.71 - 134.09: 1892 Bond angle restraints: 162652 Sorted by residual: angle pdb=" CA PRO D4641 " pdb=" N PRO D4641 " pdb=" CD PRO D4641 " ideal model delta sigma weight residual 112.00 93.12 18.88 1.40e+00 5.10e-01 1.82e+02 angle pdb=" CA PRO B4641 " pdb=" N PRO B4641 " pdb=" CD PRO B4641 " ideal model delta sigma weight residual 112.00 93.16 18.84 1.40e+00 5.10e-01 1.81e+02 angle pdb=" CA PRO A4641 " pdb=" N PRO A4641 " pdb=" CD PRO A4641 " ideal model delta sigma weight residual 112.00 93.17 18.83 1.40e+00 5.10e-01 1.81e+02 angle pdb=" CA PRO C4641 " pdb=" N PRO C4641 " pdb=" CD PRO C4641 " ideal model delta sigma weight residual 112.00 93.18 18.82 1.40e+00 5.10e-01 1.81e+02 angle pdb=" CA PRO D3972 " pdb=" N PRO D3972 " pdb=" CD PRO D3972 " ideal model delta sigma weight residual 112.00 100.33 11.67 1.40e+00 5.10e-01 6.94e+01 ... (remaining 162647 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.08: 68482 31.08 - 62.17: 2506 62.17 - 93.25: 216 93.25 - 124.34: 2 124.34 - 155.42: 6 Dihedral angle restraints: 71212 sinusoidal: 23028 harmonic: 48184 Sorted by residual: dihedral pdb=" CA ALA D3680 " pdb=" C ALA D3680 " pdb=" N GLY D3681 " pdb=" CA GLY D3681 " ideal model delta harmonic sigma weight residual 180.00 143.34 36.66 0 5.00e+00 4.00e-02 5.38e+01 dihedral pdb=" CA ALA A3680 " pdb=" C ALA A3680 " pdb=" N GLY A3681 " pdb=" CA GLY A3681 " ideal model delta harmonic sigma weight residual 180.00 143.36 36.64 0 5.00e+00 4.00e-02 5.37e+01 dihedral pdb=" CA ALA B3680 " pdb=" C ALA B3680 " pdb=" N GLY B3681 " pdb=" CA GLY B3681 " ideal model delta harmonic sigma weight residual 180.00 143.38 36.62 0 5.00e+00 4.00e-02 5.36e+01 ... (remaining 71209 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 17402 0.075 - 0.151: 1523 0.151 - 0.226: 72 0.226 - 0.302: 23 0.302 - 0.377: 8 Chirality restraints: 19028 Sorted by residual: chirality pdb=" C2' ACP D5101 " pdb=" C1' ACP D5101 " pdb=" C3' ACP D5101 " pdb=" O2' ACP D5101 " both_signs ideal model delta sigma weight residual False -2.75 -2.38 -0.38 2.00e-01 2.50e+01 3.56e+00 chirality pdb=" C2' ACP C5101 " pdb=" C1' ACP C5101 " pdb=" C3' ACP C5101 " pdb=" O2' ACP C5101 " both_signs ideal model delta sigma weight residual False -2.75 -2.38 -0.38 2.00e-01 2.50e+01 3.56e+00 chirality pdb=" C2' ACP B5101 " pdb=" C1' ACP B5101 " pdb=" C3' ACP B5101 " pdb=" O2' ACP B5101 " both_signs ideal model delta sigma weight residual False -2.75 -2.39 -0.37 2.00e-01 2.50e+01 3.36e+00 ... (remaining 19025 not shown) Planarity restraints: 21412 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU D4640 " -0.106 5.00e-02 4.00e+02 1.43e-01 3.26e+01 pdb=" N PRO D4641 " 0.246 5.00e-02 4.00e+02 pdb=" CA PRO D4641 " -0.064 5.00e-02 4.00e+02 pdb=" CD PRO D4641 " -0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B4640 " -0.106 5.00e-02 4.00e+02 1.43e-01 3.26e+01 pdb=" N PRO B4641 " 0.246 5.00e-02 4.00e+02 pdb=" CA PRO B4641 " -0.065 5.00e-02 4.00e+02 pdb=" CD PRO B4641 " -0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A4640 " -0.106 5.00e-02 4.00e+02 1.43e-01 3.26e+01 pdb=" N PRO A4641 " 0.246 5.00e-02 4.00e+02 pdb=" CA PRO A4641 " -0.065 5.00e-02 4.00e+02 pdb=" CD PRO A4641 " -0.075 5.00e-02 4.00e+02 ... (remaining 21409 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 14291 2.76 - 3.29: 113988 3.29 - 3.83: 183724 3.83 - 4.36: 191692 4.36 - 4.90: 340014 Nonbonded interactions: 843709 Sorted by model distance: nonbonded pdb=" OG1 THR C1156 " pdb=" OE1 GLU C1157 " model vdw 2.223 2.440 nonbonded pdb=" OG1 THR A1156 " pdb=" OE1 GLU A1157 " model vdw 2.223 2.440 nonbonded pdb=" OG1 THR B1156 " pdb=" OE1 GLU B1157 " model vdw 2.223 2.440 nonbonded pdb=" OG1 THR D1156 " pdb=" OE1 GLU D1157 " model vdw 2.224 2.440 nonbonded pdb=" O VAL D4848 " pdb=" OG1 THR D4852 " model vdw 2.233 2.440 ... (remaining 843704 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 22.020 Check model and map are aligned: 1.320 Set scattering table: 0.790 Process input model: 265.010 Find NCS groups from input model: 6.320 Set up NCS constraints: 0.570 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 302.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 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 : 0.005 0.232 119272 Z= 0.308 Angle : 0.909 18.883 162652 Z= 0.459 Chirality : 0.043 0.377 19028 Planarity : 0.006 0.143 21412 Dihedral : 15.737 155.419 39848 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.95 % Favored : 93.86 % Rotamer Outliers : 0.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.07), residues: 12804 helix: 1.19 (0.07), residues: 5780 sheet: -0.37 (0.16), residues: 1048 loop : -1.74 (0.07), residues: 5976 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25608 Ramachandran restraints generated. 12804 Oldfield, 0 Emsley, 12804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25608 Ramachandran restraints generated. 12804 Oldfield, 0 Emsley, 12804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1284 residues out of total 11244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 1247 time to evaluate : 9.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 9 residues processed: 1267 average time/residue: 0.9394 time to fit residues: 2138.6920 Evaluate side-chains 939 residues out of total 11244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 930 time to evaluate : 10.034 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.8829 time to fit residues: 27.1668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 6.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 ASN A 226 HIS ** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 617 ASN A 725 HIS A 735 GLN ** A 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1274 HIS ** A1691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2095 GLN ** A2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2756 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2902 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3704 HIS ** A3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3814 GLN ** A3897 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3906 GLN A3960 GLN A4043 GLN A4054 ASN ** A4130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4978 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4984 ASN B 201 ASN B 226 HIS ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 489 ASN ** B 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 617 ASN ** B 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 735 GLN ** B 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1274 HIS ** B1691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1953 HIS B2095 GLN B2184 ASN ** B2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2756 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2902 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3704 HIS ** B3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3814 GLN B3882 GLN ** B3897 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3906 GLN B3960 GLN B4043 GLN B4054 ASN B4078 GLN ** B4130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4978 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4984 ASN C 201 ASN C 226 HIS ** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 617 ASN ** C 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 725 HIS C 735 GLN ** C 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1252 HIS ** C1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1274 HIS ** C1691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1953 HIS C2095 GLN ** C2193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2756 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2902 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3704 HIS ** C3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3814 GLN C3833 GLN ** C3897 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3906 GLN C3960 GLN C4043 GLN C4054 ASN ** C4130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C4728 HIS ** C4886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4978 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C4984 ASN D 201 ASN ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 HIS ** D 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 617 ASN ** D 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 725 HIS D 735 GLN ** D 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1252 HIS ** D1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1274 HIS ** D1691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1953 HIS D2095 GLN D2184 ASN ** D2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2756 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2902 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3704 HIS ** D3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3814 GLN D3833 GLN ** D3897 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3960 GLN D4043 GLN D4054 ASN ** D4130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4978 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4984 ASN Total number of N/Q/H flips: 67 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.7060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.056 0.366 119272 Z= 3.672 Angle : 3.347 30.299 162652 Z= 1.696 Chirality : 0.156 0.758 19028 Planarity : 0.021 0.207 21412 Dihedral : 12.568 176.495 17496 Min Nonbonded Distance : 1.707 Molprobity Statistics. All-atom Clashscore : 76.06 Ramachandran Plot: Outliers : 3.34 % Allowed : 17.14 % Favored : 79.51 % Rotamer Outliers : 16.54 % Cbeta Deviations : 1.01 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.26 % Twisted General : 1.88 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.55 (0.06), residues: 12804 helix: -3.44 (0.05), residues: 5784 sheet: -2.96 (0.14), residues: 1116 loop : -4.09 (0.07), residues: 5904 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25608 Ramachandran restraints generated. 12804 Oldfield, 0 Emsley, 12804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25608 Ramachandran restraints generated. 12804 Oldfield, 0 Emsley, 12804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2350 residues out of total 11244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1663 poor density : 687 time to evaluate : 9.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1663 outliers final: 993 residues processed: 2230 average time/residue: 0.9409 time to fit residues: 3802.4863 Evaluate side-chains 1651 residues out of total 11244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 993 poor density : 658 time to evaluate : 9.735 Switching outliers to nearest non-outliers outliers start: 993 outliers final: 3 residues processed: 993 average time/residue: 0.8224 time to fit residues: 1566.5829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 6.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 ASN A 520 ASN ** A 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1274 HIS ** A1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1688 HIS ** A1691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1953 HIS A2125 HIS A2184 ASN ** A2194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2756 ASN A3833 GLN A3882 GLN A3889 GLN ** A4078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4153 HIS A4650 HIS ** A4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4984 ASN ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 520 ASN ** B 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 725 HIS ** B 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1274 HIS B1688 HIS B1691 GLN ** B1719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2204 HIS ** B2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2756 ASN B3833 GLN B3889 GLN ** B4130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4153 HIS ** B4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4984 ASN ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 489 ASN C 520 ASN ** C 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1274 HIS C1691 GLN ** C1719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2184 ASN ** C2194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2204 HIS ** C2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2756 ASN C3882 GLN C3889 GLN ** C4078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4153 HIS ** C4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4978 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C4984 ASN ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 ASN D 520 ASN ** D 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1274 HIS ** D1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1691 GLN ** D1719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2204 HIS ** D2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3882 GLN D3889 GLN ** D3906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4153 HIS ** D4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4978 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4984 ASN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.8361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.056 0.343 119272 Z= 3.618 Angle : 3.249 31.786 162652 Z= 1.648 Chirality : 0.156 0.776 19028 Planarity : 0.020 0.207 21412 Dihedral : 13.679 179.997 17496 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 86.53 Ramachandran Plot: Outliers : 3.03 % Allowed : 28.76 % Favored : 68.21 % Rotamer Outliers : 22.47 % Cbeta Deviations : 0.92 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.40 % Twisted General : 2.92 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.67 (0.05), residues: 12804 helix: -4.13 (0.04), residues: 5752 sheet: -3.74 (0.13), residues: 1024 loop : -4.92 (0.06), residues: 6028 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25608 Ramachandran restraints generated. 12804 Oldfield, 0 Emsley, 12804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25608 Ramachandran restraints generated. 12804 Oldfield, 0 Emsley, 12804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2898 residues out of total 11244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2259 poor density : 639 time to evaluate : 9.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2259 outliers final: 1483 residues processed: 2771 average time/residue: 0.9473 time to fit residues: 4717.4807 Evaluate side-chains 2109 residues out of total 11244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1483 poor density : 626 time to evaluate : 9.677 Switching outliers to nearest non-outliers outliers start: 1483 outliers final: 20 residues processed: 1483 average time/residue: 0.8331 time to fit residues: 2347.6299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 6.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 520 ASN ** A 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1691 GLN ** A1952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2125 HIS A2187 ASN ** A2194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2204 HIS ** A2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2773 ASN ** A4078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 520 ASN ** B 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1127 HIS ** B1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2125 HIS B2187 ASN ** B2194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2773 ASN ** B2892 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4650 HIS ** B4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4978 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 520 ASN ** C 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1127 HIS ** C1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1688 HIS ** C1691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2187 ASN ** C2193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2772 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2773 ASN ** C4078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4650 HIS ** C4886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4978 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 520 ASN ** D 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 889 GLN ** D 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1127 HIS ** D1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1688 HIS ** D1691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2187 ASN ** D2193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2756 ASN ** D2772 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2773 ASN ** D3906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4650 HIS ** D4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4978 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.9085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.056 0.353 119272 Z= 3.633 Angle : 3.276 34.693 162652 Z= 1.655 Chirality : 0.157 0.775 19028 Planarity : 0.020 0.200 21412 Dihedral : 14.144 178.978 17496 Min Nonbonded Distance : 1.732 Molprobity Statistics. All-atom Clashscore : 90.28 Ramachandran Plot: Outliers : 2.69 % Allowed : 32.86 % Favored : 64.45 % Rotamer Outliers : 21.33 % Cbeta Deviations : 0.84 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.72 % Twisted General : 3.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -7.08 (0.05), residues: 12804 helix: -4.30 (0.04), residues: 5792 sheet: -4.21 (0.12), residues: 1132 loop : -5.28 (0.05), residues: 5880 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25608 Ramachandran restraints generated. 12804 Oldfield, 0 Emsley, 12804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25608 Ramachandran restraints generated. 12804 Oldfield, 0 Emsley, 12804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2756 residues out of total 11244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2144 poor density : 612 time to evaluate : 9.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2144 outliers final: 1379 residues processed: 2649 average time/residue: 0.9507 time to fit residues: 4517.6127 Evaluate side-chains 2003 residues out of total 11244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1379 poor density : 624 time to evaluate : 9.765 Switching outliers to nearest non-outliers outliers start: 1379 outliers final: 21 residues processed: 1379 average time/residue: 0.8459 time to fit residues: 2202.1042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 6.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 520 ASN ** A 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1127 HIS ** A1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1252 HIS ** A1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2187 ASN ** A2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 520 ASN ** B 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1252 HIS ** B1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1683 HIS ** B1691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2125 HIS B2187 ASN ** B2188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4978 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 520 ASN ** C 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1683 HIS ** C1691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2187 ASN ** C2188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4978 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 520 ASN ** D 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1683 HIS ** D1691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2187 ASN ** D2188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4978 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.9465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.056 0.343 119272 Z= 3.634 Angle : 3.266 36.508 162652 Z= 1.651 Chirality : 0.157 0.753 19028 Planarity : 0.020 0.204 21412 Dihedral : 14.398 179.841 17496 Min Nonbonded Distance : 1.750 Molprobity Statistics. All-atom Clashscore : 92.64 Ramachandran Plot: Outliers : 2.74 % Allowed : 34.39 % Favored : 62.87 % Rotamer Outliers : 19.12 % Cbeta Deviations : 0.93 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.72 % Twisted General : 3.40 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -7.19 (0.05), residues: 12804 helix: -4.36 (0.04), residues: 5780 sheet: -4.20 (0.12), residues: 1100 loop : -5.39 (0.05), residues: 5924 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25608 Ramachandran restraints generated. 12804 Oldfield, 0 Emsley, 12804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25608 Ramachandran restraints generated. 12804 Oldfield, 0 Emsley, 12804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2533 residues out of total 11244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1922 poor density : 611 time to evaluate : 9.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1922 outliers final: 1229 residues processed: 2447 average time/residue: 0.9486 time to fit residues: 4182.2606 Evaluate side-chains 1848 residues out of total 11244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1229 poor density : 619 time to evaluate : 9.855 Switching outliers to nearest non-outliers outliers start: 1229 outliers final: 22 residues processed: 1229 average time/residue: 0.9397 time to fit residues: 2192.2995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 5.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 520 ASN ** A 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2125 HIS ** A2193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2763 HIS A3830 GLN ** A4037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4662 ASN ** A4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 520 ASN ** B 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2187 ASN ** B2188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3830 GLN ** B4037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4662 ASN ** B4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4978 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 520 ASN ** C 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2187 ASN ** C2188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2763 HIS C2788 HIS ** C3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3830 GLN ** C4078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4978 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 520 ASN ** D 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2125 HIS D2187 ASN ** D2188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4978 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.9726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.056 0.345 119272 Z= 3.638 Angle : 3.268 33.596 162652 Z= 1.652 Chirality : 0.158 0.772 19028 Planarity : 0.020 0.181 21412 Dihedral : 14.573 179.811 17496 Min Nonbonded Distance : 1.740 Molprobity Statistics. All-atom Clashscore : 93.07 Ramachandran Plot: Outliers : 2.65 % Allowed : 35.59 % Favored : 61.76 % Rotamer Outliers : 16.15 % Cbeta Deviations : 0.96 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.05 % Twisted General : 3.66 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -7.24 (0.05), residues: 12804 helix: -4.37 (0.04), residues: 5720 sheet: -4.35 (0.12), residues: 1092 loop : -5.42 (0.05), residues: 5992 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25608 Ramachandran restraints generated. 12804 Oldfield, 0 Emsley, 12804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25608 Ramachandran restraints generated. 12804 Oldfield, 0 Emsley, 12804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2219 residues out of total 11244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1623 poor density : 596 time to evaluate : 9.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1623 outliers final: 1027 residues processed: 2140 average time/residue: 0.9817 time to fit residues: 3784.6982 Evaluate side-chains 1636 residues out of total 11244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1027 poor density : 609 time to evaluate : 9.283 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1027 outliers final: 32 residues processed: 1027 average time/residue: 0.8744 time to fit residues: 1706.4900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 6.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 520 ASN ** A 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1688 HIS ** A1691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2125 HIS ** A2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2884 ASN ** A4037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 520 ASN ** B 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1688 HIS ** B1691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2187 ASN ** B2188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2763 HIS ** B3704 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4978 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2125 HIS C2187 ASN ** C2188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4978 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2125 HIS D2187 ASN ** D2188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3830 GLN D3833 GLN ** D4037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4978 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.9935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.056 0.347 119272 Z= 3.641 Angle : 3.276 34.444 162652 Z= 1.654 Chirality : 0.158 0.782 19028 Planarity : 0.020 0.305 21412 Dihedral : 14.703 179.747 17496 Min Nonbonded Distance : 1.742 Molprobity Statistics. All-atom Clashscore : 93.74 Ramachandran Plot: Outliers : 2.77 % Allowed : 36.00 % Favored : 61.22 % Rotamer Outliers : 12.68 % Cbeta Deviations : 0.96 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 10.03 % Twisted General : 3.73 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -7.25 (0.05), residues: 12804 helix: -4.38 (0.04), residues: 5748 sheet: -4.26 (0.12), residues: 1152 loop : -5.46 (0.05), residues: 5904 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25608 Ramachandran restraints generated. 12804 Oldfield, 0 Emsley, 12804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25608 Ramachandran restraints generated. 12804 Oldfield, 0 Emsley, 12804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1874 residues out of total 11244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1275 poor density : 599 time to evaluate : 9.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1275 outliers final: 787 residues processed: 1823 average time/residue: 1.0387 time to fit residues: 3419.2076 Evaluate side-chains 1396 residues out of total 11244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 787 poor density : 609 time to evaluate : 9.730 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 787 outliers final: 29 residues processed: 787 average time/residue: 0.9023 time to fit residues: 1348.8097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 5.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2125 HIS ** A2193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2788 HIS ** A3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2187 ASN ** B2188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2788 HIS ** B3704 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4978 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 383 HIS ** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2125 HIS C2187 ASN ** C2188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4978 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 520 ASN ** D 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2125 HIS D2187 ASN ** D2188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2763 HIS D2788 HIS D3833 GLN ** D4037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4978 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 1.0066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.056 0.351 119272 Z= 3.643 Angle : 3.279 32.891 162652 Z= 1.656 Chirality : 0.159 0.906 19028 Planarity : 0.020 0.215 21412 Dihedral : 14.758 179.755 17496 Min Nonbonded Distance : 1.731 Molprobity Statistics. All-atom Clashscore : 93.59 Ramachandran Plot: Outliers : 2.71 % Allowed : 36.38 % Favored : 60.91 % Rotamer Outliers : 9.07 % Cbeta Deviations : 0.96 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 10.36 % Twisted General : 3.97 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -7.28 (0.05), residues: 12804 helix: -4.40 (0.04), residues: 5792 sheet: -4.32 (0.12), residues: 1156 loop : -5.46 (0.05), residues: 5856 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25608 Ramachandran restraints generated. 12804 Oldfield, 0 Emsley, 12804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25608 Ramachandran restraints generated. 12804 Oldfield, 0 Emsley, 12804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1511 residues out of total 11244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 912 poor density : 599 time to evaluate : 9.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 912 outliers final: 496 residues processed: 1457 average time/residue: 0.9863 time to fit residues: 2567.1374 Evaluate side-chains 1097 residues out of total 11244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 496 poor density : 601 time to evaluate : 9.660 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 496 outliers final: 32 residues processed: 496 average time/residue: 0.8288 time to fit residues: 789.5733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 5.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1683 HIS ** A1691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2125 HIS ** A2193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3704 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4978 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2125 HIS C2187 ASN ** C2188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4978 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2125 HIS ** D2188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3833 GLN ** D4037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4978 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 1.0207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.056 0.348 119272 Z= 3.647 Angle : 3.285 32.818 162652 Z= 1.660 Chirality : 0.159 1.059 19028 Planarity : 0.020 0.249 21412 Dihedral : 14.834 179.782 17496 Min Nonbonded Distance : 1.738 Molprobity Statistics. All-atom Clashscore : 94.30 Ramachandran Plot: Outliers : 2.71 % Allowed : 36.74 % Favored : 60.55 % Rotamer Outliers : 7.03 % Cbeta Deviations : 1.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.70 % Twisted General : 4.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -7.31 (0.05), residues: 12804 helix: -4.40 (0.04), residues: 5780 sheet: -4.33 (0.12), residues: 1172 loop : -5.50 (0.05), residues: 5852 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25608 Ramachandran restraints generated. 12804 Oldfield, 0 Emsley, 12804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25608 Ramachandran restraints generated. 12804 Oldfield, 0 Emsley, 12804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1296 residues out of total 11244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 707 poor density : 589 time to evaluate : 9.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 707 outliers final: 398 residues processed: 1253 average time/residue: 1.0077 time to fit residues: 2260.6765 Evaluate side-chains 992 residues out of total 11244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 398 poor density : 594 time to evaluate : 8.884 Switching outliers to nearest non-outliers outliers start: 398 outliers final: 27 residues processed: 398 average time/residue: 0.9279 time to fit residues: 713.7635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 6.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2247 GLN ** A2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3704 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2125 HIS ** C2188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2125 HIS ** D2188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 1.0283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.056 0.350 119272 Z= 3.653 Angle : 3.288 32.870 162652 Z= 1.663 Chirality : 0.159 1.174 19028 Planarity : 0.021 0.310 21412 Dihedral : 14.891 179.761 17496 Min Nonbonded Distance : 1.738 Molprobity Statistics. All-atom Clashscore : 94.01 Ramachandran Plot: Outliers : 2.73 % Allowed : 36.72 % Favored : 60.55 % Rotamer Outliers : 3.55 % Cbeta Deviations : 1.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.54 % Twisted General : 4.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -7.31 (0.05), residues: 12804 helix: -4.42 (0.04), residues: 5792 sheet: -4.33 (0.12), residues: 1168 loop : -5.49 (0.05), residues: 5844 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25608 Ramachandran restraints generated. 12804 Oldfield, 0 Emsley, 12804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25608 Ramachandran restraints generated. 12804 Oldfield, 0 Emsley, 12804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 949 residues out of total 11244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 357 poor density : 592 time to evaluate : 9.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 357 outliers final: 197 residues processed: 913 average time/residue: 0.9955 time to fit residues: 1621.0509 Evaluate side-chains 787 residues out of total 11244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 590 time to evaluate : 9.729 Switching outliers to nearest non-outliers outliers start: 197 outliers final: 27 residues processed: 197 average time/residue: 0.9080 time to fit residues: 346.7136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 5.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 889 GLN ** A 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3704 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 889 GLN ** C 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2125 HIS ** C2188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2884 ASN ** C3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1688 HIS ** D1691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2125 HIS ** D2188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3833 GLN ** D4037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4978 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.070044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.055940 restraints weight = 564811.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.055014 restraints weight = 375347.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.055275 restraints weight = 387985.701| |-----------------------------------------------------------------------------| r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 1.0342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.056 0.354 119272 Z= 3.651 Angle : 3.285 32.909 162652 Z= 1.660 Chirality : 0.159 1.341 19028 Planarity : 0.021 0.345 21412 Dihedral : 14.917 179.803 17496 Min Nonbonded Distance : 1.738 Molprobity Statistics. All-atom Clashscore : 94.24 Ramachandran Plot: Outliers : 2.72 % Allowed : 37.04 % Favored : 60.25 % Rotamer Outliers : 2.96 % Cbeta Deviations : 0.98 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.87 % Twisted General : 4.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -7.31 (0.05), residues: 12804 helix: -4.41 (0.04), residues: 5792 sheet: -4.37 (0.12), residues: 1160 loop : -5.50 (0.05), residues: 5852 =============================================================================== Job complete usr+sys time: 70396.28 seconds wall clock time: 1206 minutes 22.51 seconds (72382.51 seconds total)