Starting phenix.real_space_refine (version: 1.21rc1) on Mon Apr 24 00:27:13 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tdk_25832/04_2023/7tdk_25832_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tdk_25832/04_2023/7tdk_25832.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tdk_25832/04_2023/7tdk_25832.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tdk_25832/04_2023/7tdk_25832.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tdk_25832/04_2023/7tdk_25832_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tdk_25832/04_2023/7tdk_25832_neut_updated.pdb" } resolution = 3.8 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= 0.002 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 624 5.16 5 C 74116 2.51 5 N 20752 2.21 5 O 21620 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 PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 439": "OE1" <-> "OE2" Residue "A GLU 453": "OE1" <-> "OE2" Residue "A GLU 462": "OE1" <-> "OE2" Residue "A GLU 509": "OE1" <-> "OE2" Residue "A GLU 580": "OE1" <-> "OE2" Residue "A ASP 619": "OD1" <-> "OD2" Residue "A ASP 710": "OD1" <-> "OD2" Residue "A PHE 757": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 791": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 920": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1112": "OD1" <-> "OD2" Residue "A ASP 1118": "OD1" <-> "OD2" Residue "A GLU 1119": "OE1" <-> "OE2" Residue "A PHE 1139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1644": "OE1" <-> "OE2" Residue "A GLU 1721": "OE1" <-> "OE2" Residue "A GLU 2205": "OE1" <-> "OE2" Residue "A GLU 2209": "OE1" <-> "OE2" Residue "A GLU 2347": "OE1" <-> "OE2" Residue "A GLU 3665": "OE1" <-> "OE2" Residue "A GLU 3712": "OE1" <-> "OE2" Residue "A TYR 3720": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 3789": "OE1" <-> "OE2" Residue "A ASP 3818": "OD1" <-> "OD2" Residue "A GLU 3825": "OE1" <-> "OE2" Residue "A ASP 3843": "OD1" <-> "OD2" Residue "A ASP 3878": "OD1" <-> "OD2" Residue "A GLU 3893": "OE1" <-> "OE2" Residue "A ASP 3898": "OD1" <-> "OD2" Residue "A GLU 3967": "OE1" <-> "OE2" Residue "A GLU 4011": "OE1" <-> "OE2" Residue "A ASP 4118": "OD1" <-> "OD2" Residue "A GLU 4172": "OE1" <-> "OE2" Residue "A GLU 4199": "OE1" <-> "OE2" Residue "A ASP 4240": "OD1" <-> "OD2" Residue "A PHE 4575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 4634": "OE1" <-> "OE2" Residue "A GLU 4676": "OE1" <-> "OE2" Residue "A ASP 4684": "OD1" <-> "OD2" Residue "A ASP 4695": "OD1" <-> "OD2" Residue "A ASP 4696": "OD1" <-> "OD2" Residue "A GLU 4735": "OE1" <-> "OE2" Residue "A GLU 4739": "OE1" <-> "OE2" Residue "A TYR 4804": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 4815": "OD1" <-> "OD2" Residue "A GLU 4867": "OE1" <-> "OE2" Residue "A GLU 4869": "OE1" <-> "OE2" Residue "A ASP 4899": "OD1" <-> "OD2" Residue "A PHE 4959": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 4966": "OD1" <-> "OD2" Residue "A GLU 4976": "OE1" <-> "OE2" Residue "A GLU 4981": "OE1" <-> "OE2" Residue "A GLU 4982": "OE1" <-> "OE2" Residue "A GLU 5002": "OE1" <-> "OE2" Residue "A GLU 5007": "OE1" <-> "OE2" Residue "A PHE 5021": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 5028": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 139": "OE1" <-> "OE2" Residue "B PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 439": "OE1" <-> "OE2" Residue "B GLU 453": "OE1" <-> "OE2" Residue "B GLU 462": "OE1" <-> "OE2" Residue "B GLU 509": "OE1" <-> "OE2" Residue "B GLU 580": "OE1" <-> "OE2" Residue "B ASP 619": "OD1" <-> "OD2" Residue "B ASP 710": "OD1" <-> "OD2" Residue "B PHE 757": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 791": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 920": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1112": "OD1" <-> "OD2" Residue "B ASP 1118": "OD1" <-> "OD2" Residue "B GLU 1119": "OE1" <-> "OE2" Residue "B PHE 1139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1644": "OE1" <-> "OE2" Residue "B GLU 1721": "OE1" <-> "OE2" Residue "B GLU 2205": "OE1" <-> "OE2" Residue "B GLU 2209": "OE1" <-> "OE2" Residue "B GLU 2347": "OE1" <-> "OE2" Residue "B GLU 3665": "OE1" <-> "OE2" Residue "B GLU 3712": "OE1" <-> "OE2" Residue "B TYR 3720": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 3789": "OE1" <-> "OE2" Residue "B ASP 3818": "OD1" <-> "OD2" Residue "B GLU 3825": "OE1" <-> "OE2" Residue "B ASP 3843": "OD1" <-> "OD2" Residue "B ASP 3878": "OD1" <-> "OD2" Residue "B GLU 3893": "OE1" <-> "OE2" Residue "B ASP 3898": "OD1" <-> "OD2" Residue "B GLU 3967": "OE1" <-> "OE2" Residue "B GLU 4011": "OE1" <-> "OE2" Residue "B ASP 4118": "OD1" <-> "OD2" Residue "B GLU 4172": "OE1" <-> "OE2" Residue "B GLU 4199": "OE1" <-> "OE2" Residue "B ASP 4240": "OD1" <-> "OD2" Residue "B PHE 4575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 4634": "OE1" <-> "OE2" Residue "B GLU 4676": "OE1" <-> "OE2" Residue "B ASP 4684": "OD1" <-> "OD2" Residue "B ASP 4695": "OD1" <-> "OD2" Residue "B ASP 4696": "OD1" <-> "OD2" Residue "B GLU 4735": "OE1" <-> "OE2" Residue "B GLU 4739": "OE1" <-> "OE2" Residue "B TYR 4804": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 4815": "OD1" <-> "OD2" Residue "B GLU 4867": "OE1" <-> "OE2" Residue "B GLU 4869": "OE1" <-> "OE2" Residue "B ASP 4899": "OD1" <-> "OD2" Residue "B PHE 4959": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 4966": "OD1" <-> "OD2" Residue "B GLU 4976": "OE1" <-> "OE2" Residue "B GLU 4981": "OE1" <-> "OE2" Residue "B GLU 4982": "OE1" <-> "OE2" Residue "B GLU 5002": "OE1" <-> "OE2" Residue "B GLU 5007": "OE1" <-> "OE2" Residue "B PHE 5021": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 5028": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 139": "OE1" <-> "OE2" Residue "C PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 439": "OE1" <-> "OE2" Residue "C GLU 453": "OE1" <-> "OE2" Residue "C GLU 462": "OE1" <-> "OE2" Residue "C GLU 509": "OE1" <-> "OE2" Residue "C GLU 580": "OE1" <-> "OE2" Residue "C ASP 619": "OD1" <-> "OD2" Residue "C ASP 710": "OD1" <-> "OD2" Residue "C PHE 757": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 791": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 920": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1112": "OD1" <-> "OD2" Residue "C ASP 1118": "OD1" <-> "OD2" Residue "C GLU 1119": "OE1" <-> "OE2" Residue "C PHE 1139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1644": "OE1" <-> "OE2" Residue "C GLU 1721": "OE1" <-> "OE2" Residue "C GLU 2205": "OE1" <-> "OE2" Residue "C GLU 2209": "OE1" <-> "OE2" Residue "C GLU 2347": "OE1" <-> "OE2" Residue "C GLU 3665": "OE1" <-> "OE2" Residue "C GLU 3712": "OE1" <-> "OE2" Residue "C TYR 3720": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 3789": "OE1" <-> "OE2" Residue "C ASP 3818": "OD1" <-> "OD2" Residue "C GLU 3825": "OE1" <-> "OE2" Residue "C ASP 3843": "OD1" <-> "OD2" Residue "C ASP 3878": "OD1" <-> "OD2" Residue "C GLU 3893": "OE1" <-> "OE2" Residue "C ASP 3898": "OD1" <-> "OD2" Residue "C GLU 3967": "OE1" <-> "OE2" Residue "C GLU 4011": "OE1" <-> "OE2" Residue "C ASP 4118": "OD1" <-> "OD2" Residue "C GLU 4172": "OE1" <-> "OE2" Residue "C GLU 4199": "OE1" <-> "OE2" Residue "C ASP 4240": "OD1" <-> "OD2" Residue "C PHE 4575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 4634": "OE1" <-> "OE2" Residue "C GLU 4676": "OE1" <-> "OE2" Residue "C ASP 4684": "OD1" <-> "OD2" Residue "C ASP 4695": "OD1" <-> "OD2" Residue "C ASP 4696": "OD1" <-> "OD2" Residue "C GLU 4735": "OE1" <-> "OE2" Residue "C GLU 4739": "OE1" <-> "OE2" Residue "C TYR 4804": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 4815": "OD1" <-> "OD2" Residue "C GLU 4867": "OE1" <-> "OE2" Residue "C GLU 4869": "OE1" <-> "OE2" Residue "C ASP 4899": "OD1" <-> "OD2" Residue "C PHE 4959": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 4966": "OD1" <-> "OD2" Residue "C GLU 4976": "OE1" <-> "OE2" Residue "C GLU 4981": "OE1" <-> "OE2" Residue "C GLU 4982": "OE1" <-> "OE2" Residue "C GLU 5002": "OE1" <-> "OE2" Residue "C GLU 5007": "OE1" <-> "OE2" Residue "C PHE 5021": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 5028": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 139": "OE1" <-> "OE2" Residue "D PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 439": "OE1" <-> "OE2" Residue "D GLU 453": "OE1" <-> "OE2" Residue "D GLU 462": "OE1" <-> "OE2" Residue "D GLU 509": "OE1" <-> "OE2" Residue "D GLU 580": "OE1" <-> "OE2" Residue "D ASP 619": "OD1" <-> "OD2" Residue "D ASP 710": "OD1" <-> "OD2" Residue "D PHE 757": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 791": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 920": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1112": "OD1" <-> "OD2" Residue "D ASP 1118": "OD1" <-> "OD2" Residue "D GLU 1119": "OE1" <-> "OE2" Residue "D PHE 1139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1644": "OE1" <-> "OE2" Residue "D GLU 1721": "OE1" <-> "OE2" Residue "D GLU 2205": "OE1" <-> "OE2" Residue "D GLU 2209": "OE1" <-> "OE2" Residue "D GLU 2347": "OE1" <-> "OE2" Residue "D GLU 3665": "OE1" <-> "OE2" Residue "D GLU 3712": "OE1" <-> "OE2" Residue "D TYR 3720": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 3789": "OE1" <-> "OE2" Residue "D ASP 3818": "OD1" <-> "OD2" Residue "D GLU 3825": "OE1" <-> "OE2" Residue "D ASP 3843": "OD1" <-> "OD2" Residue "D ASP 3878": "OD1" <-> "OD2" Residue "D GLU 3893": "OE1" <-> "OE2" Residue "D ASP 3898": "OD1" <-> "OD2" Residue "D GLU 3967": "OE1" <-> "OE2" Residue "D GLU 4011": "OE1" <-> "OE2" Residue "D ASP 4118": "OD1" <-> "OD2" Residue "D GLU 4172": "OE1" <-> "OE2" Residue "D GLU 4199": "OE1" <-> "OE2" Residue "D ASP 4240": "OD1" <-> "OD2" Residue "D PHE 4575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 4634": "OE1" <-> "OE2" Residue "D GLU 4676": "OE1" <-> "OE2" Residue "D ASP 4684": "OD1" <-> "OD2" Residue "D ASP 4695": "OD1" <-> "OD2" Residue "D ASP 4696": "OD1" <-> "OD2" Residue "D GLU 4735": "OE1" <-> "OE2" Residue "D GLU 4739": "OE1" <-> "OE2" Residue "D TYR 4804": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 4815": "OD1" <-> "OD2" Residue "D GLU 4867": "OE1" <-> "OE2" Residue "D GLU 4869": "OE1" <-> "OE2" Residue "D ASP 4899": "OD1" <-> "OD2" Residue "D PHE 4959": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 4966": "OD1" <-> "OD2" Residue "D GLU 4976": "OE1" <-> "OE2" Residue "D GLU 4981": "OE1" <-> "OE2" Residue "D GLU 4982": "OE1" <-> "OE2" Residue "D GLU 5002": "OE1" <-> "OE2" Residue "D GLU 5007": "OE1" <-> "OE2" Residue "D PHE 5021": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 5028": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.25s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 117136 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 29250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4134, 29250 Classifications: {'peptide': 4134} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1199} Link IDs: {'PTRANS': 152, 'TRANS': 3981} Chain breaks: 24 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2875 Unresolved non-hydrogen angles: 4034 Unresolved non-hydrogen dihedrals: 1768 Unresolved non-hydrogen chiralities: 43 Planarities with less than four sites: {'GLN:plan1': 16, 'UNK:plan-1': 900, 'ASP:plan': 38, 'TYR:plan': 2, 'ASN:plan1': 13, 'TRP:plan': 4, 'HIS:plan': 4, 'PHE:plan': 4, 'GLU:plan': 77, 'ARG:plan': 28} Unresolved non-hydrogen planarities: 1659 Chain: "B" Number of atoms: 29250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4134, 29250 Classifications: {'peptide': 4134} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1199} Link IDs: {'PTRANS': 152, 'TRANS': 3981} Chain breaks: 24 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2875 Unresolved non-hydrogen angles: 4034 Unresolved non-hydrogen dihedrals: 1768 Unresolved non-hydrogen chiralities: 43 Planarities with less than four sites: {'GLN:plan1': 16, 'UNK:plan-1': 900, 'ASP:plan': 38, 'TYR:plan': 2, 'ASN:plan1': 13, 'TRP:plan': 4, 'HIS:plan': 4, 'PHE:plan': 4, 'GLU:plan': 77, 'ARG:plan': 28} Unresolved non-hydrogen planarities: 1659 Chain: "C" Number of atoms: 29250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4134, 29250 Classifications: {'peptide': 4134} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1199} Link IDs: {'PTRANS': 152, 'TRANS': 3981} Chain breaks: 24 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2875 Unresolved non-hydrogen angles: 4034 Unresolved non-hydrogen dihedrals: 1768 Unresolved non-hydrogen chiralities: 43 Planarities with less than four sites: {'GLN:plan1': 16, 'UNK:plan-1': 900, 'ASP:plan': 38, 'TYR:plan': 2, 'ASN:plan1': 13, 'TRP:plan': 4, 'HIS:plan': 4, 'PHE:plan': 4, 'GLU:plan': 77, 'ARG:plan': 28} Unresolved non-hydrogen planarities: 1659 Chain: "D" Number of atoms: 29250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4134, 29250 Classifications: {'peptide': 4134} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1199} Link IDs: {'PTRANS': 152, 'TRANS': 3981} Chain breaks: 24 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2875 Unresolved non-hydrogen angles: 4034 Unresolved non-hydrogen dihedrals: 1768 Unresolved non-hydrogen chiralities: 43 Planarities with less than four sites: {'GLN:plan1': 16, 'UNK:plan-1': 900, 'ASP:plan': 38, 'TYR:plan': 2, 'ASN:plan1': 13, 'TRP:plan': 4, 'HIS:plan': 4, 'PHE:plan': 4, 'GLU:plan': 77, 'ARG:plan': 28} Unresolved non-hydrogen planarities: 1659 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 28578 SG CYS A4958 180.929 207.763 102.322 1.00 68.39 S ATOM 28603 SG CYS A4961 180.216 205.855 99.257 1.00 61.50 S ATOM 57828 SG CYS B4958 181.218 180.985 102.243 1.00 68.39 S ATOM 57853 SG CYS B4961 183.123 180.269 99.178 1.00 61.50 S ATOM 87078 SG CYS C4958 208.013 181.210 102.335 1.00 68.39 S ATOM 87103 SG CYS C4961 208.727 183.118 99.271 1.00 61.50 S ATOM A0CLK SG CYS D4958 207.767 208.022 102.328 1.00 68.39 S ATOM A0CM9 SG CYS D4961 205.859 208.735 99.264 1.00 61.50 S Time building chain proxies: 43.45, per 1000 atoms: 0.37 Number of scatterers: 117136 At special positions: 0 Unit cell: (390.065, 390.065, 193.375, 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 624 16.00 P 12 15.00 O 21620 8.00 N 20752 7.00 C 74116 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=2.04 Simple disulfide: pdb=" SG CYS B4876 " - pdb=" SG CYS B4882 " distance=2.04 Simple disulfide: pdb=" SG CYS C4876 " - pdb=" SG CYS C4882 " distance=2.04 Simple disulfide: pdb=" SG CYS D4876 " - pdb=" SG CYS D4882 " distance=2.04 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: 36.72 Conformation dependent library (CDL) restraints added in 11.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A5102 " pdb="ZN ZN A5102 " - pdb=" SG CYS A4958 " pdb="ZN ZN A5102 " - pdb=" SG CYS A4961 " pdb="ZN ZN A5102 " - pdb=" NE2 HIS A4978 " pdb="ZN ZN A5102 " - pdb=" ND1 HIS A4983 " pdb=" ZN B5102 " pdb="ZN ZN B5102 " - pdb=" SG CYS B4958 " pdb="ZN ZN B5102 " - pdb=" NE2 HIS B4978 " pdb="ZN ZN B5102 " - pdb=" SG CYS B4961 " pdb=" ZN C5102 " pdb="ZN ZN C5102 " - pdb=" SG CYS C4961 " pdb="ZN ZN C5102 " - pdb=" SG CYS C4958 " pdb="ZN ZN C5102 " - pdb=" ND1 HIS C4983 " pdb=" ZN D5102 " pdb="ZN ZN D5102 " - pdb=" ND1 HIS D4983 " pdb="ZN ZN D5102 " - pdb=" SG CYS D4961 " pdb="ZN ZN D5102 " - pdb=" SG CYS D4958 " Number of angles added : 1 25616 Ramachandran restraints generated. 12808 Oldfield, 0 Emsley, 12808 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 31360 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: 492 helices and 44 sheets defined 55.3% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 15.44 Creating SS restraints... Processing helix chain 'A' and resid 61 through 66 removed outlier: 4.909A 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: 4.324A pdb=" N CYS A 253 " --> pdb=" O GLY A 249 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N THR A 254 " --> pdb=" O GLY A 250 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N HIS A 255 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 5.334A 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 308 through 313 removed outlier: 6.724A pdb=" N THR A 312 " --> pdb=" O HIS A 308 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N SER A 313 " --> pdb=" O THR A 309 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 308 through 313' Processing helix chain 'A' and resid 364 through 371 removed outlier: 3.620A pdb=" N LEU A 369 " --> pdb=" O LYS A 365 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLY A 370 " --> pdb=" O ALA A 366 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N VAL A 371 " --> pdb=" O LEU A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 423 removed outlier: 3.796A pdb=" N ASP A 419 " --> pdb=" O ILE A 415 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N SER A 420 " --> pdb=" O LYS A 416 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N PHE A 421 " --> pdb=" O GLY A 417 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N SER A 422 " --> pdb=" O LEU A 418 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N GLY A 423 " --> pdb=" O ASP A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 453 removed outlier: 3.952A pdb=" N VAL A 441 " --> pdb=" O PRO A 437 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ILE A 442 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU A 443 " --> pdb=" O GLU A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 482 removed outlier: 3.799A pdb=" N GLU A 480 " --> pdb=" O SER A 476 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLU A 481 " --> pdb=" O LEU A 477 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N GLY A 482 " --> pdb=" O PHE A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 496 removed outlier: 4.376A pdb=" N VAL A 487 " --> pdb=" O MET A 483 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N CYS A 490 " --> pdb=" O LEU A 486 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL A 496 " --> pdb=" O ASP A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 532 removed outlier: 4.460A pdb=" N TRP A 515 " --> pdb=" O ALA A 511 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N LYS A 516 " --> pdb=" O ALA A 512 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N GLU A 517 " --> pdb=" O GLU A 513 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N GLY A 532 " --> pdb=" O SER A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 541 removed outlier: 3.641A pdb=" N CYS A 537 " --> pdb=" O ASN A 533 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A 539 " --> pdb=" O ALA A 535 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N PHE A 540 " --> pdb=" O ASN A 536 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N SER A 541 " --> pdb=" O CYS A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 551 removed outlier: 3.668A pdb=" N LYS A 550 " --> pdb=" O TRP A 546 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N LEU A 551 " --> pdb=" O VAL A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 571 removed outlier: 3.734A pdb=" N VAL A 567 " --> pdb=" O VAL A 563 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU A 568 " --> pdb=" O LEU A 564 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ILE A 569 " --> pdb=" O TYR A 565 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU A 570 " --> pdb=" O CYS A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 578 removed outlier: 4.550A pdb=" N ASN A 576 " --> pdb=" O PRO A 572 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ILE A 577 " --> pdb=" O GLU A 573 " (cutoff:3.500A) removed outlier: 4.007A 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: 3.558A pdb=" N LEU A 590 " --> pdb=" O ILE A 586 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP A 591 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 609 removed outlier: 3.693A pdb=" N LEU A 600 " --> pdb=" O ASN A 596 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N CYS A 607 " --> pdb=" O LEU A 603 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N VAL A 608 " --> pdb=" O CYS A 604 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N CYS A 609 " --> pdb=" O SER A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 625 removed outlier: 4.326A pdb=" N GLN A 618 " --> pdb=" O VAL A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 890 removed outlier: 3.856A pdb=" N GLU A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N LYS A 873 " --> pdb=" O ARG A 869 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TRP A 882 " --> pdb=" O ILE A 878 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA A 883 " --> pdb=" O HIS A 879 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N GLU A 888 " --> pdb=" O LEU A 884 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N GLN A 889 " --> pdb=" O THR A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 935 removed outlier: 5.178A pdb=" N LEU A 935 " --> pdb=" O THR A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 948 removed outlier: 6.279A pdb=" N GLU A 947 " --> pdb=" O ASP A 943 " (cutoff:3.500A) removed outlier: 3.949A 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 removed outlier: 3.759A pdb=" N MET A 960 " --> pdb=" O PRO A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 1001 removed outlier: 4.303A pdb=" N THR A 982 " --> pdb=" O THR A 978 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ASP A 999 " --> pdb=" O VAL A 995 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ARG A1000 " --> pdb=" O TRP A 996 " (cutoff:3.500A) Processing helix chain 'A' and resid 1029 through 1045 removed outlier: 3.569A pdb=" N ASP A1037 " --> pdb=" O ARG A1033 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N SER A1038 " --> pdb=" O SER A1034 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A1039 " --> pdb=" O ASN A1035 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N THR A1045 " --> pdb=" O GLN A1041 " (cutoff:3.500A) Processing helix chain 'A' and resid 1574 through 1581 removed outlier: 3.800A pdb=" N ALA A1578 " --> pdb=" O PRO A1574 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET A1579 " --> pdb=" O LEU A1575 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE A1580 " --> pdb=" O SER A1576 " (cutoff:3.500A) removed outlier: 3.780A 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 1654 removed outlier: 4.098A pdb=" N LEU A1653 " --> pdb=" O ASP A1649 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N SER A1654 " --> pdb=" O ILE A1650 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1649 through 1654' Processing helix chain 'A' and resid 1656 through 1675 removed outlier: 6.007A pdb=" N GLN A1660 " --> pdb=" O ARG A1656 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N ARG A1661 " --> pdb=" O LEU A1657 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N CYS A1674 " --> pdb=" O TYR A1670 " (cutoff:3.500A) Processing helix chain 'A' and resid 1678 through 1690 removed outlier: 4.688A pdb=" N ALA A1682 " --> pdb=" O ASN A1678 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N HIS A1683 " --> pdb=" O ASN A1679 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA A1684 " --> pdb=" O ARG A1680 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASP A1690 " --> pdb=" O CYS A1686 " (cutoff:3.500A) Processing helix chain 'A' and resid 1691 through 1701 removed outlier: 3.820A pdb=" N LEU A1698 " --> pdb=" O LEU A1694 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLU A1699 " --> pdb=" O LEU A1695 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASP A1700 " --> pdb=" O HIS A1696 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N ALA A1701 " --> pdb=" O ALA A1697 " (cutoff:3.500A) Processing helix chain 'A' and resid 1704 through 1719 removed outlier: 6.844A pdb=" N ARG A1708 " --> pdb=" O PRO A1704 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA A1709 " --> pdb=" O GLY A1705 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N HIS A1719 " --> pdb=" O LEU A1715 " (cutoff:3.500A) Processing helix chain 'A' and resid 1720 through 1732 removed outlier: 4.578A pdb=" N SER A1732 " --> pdb=" O ARG A1728 " (cutoff:3.500A) Processing helix chain 'A' and resid 1739 through 1745 removed outlier: 4.153A pdb=" N ILE A1745 " --> pdb=" O GLU A1741 " (cutoff:3.500A) Processing helix chain 'A' and resid 1754 through 1759 removed outlier: 4.287A pdb=" N ARG A1759 " --> pdb=" O GLY A1755 " (cutoff:3.500A) Processing helix chain 'A' and resid 1803 through 1825 removed outlier: 3.700A pdb=" N LEU A1807 " --> pdb=" O PRO A1803 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASP A1809 " --> pdb=" O GLU A1805 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL A1819 " --> pdb=" O LEU A1815 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG A1820 " --> pdb=" O GLY A1816 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLN A1824 " --> pdb=" O ARG A1820 " (cutoff:3.500A) removed outlier: 4.455A 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: 3.692A pdb=" N MET A1851 " --> pdb=" O THR A1847 " (cutoff:3.500A) Processing helix chain 'A' and resid 1855 through 1865 removed outlier: 4.020A pdb=" N MET A1865 " --> pdb=" O GLN A1861 " (cutoff:3.500A) Processing helix chain 'A' and resid 1932 through 1984 removed outlier: 7.021A pdb=" N LYS A1936 " --> pdb=" O PRO A1932 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N LEU A1937 " --> pdb=" O GLU A1933 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLN A1938 " --> pdb=" O SER A1934 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TYR A1945 " --> pdb=" O ASN A1941 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N PHE A1946 " --> pdb=" O LEU A1942 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU A1950 " --> pdb=" O PHE A1946 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU A1951 " --> pdb=" O CYS A1947 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU A1963 " --> pdb=" O ALA A1959 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG A1964 " --> pdb=" O ALA A1960 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N PHE A1984 " --> pdb=" O LEU A1980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1987 through 1999 removed outlier: 4.146A pdb=" N ARG A1996 " --> pdb=" O ALA A1992 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLU A1997 " --> pdb=" O ARG A1993 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE A1998 " --> pdb=" O ARG A1994 " (cutoff:3.500A) Processing helix chain 'A' and resid 2001 through 2015 removed outlier: 3.571A pdb=" N LEU A2009 " --> pdb=" O GLN A2005 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU A2010 " --> pdb=" O ILE A2006 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLU A2015 " --> pdb=" O HIS A2011 " (cutoff:3.500A) Processing helix chain 'A' and resid 2027 through 2043 removed outlier: 4.730A pdb=" N LEU A2031 " --> pdb=" O ILE A2027 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLN A2032 " --> pdb=" O ARG A2028 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLY A2043 " --> pdb=" O LEU A2039 " (cutoff:3.500A) Processing helix chain 'A' and resid 2093 through 2109 removed outlier: 3.519A pdb=" N VAL A2103 " --> pdb=" O SER A2099 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASP A2109 " --> pdb=" O TRP A2105 " (cutoff:3.500A) Processing helix chain 'A' and resid 2113 through 2130 removed outlier: 3.720A pdb=" N LEU A2123 " --> pdb=" O ALA A2119 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLY A2130 " --> pdb=" O ARG A2126 " (cutoff:3.500A) Processing helix chain 'A' and resid 2131 through 2142 Proline residue: A2139 - end of helix removed outlier: 5.700A pdb=" N TYR A2142 " --> pdb=" O LEU A2138 " (cutoff:3.500A) Processing helix chain 'A' and resid 2148 through 2169 removed outlier: 4.272A pdb=" N SER A2154 " --> pdb=" O GLU A2150 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU A2155 " --> pdb=" O ASP A2151 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ILE A2167 " --> pdb=" O ARG A2163 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N VAL A2168 " --> pdb=" O SER A2164 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N GLN A2169 " --> pdb=" O LEU A2165 " (cutoff:3.500A) Processing helix chain 'A' and resid 2171 through 2188 removed outlier: 3.578A pdb=" N ASN A2176 " --> pdb=" O PRO A2172 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU A2177 " --> pdb=" O GLN A2173 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ASN A2187 " --> pdb=" O GLY A2183 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ASN A2188 " --> pdb=" O ASN A2184 " (cutoff:3.500A) Processing helix chain 'A' and resid 2189 through 2195 removed outlier: 4.542A pdb=" N GLN A2193 " --> pdb=" O LYS A2189 " (cutoff:3.500A) removed outlier: 3.700A 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: 3.926A pdb=" N ASN A2213 " --> pdb=" O GLU A2209 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL A2214 " --> pdb=" O VAL A2210 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU A2215 " --> pdb=" O MET A2211 " (cutoff:3.500A) Processing helix chain 'A' and resid 2227 through 2244 removed outlier: 4.449A pdb=" N SER A2231 " --> pdb=" O LYS A2227 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N SER A2243 " --> pdb=" O PHE A2239 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N ARG A2244 " --> pdb=" O CYS A2240 " (cutoff:3.500A) Processing helix chain 'A' and resid 2245 through 2255 removed outlier: 4.199A pdb=" N SER A2249 " --> pdb=" O GLN A2245 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASP A2252 " --> pdb=" O ARG A2248 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N HIS A2253 " --> pdb=" O SER A2249 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LEU A2254 " --> pdb=" O MET A2250 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N SER A2255 " --> pdb=" O PHE A2251 " (cutoff:3.500A) Processing helix chain 'A' and resid 2256 through 2265 removed outlier: 3.631A pdb=" N ASN A2260 " --> pdb=" O TYR A2256 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLY A2262 " --> pdb=" O LEU A2258 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ILE A2263 " --> pdb=" O GLU A2259 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY A2264 " --> pdb=" O ASN A2260 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU A2265 " --> pdb=" O SER A2261 " (cutoff:3.500A) Processing helix chain 'A' and resid 2271 through 2282 removed outlier: 3.846A pdb=" N VAL A2275 " --> pdb=" O THR A2271 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA A2276 " --> pdb=" O PRO A2272 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N VAL A2280 " --> pdb=" O ALA A2276 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ILE A2281 " --> pdb=" O ALA A2277 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N ASP A2282 " --> pdb=" O ALA A2278 " (cutoff:3.500A) Processing helix chain 'A' and resid 2286 through 2291 removed outlier: 3.703A pdb=" N LEU A2290 " --> pdb=" O LEU A2286 " (cutoff:3.500A) removed outlier: 4.529A 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 2309 removed outlier: 3.780A pdb=" N VAL A2299 " --> pdb=" O LEU A2295 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N SER A2300 " --> pdb=" O GLU A2296 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N TYR A2301 " --> pdb=" O LYS A2297 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU A2302 " --> pdb=" O VAL A2298 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU A2307 " --> pdb=" O ALA A2303 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N SER A2309 " --> pdb=" O CYS A2305 " (cutoff:3.500A) Processing helix chain 'A' and resid 2310 through 2315 removed outlier: 3.830A pdb=" N LEU A2314 " --> pdb=" O CYS A2310 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA A2315 " --> pdb=" O PRO A2311 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2310 through 2315' Processing helix chain 'A' and resid 2324 through 2341 removed outlier: 3.705A pdb=" N GLY A2328 " --> pdb=" O ASN A2324 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LEU A2332 " --> pdb=" O GLY A2328 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N ASP A2333 " --> pdb=" O GLU A2329 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N PHE A2334 " --> pdb=" O ARG A2330 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LEU A2335 " --> pdb=" O TYR A2331 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N VAL A2341 " --> pdb=" O PHE A2337 " (cutoff:3.500A) Processing helix chain 'A' and resid 2346 through 2361 removed outlier: 3.856A pdb=" N VAL A2352 " --> pdb=" O GLU A2348 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG A2359 " --> pdb=" O ARG A2355 " (cutoff:3.500A) removed outlier: 4.563A 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: 4.485A pdb=" N ARG A2452 " --> pdb=" O GLY A2448 " (cutoff:3.500A) removed outlier: 3.655A 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 2472 removed outlier: 4.296A pdb=" N GLY A2468 " --> pdb=" O ASP A2464 " (cutoff:3.500A) Processing helix chain 'A' and resid 2751 through 2774 removed outlier: 5.004A pdb=" N ILE A2755 " --> pdb=" O LEU A2751 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N THR A2762 " --> pdb=" O PHE A2758 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N HIS A2763 " --> pdb=" O ALA A2759 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU A2764 " --> pdb=" O GLU A2760 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LYS A2765 " --> pdb=" O TYR A2761 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N TRP A2766 " --> pdb=" O THR A2762 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ALA A2767 " --> pdb=" O HIS A2763 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N PHE A2768 " --> pdb=" O GLU A2764 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ASP A2769 " --> pdb=" O LYS A2765 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N LYS A2770 " --> pdb=" O TRP A2766 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ILE A2771 " --> pdb=" O ALA A2767 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLN A2772 " --> pdb=" O PHE A2768 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ASN A2773 " --> pdb=" O ASP A2769 " (cutoff:3.500A) Processing helix chain 'A' and resid 2798 through 2804 removed outlier: 4.577A pdb=" N LYS A2802 " --> pdb=" O SER A2798 " (cutoff:3.500A) Processing helix chain 'A' and resid 2807 through 2813 removed outlier: 4.270A pdb=" N GLU A2811 " --> pdb=" O TRP A2807 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N SER A2812 " --> pdb=" O PRO A2808 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU A2813 " --> pdb=" O ILE A2809 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2807 through 2813' Processing helix chain 'A' and resid 2868 through 2873 removed outlier: 5.176A pdb=" N GLN A2872 " --> pdb=" O SER A2868 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ALA A2873 " --> pdb=" O ARG A2869 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2868 through 2873' Processing helix chain 'A' and resid 2874 through 2891 removed outlier: 4.589A pdb=" N ALA A2879 " --> pdb=" O ALA A2875 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ASN A2881 " --> pdb=" O GLN A2877 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N TYR A2882 " --> pdb=" O LEU A2878 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N LYS A2890 " --> pdb=" O TRP A2886 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N LYS A2891 " --> pdb=" O GLY A2887 " (cutoff:3.500A) Processing helix chain 'A' and resid 2919 through 2930 removed outlier: 4.480A pdb=" N ALA A2923 " --> pdb=" O ASP A2919 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU A2925 " --> pdb=" O GLU A2921 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LYS A2928 " --> pdb=" O GLN A2924 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE A2929 " --> pdb=" O GLU A2925 " (cutoff:3.500A) Processing helix chain 'A' and resid 3645 through 3657 removed outlier: 3.828A pdb=" N GLU A3655 " --> pdb=" O ASN A3651 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N SER A3656 " --> pdb=" O MET A3652 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N TYR A3657 " --> pdb=" O PHE A3653 " (cutoff:3.500A) Processing helix chain 'A' and resid 3668 through 3680 removed outlier: 4.364A pdb=" N ALA A3680 " --> pdb=" O ASP A3676 " (cutoff:3.500A) Processing helix chain 'A' and resid 3683 through 3688 Processing helix chain 'A' and resid 3696 through 3712 removed outlier: 5.576A pdb=" N GLU A3712 " --> pdb=" O THR A3708 " (cutoff:3.500A) Processing helix chain 'A' and resid 3719 through 3735 removed outlier: 4.085A pdb=" N ASP A3727 " --> pdb=" O MET A3723 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N CYS A3733 " --> pdb=" O MET A3729 " (cutoff:3.500A) Processing helix chain 'A' and resid 3752 through 3771 removed outlier: 3.914A pdb=" N LEU A3770 " --> pdb=" O GLN A3766 " (cutoff:3.500A) Processing helix chain 'A' and resid 3774 through 3787 removed outlier: 4.115A pdb=" N MET A3778 " --> pdb=" O GLY A3774 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N VAL A3779 " --> pdb=" O ALA A3775 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LEU A3780 " --> pdb=" O ALA A3776 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LYS A3787 " --> pdb=" O ILE A3783 " (cutoff:3.500A) Processing helix chain 'A' and resid 3791 through 3806 removed outlier: 3.656A pdb=" N SER A3795 " --> pdb=" O GLY A3791 " (cutoff:3.500A) Processing helix chain 'A' and resid 3809 through 3824 Processing helix chain 'A' and resid 3826 through 3839 removed outlier: 6.674A pdb=" N GLN A3830 " --> pdb=" O VAL A3826 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N CYS A3839 " --> pdb=" O LEU A3835 " (cutoff:3.500A) Processing helix chain 'A' and resid 3843 through 3858 removed outlier: 4.920A pdb=" N MET A3858 " --> pdb=" O GLU A3854 " (cutoff:3.500A) Processing helix chain 'A' and resid 3862 through 3872 removed outlier: 4.578A pdb=" N GLU A3872 " --> pdb=" O ARG A3868 " (cutoff:3.500A) Processing helix chain 'A' and resid 3877 through 3893 removed outlier: 3.744A pdb=" N CYS A3892 " --> pdb=" O LEU A3888 " (cutoff:3.500A) Processing helix chain 'A' and resid 3896 through 3905 removed outlier: 3.707A pdb=" N ARG A3904 " --> pdb=" O GLN A3900 " (cutoff:3.500A) Processing helix chain 'A' and resid 3914 through 3939 removed outlier: 3.947A pdb=" N CYS A3918 " --> pdb=" O ASN A3914 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N GLY A3939 " --> pdb=" O TRP A3935 " (cutoff:3.500A) Processing helix chain 'A' and resid 3944 through 3970 removed outlier: 3.709A pdb=" N GLN A3960 " --> pdb=" O SER A3956 " (cutoff:3.500A) Processing helix chain 'A' and resid 3973 through 3984 removed outlier: 4.923A pdb=" N ARG A3984 " --> pdb=" O LEU A3980 " (cutoff:3.500A) Processing helix chain 'A' and resid 3985 through 4004 Processing helix chain 'A' and resid 4009 through 4032 removed outlier: 3.740A pdb=" N LEU A4031 " --> pdb=" O LEU A4027 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLU A4032 " --> pdb=" O LEU A4028 " (cutoff:3.500A) Processing helix chain 'A' and resid 4039 through 4052 removed outlier: 5.909A pdb=" N GLN A4043 " --> pdb=" O MET A4039 " (cutoff:3.500A) Processing helix chain 'A' and resid 4053 through 4074 removed outlier: 3.512A pdb=" N PHE A4065 " --> pdb=" O PHE A4061 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY A4073 " --> pdb=" O LYS A4069 " (cutoff:3.500A) Processing helix chain 'A' and resid 4075 through 4082 removed outlier: 4.413A pdb=" N THR A4082 " --> pdb=" O GLN A4078 " (cutoff:3.500A) Processing helix chain 'A' and resid 4089 through 4101 removed outlier: 3.578A pdb=" N GLN A4094 " --> pdb=" O LYS A4090 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS A4095 " --> pdb=" O LYS A4091 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LYS A4101 " --> pdb=" O MET A4097 " (cutoff:3.500A) Processing helix chain 'A' and resid 4104 through 4116 removed outlier: 3.706A pdb=" N ILE A4108 " --> pdb=" O THR A4104 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN A4109 " --> pdb=" O GLY A4105 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N GLU A4116 " --> pdb=" O LEU A4112 " (cutoff:3.500A) Processing helix chain 'A' and resid 4124 through 4132 removed outlier: 5.408A pdb=" N PHE A4132 " --> pdb=" O PHE A4128 " (cutoff:3.500A) Processing helix chain 'A' and resid 4134 through 4155 removed outlier: 4.572A pdb=" N ASP A4138 " --> pdb=" O GLU A4134 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ILE A4139 " --> pdb=" O PRO A4135 " (cutoff:3.500A) Proline residue: A4155 - end of helix Processing helix chain 'A' and resid 4157 through 4168 removed outlier: 4.024A pdb=" N ARG A4161 " --> pdb=" O ASP A4157 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASN A4162 " --> pdb=" O PRO A4158 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE A4163 " --> pdb=" O ARG A4159 " (cutoff:3.500A) Processing helix chain 'A' and resid 4169 through 4179 Proline residue: A4176 - end of helix removed outlier: 5.790A pdb=" N GLY A4179 " --> pdb=" O ARG A4175 " (cutoff:3.500A) Processing helix chain 'A' and resid 4198 through 4207 removed outlier: 3.502A pdb=" N ARG A4202 " --> pdb=" O SER A4198 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N MET A4207 " --> pdb=" O ALA A4203 " (cutoff:3.500A) Processing helix chain 'A' and resid 4208 through 4224 Processing helix chain 'A' and resid 4229 through 4252 removed outlier: 3.569A pdb=" N PHE A4243 " --> pdb=" O GLU A4239 " (cutoff:3.500A) Processing helix chain 'A' and resid 4540 through 4559 removed outlier: 3.918A pdb=" N PHE A4559 " --> pdb=" O LEU A4555 " (cutoff:3.500A) Processing helix chain 'A' and resid 4560 through 4580 removed outlier: 5.013A pdb=" N TYR A4580 " --> pdb=" O ILE A4576 " (cutoff:3.500A) Processing helix chain 'A' and resid 4642 through 4684 removed outlier: 4.220A pdb=" N LEU A4646 " --> pdb=" O ALA A4642 " (cutoff:3.500A) removed outlier: 4.588A 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 4708 removed outlier: 3.874A pdb=" N GLN A4700 " --> pdb=" O ASP A4696 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LEU A4704 " --> pdb=" O GLN A4700 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N VAL A4705 " --> pdb=" O TRP A4701 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LEU A4706 " --> pdb=" O ASP A4702 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N ASN A4707 " --> pdb=" O ARG A4703 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N THR A4708 " --> pdb=" O LEU A4704 " (cutoff:3.500A) Processing helix chain 'A' and resid 4719 through 4728 Processing helix chain 'A' and resid 4733 through 4742 removed outlier: 4.621A pdb=" N GLY A4742 " --> pdb=" O ALA A4738 " (cutoff:3.500A) Processing helix chain 'A' and resid 4749 through 4755 Processing helix chain 'A' and resid 4772 through 4787 removed outlier: 5.450A pdb=" N ASN A4787 " --> pdb=" O ILE A4783 " (cutoff:3.500A) Processing helix chain 'A' and resid 4788 through 4802 removed outlier: 3.758A pdb=" N LEU A4792 " --> pdb=" O SER A4788 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLY A4802 " --> pdb=" O MET A4798 " (cutoff:3.500A) Processing helix chain 'A' and resid 4807 through 4820 removed outlier: 4.020A pdb=" N ALA A4811 " --> pdb=" O PHE A4807 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N HIS A4812 " --> pdb=" O PHE A4808 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LEU A4813 " --> pdb=" O PHE A4809 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N LEU A4814 " --> pdb=" O ALA A4810 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N ASP A4815 " --> pdb=" O ALA A4811 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N ILE A4816 " --> pdb=" O HIS A4812 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N ALA A4817 " --> pdb=" O LEU A4813 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N MET A4818 " --> pdb=" O LEU A4814 " (cutoff:3.500A) Processing helix chain 'A' and resid 4821 through 4835 removed outlier: 4.160A pdb=" N ASN A4833 " --> pdb=" O SER A4829 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY A4834 " --> pdb=" O VAL A4830 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N LYS A4835 " --> pdb=" O THR A4831 " (cutoff:3.500A) Processing helix chain 'A' and resid 4836 through 4859 Processing helix chain 'A' and resid 4878 through 4893 removed outlier: 3.989A pdb=" N LEU A4884 " --> pdb=" O MET A4880 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VAL A4891 " --> pdb=" O MET A4887 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ARG A4892 " --> pdb=" O TYR A4888 " (cutoff:3.500A) Processing helix chain 'A' and resid 4896 through 4902 removed outlier: 5.676A pdb=" N GLU A4902 " --> pdb=" O GLY A4898 " (cutoff:3.500A) Processing helix chain 'A' and resid 4910 through 4924 removed outlier: 6.541A pdb=" N VAL A4914 " --> pdb=" O GLU A4910 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N VAL A4915 " --> pdb=" O LEU A4911 " (cutoff:3.500A) Processing helix chain 'A' and resid 4928 through 4957 removed outlier: 3.623A pdb=" N ARG A4944 " --> pdb=" O PHE A4940 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN A4947 " --> pdb=" O LEU A4943 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N THR A4956 " --> pdb=" O GLU A4952 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N LYS A4957 " --> pdb=" O ASP A4953 " (cutoff:3.500A) Processing helix chain 'A' and resid 4964 through 4972 removed outlier: 4.452A pdb=" N PHE A4968 " --> pdb=" O GLY A4964 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N THR A4971 " --> pdb=" O TYR A4967 " (cutoff:3.500A) Proline residue: A4972 - end of helix Processing helix chain 'A' and resid 4973 through 4982 Processing helix chain 'A' and resid 4984 through 4999 removed outlier: 7.166A pdb=" N TYR A4988 " --> pdb=" O ASN A4984 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N MET A4989 " --> pdb=" O LEU A4985 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N ASP A4999 " --> pdb=" O LEU A4995 " (cutoff:3.500A) Processing helix chain 'A' and resid 5004 through 5017 Processing helix chain 'A' and resid 5027 through 5033 removed outlier: 6.049A pdb=" N GLN A5031 " --> pdb=" O CYS A5027 " (cutoff:3.500A) Processing helix chain 'A' and resid 4764 through 4769 removed outlier: 5.657A pdb=" N TRP A4767 " --> pdb=" O LEU A4764 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N LEU A4768 " --> pdb=" O LEU A4765 " (cutoff:3.500A) Processing helix chain 'A' and resid 1214 through 1219 removed outlier: 4.202A pdb=" N LEU A1219 " --> pdb=" O PHE A1214 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1214 through 1219' Processing helix chain 'A' and resid 4685 through 4690 Processing helix chain 'B' and resid 61 through 66 removed outlier: 4.909A 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: 4.324A pdb=" N CYS B 253 " --> pdb=" O GLY B 249 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N THR B 254 " --> pdb=" O GLY B 250 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N HIS B 255 " --> pdb=" O ALA B 251 " (cutoff:3.500A) removed outlier: 5.334A 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 308 through 313 removed outlier: 6.725A pdb=" N THR B 312 " --> pdb=" O HIS B 308 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N SER B 313 " --> pdb=" O THR B 309 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 308 through 313' Processing helix chain 'B' and resid 364 through 371 removed outlier: 3.619A pdb=" N LEU B 369 " --> pdb=" O LYS B 365 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLY B 370 " --> pdb=" O ALA B 366 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N VAL B 371 " --> pdb=" O LEU B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 423 removed outlier: 3.796A pdb=" N ASP B 419 " --> pdb=" O ILE B 415 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N SER B 420 " --> pdb=" O LYS B 416 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N PHE B 421 " --> pdb=" O GLY B 417 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N SER B 422 " --> pdb=" O LEU B 418 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N GLY B 423 " --> pdb=" O ASP B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 453 removed outlier: 3.953A pdb=" N VAL B 441 " --> pdb=" O PRO B 437 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ILE B 442 " --> pdb=" O ILE B 438 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU B 443 " --> pdb=" O GLU B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 482 removed outlier: 3.799A pdb=" N GLU B 480 " --> pdb=" O SER B 476 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLU B 481 " --> pdb=" O LEU B 477 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N GLY B 482 " --> pdb=" O PHE B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 496 removed outlier: 4.375A pdb=" N VAL B 487 " --> pdb=" O MET B 483 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N CYS B 490 " --> pdb=" O LEU B 486 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL B 496 " --> pdb=" O ASP B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 532 removed outlier: 4.460A pdb=" N TRP B 515 " --> pdb=" O ALA B 511 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N LYS B 516 " --> pdb=" O ALA B 512 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N GLU B 517 " --> pdb=" O GLU B 513 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N GLY B 532 " --> pdb=" O SER B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 541 removed outlier: 3.642A pdb=" N CYS B 537 " --> pdb=" O ASN B 533 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU B 539 " --> pdb=" O ALA B 535 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N PHE B 540 " --> pdb=" O ASN B 536 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N SER B 541 " --> pdb=" O CYS B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 551 removed outlier: 3.669A pdb=" N LYS B 550 " --> pdb=" O TRP B 546 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N LEU B 551 " --> pdb=" O VAL B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 571 removed outlier: 3.735A pdb=" N VAL B 567 " --> pdb=" O VAL B 563 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU B 568 " --> pdb=" O LEU B 564 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ILE B 569 " --> pdb=" O TYR B 565 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU B 570 " --> pdb=" O CYS B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 578 removed outlier: 4.549A pdb=" N ASN B 576 " --> pdb=" O PRO B 572 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ILE B 577 " --> pdb=" O GLU B 573 " (cutoff:3.500A) removed outlier: 4.007A 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: 3.558A pdb=" N LEU B 590 " --> pdb=" O ILE B 586 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP B 591 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 609 removed outlier: 3.693A pdb=" N LEU B 600 " --> pdb=" O ASN B 596 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N CYS B 607 " --> pdb=" O LEU B 603 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N VAL B 608 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N CYS B 609 " --> pdb=" O SER B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 625 removed outlier: 4.326A pdb=" N GLN B 618 " --> pdb=" O VAL B 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 868 through 890 removed outlier: 3.856A pdb=" N GLU B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N LYS B 873 " --> pdb=" O ARG B 869 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TRP B 882 " --> pdb=" O ILE B 878 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA B 883 " --> pdb=" O HIS B 879 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N GLU B 888 " --> pdb=" O LEU B 884 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N GLN B 889 " --> pdb=" O THR B 885 " (cutoff:3.500A) Processing helix chain 'B' and resid 914 through 935 removed outlier: 5.178A pdb=" N LEU B 935 " --> pdb=" O THR B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 943 through 948 removed outlier: 6.279A pdb=" N GLU B 947 " --> pdb=" O ASP B 943 " (cutoff:3.500A) removed outlier: 3.948A 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 removed outlier: 3.758A pdb=" N MET B 960 " --> pdb=" O PRO B 956 " (cutoff:3.500A) Processing helix chain 'B' and resid 978 through 1001 removed outlier: 4.303A pdb=" N THR B 982 " --> pdb=" O THR B 978 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ASP B 999 " --> pdb=" O VAL B 995 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ARG B1000 " --> pdb=" O TRP B 996 " (cutoff:3.500A) Processing helix chain 'B' and resid 1029 through 1045 removed outlier: 3.569A pdb=" N ASP B1037 " --> pdb=" O ARG B1033 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N SER B1038 " --> pdb=" O SER B1034 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU B1039 " --> pdb=" O ASN B1035 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N THR B1045 " --> pdb=" O GLN B1041 " (cutoff:3.500A) Processing helix chain 'B' and resid 1574 through 1581 removed outlier: 3.800A pdb=" N ALA B1578 " --> pdb=" O PRO B1574 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET B1579 " --> pdb=" O LEU B1575 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE B1580 " --> pdb=" O SER B1576 " (cutoff:3.500A) removed outlier: 3.781A 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 1654 removed outlier: 4.098A pdb=" N LEU B1653 " --> pdb=" O ASP B1649 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N SER B1654 " --> pdb=" O ILE B1650 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1649 through 1654' Processing helix chain 'B' and resid 1656 through 1675 removed outlier: 6.007A pdb=" N GLN B1660 " --> pdb=" O ARG B1656 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ARG B1661 " --> pdb=" O LEU B1657 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N CYS B1674 " --> pdb=" O TYR B1670 " (cutoff:3.500A) Processing helix chain 'B' and resid 1678 through 1690 removed outlier: 4.689A pdb=" N ALA B1682 " --> pdb=" O ASN B1678 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N HIS B1683 " --> pdb=" O ASN B1679 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA B1684 " --> pdb=" O ARG B1680 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASP B1690 " --> pdb=" O CYS B1686 " (cutoff:3.500A) Processing helix chain 'B' and resid 1691 through 1701 removed outlier: 3.820A pdb=" N LEU B1698 " --> pdb=" O LEU B1694 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLU B1699 " --> pdb=" O LEU B1695 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP B1700 " --> pdb=" O HIS B1696 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N ALA B1701 " --> pdb=" O ALA B1697 " (cutoff:3.500A) Processing helix chain 'B' and resid 1704 through 1719 removed outlier: 6.844A pdb=" N ARG B1708 " --> pdb=" O PRO B1704 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA B1709 " --> pdb=" O GLY B1705 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N HIS B1719 " --> pdb=" O LEU B1715 " (cutoff:3.500A) Processing helix chain 'B' and resid 1720 through 1732 removed outlier: 4.578A pdb=" N SER B1732 " --> pdb=" O ARG B1728 " (cutoff:3.500A) Processing helix chain 'B' and resid 1739 through 1745 removed outlier: 4.153A pdb=" N ILE B1745 " --> pdb=" O GLU B1741 " (cutoff:3.500A) Processing helix chain 'B' and resid 1754 through 1759 removed outlier: 4.288A pdb=" N ARG B1759 " --> pdb=" O GLY B1755 " (cutoff:3.500A) Processing helix chain 'B' and resid 1803 through 1825 removed outlier: 3.700A pdb=" N LEU B1807 " --> pdb=" O PRO B1803 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASP B1809 " --> pdb=" O GLU B1805 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL B1819 " --> pdb=" O LEU B1815 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG B1820 " --> pdb=" O GLY B1816 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLN B1824 " --> pdb=" O ARG B1820 " (cutoff:3.500A) removed outlier: 4.455A 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: 3.691A pdb=" N MET B1851 " --> pdb=" O THR B1847 " (cutoff:3.500A) Processing helix chain 'B' and resid 1855 through 1865 removed outlier: 4.019A pdb=" N MET B1865 " --> pdb=" O GLN B1861 " (cutoff:3.500A) Processing helix chain 'B' and resid 1932 through 1984 removed outlier: 7.021A pdb=" N LYS B1936 " --> pdb=" O PRO B1932 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N LEU B1937 " --> pdb=" O GLU B1933 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLN B1938 " --> pdb=" O SER B1934 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N TYR B1945 " --> pdb=" O ASN B1941 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N PHE B1946 " --> pdb=" O LEU B1942 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU B1950 " --> pdb=" O PHE B1946 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU B1951 " --> pdb=" O CYS B1947 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU B1963 " --> pdb=" O ALA B1959 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ARG B1964 " --> pdb=" O ALA B1960 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N PHE B1984 " --> pdb=" O LEU B1980 " (cutoff:3.500A) Processing helix chain 'B' and resid 1987 through 1999 removed outlier: 4.147A pdb=" N ARG B1996 " --> pdb=" O ALA B1992 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N GLU B1997 " --> pdb=" O ARG B1993 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE B1998 " --> pdb=" O ARG B1994 " (cutoff:3.500A) Processing helix chain 'B' and resid 2001 through 2015 removed outlier: 3.569A pdb=" N LEU B2009 " --> pdb=" O GLN B2005 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU B2010 " --> pdb=" O ILE B2006 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLU B2015 " --> pdb=" O HIS B2011 " (cutoff:3.500A) Processing helix chain 'B' and resid 2027 through 2043 removed outlier: 4.730A pdb=" N LEU B2031 " --> pdb=" O ILE B2027 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN B2032 " --> pdb=" O ARG B2028 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLY B2043 " --> pdb=" O LEU B2039 " (cutoff:3.500A) Processing helix chain 'B' and resid 2093 through 2109 removed outlier: 3.519A pdb=" N VAL B2103 " --> pdb=" O SER B2099 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASP B2109 " --> pdb=" O TRP B2105 " (cutoff:3.500A) Processing helix chain 'B' and resid 2113 through 2130 removed outlier: 3.720A pdb=" N LEU B2123 " --> pdb=" O ALA B2119 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY B2130 " --> pdb=" O ARG B2126 " (cutoff:3.500A) Processing helix chain 'B' and resid 2131 through 2142 Proline residue: B2139 - end of helix removed outlier: 5.701A pdb=" N TYR B2142 " --> pdb=" O LEU B2138 " (cutoff:3.500A) Processing helix chain 'B' and resid 2148 through 2169 removed outlier: 4.272A pdb=" N SER B2154 " --> pdb=" O GLU B2150 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU B2155 " --> pdb=" O ASP B2151 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ILE B2167 " --> pdb=" O ARG B2163 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N VAL B2168 " --> pdb=" O SER B2164 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N GLN B2169 " --> pdb=" O LEU B2165 " (cutoff:3.500A) Processing helix chain 'B' and resid 2171 through 2188 removed outlier: 3.577A pdb=" N ASN B2176 " --> pdb=" O PRO B2172 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU B2177 " --> pdb=" O GLN B2173 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ASN B2187 " --> pdb=" O GLY B2183 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ASN B2188 " --> pdb=" O ASN B2184 " (cutoff:3.500A) Processing helix chain 'B' and resid 2189 through 2195 removed outlier: 4.542A pdb=" N GLN B2193 " --> pdb=" O LYS B2189 " (cutoff:3.500A) removed outlier: 3.700A 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: 3.926A pdb=" N ASN B2213 " --> pdb=" O GLU B2209 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL B2214 " --> pdb=" O VAL B2210 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU B2215 " --> pdb=" O MET B2211 " (cutoff:3.500A) Processing helix chain 'B' and resid 2227 through 2244 removed outlier: 4.449A pdb=" N SER B2231 " --> pdb=" O LYS B2227 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N SER B2243 " --> pdb=" O PHE B2239 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N ARG B2244 " --> pdb=" O CYS B2240 " (cutoff:3.500A) Processing helix chain 'B' and resid 2245 through 2255 removed outlier: 4.199A pdb=" N SER B2249 " --> pdb=" O GLN B2245 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP B2252 " --> pdb=" O ARG B2248 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N HIS B2253 " --> pdb=" O SER B2249 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LEU B2254 " --> pdb=" O MET B2250 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N SER B2255 " --> pdb=" O PHE B2251 " (cutoff:3.500A) Processing helix chain 'B' and resid 2256 through 2265 removed outlier: 3.630A pdb=" N ASN B2260 " --> pdb=" O TYR B2256 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLY B2262 " --> pdb=" O LEU B2258 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ILE B2263 " --> pdb=" O GLU B2259 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY B2264 " --> pdb=" O ASN B2260 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU B2265 " --> pdb=" O SER B2261 " (cutoff:3.500A) Processing helix chain 'B' and resid 2271 through 2282 removed outlier: 3.847A pdb=" N VAL B2275 " --> pdb=" O THR B2271 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA B2276 " --> pdb=" O PRO B2272 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL B2280 " --> pdb=" O ALA B2276 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ILE B2281 " --> pdb=" O ALA B2277 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N ASP B2282 " --> pdb=" O ALA B2278 " (cutoff:3.500A) Processing helix chain 'B' and resid 2286 through 2291 removed outlier: 3.702A pdb=" N LEU B2290 " --> pdb=" O LEU B2286 " (cutoff:3.500A) removed outlier: 4.530A 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 2309 removed outlier: 3.780A pdb=" N VAL B2299 " --> pdb=" O LEU B2295 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N SER B2300 " --> pdb=" O GLU B2296 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N TYR B2301 " --> pdb=" O LYS B2297 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU B2302 " --> pdb=" O VAL B2298 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU B2307 " --> pdb=" O ALA B2303 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N SER B2309 " --> pdb=" O CYS B2305 " (cutoff:3.500A) Processing helix chain 'B' and resid 2310 through 2315 removed outlier: 3.831A pdb=" N LEU B2314 " --> pdb=" O CYS B2310 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA B2315 " --> pdb=" O PRO B2311 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2310 through 2315' Processing helix chain 'B' and resid 2324 through 2341 removed outlier: 3.704A pdb=" N GLY B2328 " --> pdb=" O ASN B2324 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LEU B2332 " --> pdb=" O GLY B2328 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N ASP B2333 " --> pdb=" O GLU B2329 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N PHE B2334 " --> pdb=" O ARG B2330 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LEU B2335 " --> pdb=" O TYR B2331 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N VAL B2341 " --> pdb=" O PHE B2337 " (cutoff:3.500A) Processing helix chain 'B' and resid 2346 through 2361 removed outlier: 3.855A pdb=" N VAL B2352 " --> pdb=" O GLU B2348 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG B2359 " --> pdb=" O ARG B2355 " (cutoff:3.500A) removed outlier: 4.564A 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: 4.484A pdb=" N ARG B2452 " --> pdb=" O GLY B2448 " (cutoff:3.500A) removed outlier: 3.655A 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 2472 removed outlier: 4.294A pdb=" N GLY B2468 " --> pdb=" O ASP B2464 " (cutoff:3.500A) Processing helix chain 'B' and resid 2751 through 2774 removed outlier: 5.005A pdb=" N ILE B2755 " --> pdb=" O LEU B2751 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N THR B2762 " --> pdb=" O PHE B2758 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N HIS B2763 " --> pdb=" O ALA B2759 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU B2764 " --> pdb=" O GLU B2760 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LYS B2765 " --> pdb=" O TYR B2761 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N TRP B2766 " --> pdb=" O THR B2762 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ALA B2767 " --> pdb=" O HIS B2763 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N PHE B2768 " --> pdb=" O GLU B2764 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ASP B2769 " --> pdb=" O LYS B2765 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N LYS B2770 " --> pdb=" O TRP B2766 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N ILE B2771 " --> pdb=" O ALA B2767 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLN B2772 " --> pdb=" O PHE B2768 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ASN B2773 " --> pdb=" O ASP B2769 " (cutoff:3.500A) Processing helix chain 'B' and resid 2798 through 2804 removed outlier: 4.578A pdb=" N LYS B2802 " --> pdb=" O SER B2798 " (cutoff:3.500A) Processing helix chain 'B' and resid 2807 through 2813 removed outlier: 4.270A pdb=" N GLU B2811 " --> pdb=" O TRP B2807 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N SER B2812 " --> pdb=" O PRO B2808 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU B2813 " --> pdb=" O ILE B2809 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2807 through 2813' Processing helix chain 'B' and resid 2868 through 2873 removed outlier: 5.175A pdb=" N GLN B2872 " --> pdb=" O SER B2868 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ALA B2873 " --> pdb=" O ARG B2869 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2868 through 2873' Processing helix chain 'B' and resid 2874 through 2891 removed outlier: 4.589A pdb=" N ALA B2879 " --> pdb=" O ALA B2875 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ASN B2881 " --> pdb=" O GLN B2877 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N TYR B2882 " --> pdb=" O LEU B2878 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N LYS B2890 " --> pdb=" O TRP B2886 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N LYS B2891 " --> pdb=" O GLY B2887 " (cutoff:3.500A) Processing helix chain 'B' and resid 2919 through 2930 removed outlier: 4.481A pdb=" N ALA B2923 " --> pdb=" O ASP B2919 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU B2925 " --> pdb=" O GLU B2921 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LYS B2928 " --> pdb=" O GLN B2924 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE B2929 " --> pdb=" O GLU B2925 " (cutoff:3.500A) Processing helix chain 'B' and resid 3645 through 3657 removed outlier: 3.828A pdb=" N GLU B3655 " --> pdb=" O ASN B3651 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N SER B3656 " --> pdb=" O MET B3652 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N TYR B3657 " --> pdb=" O PHE B3653 " (cutoff:3.500A) Processing helix chain 'B' and resid 3668 through 3680 removed outlier: 4.364A pdb=" N ALA B3680 " --> pdb=" O ASP B3676 " (cutoff:3.500A) Processing helix chain 'B' and resid 3683 through 3688 Processing helix chain 'B' and resid 3696 through 3712 removed outlier: 5.577A pdb=" N GLU B3712 " --> pdb=" O THR B3708 " (cutoff:3.500A) Processing helix chain 'B' and resid 3719 through 3735 removed outlier: 4.085A pdb=" N ASP B3727 " --> pdb=" O MET B3723 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N CYS B3733 " --> pdb=" O MET B3729 " (cutoff:3.500A) Processing helix chain 'B' and resid 3752 through 3771 removed outlier: 3.913A pdb=" N LEU B3770 " --> pdb=" O GLN B3766 " (cutoff:3.500A) Processing helix chain 'B' and resid 3774 through 3787 removed outlier: 4.115A pdb=" N MET B3778 " --> pdb=" O GLY B3774 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N VAL B3779 " --> pdb=" O ALA B3775 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LEU B3780 " --> pdb=" O ALA B3776 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LYS B3787 " --> pdb=" O ILE B3783 " (cutoff:3.500A) Processing helix chain 'B' and resid 3791 through 3806 removed outlier: 3.655A pdb=" N SER B3795 " --> pdb=" O GLY B3791 " (cutoff:3.500A) Processing helix chain 'B' and resid 3809 through 3824 Processing helix chain 'B' and resid 3826 through 3839 removed outlier: 6.674A pdb=" N GLN B3830 " --> pdb=" O VAL B3826 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N CYS B3839 " --> pdb=" O LEU B3835 " (cutoff:3.500A) Processing helix chain 'B' and resid 3843 through 3858 removed outlier: 4.920A pdb=" N MET B3858 " --> pdb=" O GLU B3854 " (cutoff:3.500A) Processing helix chain 'B' and resid 3862 through 3872 removed outlier: 4.577A pdb=" N GLU B3872 " --> pdb=" O ARG B3868 " (cutoff:3.500A) Processing helix chain 'B' and resid 3877 through 3893 removed outlier: 3.744A pdb=" N CYS B3892 " --> pdb=" O LEU B3888 " (cutoff:3.500A) Processing helix chain 'B' and resid 3896 through 3905 removed outlier: 3.709A pdb=" N ARG B3904 " --> pdb=" O GLN B3900 " (cutoff:3.500A) Processing helix chain 'B' and resid 3914 through 3939 removed outlier: 3.947A pdb=" N CYS B3918 " --> pdb=" O ASN B3914 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N GLY B3939 " --> pdb=" O TRP B3935 " (cutoff:3.500A) Processing helix chain 'B' and resid 3944 through 3970 removed outlier: 3.708A pdb=" N GLN B3960 " --> pdb=" O SER B3956 " (cutoff:3.500A) Processing helix chain 'B' and resid 3973 through 3984 removed outlier: 4.922A pdb=" N ARG B3984 " --> pdb=" O LEU B3980 " (cutoff:3.500A) Processing helix chain 'B' and resid 3985 through 4004 Processing helix chain 'B' and resid 4009 through 4032 removed outlier: 3.740A pdb=" N LEU B4031 " --> pdb=" O LEU B4027 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLU B4032 " --> pdb=" O LEU B4028 " (cutoff:3.500A) Processing helix chain 'B' and resid 4039 through 4052 removed outlier: 5.910A pdb=" N GLN B4043 " --> pdb=" O MET B4039 " (cutoff:3.500A) Processing helix chain 'B' and resid 4053 through 4074 removed outlier: 3.512A pdb=" N PHE B4065 " --> pdb=" O PHE B4061 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY B4073 " --> pdb=" O LYS B4069 " (cutoff:3.500A) Processing helix chain 'B' and resid 4075 through 4082 removed outlier: 4.412A pdb=" N THR B4082 " --> pdb=" O GLN B4078 " (cutoff:3.500A) Processing helix chain 'B' and resid 4089 through 4101 removed outlier: 3.578A pdb=" N GLN B4094 " --> pdb=" O LYS B4090 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS B4095 " --> pdb=" O LYS B4091 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LYS B4101 " --> pdb=" O MET B4097 " (cutoff:3.500A) Processing helix chain 'B' and resid 4104 through 4116 removed outlier: 3.706A pdb=" N ILE B4108 " --> pdb=" O THR B4104 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN B4109 " --> pdb=" O GLY B4105 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N GLU B4116 " --> pdb=" O LEU B4112 " (cutoff:3.500A) Processing helix chain 'B' and resid 4124 through 4132 removed outlier: 5.407A pdb=" N PHE B4132 " --> pdb=" O PHE B4128 " (cutoff:3.500A) Processing helix chain 'B' and resid 4134 through 4155 removed outlier: 4.573A pdb=" N ASP B4138 " --> pdb=" O GLU B4134 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ILE B4139 " --> pdb=" O PRO B4135 " (cutoff:3.500A) Proline residue: B4155 - end of helix Processing helix chain 'B' and resid 4157 through 4168 removed outlier: 4.024A pdb=" N ARG B4161 " --> pdb=" O ASP B4157 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASN B4162 " --> pdb=" O PRO B4158 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE B4163 " --> pdb=" O ARG B4159 " (cutoff:3.500A) Processing helix chain 'B' and resid 4169 through 4179 Proline residue: B4176 - end of helix removed outlier: 5.790A pdb=" N GLY B4179 " --> pdb=" O ARG B4175 " (cutoff:3.500A) Processing helix chain 'B' and resid 4198 through 4207 removed outlier: 3.501A pdb=" N ARG B4202 " --> pdb=" O SER B4198 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N MET B4207 " --> pdb=" O ALA B4203 " (cutoff:3.500A) Processing helix chain 'B' and resid 4208 through 4224 Processing helix chain 'B' and resid 4229 through 4252 removed outlier: 3.569A pdb=" N PHE B4243 " --> pdb=" O GLU B4239 " (cutoff:3.500A) Processing helix chain 'B' and resid 4540 through 4559 removed outlier: 3.919A pdb=" N PHE B4559 " --> pdb=" O LEU B4555 " (cutoff:3.500A) Processing helix chain 'B' and resid 4560 through 4580 removed outlier: 5.013A pdb=" N TYR B4580 " --> pdb=" O ILE B4576 " (cutoff:3.500A) Processing helix chain 'B' and resid 4642 through 4684 removed outlier: 4.220A pdb=" N LEU B4646 " --> pdb=" O ALA B4642 " (cutoff:3.500A) removed outlier: 4.588A 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 4708 removed outlier: 3.874A pdb=" N GLN B4700 " --> pdb=" O ASP B4696 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LEU B4704 " --> pdb=" O GLN B4700 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N VAL B4705 " --> pdb=" O TRP B4701 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LEU B4706 " --> pdb=" O ASP B4702 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N ASN B4707 " --> pdb=" O ARG B4703 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N THR B4708 " --> pdb=" O LEU B4704 " (cutoff:3.500A) Processing helix chain 'B' and resid 4719 through 4728 Processing helix chain 'B' and resid 4733 through 4742 removed outlier: 4.620A pdb=" N GLY B4742 " --> pdb=" O ALA B4738 " (cutoff:3.500A) Processing helix chain 'B' and resid 4749 through 4755 Processing helix chain 'B' and resid 4772 through 4787 removed outlier: 5.450A pdb=" N ASN B4787 " --> pdb=" O ILE B4783 " (cutoff:3.500A) Processing helix chain 'B' and resid 4788 through 4802 removed outlier: 3.757A pdb=" N LEU B4792 " --> pdb=" O SER B4788 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLY B4802 " --> pdb=" O MET B4798 " (cutoff:3.500A) Processing helix chain 'B' and resid 4807 through 4820 removed outlier: 4.020A pdb=" N ALA B4811 " --> pdb=" O PHE B4807 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N HIS B4812 " --> pdb=" O PHE B4808 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N LEU B4813 " --> pdb=" O PHE B4809 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N LEU B4814 " --> pdb=" O ALA B4810 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N ASP B4815 " --> pdb=" O ALA B4811 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N ILE B4816 " --> pdb=" O HIS B4812 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N ALA B4817 " --> pdb=" O LEU B4813 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N MET B4818 " --> pdb=" O LEU B4814 " (cutoff:3.500A) Processing helix chain 'B' and resid 4821 through 4835 removed outlier: 4.161A pdb=" N ASN B4833 " --> pdb=" O SER B4829 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY B4834 " --> pdb=" O VAL B4830 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N LYS B4835 " --> pdb=" O THR B4831 " (cutoff:3.500A) Processing helix chain 'B' and resid 4836 through 4859 Processing helix chain 'B' and resid 4878 through 4893 removed outlier: 3.989A pdb=" N LEU B4884 " --> pdb=" O MET B4880 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL B4891 " --> pdb=" O MET B4887 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ARG B4892 " --> pdb=" O TYR B4888 " (cutoff:3.500A) Processing helix chain 'B' and resid 4896 through 4902 removed outlier: 5.677A pdb=" N GLU B4902 " --> pdb=" O GLY B4898 " (cutoff:3.500A) Processing helix chain 'B' and resid 4910 through 4924 removed outlier: 6.541A pdb=" N VAL B4914 " --> pdb=" O GLU B4910 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N VAL B4915 " --> pdb=" O LEU B4911 " (cutoff:3.500A) Processing helix chain 'B' and resid 4928 through 4957 removed outlier: 3.623A pdb=" N ARG B4944 " --> pdb=" O PHE B4940 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN B4947 " --> pdb=" O LEU B4943 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N THR B4956 " --> pdb=" O GLU B4952 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N LYS B4957 " --> pdb=" O ASP B4953 " (cutoff:3.500A) Processing helix chain 'B' and resid 4964 through 4972 removed outlier: 4.452A pdb=" N PHE B4968 " --> pdb=" O GLY B4964 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N THR B4971 " --> pdb=" O TYR B4967 " (cutoff:3.500A) Proline residue: B4972 - end of helix Processing helix chain 'B' and resid 4973 through 4982 Processing helix chain 'B' and resid 4984 through 4999 removed outlier: 7.166A pdb=" N TYR B4988 " --> pdb=" O ASN B4984 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N MET B4989 " --> pdb=" O LEU B4985 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N ASP B4999 " --> pdb=" O LEU B4995 " (cutoff:3.500A) Processing helix chain 'B' and resid 5004 through 5017 Processing helix chain 'B' and resid 5027 through 5033 removed outlier: 6.050A pdb=" N GLN B5031 " --> pdb=" O CYS B5027 " (cutoff:3.500A) Processing helix chain 'B' and resid 4764 through 4769 removed outlier: 5.657A pdb=" N TRP B4767 " --> pdb=" O LEU B4764 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N LEU B4768 " --> pdb=" O LEU B4765 " (cutoff:3.500A) Processing helix chain 'B' and resid 1214 through 1219 removed outlier: 4.202A pdb=" N LEU B1219 " --> pdb=" O PHE B1214 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1214 through 1219' Processing helix chain 'B' and resid 4685 through 4690 Processing helix chain 'C' and resid 61 through 66 removed outlier: 4.909A 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: 4.324A pdb=" N CYS C 253 " --> pdb=" O GLY C 249 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N THR C 254 " --> pdb=" O GLY C 250 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N HIS C 255 " --> pdb=" O ALA C 251 " (cutoff:3.500A) removed outlier: 5.333A 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 308 through 313 removed outlier: 6.726A pdb=" N THR C 312 " --> pdb=" O HIS C 308 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N SER C 313 " --> pdb=" O THR C 309 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 308 through 313' Processing helix chain 'C' and resid 364 through 371 removed outlier: 3.620A pdb=" N LEU C 369 " --> pdb=" O LYS C 365 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLY C 370 " --> pdb=" O ALA C 366 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N VAL C 371 " --> pdb=" O LEU C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 423 removed outlier: 3.796A pdb=" N ASP C 419 " --> pdb=" O ILE C 415 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N SER C 420 " --> pdb=" O LYS C 416 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N PHE C 421 " --> pdb=" O GLY C 417 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N SER C 422 " --> pdb=" O LEU C 418 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N GLY C 423 " --> pdb=" O ASP C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 453 removed outlier: 3.952A pdb=" N VAL C 441 " --> pdb=" O PRO C 437 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ILE C 442 " --> pdb=" O ILE C 438 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU C 443 " --> pdb=" O GLU C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 482 removed outlier: 3.800A pdb=" N GLU C 480 " --> pdb=" O SER C 476 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLU C 481 " --> pdb=" O LEU C 477 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N GLY C 482 " --> pdb=" O PHE C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 496 removed outlier: 4.376A pdb=" N VAL C 487 " --> pdb=" O MET C 483 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N CYS C 490 " --> pdb=" O LEU C 486 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL C 496 " --> pdb=" O ASP C 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 511 through 532 removed outlier: 4.461A pdb=" N TRP C 515 " --> pdb=" O ALA C 511 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N LYS C 516 " --> pdb=" O ALA C 512 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N GLU C 517 " --> pdb=" O GLU C 513 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N GLY C 532 " --> pdb=" O SER C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 541 removed outlier: 3.642A pdb=" N CYS C 537 " --> pdb=" O ASN C 533 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU C 539 " --> pdb=" O ALA C 535 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N PHE C 540 " --> pdb=" O ASN C 536 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N SER C 541 " --> pdb=" O CYS C 537 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 551 removed outlier: 3.670A pdb=" N LYS C 550 " --> pdb=" O TRP C 546 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N LEU C 551 " --> pdb=" O VAL C 547 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 571 removed outlier: 3.735A pdb=" N VAL C 567 " --> pdb=" O VAL C 563 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU C 568 " --> pdb=" O LEU C 564 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ILE C 569 " --> pdb=" O TYR C 565 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU C 570 " --> pdb=" O CYS C 566 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 578 removed outlier: 4.549A pdb=" N ASN C 576 " --> pdb=" O PRO C 572 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ILE C 577 " --> pdb=" O GLU C 573 " (cutoff:3.500A) removed outlier: 4.007A 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: 3.558A pdb=" N LEU C 590 " --> pdb=" O ILE C 586 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP C 591 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 609 removed outlier: 3.692A pdb=" N LEU C 600 " --> pdb=" O ASN C 596 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N CYS C 607 " --> pdb=" O LEU C 603 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N VAL C 608 " --> pdb=" O CYS C 604 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N CYS C 609 " --> pdb=" O SER C 605 " (cutoff:3.500A) Processing helix chain 'C' and resid 614 through 625 removed outlier: 4.326A pdb=" N GLN C 618 " --> pdb=" O VAL C 614 " (cutoff:3.500A) Processing helix chain 'C' and resid 868 through 890 removed outlier: 3.855A pdb=" N GLU C 872 " --> pdb=" O GLU C 868 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N LYS C 873 " --> pdb=" O ARG C 869 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N TRP C 882 " --> pdb=" O ILE C 878 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA C 883 " --> pdb=" O HIS C 879 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N GLU C 888 " --> pdb=" O LEU C 884 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N GLN C 889 " --> pdb=" O THR C 885 " (cutoff:3.500A) Processing helix chain 'C' and resid 914 through 935 removed outlier: 5.178A pdb=" N LEU C 935 " --> pdb=" O THR C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 943 through 948 removed outlier: 6.279A pdb=" N GLU C 947 " --> pdb=" O ASP C 943 " (cutoff:3.500A) removed outlier: 3.949A 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 removed outlier: 3.759A pdb=" N MET C 960 " --> pdb=" O PRO C 956 " (cutoff:3.500A) Processing helix chain 'C' and resid 978 through 1001 removed outlier: 4.303A pdb=" N THR C 982 " --> pdb=" O THR C 978 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ASP C 999 " --> pdb=" O VAL C 995 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ARG C1000 " --> pdb=" O TRP C 996 " (cutoff:3.500A) Processing helix chain 'C' and resid 1029 through 1045 removed outlier: 3.569A pdb=" N ASP C1037 " --> pdb=" O ARG C1033 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N SER C1038 " --> pdb=" O SER C1034 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU C1039 " --> pdb=" O ASN C1035 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N THR C1045 " --> pdb=" O GLN C1041 " (cutoff:3.500A) Processing helix chain 'C' and resid 1574 through 1581 removed outlier: 3.800A pdb=" N ALA C1578 " --> pdb=" O PRO C1574 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET C1579 " --> pdb=" O LEU C1575 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHE C1580 " --> pdb=" O SER C1576 " (cutoff:3.500A) removed outlier: 3.781A 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 1654 removed outlier: 4.097A pdb=" N LEU C1653 " --> pdb=" O ASP C1649 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N SER C1654 " --> pdb=" O ILE C1650 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1649 through 1654' Processing helix chain 'C' and resid 1656 through 1675 removed outlier: 6.007A pdb=" N GLN C1660 " --> pdb=" O ARG C1656 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N ARG C1661 " --> pdb=" O LEU C1657 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N CYS C1674 " --> pdb=" O TYR C1670 " (cutoff:3.500A) Processing helix chain 'C' and resid 1678 through 1690 removed outlier: 4.689A pdb=" N ALA C1682 " --> pdb=" O ASN C1678 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N HIS C1683 " --> pdb=" O ASN C1679 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA C1684 " --> pdb=" O ARG C1680 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASP C1690 " --> pdb=" O CYS C1686 " (cutoff:3.500A) Processing helix chain 'C' and resid 1691 through 1701 removed outlier: 3.820A pdb=" N LEU C1698 " --> pdb=" O LEU C1694 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLU C1699 " --> pdb=" O LEU C1695 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP C1700 " --> pdb=" O HIS C1696 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N ALA C1701 " --> pdb=" O ALA C1697 " (cutoff:3.500A) Processing helix chain 'C' and resid 1704 through 1719 removed outlier: 6.843A pdb=" N ARG C1708 " --> pdb=" O PRO C1704 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA C1709 " --> pdb=" O GLY C1705 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N HIS C1719 " --> pdb=" O LEU C1715 " (cutoff:3.500A) Processing helix chain 'C' and resid 1720 through 1732 removed outlier: 4.578A pdb=" N SER C1732 " --> pdb=" O ARG C1728 " (cutoff:3.500A) Processing helix chain 'C' and resid 1739 through 1745 removed outlier: 4.153A pdb=" N ILE C1745 " --> pdb=" O GLU C1741 " (cutoff:3.500A) Processing helix chain 'C' and resid 1754 through 1759 removed outlier: 4.287A pdb=" N ARG C1759 " --> pdb=" O GLY C1755 " (cutoff:3.500A) Processing helix chain 'C' and resid 1803 through 1825 removed outlier: 3.701A pdb=" N LEU C1807 " --> pdb=" O PRO C1803 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASP C1809 " --> pdb=" O GLU C1805 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL C1819 " --> pdb=" O LEU C1815 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG C1820 " --> pdb=" O GLY C1816 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLN C1824 " --> pdb=" O ARG C1820 " (cutoff:3.500A) removed outlier: 4.455A 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: 3.692A pdb=" N MET C1851 " --> pdb=" O THR C1847 " (cutoff:3.500A) Processing helix chain 'C' and resid 1855 through 1865 removed outlier: 4.020A pdb=" N MET C1865 " --> pdb=" O GLN C1861 " (cutoff:3.500A) Processing helix chain 'C' and resid 1932 through 1984 removed outlier: 7.022A pdb=" N LYS C1936 " --> pdb=" O PRO C1932 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N LEU C1937 " --> pdb=" O GLU C1933 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLN C1938 " --> pdb=" O SER C1934 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N TYR C1945 " --> pdb=" O ASN C1941 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHE C1946 " --> pdb=" O LEU C1942 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU C1950 " --> pdb=" O PHE C1946 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU C1951 " --> pdb=" O CYS C1947 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU C1963 " --> pdb=" O ALA C1959 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG C1964 " --> pdb=" O ALA C1960 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N PHE C1984 " --> pdb=" O LEU C1980 " (cutoff:3.500A) Processing helix chain 'C' and resid 1987 through 1999 removed outlier: 4.146A pdb=" N ARG C1996 " --> pdb=" O ALA C1992 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLU C1997 " --> pdb=" O ARG C1993 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE C1998 " --> pdb=" O ARG C1994 " (cutoff:3.500A) Processing helix chain 'C' and resid 2001 through 2015 removed outlier: 3.571A pdb=" N LEU C2009 " --> pdb=" O GLN C2005 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU C2010 " --> pdb=" O ILE C2006 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLU C2015 " --> pdb=" O HIS C2011 " (cutoff:3.500A) Processing helix chain 'C' and resid 2027 through 2043 removed outlier: 4.730A pdb=" N LEU C2031 " --> pdb=" O ILE C2027 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN C2032 " --> pdb=" O ARG C2028 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N GLY C2043 " --> pdb=" O LEU C2039 " (cutoff:3.500A) Processing helix chain 'C' and resid 2093 through 2109 removed outlier: 3.519A pdb=" N VAL C2103 " --> pdb=" O SER C2099 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASP C2109 " --> pdb=" O TRP C2105 " (cutoff:3.500A) Processing helix chain 'C' and resid 2113 through 2130 removed outlier: 3.721A pdb=" N LEU C2123 " --> pdb=" O ALA C2119 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLY C2130 " --> pdb=" O ARG C2126 " (cutoff:3.500A) Processing helix chain 'C' and resid 2131 through 2142 Proline residue: C2139 - end of helix removed outlier: 5.700A pdb=" N TYR C2142 " --> pdb=" O LEU C2138 " (cutoff:3.500A) Processing helix chain 'C' and resid 2148 through 2169 removed outlier: 4.273A pdb=" N SER C2154 " --> pdb=" O GLU C2150 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU C2155 " --> pdb=" O ASP C2151 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE C2167 " --> pdb=" O ARG C2163 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N VAL C2168 " --> pdb=" O SER C2164 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N GLN C2169 " --> pdb=" O LEU C2165 " (cutoff:3.500A) Processing helix chain 'C' and resid 2171 through 2188 removed outlier: 3.578A pdb=" N ASN C2176 " --> pdb=" O PRO C2172 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU C2177 " --> pdb=" O GLN C2173 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ASN C2187 " --> pdb=" O GLY C2183 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ASN C2188 " --> pdb=" O ASN C2184 " (cutoff:3.500A) Processing helix chain 'C' and resid 2189 through 2195 removed outlier: 4.542A pdb=" N GLN C2193 " --> pdb=" O LYS C2189 " (cutoff:3.500A) removed outlier: 3.701A 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: 3.927A pdb=" N ASN C2213 " --> pdb=" O GLU C2209 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL C2214 " --> pdb=" O VAL C2210 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU C2215 " --> pdb=" O MET C2211 " (cutoff:3.500A) Processing helix chain 'C' and resid 2227 through 2244 removed outlier: 4.449A pdb=" N SER C2231 " --> pdb=" O LYS C2227 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N SER C2243 " --> pdb=" O PHE C2239 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N ARG C2244 " --> pdb=" O CYS C2240 " (cutoff:3.500A) Processing helix chain 'C' and resid 2245 through 2255 removed outlier: 4.199A pdb=" N SER C2249 " --> pdb=" O GLN C2245 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP C2252 " --> pdb=" O ARG C2248 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N HIS C2253 " --> pdb=" O SER C2249 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LEU C2254 " --> pdb=" O MET C2250 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N SER C2255 " --> pdb=" O PHE C2251 " (cutoff:3.500A) Processing helix chain 'C' and resid 2256 through 2265 removed outlier: 3.631A pdb=" N ASN C2260 " --> pdb=" O TYR C2256 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLY C2262 " --> pdb=" O LEU C2258 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ILE C2263 " --> pdb=" O GLU C2259 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY C2264 " --> pdb=" O ASN C2260 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU C2265 " --> pdb=" O SER C2261 " (cutoff:3.500A) Processing helix chain 'C' and resid 2271 through 2282 removed outlier: 3.847A pdb=" N VAL C2275 " --> pdb=" O THR C2271 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA C2276 " --> pdb=" O PRO C2272 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N VAL C2280 " --> pdb=" O ALA C2276 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ILE C2281 " --> pdb=" O ALA C2277 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N ASP C2282 " --> pdb=" O ALA C2278 " (cutoff:3.500A) Processing helix chain 'C' and resid 2286 through 2291 removed outlier: 3.703A pdb=" N LEU C2290 " --> pdb=" O LEU C2286 " (cutoff:3.500A) removed outlier: 4.529A 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 2309 removed outlier: 3.780A pdb=" N VAL C2299 " --> pdb=" O LEU C2295 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N SER C2300 " --> pdb=" O GLU C2296 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TYR C2301 " --> pdb=" O LYS C2297 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU C2302 " --> pdb=" O VAL C2298 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU C2307 " --> pdb=" O ALA C2303 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N SER C2309 " --> pdb=" O CYS C2305 " (cutoff:3.500A) Processing helix chain 'C' and resid 2310 through 2315 removed outlier: 3.831A pdb=" N LEU C2314 " --> pdb=" O CYS C2310 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA C2315 " --> pdb=" O PRO C2311 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2310 through 2315' Processing helix chain 'C' and resid 2324 through 2341 removed outlier: 3.705A pdb=" N GLY C2328 " --> pdb=" O ASN C2324 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LEU C2332 " --> pdb=" O GLY C2328 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N ASP C2333 " --> pdb=" O GLU C2329 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N PHE C2334 " --> pdb=" O ARG C2330 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LEU C2335 " --> pdb=" O TYR C2331 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N VAL C2341 " --> pdb=" O PHE C2337 " (cutoff:3.500A) Processing helix chain 'C' and resid 2346 through 2361 removed outlier: 3.856A pdb=" N VAL C2352 " --> pdb=" O GLU C2348 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG C2359 " --> pdb=" O ARG C2355 " (cutoff:3.500A) removed outlier: 4.563A 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: 4.485A pdb=" N ARG C2452 " --> pdb=" O GLY C2448 " (cutoff:3.500A) removed outlier: 3.655A 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 2472 removed outlier: 4.295A pdb=" N GLY C2468 " --> pdb=" O ASP C2464 " (cutoff:3.500A) Processing helix chain 'C' and resid 2751 through 2774 removed outlier: 5.004A pdb=" N ILE C2755 " --> pdb=" O LEU C2751 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N THR C2762 " --> pdb=" O PHE C2758 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N HIS C2763 " --> pdb=" O ALA C2759 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLU C2764 " --> pdb=" O GLU C2760 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LYS C2765 " --> pdb=" O TYR C2761 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N TRP C2766 " --> pdb=" O THR C2762 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ALA C2767 " --> pdb=" O HIS C2763 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N PHE C2768 " --> pdb=" O GLU C2764 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ASP C2769 " --> pdb=" O LYS C2765 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N LYS C2770 " --> pdb=" O TRP C2766 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ILE C2771 " --> pdb=" O ALA C2767 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLN C2772 " --> pdb=" O PHE C2768 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ASN C2773 " --> pdb=" O ASP C2769 " (cutoff:3.500A) Processing helix chain 'C' and resid 2798 through 2804 removed outlier: 4.578A pdb=" N LYS C2802 " --> pdb=" O SER C2798 " (cutoff:3.500A) Processing helix chain 'C' and resid 2807 through 2813 removed outlier: 4.271A pdb=" N GLU C2811 " --> pdb=" O TRP C2807 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N SER C2812 " --> pdb=" O PRO C2808 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU C2813 " --> pdb=" O ILE C2809 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2807 through 2813' Processing helix chain 'C' and resid 2868 through 2873 removed outlier: 5.175A pdb=" N GLN C2872 " --> pdb=" O SER C2868 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ALA C2873 " --> pdb=" O ARG C2869 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2868 through 2873' Processing helix chain 'C' and resid 2874 through 2891 removed outlier: 4.589A pdb=" N ALA C2879 " --> pdb=" O ALA C2875 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ASN C2881 " --> pdb=" O GLN C2877 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N TYR C2882 " --> pdb=" O LEU C2878 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N LYS C2890 " --> pdb=" O TRP C2886 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N LYS C2891 " --> pdb=" O GLY C2887 " (cutoff:3.500A) Processing helix chain 'C' and resid 2919 through 2930 removed outlier: 4.481A pdb=" N ALA C2923 " --> pdb=" O ASP C2919 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU C2925 " --> pdb=" O GLU C2921 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N LYS C2928 " --> pdb=" O GLN C2924 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE C2929 " --> pdb=" O GLU C2925 " (cutoff:3.500A) Processing helix chain 'C' and resid 3645 through 3657 removed outlier: 3.827A pdb=" N GLU C3655 " --> pdb=" O ASN C3651 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N SER C3656 " --> pdb=" O MET C3652 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N TYR C3657 " --> pdb=" O PHE C3653 " (cutoff:3.500A) Processing helix chain 'C' and resid 3668 through 3680 removed outlier: 4.364A pdb=" N ALA C3680 " --> pdb=" O ASP C3676 " (cutoff:3.500A) Processing helix chain 'C' and resid 3683 through 3688 Processing helix chain 'C' and resid 3696 through 3712 removed outlier: 5.576A pdb=" N GLU C3712 " --> pdb=" O THR C3708 " (cutoff:3.500A) Processing helix chain 'C' and resid 3719 through 3735 removed outlier: 4.086A pdb=" N ASP C3727 " --> pdb=" O MET C3723 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N CYS C3733 " --> pdb=" O MET C3729 " (cutoff:3.500A) Processing helix chain 'C' and resid 3752 through 3771 removed outlier: 3.913A pdb=" N LEU C3770 " --> pdb=" O GLN C3766 " (cutoff:3.500A) Processing helix chain 'C' and resid 3774 through 3787 removed outlier: 4.116A pdb=" N MET C3778 " --> pdb=" O GLY C3774 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N VAL C3779 " --> pdb=" O ALA C3775 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LEU C3780 " --> pdb=" O ALA C3776 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LYS C3787 " --> pdb=" O ILE C3783 " (cutoff:3.500A) Processing helix chain 'C' and resid 3791 through 3806 removed outlier: 3.656A pdb=" N SER C3795 " --> pdb=" O GLY C3791 " (cutoff:3.500A) Processing helix chain 'C' and resid 3809 through 3824 Processing helix chain 'C' and resid 3826 through 3839 removed outlier: 6.674A pdb=" N GLN C3830 " --> pdb=" O VAL C3826 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N CYS C3839 " --> pdb=" O LEU C3835 " (cutoff:3.500A) Processing helix chain 'C' and resid 3843 through 3858 removed outlier: 4.920A pdb=" N MET C3858 " --> pdb=" O GLU C3854 " (cutoff:3.500A) Processing helix chain 'C' and resid 3862 through 3872 removed outlier: 4.577A pdb=" N GLU C3872 " --> pdb=" O ARG C3868 " (cutoff:3.500A) Processing helix chain 'C' and resid 3877 through 3893 removed outlier: 3.744A pdb=" N CYS C3892 " --> pdb=" O LEU C3888 " (cutoff:3.500A) Processing helix chain 'C' and resid 3896 through 3905 removed outlier: 3.709A pdb=" N ARG C3904 " --> pdb=" O GLN C3900 " (cutoff:3.500A) Processing helix chain 'C' and resid 3914 through 3939 removed outlier: 3.948A pdb=" N CYS C3918 " --> pdb=" O ASN C3914 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N GLY C3939 " --> pdb=" O TRP C3935 " (cutoff:3.500A) Processing helix chain 'C' and resid 3944 through 3970 removed outlier: 3.708A pdb=" N GLN C3960 " --> pdb=" O SER C3956 " (cutoff:3.500A) Processing helix chain 'C' and resid 3973 through 3984 removed outlier: 4.922A pdb=" N ARG C3984 " --> pdb=" O LEU C3980 " (cutoff:3.500A) Processing helix chain 'C' and resid 3985 through 4004 Processing helix chain 'C' and resid 4009 through 4032 removed outlier: 3.740A pdb=" N LEU C4031 " --> pdb=" O LEU C4027 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLU C4032 " --> pdb=" O LEU C4028 " (cutoff:3.500A) Processing helix chain 'C' and resid 4039 through 4052 removed outlier: 5.909A pdb=" N GLN C4043 " --> pdb=" O MET C4039 " (cutoff:3.500A) Processing helix chain 'C' and resid 4053 through 4074 removed outlier: 3.513A pdb=" N PHE C4065 " --> pdb=" O PHE C4061 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY C4073 " --> pdb=" O LYS C4069 " (cutoff:3.500A) Processing helix chain 'C' and resid 4075 through 4082 removed outlier: 4.413A pdb=" N THR C4082 " --> pdb=" O GLN C4078 " (cutoff:3.500A) Processing helix chain 'C' and resid 4089 through 4101 removed outlier: 3.579A pdb=" N GLN C4094 " --> pdb=" O LYS C4090 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS C4095 " --> pdb=" O LYS C4091 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LYS C4101 " --> pdb=" O MET C4097 " (cutoff:3.500A) Processing helix chain 'C' and resid 4104 through 4116 removed outlier: 3.706A pdb=" N ILE C4108 " --> pdb=" O THR C4104 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN C4109 " --> pdb=" O GLY C4105 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N GLU C4116 " --> pdb=" O LEU C4112 " (cutoff:3.500A) Processing helix chain 'C' and resid 4124 through 4132 removed outlier: 5.407A pdb=" N PHE C4132 " --> pdb=" O PHE C4128 " (cutoff:3.500A) Processing helix chain 'C' and resid 4134 through 4155 removed outlier: 4.573A pdb=" N ASP C4138 " --> pdb=" O GLU C4134 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ILE C4139 " --> pdb=" O PRO C4135 " (cutoff:3.500A) Proline residue: C4155 - end of helix Processing helix chain 'C' and resid 4157 through 4168 removed outlier: 4.024A pdb=" N ARG C4161 " --> pdb=" O ASP C4157 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ASN C4162 " --> pdb=" O PRO C4158 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE C4163 " --> pdb=" O ARG C4159 " (cutoff:3.500A) Processing helix chain 'C' and resid 4169 through 4179 Proline residue: C4176 - end of helix removed outlier: 5.791A pdb=" N GLY C4179 " --> pdb=" O ARG C4175 " (cutoff:3.500A) Processing helix chain 'C' and resid 4198 through 4207 removed outlier: 3.503A pdb=" N ARG C4202 " --> pdb=" O SER C4198 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N MET C4207 " --> pdb=" O ALA C4203 " (cutoff:3.500A) Processing helix chain 'C' and resid 4208 through 4224 Processing helix chain 'C' and resid 4229 through 4252 removed outlier: 3.569A pdb=" N PHE C4243 " --> pdb=" O GLU C4239 " (cutoff:3.500A) Processing helix chain 'C' and resid 4540 through 4559 removed outlier: 3.919A pdb=" N PHE C4559 " --> pdb=" O LEU C4555 " (cutoff:3.500A) Processing helix chain 'C' and resid 4560 through 4580 removed outlier: 5.012A pdb=" N TYR C4580 " --> pdb=" O ILE C4576 " (cutoff:3.500A) Processing helix chain 'C' and resid 4642 through 4684 removed outlier: 4.219A pdb=" N LEU C4646 " --> pdb=" O ALA C4642 " (cutoff:3.500A) removed outlier: 4.588A 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 4708 removed outlier: 3.874A pdb=" N GLN C4700 " --> pdb=" O ASP C4696 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LEU C4704 " --> pdb=" O GLN C4700 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N VAL C4705 " --> pdb=" O TRP C4701 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LEU C4706 " --> pdb=" O ASP C4702 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N ASN C4707 " --> pdb=" O ARG C4703 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N THR C4708 " --> pdb=" O LEU C4704 " (cutoff:3.500A) Processing helix chain 'C' and resid 4719 through 4728 Processing helix chain 'C' and resid 4733 through 4742 removed outlier: 4.621A pdb=" N GLY C4742 " --> pdb=" O ALA C4738 " (cutoff:3.500A) Processing helix chain 'C' and resid 4749 through 4755 Processing helix chain 'C' and resid 4772 through 4787 removed outlier: 5.450A pdb=" N ASN C4787 " --> pdb=" O ILE C4783 " (cutoff:3.500A) Processing helix chain 'C' and resid 4788 through 4802 removed outlier: 3.759A pdb=" N LEU C4792 " --> pdb=" O SER C4788 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLY C4802 " --> pdb=" O MET C4798 " (cutoff:3.500A) Processing helix chain 'C' and resid 4807 through 4820 removed outlier: 4.019A pdb=" N ALA C4811 " --> pdb=" O PHE C4807 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N HIS C4812 " --> pdb=" O PHE C4808 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LEU C4813 " --> pdb=" O PHE C4809 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N LEU C4814 " --> pdb=" O ALA C4810 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N ASP C4815 " --> pdb=" O ALA C4811 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N ILE C4816 " --> pdb=" O HIS C4812 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N ALA C4817 " --> pdb=" O LEU C4813 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N MET C4818 " --> pdb=" O LEU C4814 " (cutoff:3.500A) Processing helix chain 'C' and resid 4821 through 4835 removed outlier: 4.160A pdb=" N ASN C4833 " --> pdb=" O SER C4829 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY C4834 " --> pdb=" O VAL C4830 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N LYS C4835 " --> pdb=" O THR C4831 " (cutoff:3.500A) Processing helix chain 'C' and resid 4836 through 4859 Processing helix chain 'C' and resid 4878 through 4893 removed outlier: 3.989A pdb=" N LEU C4884 " --> pdb=" O MET C4880 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VAL C4891 " --> pdb=" O MET C4887 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ARG C4892 " --> pdb=" O TYR C4888 " (cutoff:3.500A) Processing helix chain 'C' and resid 4896 through 4902 removed outlier: 5.676A pdb=" N GLU C4902 " --> pdb=" O GLY C4898 " (cutoff:3.500A) Processing helix chain 'C' and resid 4910 through 4924 removed outlier: 6.542A pdb=" N VAL C4914 " --> pdb=" O GLU C4910 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N VAL C4915 " --> pdb=" O LEU C4911 " (cutoff:3.500A) Processing helix chain 'C' and resid 4928 through 4957 removed outlier: 3.622A pdb=" N ARG C4944 " --> pdb=" O PHE C4940 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN C4947 " --> pdb=" O LEU C4943 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N THR C4956 " --> pdb=" O GLU C4952 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N LYS C4957 " --> pdb=" O ASP C4953 " (cutoff:3.500A) Processing helix chain 'C' and resid 4964 through 4972 removed outlier: 4.452A pdb=" N PHE C4968 " --> pdb=" O GLY C4964 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N THR C4971 " --> pdb=" O TYR C4967 " (cutoff:3.500A) Proline residue: C4972 - end of helix Processing helix chain 'C' and resid 4973 through 4982 Processing helix chain 'C' and resid 4984 through 4999 removed outlier: 7.166A pdb=" N TYR C4988 " --> pdb=" O ASN C4984 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N MET C4989 " --> pdb=" O LEU C4985 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N ASP C4999 " --> pdb=" O LEU C4995 " (cutoff:3.500A) Processing helix chain 'C' and resid 5004 through 5017 Processing helix chain 'C' and resid 5027 through 5033 removed outlier: 6.050A pdb=" N GLN C5031 " --> pdb=" O CYS C5027 " (cutoff:3.500A) Processing helix chain 'C' and resid 4764 through 4769 removed outlier: 5.657A pdb=" N TRP C4767 " --> pdb=" O LEU C4764 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N LEU C4768 " --> pdb=" O LEU C4765 " (cutoff:3.500A) Processing helix chain 'C' and resid 1214 through 1219 removed outlier: 4.202A pdb=" N LEU C1219 " --> pdb=" O PHE C1214 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1214 through 1219' Processing helix chain 'C' and resid 4685 through 4690 Processing helix chain 'D' and resid 61 through 66 removed outlier: 4.909A 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: 4.324A pdb=" N CYS D 253 " --> pdb=" O GLY D 249 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N THR D 254 " --> pdb=" O GLY D 250 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N HIS D 255 " --> pdb=" O ALA D 251 " (cutoff:3.500A) removed outlier: 5.334A 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 308 through 313 removed outlier: 6.725A pdb=" N THR D 312 " --> pdb=" O HIS D 308 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N SER D 313 " --> pdb=" O THR D 309 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 308 through 313' Processing helix chain 'D' and resid 364 through 371 removed outlier: 3.619A pdb=" N LEU D 369 " --> pdb=" O LYS D 365 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLY D 370 " --> pdb=" O ALA D 366 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N VAL D 371 " --> pdb=" O LEU D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 423 removed outlier: 3.796A pdb=" N ASP D 419 " --> pdb=" O ILE D 415 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N SER D 420 " --> pdb=" O LYS D 416 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N PHE D 421 " --> pdb=" O GLY D 417 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N SER D 422 " --> pdb=" O LEU D 418 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N GLY D 423 " --> pdb=" O ASP D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 453 removed outlier: 3.952A pdb=" N VAL D 441 " --> pdb=" O PRO D 437 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ILE D 442 " --> pdb=" O ILE D 438 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU D 443 " --> pdb=" O GLU D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 482 removed outlier: 3.800A pdb=" N GLU D 480 " --> pdb=" O SER D 476 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLU D 481 " --> pdb=" O LEU D 477 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N GLY D 482 " --> pdb=" O PHE D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 483 through 496 removed outlier: 4.376A pdb=" N VAL D 487 " --> pdb=" O MET D 483 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N CYS D 490 " --> pdb=" O LEU D 486 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL D 496 " --> pdb=" O ASP D 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 511 through 532 removed outlier: 4.460A pdb=" N TRP D 515 " --> pdb=" O ALA D 511 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N LYS D 516 " --> pdb=" O ALA D 512 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N GLU D 517 " --> pdb=" O GLU D 513 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N GLY D 532 " --> pdb=" O SER D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 541 removed outlier: 3.641A pdb=" N CYS D 537 " --> pdb=" O ASN D 533 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU D 539 " --> pdb=" O ALA D 535 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N PHE D 540 " --> pdb=" O ASN D 536 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N SER D 541 " --> pdb=" O CYS D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 551 removed outlier: 3.668A pdb=" N LYS D 550 " --> pdb=" O TRP D 546 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N LEU D 551 " --> pdb=" O VAL D 547 " (cutoff:3.500A) Processing helix chain 'D' and resid 556 through 571 removed outlier: 3.735A pdb=" N VAL D 567 " --> pdb=" O VAL D 563 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU D 568 " --> pdb=" O LEU D 564 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ILE D 569 " --> pdb=" O TYR D 565 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU D 570 " --> pdb=" O CYS D 566 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 578 removed outlier: 4.549A pdb=" N ASN D 576 " --> pdb=" O PRO D 572 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ILE D 577 " --> pdb=" O GLU D 573 " (cutoff:3.500A) removed outlier: 4.007A 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: 3.558A pdb=" N LEU D 590 " --> pdb=" O ILE D 586 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP D 591 " --> pdb=" O ILE D 587 " (cutoff:3.500A) Processing helix chain 'D' and resid 596 through 609 removed outlier: 3.692A pdb=" N LEU D 600 " --> pdb=" O ASN D 596 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N CYS D 607 " --> pdb=" O LEU D 603 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N VAL D 608 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N CYS D 609 " --> pdb=" O SER D 605 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 625 removed outlier: 4.326A pdb=" N GLN D 618 " --> pdb=" O VAL D 614 " (cutoff:3.500A) Processing helix chain 'D' and resid 868 through 890 removed outlier: 3.856A pdb=" N GLU D 872 " --> pdb=" O GLU D 868 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N LYS D 873 " --> pdb=" O ARG D 869 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TRP D 882 " --> pdb=" O ILE D 878 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA D 883 " --> pdb=" O HIS D 879 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N GLU D 888 " --> pdb=" O LEU D 884 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N GLN D 889 " --> pdb=" O THR D 885 " (cutoff:3.500A) Processing helix chain 'D' and resid 914 through 935 removed outlier: 5.178A pdb=" N LEU D 935 " --> pdb=" O THR D 931 " (cutoff:3.500A) Processing helix chain 'D' and resid 943 through 948 removed outlier: 6.279A pdb=" N GLU D 947 " --> pdb=" O ASP D 943 " (cutoff:3.500A) removed outlier: 3.949A 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 removed outlier: 3.759A pdb=" N MET D 960 " --> pdb=" O PRO D 956 " (cutoff:3.500A) Processing helix chain 'D' and resid 978 through 1001 removed outlier: 4.303A pdb=" N THR D 982 " --> pdb=" O THR D 978 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ASP D 999 " --> pdb=" O VAL D 995 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ARG D1000 " --> pdb=" O TRP D 996 " (cutoff:3.500A) Processing helix chain 'D' and resid 1029 through 1045 removed outlier: 3.569A pdb=" N ASP D1037 " --> pdb=" O ARG D1033 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N SER D1038 " --> pdb=" O SER D1034 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU D1039 " --> pdb=" O ASN D1035 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N THR D1045 " --> pdb=" O GLN D1041 " (cutoff:3.500A) Processing helix chain 'D' and resid 1574 through 1581 removed outlier: 3.801A pdb=" N ALA D1578 " --> pdb=" O PRO D1574 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET D1579 " --> pdb=" O LEU D1575 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHE D1580 " --> pdb=" O SER D1576 " (cutoff:3.500A) removed outlier: 3.780A 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 1654 removed outlier: 4.097A pdb=" N LEU D1653 " --> pdb=" O ASP D1649 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N SER D1654 " --> pdb=" O ILE D1650 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1649 through 1654' Processing helix chain 'D' and resid 1656 through 1675 removed outlier: 6.006A pdb=" N GLN D1660 " --> pdb=" O ARG D1656 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N ARG D1661 " --> pdb=" O LEU D1657 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N CYS D1674 " --> pdb=" O TYR D1670 " (cutoff:3.500A) Processing helix chain 'D' and resid 1678 through 1690 removed outlier: 4.688A pdb=" N ALA D1682 " --> pdb=" O ASN D1678 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N HIS D1683 " --> pdb=" O ASN D1679 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA D1684 " --> pdb=" O ARG D1680 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASP D1690 " --> pdb=" O CYS D1686 " (cutoff:3.500A) Processing helix chain 'D' and resid 1691 through 1701 removed outlier: 3.821A pdb=" N LEU D1698 " --> pdb=" O LEU D1694 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLU D1699 " --> pdb=" O LEU D1695 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP D1700 " --> pdb=" O HIS D1696 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N ALA D1701 " --> pdb=" O ALA D1697 " (cutoff:3.500A) Processing helix chain 'D' and resid 1704 through 1719 removed outlier: 6.844A pdb=" N ARG D1708 " --> pdb=" O PRO D1704 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA D1709 " --> pdb=" O GLY D1705 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N HIS D1719 " --> pdb=" O LEU D1715 " (cutoff:3.500A) Processing helix chain 'D' and resid 1720 through 1732 removed outlier: 4.577A pdb=" N SER D1732 " --> pdb=" O ARG D1728 " (cutoff:3.500A) Processing helix chain 'D' and resid 1739 through 1745 removed outlier: 4.153A pdb=" N ILE D1745 " --> pdb=" O GLU D1741 " (cutoff:3.500A) Processing helix chain 'D' and resid 1754 through 1759 removed outlier: 4.287A pdb=" N ARG D1759 " --> pdb=" O GLY D1755 " (cutoff:3.500A) Processing helix chain 'D' and resid 1803 through 1825 removed outlier: 3.699A pdb=" N LEU D1807 " --> pdb=" O PRO D1803 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP D1809 " --> pdb=" O GLU D1805 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL D1819 " --> pdb=" O LEU D1815 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG D1820 " --> pdb=" O GLY D1816 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLN D1824 " --> pdb=" O ARG D1820 " (cutoff:3.500A) removed outlier: 4.455A 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: 3.692A pdb=" N MET D1851 " --> pdb=" O THR D1847 " (cutoff:3.500A) Processing helix chain 'D' and resid 1855 through 1865 removed outlier: 4.020A pdb=" N MET D1865 " --> pdb=" O GLN D1861 " (cutoff:3.500A) Processing helix chain 'D' and resid 1932 through 1984 removed outlier: 7.021A pdb=" N LYS D1936 " --> pdb=" O PRO D1932 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N LEU D1937 " --> pdb=" O GLU D1933 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLN D1938 " --> pdb=" O SER D1934 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TYR D1945 " --> pdb=" O ASN D1941 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N PHE D1946 " --> pdb=" O LEU D1942 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU D1950 " --> pdb=" O PHE D1946 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU D1951 " --> pdb=" O CYS D1947 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU D1963 " --> pdb=" O ALA D1959 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG D1964 " --> pdb=" O ALA D1960 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N PHE D1984 " --> pdb=" O LEU D1980 " (cutoff:3.500A) Processing helix chain 'D' and resid 1987 through 1999 removed outlier: 4.146A pdb=" N ARG D1996 " --> pdb=" O ALA D1992 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLU D1997 " --> pdb=" O ARG D1993 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE D1998 " --> pdb=" O ARG D1994 " (cutoff:3.500A) Processing helix chain 'D' and resid 2001 through 2015 removed outlier: 3.569A pdb=" N LEU D2009 " --> pdb=" O GLN D2005 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU D2010 " --> pdb=" O ILE D2006 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLU D2015 " --> pdb=" O HIS D2011 " (cutoff:3.500A) Processing helix chain 'D' and resid 2027 through 2043 removed outlier: 4.730A pdb=" N LEU D2031 " --> pdb=" O ILE D2027 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN D2032 " --> pdb=" O ARG D2028 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N GLY D2043 " --> pdb=" O LEU D2039 " (cutoff:3.500A) Processing helix chain 'D' and resid 2093 through 2109 removed outlier: 3.519A pdb=" N VAL D2103 " --> pdb=" O SER D2099 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASP D2109 " --> pdb=" O TRP D2105 " (cutoff:3.500A) Processing helix chain 'D' and resid 2113 through 2130 removed outlier: 3.720A pdb=" N LEU D2123 " --> pdb=" O ALA D2119 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLY D2130 " --> pdb=" O ARG D2126 " (cutoff:3.500A) Processing helix chain 'D' and resid 2131 through 2142 Proline residue: D2139 - end of helix removed outlier: 5.700A pdb=" N TYR D2142 " --> pdb=" O LEU D2138 " (cutoff:3.500A) Processing helix chain 'D' and resid 2148 through 2169 removed outlier: 4.273A pdb=" N SER D2154 " --> pdb=" O GLU D2150 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LEU D2155 " --> pdb=" O ASP D2151 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ILE D2167 " --> pdb=" O ARG D2163 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N VAL D2168 " --> pdb=" O SER D2164 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N GLN D2169 " --> pdb=" O LEU D2165 " (cutoff:3.500A) Processing helix chain 'D' and resid 2171 through 2188 removed outlier: 3.577A pdb=" N ASN D2176 " --> pdb=" O PRO D2172 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU D2177 " --> pdb=" O GLN D2173 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ASN D2187 " --> pdb=" O GLY D2183 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ASN D2188 " --> pdb=" O ASN D2184 " (cutoff:3.500A) Processing helix chain 'D' and resid 2189 through 2195 removed outlier: 4.542A pdb=" N GLN D2193 " --> pdb=" O LYS D2189 " (cutoff:3.500A) removed outlier: 3.700A 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: 3.925A pdb=" N ASN D2213 " --> pdb=" O GLU D2209 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL D2214 " --> pdb=" O VAL D2210 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU D2215 " --> pdb=" O MET D2211 " (cutoff:3.500A) Processing helix chain 'D' and resid 2227 through 2244 removed outlier: 4.449A pdb=" N SER D2231 " --> pdb=" O LYS D2227 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N SER D2243 " --> pdb=" O PHE D2239 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N ARG D2244 " --> pdb=" O CYS D2240 " (cutoff:3.500A) Processing helix chain 'D' and resid 2245 through 2255 removed outlier: 4.199A pdb=" N SER D2249 " --> pdb=" O GLN D2245 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP D2252 " --> pdb=" O ARG D2248 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N HIS D2253 " --> pdb=" O SER D2249 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LEU D2254 " --> pdb=" O MET D2250 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N SER D2255 " --> pdb=" O PHE D2251 " (cutoff:3.500A) Processing helix chain 'D' and resid 2256 through 2265 removed outlier: 3.630A pdb=" N ASN D2260 " --> pdb=" O TYR D2256 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLY D2262 " --> pdb=" O LEU D2258 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N ILE D2263 " --> pdb=" O GLU D2259 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY D2264 " --> pdb=" O ASN D2260 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU D2265 " --> pdb=" O SER D2261 " (cutoff:3.500A) Processing helix chain 'D' and resid 2271 through 2282 removed outlier: 3.847A pdb=" N VAL D2275 " --> pdb=" O THR D2271 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA D2276 " --> pdb=" O PRO D2272 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL D2280 " --> pdb=" O ALA D2276 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ILE D2281 " --> pdb=" O ALA D2277 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N ASP D2282 " --> pdb=" O ALA D2278 " (cutoff:3.500A) Processing helix chain 'D' and resid 2286 through 2291 removed outlier: 3.702A pdb=" N LEU D2290 " --> pdb=" O LEU D2286 " (cutoff:3.500A) removed outlier: 4.530A 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 2309 removed outlier: 3.780A pdb=" N VAL D2299 " --> pdb=" O LEU D2295 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N SER D2300 " --> pdb=" O GLU D2296 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N TYR D2301 " --> pdb=" O LYS D2297 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU D2302 " --> pdb=" O VAL D2298 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU D2307 " --> pdb=" O ALA D2303 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N SER D2309 " --> pdb=" O CYS D2305 " (cutoff:3.500A) Processing helix chain 'D' and resid 2310 through 2315 removed outlier: 3.831A pdb=" N LEU D2314 " --> pdb=" O CYS D2310 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA D2315 " --> pdb=" O PRO D2311 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2310 through 2315' Processing helix chain 'D' and resid 2324 through 2341 removed outlier: 3.705A pdb=" N GLY D2328 " --> pdb=" O ASN D2324 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LEU D2332 " --> pdb=" O GLY D2328 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N ASP D2333 " --> pdb=" O GLU D2329 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N PHE D2334 " --> pdb=" O ARG D2330 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LEU D2335 " --> pdb=" O TYR D2331 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N VAL D2341 " --> pdb=" O PHE D2337 " (cutoff:3.500A) Processing helix chain 'D' and resid 2346 through 2361 removed outlier: 3.856A pdb=" N VAL D2352 " --> pdb=" O GLU D2348 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG D2359 " --> pdb=" O ARG D2355 " (cutoff:3.500A) removed outlier: 4.563A 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: 4.484A pdb=" N ARG D2452 " --> pdb=" O GLY D2448 " (cutoff:3.500A) removed outlier: 3.655A 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 2472 removed outlier: 4.295A pdb=" N GLY D2468 " --> pdb=" O ASP D2464 " (cutoff:3.500A) Processing helix chain 'D' and resid 2751 through 2774 removed outlier: 5.005A pdb=" N ILE D2755 " --> pdb=" O LEU D2751 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N THR D2762 " --> pdb=" O PHE D2758 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N HIS D2763 " --> pdb=" O ALA D2759 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU D2764 " --> pdb=" O GLU D2760 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LYS D2765 " --> pdb=" O TYR D2761 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N TRP D2766 " --> pdb=" O THR D2762 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ALA D2767 " --> pdb=" O HIS D2763 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N PHE D2768 " --> pdb=" O GLU D2764 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ASP D2769 " --> pdb=" O LYS D2765 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N LYS D2770 " --> pdb=" O TRP D2766 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N ILE D2771 " --> pdb=" O ALA D2767 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLN D2772 " --> pdb=" O PHE D2768 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ASN D2773 " --> pdb=" O ASP D2769 " (cutoff:3.500A) Processing helix chain 'D' and resid 2798 through 2804 removed outlier: 4.578A pdb=" N LYS D2802 " --> pdb=" O SER D2798 " (cutoff:3.500A) Processing helix chain 'D' and resid 2807 through 2813 removed outlier: 4.270A pdb=" N GLU D2811 " --> pdb=" O TRP D2807 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N SER D2812 " --> pdb=" O PRO D2808 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU D2813 " --> pdb=" O ILE D2809 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2807 through 2813' Processing helix chain 'D' and resid 2868 through 2873 removed outlier: 5.175A pdb=" N GLN D2872 " --> pdb=" O SER D2868 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ALA D2873 " --> pdb=" O ARG D2869 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2868 through 2873' Processing helix chain 'D' and resid 2874 through 2891 removed outlier: 4.589A pdb=" N ALA D2879 " --> pdb=" O ALA D2875 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ASN D2881 " --> pdb=" O GLN D2877 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N TYR D2882 " --> pdb=" O LEU D2878 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N LYS D2890 " --> pdb=" O TRP D2886 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N LYS D2891 " --> pdb=" O GLY D2887 " (cutoff:3.500A) Processing helix chain 'D' and resid 2919 through 2930 removed outlier: 4.481A pdb=" N ALA D2923 " --> pdb=" O ASP D2919 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU D2925 " --> pdb=" O GLU D2921 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N LYS D2928 " --> pdb=" O GLN D2924 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE D2929 " --> pdb=" O GLU D2925 " (cutoff:3.500A) Processing helix chain 'D' and resid 3645 through 3657 removed outlier: 3.829A pdb=" N GLU D3655 " --> pdb=" O ASN D3651 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N SER D3656 " --> pdb=" O MET D3652 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N TYR D3657 " --> pdb=" O PHE D3653 " (cutoff:3.500A) Processing helix chain 'D' and resid 3668 through 3680 removed outlier: 4.364A pdb=" N ALA D3680 " --> pdb=" O ASP D3676 " (cutoff:3.500A) Processing helix chain 'D' and resid 3683 through 3688 Processing helix chain 'D' and resid 3696 through 3712 removed outlier: 5.576A pdb=" N GLU D3712 " --> pdb=" O THR D3708 " (cutoff:3.500A) Processing helix chain 'D' and resid 3719 through 3735 removed outlier: 4.085A pdb=" N ASP D3727 " --> pdb=" O MET D3723 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N CYS D3733 " --> pdb=" O MET D3729 " (cutoff:3.500A) Processing helix chain 'D' and resid 3752 through 3771 removed outlier: 3.913A pdb=" N LEU D3770 " --> pdb=" O GLN D3766 " (cutoff:3.500A) Processing helix chain 'D' and resid 3774 through 3787 removed outlier: 4.116A pdb=" N MET D3778 " --> pdb=" O GLY D3774 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL D3779 " --> pdb=" O ALA D3775 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LEU D3780 " --> pdb=" O ALA D3776 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LYS D3787 " --> pdb=" O ILE D3783 " (cutoff:3.500A) Processing helix chain 'D' and resid 3791 through 3806 removed outlier: 3.655A pdb=" N SER D3795 " --> pdb=" O GLY D3791 " (cutoff:3.500A) Processing helix chain 'D' and resid 3809 through 3824 Processing helix chain 'D' and resid 3826 through 3839 removed outlier: 6.674A pdb=" N GLN D3830 " --> pdb=" O VAL D3826 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N CYS D3839 " --> pdb=" O LEU D3835 " (cutoff:3.500A) Processing helix chain 'D' and resid 3843 through 3858 removed outlier: 4.920A pdb=" N MET D3858 " --> pdb=" O GLU D3854 " (cutoff:3.500A) Processing helix chain 'D' and resid 3862 through 3872 removed outlier: 4.578A pdb=" N GLU D3872 " --> pdb=" O ARG D3868 " (cutoff:3.500A) Processing helix chain 'D' and resid 3877 through 3893 removed outlier: 3.744A pdb=" N CYS D3892 " --> pdb=" O LEU D3888 " (cutoff:3.500A) Processing helix chain 'D' and resid 3896 through 3905 removed outlier: 3.707A pdb=" N ARG D3904 " --> pdb=" O GLN D3900 " (cutoff:3.500A) Processing helix chain 'D' and resid 3914 through 3939 removed outlier: 3.949A pdb=" N CYS D3918 " --> pdb=" O ASN D3914 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N GLY D3939 " --> pdb=" O TRP D3935 " (cutoff:3.500A) Processing helix chain 'D' and resid 3944 through 3970 removed outlier: 3.708A pdb=" N GLN D3960 " --> pdb=" O SER D3956 " (cutoff:3.500A) Processing helix chain 'D' and resid 3973 through 3984 removed outlier: 4.921A pdb=" N ARG D3984 " --> pdb=" O LEU D3980 " (cutoff:3.500A) Processing helix chain 'D' and resid 3985 through 4004 Processing helix chain 'D' and resid 4009 through 4032 removed outlier: 3.740A pdb=" N LEU D4031 " --> pdb=" O LEU D4027 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLU D4032 " --> pdb=" O LEU D4028 " (cutoff:3.500A) Processing helix chain 'D' and resid 4039 through 4052 removed outlier: 5.909A pdb=" N GLN D4043 " --> pdb=" O MET D4039 " (cutoff:3.500A) Processing helix chain 'D' and resid 4053 through 4074 removed outlier: 3.513A pdb=" N PHE D4065 " --> pdb=" O PHE D4061 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY D4073 " --> pdb=" O LYS D4069 " (cutoff:3.500A) Processing helix chain 'D' and resid 4075 through 4082 removed outlier: 4.413A pdb=" N THR D4082 " --> pdb=" O GLN D4078 " (cutoff:3.500A) Processing helix chain 'D' and resid 4089 through 4101 removed outlier: 3.579A pdb=" N GLN D4094 " --> pdb=" O LYS D4090 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS D4095 " --> pdb=" O LYS D4091 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LYS D4101 " --> pdb=" O MET D4097 " (cutoff:3.500A) Processing helix chain 'D' and resid 4104 through 4116 removed outlier: 3.706A pdb=" N ILE D4108 " --> pdb=" O THR D4104 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN D4109 " --> pdb=" O GLY D4105 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N GLU D4116 " --> pdb=" O LEU D4112 " (cutoff:3.500A) Processing helix chain 'D' and resid 4124 through 4132 removed outlier: 5.407A pdb=" N PHE D4132 " --> pdb=" O PHE D4128 " (cutoff:3.500A) Processing helix chain 'D' and resid 4134 through 4155 removed outlier: 4.572A pdb=" N ASP D4138 " --> pdb=" O GLU D4134 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ILE D4139 " --> pdb=" O PRO D4135 " (cutoff:3.500A) Proline residue: D4155 - end of helix Processing helix chain 'D' and resid 4157 through 4168 removed outlier: 4.024A pdb=" N ARG D4161 " --> pdb=" O ASP D4157 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASN D4162 " --> pdb=" O PRO D4158 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE D4163 " --> pdb=" O ARG D4159 " (cutoff:3.500A) Processing helix chain 'D' and resid 4169 through 4179 Proline residue: D4176 - end of helix removed outlier: 5.791A pdb=" N GLY D4179 " --> pdb=" O ARG D4175 " (cutoff:3.500A) Processing helix chain 'D' and resid 4198 through 4207 removed outlier: 3.502A pdb=" N ARG D4202 " --> pdb=" O SER D4198 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N MET D4207 " --> pdb=" O ALA D4203 " (cutoff:3.500A) Processing helix chain 'D' and resid 4208 through 4224 Processing helix chain 'D' and resid 4229 through 4252 removed outlier: 3.570A pdb=" N PHE D4243 " --> pdb=" O GLU D4239 " (cutoff:3.500A) Processing helix chain 'D' and resid 4540 through 4559 removed outlier: 3.918A pdb=" N PHE D4559 " --> pdb=" O LEU D4555 " (cutoff:3.500A) Processing helix chain 'D' and resid 4560 through 4580 removed outlier: 5.013A pdb=" N TYR D4580 " --> pdb=" O ILE D4576 " (cutoff:3.500A) Processing helix chain 'D' and resid 4642 through 4684 removed outlier: 4.219A pdb=" N LEU D4646 " --> pdb=" O ALA D4642 " (cutoff:3.500A) removed outlier: 4.587A 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 4708 removed outlier: 3.874A pdb=" N GLN D4700 " --> pdb=" O ASP D4696 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LEU D4704 " --> pdb=" O GLN D4700 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N VAL D4705 " --> pdb=" O TRP D4701 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU D4706 " --> pdb=" O ASP D4702 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N ASN D4707 " --> pdb=" O ARG D4703 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N THR D4708 " --> pdb=" O LEU D4704 " (cutoff:3.500A) Processing helix chain 'D' and resid 4719 through 4728 Processing helix chain 'D' and resid 4733 through 4742 removed outlier: 4.620A pdb=" N GLY D4742 " --> pdb=" O ALA D4738 " (cutoff:3.500A) Processing helix chain 'D' and resid 4749 through 4755 Processing helix chain 'D' and resid 4772 through 4787 removed outlier: 5.450A pdb=" N ASN D4787 " --> pdb=" O ILE D4783 " (cutoff:3.500A) Processing helix chain 'D' and resid 4788 through 4802 removed outlier: 3.758A pdb=" N LEU D4792 " --> pdb=" O SER D4788 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLY D4802 " --> pdb=" O MET D4798 " (cutoff:3.500A) Processing helix chain 'D' and resid 4807 through 4820 removed outlier: 4.019A pdb=" N ALA D4811 " --> pdb=" O PHE D4807 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N HIS D4812 " --> pdb=" O PHE D4808 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LEU D4813 " --> pdb=" O PHE D4809 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N LEU D4814 " --> pdb=" O ALA D4810 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N ASP D4815 " --> pdb=" O ALA D4811 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N ILE D4816 " --> pdb=" O HIS D4812 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N ALA D4817 " --> pdb=" O LEU D4813 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N MET D4818 " --> pdb=" O LEU D4814 " (cutoff:3.500A) Processing helix chain 'D' and resid 4821 through 4835 removed outlier: 4.160A pdb=" N ASN D4833 " --> pdb=" O SER D4829 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY D4834 " --> pdb=" O VAL D4830 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N LYS D4835 " --> pdb=" O THR D4831 " (cutoff:3.500A) Processing helix chain 'D' and resid 4836 through 4859 Processing helix chain 'D' and resid 4878 through 4893 removed outlier: 3.989A pdb=" N LEU D4884 " --> pdb=" O MET D4880 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VAL D4891 " --> pdb=" O MET D4887 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ARG D4892 " --> pdb=" O TYR D4888 " (cutoff:3.500A) Processing helix chain 'D' and resid 4896 through 4902 removed outlier: 5.676A pdb=" N GLU D4902 " --> pdb=" O GLY D4898 " (cutoff:3.500A) Processing helix chain 'D' and resid 4910 through 4924 removed outlier: 6.541A pdb=" N VAL D4914 " --> pdb=" O GLU D4910 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N VAL D4915 " --> pdb=" O LEU D4911 " (cutoff:3.500A) Processing helix chain 'D' and resid 4928 through 4957 removed outlier: 3.622A pdb=" N ARG D4944 " --> pdb=" O PHE D4940 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN D4947 " --> pdb=" O LEU D4943 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N THR D4956 " --> pdb=" O GLU D4952 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N LYS D4957 " --> pdb=" O ASP D4953 " (cutoff:3.500A) Processing helix chain 'D' and resid 4964 through 4972 removed outlier: 4.452A pdb=" N PHE D4968 " --> pdb=" O GLY D4964 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N THR D4971 " --> pdb=" O TYR D4967 " (cutoff:3.500A) Proline residue: D4972 - end of helix Processing helix chain 'D' and resid 4973 through 4982 Processing helix chain 'D' and resid 4984 through 4999 removed outlier: 7.165A pdb=" N TYR D4988 " --> pdb=" O ASN D4984 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N MET D4989 " --> pdb=" O LEU D4985 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N ASP D4999 " --> pdb=" O LEU D4995 " (cutoff:3.500A) Processing helix chain 'D' and resid 5004 through 5017 Processing helix chain 'D' and resid 5027 through 5033 removed outlier: 6.050A pdb=" N GLN D5031 " --> pdb=" O CYS D5027 " (cutoff:3.500A) Processing helix chain 'D' and resid 4764 through 4769 removed outlier: 5.657A pdb=" N TRP D4767 " --> pdb=" O LEU D4764 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N LEU D4768 " --> pdb=" O LEU D4765 " (cutoff:3.500A) Processing helix chain 'D' and resid 1214 through 1219 removed outlier: 4.202A pdb=" N LEU D1219 " --> pdb=" O PHE D1214 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1214 through 1219' Processing helix chain 'D' and resid 4685 through 4690 Processing sheet with id= 1, first strand: chain 'A' and resid 47 through 52 removed outlier: 6.742A pdb=" N LYS A 34 " --> pdb=" O THR A 52 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LEU A 33 " --> pdb=" O ALA A 26 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LEU A 37 " --> pdb=" O LEU A 22 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N LEU A 22 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 10.455A pdb=" N ALA A 39 " --> pdb=" O VAL A 20 " (cutoff:3.500A) removed outlier: 13.579A pdb=" N VAL A 20 " --> pdb=" O ALA A 39 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N GLU A 19 " --> pdb=" O ILE A 205 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 105 through 108 removed outlier: 4.565A pdb=" N HIS A 105 " --> pdb=" O MET A 150 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N TRP A 147 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ALA A 153 " --> pdb=" O ASP A 168 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N ASP A 168 " --> pdb=" O ALA A 153 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 116 through 120 Processing sheet with id= 4, first strand: chain 'A' and resid 181 through 185 Processing sheet with id= 5, first strand: chain 'A' and resid 230 through 233 removed outlier: 5.219A pdb=" N VAL A 245 " --> pdb=" O ALA A 376 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS A 374 " --> pdb=" O TYR A 247 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'A' and resid 260 through 264 Processing sheet with id= 7, first strand: chain 'A' and resid 681 through 686 removed outlier: 4.535A pdb=" N TRP A1626 " --> pdb=" O PHE A 791 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE A 791 " --> pdb=" O TRP A1626 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N LYS A 788 " --> pdb=" O ASP A 669 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASP A 669 " --> pdb=" O LYS A 788 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N TRP A 662 " --> pdb=" O CYS A 747 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N CYS A 747 " --> pdb=" O TRP A 662 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N PHE A 664 " --> pdb=" O SER A 745 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N SER A 745 " --> pdb=" O PHE A 664 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL A 666 " --> pdb=" O VAL A 743 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N VAL A 743 " --> pdb=" O VAL A 666 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL A 668 " --> pdb=" O GLU A 741 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'A' and resid 830 through 833 removed outlier: 4.371A pdb=" N GLY A 836 " --> pdb=" O GLY A 833 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N LEU A1202 " --> pdb=" O PRO A 837 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N GLN A1198 " --> pdb=" O GLY A 841 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL A1199 " --> pdb=" O VAL A1095 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'A' and resid 1134 through 1138 removed outlier: 4.817A pdb=" N VAL A1123 " --> pdb=" O TRP A1132 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLY A1126 " --> pdb=" O MET A1100 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N MET A1100 " --> pdb=" O GLY A1126 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N GLU A1099 " --> pdb=" O GLY A1195 " (cutoff:3.500A) removed outlier: 10.314A pdb=" N VAL A1072 " --> pdb=" O SER A1241 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N SER A1241 " --> pdb=" O VAL A1072 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N ILE A1074 " --> pdb=" O SER A1239 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N GLU A1078 " --> pdb=" O THR A1235 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N THR A1235 " --> pdb=" O GLU A1078 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'A' and resid 4180 through 4184 Processing sheet with id= 11, first strand: chain 'A' and resid 1615 through 1619 Processing sheet with id= 12, first strand: chain 'B' and resid 47 through 52 removed outlier: 6.741A pdb=" N LYS B 34 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LEU B 33 " --> pdb=" O ALA B 26 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LEU B 37 " --> pdb=" O LEU B 22 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N LEU B 22 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 10.455A pdb=" N ALA B 39 " --> pdb=" O VAL B 20 " (cutoff:3.500A) removed outlier: 13.578A pdb=" N VAL B 20 " --> pdb=" O ALA B 39 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N GLU B 19 " --> pdb=" O ILE B 205 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'B' and resid 105 through 108 removed outlier: 4.564A pdb=" N HIS B 105 " --> pdb=" O MET B 150 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N TRP B 147 " --> pdb=" O VAL B 174 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ALA B 153 " --> pdb=" O ASP B 168 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N ASP B 168 " --> pdb=" O ALA B 153 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'B' and resid 116 through 120 Processing sheet with id= 15, first strand: chain 'B' and resid 181 through 185 Processing sheet with id= 16, first strand: chain 'B' and resid 230 through 233 removed outlier: 5.218A pdb=" N VAL B 245 " --> pdb=" O ALA B 376 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS B 374 " --> pdb=" O TYR B 247 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'B' and resid 260 through 264 Processing sheet with id= 18, first strand: chain 'B' and resid 681 through 686 removed outlier: 4.535A pdb=" N TRP B1626 " --> pdb=" O PHE B 791 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE B 791 " --> pdb=" O TRP B1626 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N LYS B 788 " --> pdb=" O ASP B 669 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASP B 669 " --> pdb=" O LYS B 788 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N TRP B 662 " --> pdb=" O CYS B 747 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N CYS B 747 " --> pdb=" O TRP B 662 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N PHE B 664 " --> pdb=" O SER B 745 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N SER B 745 " --> pdb=" O PHE B 664 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL B 666 " --> pdb=" O VAL B 743 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N VAL B 743 " --> pdb=" O VAL B 666 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL B 668 " --> pdb=" O GLU B 741 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'B' and resid 830 through 833 removed outlier: 4.370A pdb=" N GLY B 836 " --> pdb=" O GLY B 833 " (cutoff:3.500A) removed outlier: 5.221A 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: 6.620A pdb=" N VAL B1199 " --> pdb=" O VAL B1095 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'B' and resid 1134 through 1138 removed outlier: 4.816A pdb=" N VAL B1123 " --> pdb=" O TRP B1132 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLY B1126 " --> pdb=" O MET B1100 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N MET B1100 " --> pdb=" O GLY B1126 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N GLU B1099 " --> pdb=" O GLY B1195 " (cutoff:3.500A) removed outlier: 10.314A pdb=" N VAL B1072 " --> pdb=" O SER B1241 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N SER B1241 " --> pdb=" O VAL B1072 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N ILE B1074 " --> pdb=" O SER B1239 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLU B1078 " --> pdb=" O THR B1235 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N THR B1235 " --> pdb=" O GLU B1078 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'B' and resid 4180 through 4184 Processing sheet with id= 22, first strand: chain 'B' and resid 1615 through 1619 Processing sheet with id= 23, first strand: chain 'C' and resid 47 through 52 removed outlier: 6.742A pdb=" N LYS C 34 " --> pdb=" O THR C 52 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LEU C 33 " --> pdb=" O ALA C 26 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LEU C 37 " --> pdb=" O LEU C 22 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N LEU C 22 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 10.455A pdb=" N ALA C 39 " --> pdb=" O VAL C 20 " (cutoff:3.500A) removed outlier: 13.579A pdb=" N VAL C 20 " --> pdb=" O ALA C 39 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N GLU C 19 " --> pdb=" O ILE C 205 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'C' and resid 105 through 108 removed outlier: 4.564A pdb=" N HIS C 105 " --> pdb=" O MET C 150 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N TRP C 147 " --> pdb=" O VAL C 174 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ALA C 153 " --> pdb=" O ASP C 168 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N ASP C 168 " --> pdb=" O ALA C 153 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'C' and resid 116 through 120 Processing sheet with id= 26, first strand: chain 'C' and resid 181 through 185 Processing sheet with id= 27, first strand: chain 'C' and resid 230 through 233 removed outlier: 5.218A pdb=" N VAL C 245 " --> pdb=" O ALA C 376 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS C 374 " --> pdb=" O TYR C 247 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'C' and resid 260 through 264 Processing sheet with id= 29, first strand: chain 'C' and resid 681 through 686 removed outlier: 4.535A pdb=" N TRP C1626 " --> pdb=" O PHE C 791 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE C 791 " --> pdb=" O TRP C1626 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N LYS C 788 " --> pdb=" O ASP C 669 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASP C 669 " --> pdb=" O LYS C 788 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N TRP C 662 " --> pdb=" O CYS C 747 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N CYS C 747 " --> pdb=" O TRP C 662 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N PHE C 664 " --> pdb=" O SER C 745 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N SER C 745 " --> pdb=" O PHE C 664 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL C 666 " --> pdb=" O VAL C 743 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N VAL C 743 " --> pdb=" O VAL C 666 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL C 668 " --> pdb=" O GLU C 741 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'C' and resid 830 through 833 removed outlier: 4.370A pdb=" N GLY C 836 " --> pdb=" O GLY C 833 " (cutoff:3.500A) removed outlier: 5.221A 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: 6.620A pdb=" N VAL C1199 " --> pdb=" O VAL C1095 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'C' and resid 1134 through 1138 removed outlier: 4.817A pdb=" N VAL C1123 " --> pdb=" O TRP C1132 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLY C1126 " --> pdb=" O MET C1100 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N MET C1100 " --> pdb=" O GLY C1126 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N GLU C1099 " --> pdb=" O GLY C1195 " (cutoff:3.500A) removed outlier: 10.314A pdb=" N VAL C1072 " --> pdb=" O SER C1241 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N SER C1241 " --> pdb=" O VAL C1072 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N ILE C1074 " --> pdb=" O SER C1239 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N GLU C1078 " --> pdb=" O THR C1235 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N THR C1235 " --> pdb=" O GLU C1078 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'C' and resid 4180 through 4184 Processing sheet with id= 33, first strand: chain 'C' and resid 1615 through 1619 Processing sheet with id= 34, first strand: chain 'D' and resid 47 through 52 removed outlier: 6.742A pdb=" N LYS D 34 " --> pdb=" O THR D 52 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LEU D 33 " --> pdb=" O ALA D 26 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LEU D 37 " --> pdb=" O LEU D 22 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N LEU D 22 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 10.455A pdb=" N ALA D 39 " --> pdb=" O VAL D 20 " (cutoff:3.500A) removed outlier: 13.579A pdb=" N VAL D 20 " --> pdb=" O ALA D 39 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N GLU D 19 " --> pdb=" O ILE D 205 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'D' and resid 105 through 108 removed outlier: 4.565A pdb=" N HIS D 105 " --> pdb=" O MET D 150 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N TRP D 147 " --> pdb=" O VAL D 174 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ALA D 153 " --> pdb=" O ASP D 168 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N ASP D 168 " --> pdb=" O ALA D 153 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'D' and resid 116 through 120 Processing sheet with id= 37, first strand: chain 'D' and resid 181 through 185 Processing sheet with id= 38, first strand: chain 'D' and resid 230 through 233 removed outlier: 5.219A pdb=" N VAL D 245 " --> pdb=" O ALA D 376 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS D 374 " --> pdb=" O TYR D 247 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'D' and resid 260 through 264 Processing sheet with id= 40, first strand: chain 'D' and resid 681 through 686 removed outlier: 4.536A pdb=" N TRP D1626 " --> pdb=" O PHE D 791 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE D 791 " --> pdb=" O TRP D1626 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N LYS D 788 " --> pdb=" O ASP D 669 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASP D 669 " --> pdb=" O LYS D 788 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N TRP D 662 " --> pdb=" O CYS D 747 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N CYS D 747 " --> pdb=" O TRP D 662 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N PHE D 664 " --> pdb=" O SER D 745 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N SER D 745 " --> pdb=" O PHE D 664 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL D 666 " --> pdb=" O VAL D 743 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N VAL D 743 " --> pdb=" O VAL D 666 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL D 668 " --> pdb=" O GLU D 741 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'D' and resid 830 through 833 removed outlier: 4.370A pdb=" N GLY D 836 " --> pdb=" O GLY D 833 " (cutoff:3.500A) removed outlier: 5.220A 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: 6.620A pdb=" N VAL D1199 " --> pdb=" O VAL D1095 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'D' and resid 1134 through 1138 removed outlier: 4.816A pdb=" N VAL D1123 " --> pdb=" O TRP D1132 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLY D1126 " --> pdb=" O MET D1100 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N MET D1100 " --> pdb=" O GLY D1126 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N GLU D1099 " --> pdb=" O GLY D1195 " (cutoff:3.500A) removed outlier: 10.314A pdb=" N VAL D1072 " --> pdb=" O SER D1241 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N SER D1241 " --> pdb=" O VAL D1072 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N ILE D1074 " --> pdb=" O SER D1239 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N GLU D1078 " --> pdb=" O THR D1235 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N THR D1235 " --> pdb=" O GLU D1078 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'D' and resid 4180 through 4184 Processing sheet with id= 44, first strand: chain 'D' and resid 1615 through 1619 4384 hydrogen bonds defined for protein. 13092 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: 58.57 Time building geometry restraints manager: 40.43 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: 40029 1.35 - 1.48: 28058 1.48 - 1.61: 50213 1.61 - 1.74: 16 1.74 - 1.87: 996 Bond restraints: 119312 Sorted by residual: bond pdb=" C1' ACP A5101 " pdb=" O4' ACP A5101 " ideal model delta sigma weight residual 1.390 1.625 -0.235 2.00e-02 2.50e+03 1.38e+02 bond pdb=" C1' ACP B5101 " pdb=" O4' ACP B5101 " ideal model delta sigma weight residual 1.390 1.624 -0.234 2.00e-02 2.50e+03 1.37e+02 bond pdb=" C1' ACP D5101 " pdb=" O4' ACP D5101 " 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 A5101 " pdb=" C2' ACP A5101 " ideal model delta sigma weight residual 1.527 1.296 0.231 2.00e-02 2.50e+03 1.34e+02 bond pdb=" C1' ACP C5101 " pdb=" O4' ACP C5101 " ideal model delta sigma weight residual 1.390 1.621 -0.231 2.00e-02 2.50e+03 1.34e+02 ... (remaining 119307 not shown) Histogram of bond angle deviations from ideal: 94.75 - 102.62: 448 102.62 - 110.49: 29395 110.49 - 118.35: 62539 118.35 - 126.22: 68537 126.22 - 134.09: 1801 Bond angle restraints: 162720 Sorted by residual: angle pdb=" O3A ACP B5101 " pdb=" PA ACP B5101 " pdb=" O5' ACP B5101 " ideal model delta sigma weight residual 93.75 110.88 -17.13 3.00e+00 1.11e-01 3.26e+01 angle pdb=" C HIS B4153 " pdb=" N VAL B4154 " pdb=" CA VAL B4154 " ideal model delta sigma weight residual 122.60 118.75 3.85 6.80e-01 2.16e+00 3.21e+01 angle pdb=" C HIS C4153 " pdb=" N VAL C4154 " pdb=" CA VAL C4154 " ideal model delta sigma weight residual 122.60 118.76 3.84 6.80e-01 2.16e+00 3.20e+01 angle pdb=" C HIS D4153 " pdb=" N VAL D4154 " pdb=" CA VAL D4154 " ideal model delta sigma weight residual 122.60 118.76 3.84 6.80e-01 2.16e+00 3.20e+01 angle pdb=" C HIS A4153 " pdb=" N VAL A4154 " pdb=" CA VAL A4154 " ideal model delta sigma weight residual 122.60 118.76 3.84 6.80e-01 2.16e+00 3.19e+01 ... (remaining 162715 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.78: 65315 21.78 - 43.56: 5060 43.56 - 65.35: 642 65.35 - 87.13: 167 87.13 - 108.91: 24 Dihedral angle restraints: 71208 sinusoidal: 23008 harmonic: 48200 Sorted by residual: dihedral pdb=" CA ILE A 759 " pdb=" C ILE A 759 " pdb=" N ASN A 760 " pdb=" CA ASN A 760 " ideal model delta harmonic sigma weight residual 180.00 154.58 25.42 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA ILE B 759 " pdb=" C ILE B 759 " pdb=" N ASN B 760 " pdb=" CA ASN B 760 " ideal model delta harmonic sigma weight residual 180.00 154.58 25.42 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA ILE D 759 " pdb=" C ILE D 759 " pdb=" N ASN D 760 " pdb=" CA ASN D 760 " ideal model delta harmonic sigma weight residual 180.00 154.59 25.41 0 5.00e+00 4.00e-02 2.58e+01 ... (remaining 71205 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 17847 0.084 - 0.168: 1149 0.168 - 0.252: 28 0.252 - 0.336: 12 0.336 - 0.420: 4 Chirality restraints: 19040 Sorted by residual: chirality pdb=" C2' ACP A5101 " pdb=" C1' ACP A5101 " pdb=" C3' ACP A5101 " pdb=" O2' ACP A5101 " both_signs ideal model delta sigma weight residual False -2.75 -2.33 -0.42 2.00e-01 2.50e+01 4.42e+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 -2.37 -0.38 2.00e-01 2.50e+01 3.69e+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 -2.38 -0.37 2.00e-01 2.50e+01 3.48e+00 ... (remaining 19037 not shown) Planarity restraints: 21416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET B1573 " 0.072 5.00e-02 4.00e+02 1.08e-01 1.88e+01 pdb=" N PRO B1574 " -0.187 5.00e-02 4.00e+02 pdb=" CA PRO B1574 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO B1574 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET C1573 " 0.072 5.00e-02 4.00e+02 1.08e-01 1.88e+01 pdb=" N PRO C1574 " -0.187 5.00e-02 4.00e+02 pdb=" CA PRO C1574 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO C1574 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A1573 " -0.072 5.00e-02 4.00e+02 1.08e-01 1.87e+01 pdb=" N PRO A1574 " 0.187 5.00e-02 4.00e+02 pdb=" CA PRO A1574 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO A1574 " -0.059 5.00e-02 4.00e+02 ... (remaining 21413 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 10274 2.75 - 3.29: 115960 3.29 - 3.82: 184550 3.82 - 4.36: 192214 4.36 - 4.90: 340222 Nonbonded interactions: 843220 Sorted by model distance: nonbonded pdb=" NH1 ARG B4736 " pdb=" OD2 ASP C4079 " model vdw 2.210 2.520 nonbonded pdb=" OD1 ASP B4938 " pdb=" NH1 ARG C4944 " model vdw 2.214 2.520 nonbonded pdb=" O GLN D 56 " pdb=" OG1 THR D 309 " model vdw 2.236 2.440 nonbonded pdb=" O GLN C 56 " pdb=" OG1 THR C 309 " model vdw 2.237 2.440 nonbonded pdb=" O GLN A 56 " pdb=" OG1 THR A 309 " model vdw 2.237 2.440 ... (remaining 843215 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: 2.710 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: 22.750 Check model and map are aligned: 1.260 Set scattering table: 0.740 Process input model: 261.230 Find NCS groups from input model: 5.940 Set up NCS constraints: 0.550 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 297.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 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 : 0.004 0.235 119312 Z= 0.276 Angle : 0.866 17.133 162720 Z= 0.435 Chirality : 0.042 0.420 19040 Planarity : 0.005 0.108 21416 Dihedral : 15.754 108.909 39836 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.73 % Favored : 94.14 % Rotamer Outliers : 0.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.07), residues: 12808 helix: 1.24 (0.07), residues: 5932 sheet: -0.28 (0.15), residues: 1180 loop : -1.62 (0.08), residues: 5696 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25616 Ramachandran restraints generated. 12808 Oldfield, 0 Emsley, 12808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25616 Ramachandran restraints generated. 12808 Oldfield, 0 Emsley, 12808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1185 residues out of total 11248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 1139 time to evaluate : 9.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 19 residues processed: 1173 average time/residue: 0.8823 time to fit residues: 1876.6516 Evaluate side-chains 902 residues out of total 11248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 883 time to evaluate : 9.289 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.8336 time to fit residues: 42.1142 ------------------------------------------------------------------------------- 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 98 HIS ** A 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 705 ASN A 725 HIS ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 911 HIS A1041 GLN ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1206 GLN A1254 HIS ** A1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1693 GLN ** A1825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2245 GLN A2247 GLN A2349 ASN A2756 ASN ** A2788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3699 HIS A3700 GLN A3761 GLN ** A3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3781 GLN A3976 ASN A3994 HIS A4043 GLN A4120 ASN A4204 GLN ** A4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4805 ASN A4832 HIS A4949 GLN A4984 ASN A5015 GLN B 56 GLN B 98 HIS ** B 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 ASN ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 597 HIS ** B 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 705 ASN B 725 HIS ** B 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 911 HIS B1041 GLN ** B1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1206 GLN B1254 HIS ** B1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1693 GLN ** B1825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2245 GLN B2247 GLN B2349 ASN B2756 ASN ** B2788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3699 HIS ** B3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3781 GLN B3976 ASN B3994 HIS B4043 GLN B4120 ASN B4204 GLN ** B4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4805 ASN B4832 HIS B4949 GLN B4973 HIS B4984 ASN B5015 GLN C 98 HIS ** C 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 705 ASN C 725 HIS ** C 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 911 HIS C1041 GLN ** C1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1206 GLN C1254 HIS C1274 HIS ** C1683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1693 GLN ** C1825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2245 GLN C2247 GLN C2349 ASN C2756 ASN ** C2788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3699 HIS C3700 GLN C3761 GLN ** C3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3781 GLN C3976 ASN C3994 HIS C4043 GLN C4120 ASN ** C4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C4805 ASN C4832 HIS C4949 GLN C4984 ASN C5003 HIS C5015 GLN D 98 HIS ** D 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 705 ASN D 725 HIS ** D 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 911 HIS D1041 GLN ** D1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1206 GLN D1254 HIS ** D1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1693 GLN ** D1825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2245 GLN D2247 GLN D2349 ASN D2756 ASN ** D2788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3699 HIS D3700 GLN D3761 GLN ** D3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3781 GLN D3976 ASN D3994 HIS D4043 GLN D4120 ASN ** D4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4805 ASN D4832 HIS D4949 GLN D4984 ASN D5015 GLN Total number of N/Q/H flips: 106 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.7108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.052 0.360 119312 Z= 3.372 Angle : 3.218 36.008 162720 Z= 1.607 Chirality : 0.142 0.655 19040 Planarity : 0.020 0.263 21416 Dihedral : 11.933 117.979 17504 Min Nonbonded Distance : 1.441 Molprobity Statistics. All-atom Clashscore : 80.91 Ramachandran Plot: Outliers : 2.83 % Allowed : 18.54 % Favored : 78.63 % Rotamer Outliers : 16.93 % Cbeta Deviations : 0.50 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.78 % Twisted General : 1.45 % 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: -5.73 (0.05), residues: 12808 helix: -3.54 (0.04), residues: 5992 sheet: -2.84 (0.14), residues: 1236 loop : -4.30 (0.06), residues: 5580 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25616 Ramachandran restraints generated. 12808 Oldfield, 0 Emsley, 12808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25616 Ramachandran restraints generated. 12808 Oldfield, 0 Emsley, 12808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2319 residues out of total 11248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1702 poor density : 617 time to evaluate : 9.259 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 outliers start: 1702 outliers final: 1058 residues processed: 2169 average time/residue: 0.9200 time to fit residues: 3653.2262 Evaluate side-chains 1626 residues out of total 11248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1058 poor density : 568 time to evaluate : 9.265 Switching outliers to nearest non-outliers 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: 1058 outliers final: 23 residues processed: 1058 average time/residue: 0.7904 time to fit residues: 1595.5826 ------------------------------------------------------------------------------- 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: 7.9990 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 56 GLN ** A 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 ASN ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 GLN ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 597 HIS ** A 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 647 ASN A 735 GLN ** A 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1691 GLN ** A1825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2011 HIS A2100 HIS ** A2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 380 GLN ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 617 ASN B 647 ASN B 735 GLN ** B 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1691 GLN ** B1825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2011 HIS B2100 HIS ** B2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4832 HIS C 56 GLN ** C 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 380 GLN ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 597 HIS ** C 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 647 ASN C 735 GLN ** C 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 911 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1691 GLN ** C1825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2011 HIS C2100 HIS ** C2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3667 HIS ** C3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 56 GLN ** D 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 201 ASN ** D 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 380 GLN ** D 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 597 HIS ** D 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 647 ASN D 735 GLN ** D 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1691 GLN ** D1825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2011 HIS D2100 HIS ** D2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D5003 HIS Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.8364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.051 0.358 119312 Z= 3.273 Angle : 3.100 34.358 162720 Z= 1.546 Chirality : 0.139 0.703 19040 Planarity : 0.019 0.229 21416 Dihedral : 13.005 136.024 17504 Min Nonbonded Distance : 1.358 Molprobity Statistics. All-atom Clashscore : 91.41 Ramachandran Plot: Outliers : 2.58 % Allowed : 29.18 % Favored : 68.25 % Rotamer Outliers : 22.10 % Cbeta Deviations : 0.40 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.25 % Twisted General : 2.29 % 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: -6.84 (0.05), residues: 12808 helix: -4.30 (0.04), residues: 5968 sheet: -3.92 (0.12), residues: 1196 loop : -4.93 (0.06), residues: 5644 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25616 Ramachandran restraints generated. 12808 Oldfield, 0 Emsley, 12808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25616 Ramachandran restraints generated. 12808 Oldfield, 0 Emsley, 12808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2790 residues out of total 11248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2221 poor density : 569 time to evaluate : 9.522 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 outliers start: 2221 outliers final: 1478 residues processed: 2665 average time/residue: 0.9137 time to fit residues: 4414.5884 Evaluate side-chains 2054 residues out of total 11248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1478 poor density : 576 time to evaluate : 9.351 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1478 outliers final: 28 residues processed: 1478 average time/residue: 0.8333 time to fit residues: 2345.4775 ------------------------------------------------------------------------------- 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 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1691 GLN ** A1825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2035 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2176 ASN ** A2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4886 HIS A5003 HIS ** B 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1691 GLN ** B1825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2176 ASN ** B2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B5003 HIS ** C 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 ASN ** C 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 911 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1691 GLN ** C1825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2035 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3667 HIS ** C3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C4102 GLN ** C4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 197 GLN ** D 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 647 ASN ** D 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1691 GLN ** D1825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2035 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4102 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.9032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.051 0.365 119312 Z= 3.310 Angle : 3.117 36.542 162720 Z= 1.552 Chirality : 0.140 0.663 19040 Planarity : 0.020 0.260 21416 Dihedral : 13.487 143.149 17504 Min Nonbonded Distance : 1.309 Molprobity Statistics. All-atom Clashscore : 96.19 Ramachandran Plot: Outliers : 2.60 % Allowed : 34.00 % Favored : 63.40 % Rotamer Outliers : 19.65 % Cbeta Deviations : 0.43 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.91 % Twisted General : 2.93 % 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: -7.13 (0.05), residues: 12808 helix: -4.49 (0.03), residues: 5920 sheet: -4.24 (0.12), residues: 1140 loop : -5.11 (0.06), residues: 5748 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25616 Ramachandran restraints generated. 12808 Oldfield, 0 Emsley, 12808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25616 Ramachandran restraints generated. 12808 Oldfield, 0 Emsley, 12808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2532 residues out of total 11248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1975 poor density : 557 time to evaluate : 9.080 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: 1975 outliers final: 1238 residues processed: 2431 average time/residue: 0.9118 time to fit residues: 4012.3404 Evaluate side-chains 1791 residues out of total 11248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1238 poor density : 553 time to evaluate : 9.352 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 1238 outliers final: 29 residues processed: 1238 average time/residue: 0.9112 time to fit residues: 2141.5214 ------------------------------------------------------------------------------- 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 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 350 HIS ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1691 GLN ** A1825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2035 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3667 HIS ** A3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4102 GLN A4133 GLN ** A4886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 350 HIS ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 536 ASN ** B 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2035 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3667 HIS ** B3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4102 GLN B4133 GLN ** C 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 350 HIS ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 617 ASN ** C 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2035 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3667 HIS ** C3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C4133 GLN ** D 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 647 ASN ** D 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1691 GLN ** D1825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2035 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4133 GLN ** D4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.9378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.051 0.363 119312 Z= 3.303 Angle : 3.108 39.051 162720 Z= 1.550 Chirality : 0.140 0.667 19040 Planarity : 0.020 0.277 21416 Dihedral : 13.725 175.581 17504 Min Nonbonded Distance : 1.277 Molprobity Statistics. All-atom Clashscore : 97.14 Ramachandran Plot: Outliers : 2.48 % Allowed : 35.89 % Favored : 61.63 % Rotamer Outliers : 17.71 % Cbeta Deviations : 0.42 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.40 % Twisted General : 3.29 % 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: -7.27 (0.04), residues: 12808 helix: -4.53 (0.03), residues: 5972 sheet: -4.52 (0.12), residues: 1076 loop : -5.23 (0.06), residues: 5760 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25616 Ramachandran restraints generated. 12808 Oldfield, 0 Emsley, 12808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25616 Ramachandran restraints generated. 12808 Oldfield, 0 Emsley, 12808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2327 residues out of total 11248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1780 poor density : 547 time to evaluate : 9.437 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 outliers start: 1780 outliers final: 1171 residues processed: 2242 average time/residue: 0.9419 time to fit residues: 3837.7163 Evaluate side-chains 1725 residues out of total 11248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1171 poor density : 554 time to evaluate : 8.378 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1171 outliers final: 34 residues processed: 1171 average time/residue: 0.8472 time to fit residues: 1892.1458 ------------------------------------------------------------------------------- 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: 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 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 HIS ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2035 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3667 HIS ** A3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3781 GLN ** A3833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 HIS ** B 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1691 GLN ** B1825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2035 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3667 HIS ** B3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2035 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2176 ASN ** C2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3667 HIS ** C3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 HIS ** D 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 350 HIS ** D 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 647 ASN ** D 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2035 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2176 ASN ** D2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.9621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.051 0.364 119312 Z= 3.305 Angle : 3.110 40.211 162720 Z= 1.551 Chirality : 0.141 0.712 19040 Planarity : 0.020 0.245 21416 Dihedral : 13.906 175.081 17504 Min Nonbonded Distance : 1.310 Molprobity Statistics. All-atom Clashscore : 97.95 Ramachandran Plot: Outliers : 2.33 % Allowed : 36.92 % Favored : 60.74 % Rotamer Outliers : 15.44 % Cbeta Deviations : 0.39 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.07 % Twisted General : 3.63 % 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: -7.35 (0.04), residues: 12808 helix: -4.57 (0.03), residues: 6004 sheet: -4.30 (0.12), residues: 1176 loop : -5.36 (0.05), residues: 5628 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25616 Ramachandran restraints generated. 12808 Oldfield, 0 Emsley, 12808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25616 Ramachandran restraints generated. 12808 Oldfield, 0 Emsley, 12808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2096 residues out of total 11248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1552 poor density : 544 time to evaluate : 9.400 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 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: 1552 outliers final: 962 residues processed: 2025 average time/residue: 0.9385 time to fit residues: 3431.0029 Evaluate side-chains 1505 residues out of total 11248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 962 poor density : 543 time to evaluate : 9.325 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 962 outliers final: 37 residues processed: 962 average time/residue: 0.8577 time to fit residues: 1560.8205 ------------------------------------------------------------------------------- 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 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2035 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3734 HIS ** A3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3781 GLN ** A3833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 ASN ** B 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 536 ASN ** B 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2035 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3667 HIS ** B3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 911 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2035 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3667 HIS ** C3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 647 ASN ** D 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2035 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3667 HIS D3734 HIS ** D3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.9796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.051 0.354 119312 Z= 3.310 Angle : 3.115 40.165 162720 Z= 1.556 Chirality : 0.141 0.741 19040 Planarity : 0.020 0.277 21416 Dihedral : 14.061 171.443 17504 Min Nonbonded Distance : 1.303 Molprobity Statistics. All-atom Clashscore : 98.59 Ramachandran Plot: Outliers : 2.37 % Allowed : 37.45 % Favored : 60.17 % Rotamer Outliers : 10.86 % Cbeta Deviations : 0.45 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.57 % Twisted General : 3.78 % 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: -7.37 (0.04), residues: 12808 helix: -4.58 (0.03), residues: 5984 sheet: -4.26 (0.12), residues: 1188 loop : -5.39 (0.05), residues: 5636 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25616 Ramachandran restraints generated. 12808 Oldfield, 0 Emsley, 12808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25616 Ramachandran restraints generated. 12808 Oldfield, 0 Emsley, 12808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1626 residues out of total 11248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1092 poor density : 534 time to evaluate : 9.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1092 outliers final: 645 residues processed: 1570 average time/residue: 0.9583 time to fit residues: 2712.6237 Evaluate side-chains 1184 residues out of total 11248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 645 poor density : 539 time to evaluate : 8.480 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 645 outliers final: 35 residues processed: 645 average time/residue: 0.8490 time to fit residues: 1037.6557 ------------------------------------------------------------------------------- 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: 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 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2035 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2035 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3667 HIS ** B3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 911 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2035 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3667 HIS ** C3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 647 ASN ** D 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2035 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3667 HIS ** D3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.9946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.051 0.355 119312 Z= 3.313 Angle : 3.119 40.551 162720 Z= 1.558 Chirality : 0.142 0.758 19040 Planarity : 0.020 0.375 21416 Dihedral : 14.194 169.568 17504 Min Nonbonded Distance : 1.280 Molprobity Statistics. All-atom Clashscore : 99.34 Ramachandran Plot: Outliers : 2.44 % Allowed : 37.74 % Favored : 59.82 % Rotamer Outliers : 9.22 % Cbeta Deviations : 0.47 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.57 % Twisted General : 3.91 % 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: -7.39 (0.04), residues: 12808 helix: -4.60 (0.03), residues: 5996 sheet: -4.34 (0.12), residues: 1196 loop : -5.36 (0.05), residues: 5616 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25616 Ramachandran restraints generated. 12808 Oldfield, 0 Emsley, 12808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25616 Ramachandran restraints generated. 12808 Oldfield, 0 Emsley, 12808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1463 residues out of total 11248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 927 poor density : 536 time to evaluate : 9.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 927 outliers final: 537 residues processed: 1413 average time/residue: 0.9441 time to fit residues: 2425.2838 Evaluate side-chains 1075 residues out of total 11248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 537 poor density : 538 time to evaluate : 9.331 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 537 outliers final: 35 residues processed: 537 average time/residue: 0.8746 time to fit residues: 901.9609 ------------------------------------------------------------------------------- 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: 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 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2035 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2035 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3667 HIS ** B3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3781 GLN ** B3833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 ASN ** C 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 725 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 911 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2035 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3667 HIS ** C3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3781 GLN ** C3833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 ASN ** D 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 647 ASN ** D 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2035 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3667 HIS ** D3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3781 GLN ** D3833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 1.0085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.051 0.372 119312 Z= 3.318 Angle : 3.128 40.659 162720 Z= 1.563 Chirality : 0.142 0.708 19040 Planarity : 0.020 0.470 21416 Dihedral : 14.290 168.726 17504 Min Nonbonded Distance : 1.271 Molprobity Statistics. All-atom Clashscore : 99.73 Ramachandran Plot: Outliers : 2.45 % Allowed : 38.02 % Favored : 59.53 % Rotamer Outliers : 6.83 % Cbeta Deviations : 0.48 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.07 % Twisted General : 4.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -7.43 (0.04), residues: 12808 helix: -4.64 (0.03), residues: 6020 sheet: -4.59 (0.11), residues: 1168 loop : -5.33 (0.06), residues: 5620 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25616 Ramachandran restraints generated. 12808 Oldfield, 0 Emsley, 12808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25616 Ramachandran restraints generated. 12808 Oldfield, 0 Emsley, 12808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1217 residues out of total 11248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 687 poor density : 530 time to evaluate : 9.470 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 outliers start: 687 outliers final: 399 residues processed: 1171 average time/residue: 0.9616 time to fit residues: 2039.0252 Evaluate side-chains 926 residues out of total 11248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 399 poor density : 527 time to evaluate : 9.456 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 399 outliers final: 30 residues processed: 399 average time/residue: 0.8684 time to fit residues: 665.2973 ------------------------------------------------------------------------------- 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 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2035 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3667 HIS ** B3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3781 GLN ** B3833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 911 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2035 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2763 HIS C3667 HIS ** C3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3781 GLN ** C3833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 536 ASN ** D 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 647 ASN ** D 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3667 HIS ** D3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3781 GLN ** D3833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 1.0188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.051 0.374 119312 Z= 3.320 Angle : 3.142 40.487 162720 Z= 1.569 Chirality : 0.143 0.890 19040 Planarity : 0.021 0.481 21416 Dihedral : 14.362 167.541 17504 Min Nonbonded Distance : 1.267 Molprobity Statistics. All-atom Clashscore : 99.64 Ramachandran Plot: Outliers : 2.49 % Allowed : 38.39 % Favored : 59.12 % Rotamer Outliers : 3.17 % Cbeta Deviations : 0.50 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.73 % Twisted General : 4.17 % 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: -7.45 (0.04), residues: 12808 helix: -4.66 (0.03), residues: 6016 sheet: -4.37 (0.12), residues: 1168 loop : -5.40 (0.05), residues: 5624 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25616 Ramachandran restraints generated. 12808 Oldfield, 0 Emsley, 12808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25616 Ramachandran restraints generated. 12808 Oldfield, 0 Emsley, 12808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 841 residues out of total 11248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 319 poor density : 522 time to evaluate : 9.330 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: 319 outliers final: 160 residues processed: 822 average time/residue: 1.0082 time to fit residues: 1494.0295 Evaluate side-chains 683 residues out of total 11248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 523 time to evaluate : 8.384 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 160 outliers final: 31 residues processed: 160 average time/residue: 0.8873 time to fit residues: 277.7303 ------------------------------------------------------------------------------- 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 44 ASN ** A 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 725 HIS ** B 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3667 HIS ** B3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 911 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3667 HIS ** C3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 536 ASN ** D 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 647 ASN ** D 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3667 HIS ** D3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3977 GLN ** D4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.065455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.051765 restraints weight = 640442.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.051562 restraints weight = 466449.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.051737 restraints weight = 358000.517| |-----------------------------------------------------------------------------| r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 1.0267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.051 0.376 119312 Z= 3.321 Angle : 3.143 40.576 162720 Z= 1.569 Chirality : 0.143 0.777 19040 Planarity : 0.021 0.486 21416 Dihedral : 14.394 167.582 17504 Min Nonbonded Distance : 1.268 Molprobity Statistics. All-atom Clashscore : 100.22 Ramachandran Plot: Outliers : 2.51 % Allowed : 38.37 % Favored : 59.12 % Rotamer Outliers : 3.49 % Cbeta Deviations : 0.45 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.22 % Twisted General : 4.18 % 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: -7.48 (0.04), residues: 12808 helix: -4.66 (0.03), residues: 6012 sheet: -4.61 (0.11), residues: 1132 loop : -5.39 (0.05), residues: 5664 =============================================================================== Job complete usr+sys time: 70046.96 seconds wall clock time: 1200 minutes 48.92 seconds (72048.92 seconds total)