Starting phenix.real_space_refine on Sun Mar 10 14:20:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w1n_21513/03_2024/6w1n_21513_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w1n_21513/03_2024/6w1n_21513.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w1n_21513/03_2024/6w1n_21513.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w1n_21513/03_2024/6w1n_21513.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w1n_21513/03_2024/6w1n_21513_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w1n_21513/03_2024/6w1n_21513_neut.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.127 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: 5 Type Number sf(0) Gaussians Zn 4 6.06 5 S 616 5.16 5 C 67488 2.51 5 N 18244 2.21 5 O 18880 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 40": "NH1" <-> "NH2" Residue "A ARG 42": "NH1" <-> "NH2" Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 40": "OE1" <-> "OE2" Residue "B GLU 50": "OE1" <-> "OE2" Residue "B ARG 178": "NH1" <-> "NH2" Residue "B ARG 242": "NH1" <-> "NH2" Residue "B GLU 248": "OE1" <-> "OE2" Residue "B ARG 266": "NH1" <-> "NH2" Residue "B ARG 469": "NH1" <-> "NH2" Residue "B ARG 474": "NH1" <-> "NH2" Residue "B GLU 481": "OE1" <-> "OE2" Residue "B GLU 524": "OE1" <-> "OE2" Residue "B ARG 553": "NH1" <-> "NH2" Residue "B GLU 580": "OE1" <-> "OE2" Residue "B ARG 645": "NH1" <-> "NH2" Residue "B ARG 683": "NH1" <-> "NH2" Residue "B ARG 830": "NH1" <-> "NH2" Residue "B GLU 1114": "OE1" <-> "OE2" Residue "B GLU 1221": "OE1" <-> "OE2" Residue "B GLU 1285": "OE1" <-> "OE2" Residue "B ARG 1290": "NH1" <-> "NH2" Residue "B ARG 1594": "NH1" <-> "NH2" Residue "B ARG 1607": "NH1" <-> "NH2" Residue "B ARG 1618": "NH1" <-> "NH2" Residue "B ARG 1656": "NH1" <-> "NH2" Residue "B ARG 1725": "NH1" <-> "NH2" Residue "B ARG 1743": "NH1" <-> "NH2" Residue "B ARG 1798": "NH1" <-> "NH2" Residue "B GLU 1998": "OE1" <-> "OE2" Residue "B ARG 2141": "NH1" <-> "NH2" Residue "B TYR 2319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 2509": "NH1" <-> "NH2" Residue "B ARG 3881": "NH1" <-> "NH2" Residue "B ARG 3899": "NH1" <-> "NH2" Residue "B GLU 4006": "OE1" <-> "OE2" Residue "B GLU 4027": "OE1" <-> "OE2" Residue "B ARG 4132": "NH1" <-> "NH2" Residue "B GLU 4147": "OE1" <-> "OE2" Residue "B GLU 4177": "OE1" <-> "OE2" Residue "B GLU 4186": "OE1" <-> "OE2" Residue "B ARG 4187": "NH1" <-> "NH2" Residue "B GLU 4194": "OE1" <-> "OE2" Residue "B ARG 4197": "NH1" <-> "NH2" Residue "B GLU 4234": "OE1" <-> "OE2" Residue "B GLU 4239": "OE1" <-> "OE2" Residue "B ARG 4671": "NH1" <-> "NH2" Residue "B GLU 4680": "OE1" <-> "OE2" Residue "B ARG 4701": "NH1" <-> "NH2" Residue "B GLU 4733": "OE1" <-> "OE2" Residue "B GLU 4946": "OE1" <-> "OE2" Residue "B GLU 4950": "OE1" <-> "OE2" Residue "B GLU 4974": "OE1" <-> "OE2" Residue "B GLU 4998": "OE1" <-> "OE2" Residue "B ARG 5015": "NH1" <-> "NH2" Residue "B ARG 5027": "NH1" <-> "NH2" Residue "B GLU 5031": "OE1" <-> "OE2" Residue "C ARG 40": "NH1" <-> "NH2" Residue "C ARG 42": "NH1" <-> "NH2" Residue "C PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 40": "OE1" <-> "OE2" Residue "D GLU 50": "OE1" <-> "OE2" Residue "D ARG 178": "NH1" <-> "NH2" Residue "D ARG 242": "NH1" <-> "NH2" Residue "D GLU 248": "OE1" <-> "OE2" Residue "D ARG 266": "NH1" <-> "NH2" Residue "D ARG 469": "NH1" <-> "NH2" Residue "D ARG 474": "NH1" <-> "NH2" Residue "D GLU 481": "OE1" <-> "OE2" Residue "D GLU 524": "OE1" <-> "OE2" Residue "D ARG 553": "NH1" <-> "NH2" Residue "D GLU 580": "OE1" <-> "OE2" Residue "D ARG 645": "NH1" <-> "NH2" Residue "D ARG 683": "NH1" <-> "NH2" Residue "D ARG 830": "NH1" <-> "NH2" Residue "D GLU 1114": "OE1" <-> "OE2" Residue "D GLU 1221": "OE1" <-> "OE2" Residue "D GLU 1285": "OE1" <-> "OE2" Residue "D ARG 1290": "NH1" <-> "NH2" Residue "D ARG 1594": "NH1" <-> "NH2" Residue "D ARG 1607": "NH1" <-> "NH2" Residue "D ARG 1618": "NH1" <-> "NH2" Residue "D ARG 1656": "NH1" <-> "NH2" Residue "D ARG 1725": "NH1" <-> "NH2" Residue "D ARG 1743": "NH1" <-> "NH2" Residue "D ARG 1798": "NH1" <-> "NH2" Residue "D GLU 1998": "OE1" <-> "OE2" Residue "D ARG 2141": "NH1" <-> "NH2" Residue "D TYR 2319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 2509": "NH1" <-> "NH2" Residue "D ARG 3881": "NH1" <-> "NH2" Residue "D ARG 3899": "NH1" <-> "NH2" Residue "D GLU 4006": "OE1" <-> "OE2" Residue "D GLU 4027": "OE1" <-> "OE2" Residue "D ARG 4132": "NH1" <-> "NH2" Residue "D GLU 4147": "OE1" <-> "OE2" Residue "D GLU 4177": "OE1" <-> "OE2" Residue "D GLU 4186": "OE1" <-> "OE2" Residue "D ARG 4187": "NH1" <-> "NH2" Residue "D GLU 4194": "OE1" <-> "OE2" Residue "D ARG 4197": "NH1" <-> "NH2" Residue "D GLU 4234": "OE1" <-> "OE2" Residue "D GLU 4239": "OE1" <-> "OE2" Residue "D ARG 4671": "NH1" <-> "NH2" Residue "D GLU 4680": "OE1" <-> "OE2" Residue "D ARG 4701": "NH1" <-> "NH2" Residue "D GLU 4733": "OE1" <-> "OE2" Residue "D GLU 4946": "OE1" <-> "OE2" Residue "D GLU 4950": "OE1" <-> "OE2" Residue "D GLU 4974": "OE1" <-> "OE2" Residue "D GLU 4998": "OE1" <-> "OE2" Residue "D ARG 5015": "NH1" <-> "NH2" Residue "D ARG 5027": "NH1" <-> "NH2" Residue "D GLU 5031": "OE1" <-> "OE2" Residue "E ARG 40": "NH1" <-> "NH2" Residue "E ARG 42": "NH1" <-> "NH2" Residue "E PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 40": "OE1" <-> "OE2" Residue "F GLU 50": "OE1" <-> "OE2" Residue "F ARG 178": "NH1" <-> "NH2" Residue "F ARG 242": "NH1" <-> "NH2" Residue "F GLU 248": "OE1" <-> "OE2" Residue "F ARG 266": "NH1" <-> "NH2" Residue "F ARG 469": "NH1" <-> "NH2" Residue "F ARG 474": "NH1" <-> "NH2" Residue "F GLU 481": "OE1" <-> "OE2" Residue "F GLU 524": "OE1" <-> "OE2" Residue "F ARG 553": "NH1" <-> "NH2" Residue "F GLU 580": "OE1" <-> "OE2" Residue "F ARG 645": "NH1" <-> "NH2" Residue "F ARG 683": "NH1" <-> "NH2" Residue "F ARG 830": "NH1" <-> "NH2" Residue "F GLU 1114": "OE1" <-> "OE2" Residue "F GLU 1221": "OE1" <-> "OE2" Residue "F GLU 1285": "OE1" <-> "OE2" Residue "F ARG 1290": "NH1" <-> "NH2" Residue "F ARG 1594": "NH1" <-> "NH2" Residue "F ARG 1607": "NH1" <-> "NH2" Residue "F ARG 1618": "NH1" <-> "NH2" Residue "F ARG 1656": "NH1" <-> "NH2" Residue "F ARG 1725": "NH1" <-> "NH2" Residue "F ARG 1743": "NH1" <-> "NH2" Residue "F ARG 1798": "NH1" <-> "NH2" Residue "F GLU 1998": "OE1" <-> "OE2" Residue "F ARG 2141": "NH1" <-> "NH2" Residue "F TYR 2319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 2509": "NH1" <-> "NH2" Residue "F ARG 3881": "NH1" <-> "NH2" Residue "F ARG 3899": "NH1" <-> "NH2" Residue "F GLU 4006": "OE1" <-> "OE2" Residue "F GLU 4027": "OE1" <-> "OE2" Residue "F ARG 4132": "NH1" <-> "NH2" Residue "F GLU 4147": "OE1" <-> "OE2" Residue "F GLU 4177": "OE1" <-> "OE2" Residue "F GLU 4186": "OE1" <-> "OE2" Residue "F ARG 4187": "NH1" <-> "NH2" Residue "F GLU 4194": "OE1" <-> "OE2" Residue "F ARG 4197": "NH1" <-> "NH2" Residue "F GLU 4234": "OE1" <-> "OE2" Residue "F GLU 4239": "OE1" <-> "OE2" Residue "F ARG 4671": "NH1" <-> "NH2" Residue "F GLU 4680": "OE1" <-> "OE2" Residue "F ARG 4701": "NH1" <-> "NH2" Residue "F GLU 4733": "OE1" <-> "OE2" Residue "F GLU 4946": "OE1" <-> "OE2" Residue "F GLU 4950": "OE1" <-> "OE2" Residue "F GLU 4974": "OE1" <-> "OE2" Residue "F GLU 4998": "OE1" <-> "OE2" Residue "F ARG 5015": "NH1" <-> "NH2" Residue "F ARG 5027": "NH1" <-> "NH2" Residue "F GLU 5031": "OE1" <-> "OE2" Residue "G ARG 40": "NH1" <-> "NH2" Residue "G ARG 42": "NH1" <-> "NH2" Residue "G PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 40": "OE1" <-> "OE2" Residue "H GLU 50": "OE1" <-> "OE2" Residue "H ARG 178": "NH1" <-> "NH2" Residue "H ARG 242": "NH1" <-> "NH2" Residue "H GLU 248": "OE1" <-> "OE2" Residue "H ARG 266": "NH1" <-> "NH2" Residue "H ARG 469": "NH1" <-> "NH2" Residue "H ARG 474": "NH1" <-> "NH2" Residue "H GLU 481": "OE1" <-> "OE2" Residue "H GLU 524": "OE1" <-> "OE2" Residue "H ARG 553": "NH1" <-> "NH2" Residue "H GLU 580": "OE1" <-> "OE2" Residue "H ARG 645": "NH1" <-> "NH2" Residue "H ARG 683": "NH1" <-> "NH2" Residue "H ARG 830": "NH1" <-> "NH2" Residue "H GLU 1114": "OE1" <-> "OE2" Residue "H GLU 1221": "OE1" <-> "OE2" Residue "H GLU 1285": "OE1" <-> "OE2" Residue "H ARG 1290": "NH1" <-> "NH2" Residue "H ARG 1594": "NH1" <-> "NH2" Residue "H ARG 1607": "NH1" <-> "NH2" Residue "H ARG 1618": "NH1" <-> "NH2" Residue "H ARG 1656": "NH1" <-> "NH2" Residue "H ARG 1725": "NH1" <-> "NH2" Residue "H ARG 1743": "NH1" <-> "NH2" Residue "H ARG 1798": "NH1" <-> "NH2" Residue "H GLU 1998": "OE1" <-> "OE2" Residue "H ARG 2141": "NH1" <-> "NH2" Residue "H TYR 2319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 2509": "NH1" <-> "NH2" Residue "H ARG 3881": "NH1" <-> "NH2" Residue "H ARG 3899": "NH1" <-> "NH2" Residue "H GLU 4006": "OE1" <-> "OE2" Residue "H GLU 4027": "OE1" <-> "OE2" Residue "H ARG 4132": "NH1" <-> "NH2" Residue "H GLU 4147": "OE1" <-> "OE2" Residue "H GLU 4177": "OE1" <-> "OE2" Residue "H GLU 4186": "OE1" <-> "OE2" Residue "H ARG 4187": "NH1" <-> "NH2" Residue "H GLU 4194": "OE1" <-> "OE2" Residue "H ARG 4197": "NH1" <-> "NH2" Residue "H GLU 4234": "OE1" <-> "OE2" Residue "H GLU 4239": "OE1" <-> "OE2" Residue "H ARG 4671": "NH1" <-> "NH2" Residue "H GLU 4680": "OE1" <-> "OE2" Residue "H ARG 4701": "NH1" <-> "NH2" Residue "H GLU 4733": "OE1" <-> "OE2" Residue "H GLU 4946": "OE1" <-> "OE2" Residue "H GLU 4950": "OE1" <-> "OE2" Residue "H GLU 4974": "OE1" <-> "OE2" Residue "H GLU 4998": "OE1" <-> "OE2" Residue "H ARG 5015": "NH1" <-> "NH2" Residue "H ARG 5027": "NH1" <-> "NH2" Residue "H GLU 5031": "OE1" <-> "OE2" Time to flip residues: 0.22s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 105232 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 730 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 7, 'TRANS': 98} Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 Chain: "B" Number of atoms: 25577 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 3719, 25575 Classifications: {'peptide': 3719} Incomplete info: {'truncation_to_alanine': 1181} Link IDs: {'PTRANS': 154, 'TRANS': 3564} Chain breaks: 56 Unresolved chain link angles: 17 Unresolved non-hydrogen bonds: 3970 Unresolved non-hydrogen angles: 5048 Unresolved non-hydrogen dihedrals: 3045 Unresolved non-hydrogen chiralities: 136 Planarities with less than four sites: {'GLN:plan1': 42, 'UNK:plan-1': 329, 'ASP:plan': 98, 'TYR:plan': 12, 'ASN:plan1': 27, 'TRP:plan': 6, 'HIS:plan': 18, 'PHE:plan': 11, 'GLU:plan': 187, 'ARG:plan': 118} Unresolved non-hydrogen planarities: 2504 Conformer: "B" Number of residues, atoms: 3719, 25575 Classifications: {'peptide': 3719} Incomplete info: {'truncation_to_alanine': 1181} Link IDs: {'PTRANS': 154, 'TRANS': 3564} Chain breaks: 56 Unresolved chain link angles: 17 Unresolved non-hydrogen bonds: 3970 Unresolved non-hydrogen angles: 5048 Unresolved non-hydrogen dihedrals: 3045 Unresolved non-hydrogen chiralities: 136 Planarities with less than four sites: {'GLN:plan1': 42, 'UNK:plan-1': 329, 'ASP:plan': 98, 'TYR:plan': 12, 'ASN:plan1': 27, 'TRP:plan': 6, 'HIS:plan': 18, 'PHE:plan': 11, 'GLU:plan': 187, 'ARG:plan': 118} Unresolved non-hydrogen planarities: 2504 bond proxies already assigned to first conformer: 26080 Chain: "C" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 730 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 7, 'TRANS': 98} Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 Chain: "D" Number of atoms: 25577 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 3719, 25575 Classifications: {'peptide': 3719} Incomplete info: {'truncation_to_alanine': 1181} Link IDs: {'PTRANS': 154, 'TRANS': 3564} Chain breaks: 56 Unresolved chain link angles: 17 Unresolved non-hydrogen bonds: 3970 Unresolved non-hydrogen angles: 5048 Unresolved non-hydrogen dihedrals: 3045 Unresolved non-hydrogen chiralities: 136 Planarities with less than four sites: {'GLN:plan1': 42, 'UNK:plan-1': 329, 'ASP:plan': 98, 'TYR:plan': 12, 'ASN:plan1': 27, 'TRP:plan': 6, 'HIS:plan': 18, 'PHE:plan': 11, 'GLU:plan': 187, 'ARG:plan': 118} Unresolved non-hydrogen planarities: 2504 Conformer: "B" Number of residues, atoms: 3719, 25575 Classifications: {'peptide': 3719} Incomplete info: {'truncation_to_alanine': 1181} Link IDs: {'PTRANS': 154, 'TRANS': 3564} Chain breaks: 56 Unresolved chain link angles: 17 Unresolved non-hydrogen bonds: 3970 Unresolved non-hydrogen angles: 5048 Unresolved non-hydrogen dihedrals: 3045 Unresolved non-hydrogen chiralities: 136 Planarities with less than four sites: {'GLN:plan1': 42, 'UNK:plan-1': 329, 'ASP:plan': 98, 'TYR:plan': 12, 'ASN:plan1': 27, 'TRP:plan': 6, 'HIS:plan': 18, 'PHE:plan': 11, 'GLU:plan': 187, 'ARG:plan': 118} Unresolved non-hydrogen planarities: 2504 bond proxies already assigned to first conformer: 26080 Chain: "E" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 730 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 7, 'TRANS': 98} Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 Chain: "F" Number of atoms: 25577 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 3719, 25575 Classifications: {'peptide': 3719} Incomplete info: {'truncation_to_alanine': 1181} Link IDs: {'PTRANS': 154, 'TRANS': 3564} Chain breaks: 56 Unresolved chain link angles: 17 Unresolved non-hydrogen bonds: 3970 Unresolved non-hydrogen angles: 5048 Unresolved non-hydrogen dihedrals: 3045 Unresolved non-hydrogen chiralities: 136 Planarities with less than four sites: {'GLN:plan1': 42, 'UNK:plan-1': 329, 'ASP:plan': 98, 'TYR:plan': 12, 'ASN:plan1': 27, 'TRP:plan': 6, 'HIS:plan': 18, 'PHE:plan': 11, 'GLU:plan': 187, 'ARG:plan': 118} Unresolved non-hydrogen planarities: 2504 Conformer: "B" Number of residues, atoms: 3719, 25575 Classifications: {'peptide': 3719} Incomplete info: {'truncation_to_alanine': 1181} Link IDs: {'PTRANS': 154, 'TRANS': 3564} Chain breaks: 56 Unresolved chain link angles: 17 Unresolved non-hydrogen bonds: 3970 Unresolved non-hydrogen angles: 5048 Unresolved non-hydrogen dihedrals: 3045 Unresolved non-hydrogen chiralities: 136 Planarities with less than four sites: {'GLN:plan1': 42, 'UNK:plan-1': 329, 'ASP:plan': 98, 'TYR:plan': 12, 'ASN:plan1': 27, 'TRP:plan': 6, 'HIS:plan': 18, 'PHE:plan': 11, 'GLU:plan': 187, 'ARG:plan': 118} Unresolved non-hydrogen planarities: 2504 bond proxies already assigned to first conformer: 26080 Chain: "G" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 730 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 7, 'TRANS': 98} Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 Chain: "H" Number of atoms: 25577 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 3719, 25575 Classifications: {'peptide': 3719} Incomplete info: {'truncation_to_alanine': 1181} Link IDs: {'PTRANS': 154, 'TRANS': 3564} Chain breaks: 56 Unresolved chain link angles: 17 Unresolved non-hydrogen bonds: 3970 Unresolved non-hydrogen angles: 5048 Unresolved non-hydrogen dihedrals: 3045 Unresolved non-hydrogen chiralities: 136 Planarities with less than four sites: {'GLN:plan1': 42, 'UNK:plan-1': 329, 'ASP:plan': 98, 'TYR:plan': 12, 'ASN:plan1': 27, 'TRP:plan': 6, 'HIS:plan': 18, 'PHE:plan': 11, 'GLU:plan': 187, 'ARG:plan': 118} Unresolved non-hydrogen planarities: 2504 Conformer: "B" Number of residues, atoms: 3719, 25575 Classifications: {'peptide': 3719} Incomplete info: {'truncation_to_alanine': 1181} Link IDs: {'PTRANS': 154, 'TRANS': 3564} Chain breaks: 56 Unresolved chain link angles: 17 Unresolved non-hydrogen bonds: 3970 Unresolved non-hydrogen angles: 5048 Unresolved non-hydrogen dihedrals: 3045 Unresolved non-hydrogen chiralities: 136 Planarities with less than four sites: {'GLN:plan1': 42, 'UNK:plan-1': 329, 'ASP:plan': 98, 'TYR:plan': 12, 'ASN:plan1': 27, 'TRP:plan': 6, 'HIS:plan': 18, 'PHE:plan': 11, 'GLU:plan': 187, 'ARG:plan': 118} Unresolved non-hydrogen planarities: 2504 bond proxies already assigned to first conformer: 26080 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 25674 SG CYS B4956 180.520 206.653 121.800 1.00126.28 S ATOM 51981 SG CYS D4956 177.195 180.514 121.799 1.00123.72 S ATOM 78288 SG CYS F4956 203.333 177.189 121.799 1.00122.21 S ATOM A03JN SG CYS H4956 206.659 203.329 121.800 1.00124.60 S Time building chain proxies: 77.27, per 1000 atoms: 0.73 Number of scatterers: 105232 At special positions: 0 Unit cell: (385.204, 385.204, 202.883, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 4 29.99 S 616 16.00 O 18880 8.00 N 18244 7.00 C 67488 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 28.70 Conformation dependent library (CDL) restraints added in 26.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B5101 " pdb="ZN ZN B5101 " - pdb=" NE2 HIS B4976 " pdb="ZN ZN B5101 " - pdb=" ND1 HIS B4981 " pdb="ZN ZN B5101 " - pdb=" SG CYS B4956 " pdb=" ZN D5101 " pdb="ZN ZN D5101 " - pdb=" NE2 HIS D4976 " pdb="ZN ZN D5101 " - pdb=" ND1 HIS D4981 " pdb="ZN ZN D5101 " - pdb=" SG CYS D4956 " pdb=" ZN F5101 " pdb="ZN ZN F5101 " - pdb=" NE2 HIS F4976 " pdb="ZN ZN F5101 " - pdb=" SG CYS F4956 " pdb="ZN ZN F5101 " - pdb=" ND1 HIS F4981 " pdb=" ZN H5101 " pdb="ZN ZN H5101 " - pdb=" NE2 HIS H4976 " pdb="ZN ZN H5101 " - pdb=" ND1 HIS H4981 " pdb="ZN ZN H5101 " - pdb=" SG CYS H4956 " 27384 Ramachandran restraints generated. 13692 Oldfield, 0 Emsley, 13692 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 28840 Finding SS restraints... Secondary structure from input PDB file: 644 helices and 124 sheets defined 62.0% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 17.07 Creating SS restraints... Processing helix chain 'A' and resid 40 through 42 No H-bonds generated for 'chain 'A' and resid 40 through 42' Processing helix chain 'A' and resid 56 through 66 Processing helix chain 'A' and resid 78 through 81 Processing helix chain 'B' and resid 74 through 84 Processing helix chain 'B' and resid 249 through 254 removed outlier: 4.300A pdb=" N THR B 254 " --> pdb=" O GLY B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 257 No H-bonds generated for 'chain 'B' and resid 255 through 257' Processing helix chain 'B' and resid 394 through 424 removed outlier: 3.586A pdb=" N SER B 420 " --> pdb=" O LYS B 416 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE B 421 " --> pdb=" O GLY B 417 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LYS B 424 " --> pdb=" O SER B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 450 Processing helix chain 'B' and resid 460 through 480 removed outlier: 3.881A pdb=" N GLU B 480 " --> pdb=" O SER B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 495 Processing helix chain 'B' and resid 508 through 513 removed outlier: 3.801A pdb=" N GLU B 513 " --> pdb=" O GLU B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 531 removed outlier: 3.642A pdb=" N VAL B 519 " --> pdb=" O TRP B 515 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN B 520 " --> pdb=" O LYS B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 540 removed outlier: 3.579A pdb=" N CYS B 537 " --> pdb=" O ASN B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 552 removed outlier: 3.504A pdb=" N LYS B 550 " --> pdb=" O TRP B 546 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ASP B 552 " --> pdb=" O VAL B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 571 removed outlier: 3.676A pdb=" N ILE B 560 " --> pdb=" O ALA B 556 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU B 568 " --> pdb=" O LEU B 564 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE B 569 " --> pdb=" O TYR B 565 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU B 570 " --> pdb=" O CYS B 566 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER B 571 " --> pdb=" O VAL B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 578 removed outlier: 3.742A pdb=" N ILE B 578 " --> pdb=" O LEU B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 593 removed outlier: 3.569A pdb=" N ILE B 583 " --> pdb=" O GLN B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 607 removed outlier: 3.658A pdb=" N LEU B 600 " --> pdb=" O ASN B 596 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU B 603 " --> pdb=" O VAL B 599 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N CYS B 604 " --> pdb=" O LEU B 600 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER B 605 " --> pdb=" O ASP B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 625 removed outlier: 3.618A pdb=" N GLN B 618 " --> pdb=" O VAL B 614 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU B 623 " --> pdb=" O ASP B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 674 through 678 removed outlier: 4.128A pdb=" N ALA B 677 " --> pdb=" O PHE B 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 812 through 815 removed outlier: 3.681A pdb=" N VAL B 815 " --> pdb=" O HIS B 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 812 through 815' Processing helix chain 'B' and resid 867 through 889 Processing helix chain 'B' and resid 905 through 908 removed outlier: 4.023A pdb=" N VAL B 908 " --> pdb=" O PRO B 905 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 905 through 908' Processing helix chain 'B' and resid 914 through 936 removed outlier: 3.633A pdb=" N LEU B 933 " --> pdb=" O LEU B 929 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA B 934 " --> pdb=" O LYS B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 943 through 949 removed outlier: 3.990A pdb=" N GLU B 947 " --> pdb=" O ASP B 943 " (cutoff:3.500A) Processing helix chain 'B' and resid 978 through 1004 removed outlier: 3.776A pdb=" N THR B 983 " --> pdb=" O PRO B 979 " (cutoff:3.500A) Processing helix chain 'B' and resid 1018 through 1022 removed outlier: 3.973A pdb=" N LEU B1021 " --> pdb=" O ASN B1018 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N VAL B1022 " --> pdb=" O PRO B1019 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1018 through 1022' Processing helix chain 'B' and resid 1023 through 1027 Processing helix chain 'B' and resid 1028 through 1049 removed outlier: 3.531A pdb=" N ALA B1042 " --> pdb=" O SER B1038 " (cutoff:3.500A) Processing helix chain 'B' and resid 1079 through 1082 Processing helix chain 'B' and resid 1213 through 1222 removed outlier: 4.778A pdb=" N LEU B1219 " --> pdb=" O ALA B1215 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N GLN B1220 " --> pdb=" O ILE B1216 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU B1221 " --> pdb=" O CYS B1217 " (cutoff:3.500A) Processing helix chain 'B' and resid 1444 through 1446 No H-bonds generated for 'chain 'B' and resid 1444 through 1446' Processing helix chain 'B' and resid 1465 through 1469 removed outlier: 3.648A pdb=" N VAL B1469 " --> pdb=" O LEU B1466 " (cutoff:3.500A) Processing helix chain 'B' and resid 1575 through 1580 Processing helix chain 'B' and resid 1651 through 1655 removed outlier: 3.780A pdb=" N SER B1654 " --> pdb=" O LEU B1651 " (cutoff:3.500A) Processing helix chain 'B' and resid 1656 through 1673 removed outlier: 3.804A pdb=" N GLN B1661 " --> pdb=" O LEU B1657 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N PHE B1662 " --> pdb=" O ASP B1658 " (cutoff:3.500A) Processing helix chain 'B' and resid 1679 through 1689 removed outlier: 3.593A pdb=" N HIS B1683 " --> pdb=" O ASN B1679 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA B1684 " --> pdb=" O ARG B1680 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N CYS B1686 " --> pdb=" O ALA B1682 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N SER B1687 " --> pdb=" O HIS B1683 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N HIS B1688 " --> pdb=" O ALA B1684 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL B1689 " --> pdb=" O LEU B1685 " (cutoff:3.500A) Processing helix chain 'B' and resid 1690 through 1700 removed outlier: 3.728A pdb=" N GLU B1699 " --> pdb=" O LEU B1695 " (cutoff:3.500A) Processing helix chain 'B' and resid 1704 through 1720 Processing helix chain 'B' and resid 1720 through 1730 removed outlier: 3.725A pdb=" N CYS B1724 " --> pdb=" O LEU B1720 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG B1725 " --> pdb=" O GLU B1721 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER B1726 " --> pdb=" O SER B1722 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N MET B1730 " --> pdb=" O SER B1726 " (cutoff:3.500A) Processing helix chain 'B' and resid 1739 through 1744 Processing helix chain 'B' and resid 1804 through 1826 removed outlier: 3.501A pdb=" N LEU B1808 " --> pdb=" O PRO B1804 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL B1820 " --> pdb=" O LEU B1816 " (cutoff:3.500A) Processing helix chain 'B' and resid 1830 through 1833 Processing helix chain 'B' and resid 1834 through 1853 Proline residue: B1841 - end of helix removed outlier: 3.800A pdb=" N LEU B1845 " --> pdb=" O PRO B1841 " (cutoff:3.500A) Processing helix chain 'B' and resid 1856 through 1868 removed outlier: 3.506A pdb=" N LYS B1861 " --> pdb=" O ASP B1857 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU B1868 " --> pdb=" O LEU B1864 " (cutoff:3.500A) Processing helix chain 'B' and resid 1933 through 1984 removed outlier: 3.535A pdb=" N GLN B1939 " --> pdb=" O SER B1935 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE B1947 " --> pdb=" O LEU B1943 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU B1951 " --> pdb=" O PHE B1947 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU B1952 " --> pdb=" O CYS B1948 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS B1969 " --> pdb=" O ARG B1965 " (cutoff:3.500A) Processing helix chain 'B' and resid 1988 through 2000 Processing helix chain 'B' and resid 2002 through 2012 Processing helix chain 'B' and resid 2025 through 2044 removed outlier: 3.885A pdb=" N ASP B2031 " --> pdb=" O GLU B2027 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU B2032 " --> pdb=" O ILE B2028 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU B2033 " --> pdb=" O ARG B2029 " (cutoff:3.500A) Processing helix chain 'B' and resid 2094 through 2110 removed outlier: 3.538A pdb=" N VAL B2104 " --> pdb=" O SER B2100 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA B2107 " --> pdb=" O VAL B2103 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASP B2110 " --> pdb=" O TRP B2106 " (cutoff:3.500A) Processing helix chain 'B' and resid 2114 through 2128 removed outlier: 3.650A pdb=" N ARG B2119 " --> pdb=" O PRO B2115 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA B2120 " --> pdb=" O GLU B2116 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG B2127 " --> pdb=" O SER B2123 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN B2128 " --> pdb=" O LEU B2124 " (cutoff:3.500A) Processing helix chain 'B' and resid 2130 through 2139 Processing helix chain 'B' and resid 2146 through 2148 No H-bonds generated for 'chain 'B' and resid 2146 through 2148' Processing helix chain 'B' and resid 2149 through 2169 removed outlier: 3.534A pdb=" N GLN B2162 " --> pdb=" O GLU B2158 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ILE B2168 " --> pdb=" O ARG B2164 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL B2169 " --> pdb=" O SER B2165 " (cutoff:3.500A) Processing helix chain 'B' and resid 2172 through 2188 Processing helix chain 'B' and resid 2189 through 2195 removed outlier: 4.054A pdb=" N TYR B2193 " --> pdb=" O ASN B2189 " (cutoff:3.500A) Processing helix chain 'B' and resid 2195 through 2202 removed outlier: 3.694A pdb=" N MET B2199 " --> pdb=" O HIS B2195 " (cutoff:3.500A) Processing helix chain 'B' and resid 2203 through 2217 removed outlier: 3.542A pdb=" N THR B2207 " --> pdb=" O GLY B2203 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL B2215 " --> pdb=" O VAL B2211 " (cutoff:3.500A) Processing helix chain 'B' and resid 2226 through 2244 removed outlier: 3.815A pdb=" N VAL B2230 " --> pdb=" O PHE B2226 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR B2231 " --> pdb=" O PRO B2227 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER B2232 " --> pdb=" O LYS B2228 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N CYS B2234 " --> pdb=" O VAL B2230 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG B2242 " --> pdb=" O CYS B2238 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE B2243 " --> pdb=" O TYR B2239 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N SER B2244 " --> pdb=" O PHE B2240 " (cutoff:3.500A) Processing helix chain 'B' and resid 2244 through 2254 removed outlier: 3.505A pdb=" N MET B2251 " --> pdb=" O ASN B2247 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP B2253 " --> pdb=" O ARG B2249 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N HIS B2254 " --> pdb=" O SER B2250 " (cutoff:3.500A) Processing helix chain 'B' and resid 2254 through 2263 removed outlier: 3.695A pdb=" N GLY B2263 " --> pdb=" O LEU B2259 " (cutoff:3.500A) Processing helix chain 'B' and resid 2272 through 2282 removed outlier: 3.680A pdb=" N VAL B2276 " --> pdb=" O THR B2272 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL B2281 " --> pdb=" O ALA B2277 " (cutoff:3.500A) Processing helix chain 'B' and resid 2284 through 2290 removed outlier: 3.545A pdb=" N ALA B2288 " --> pdb=" O ASN B2284 " (cutoff:3.500A) Processing helix chain 'B' and resid 2292 through 2307 removed outlier: 3.507A pdb=" N LEU B2296 " --> pdb=" O GLN B2292 " (cutoff:3.500A) Processing helix chain 'B' and resid 2325 through 2340 removed outlier: 3.790A pdb=" N GLY B2329 " --> pdb=" O ASN B2325 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ARG B2331 " --> pdb=" O CYS B2327 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TYR B2332 " --> pdb=" O GLY B2328 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE B2338 " --> pdb=" O ASP B2334 " (cutoff:3.500A) Processing helix chain 'B' and resid 2347 through 2361 removed outlier: 3.573A pdb=" N LYS B2361 " --> pdb=" O LEU B2357 " (cutoff:3.500A) Processing helix chain 'B' and resid 2378 through 2383 Processing helix chain 'B' and resid 2421 through 2437 removed outlier: 3.509A pdb=" N TYR B2427 " --> pdb=" O ILE B2423 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N CYS B2437 " --> pdb=" O LEU B2433 " (cutoff:3.500A) Processing helix chain 'B' and resid 2441 through 2446 Processing helix chain 'B' and resid 2451 through 2462 Processing helix chain 'B' and resid 2463 through 2472 Processing helix chain 'B' and resid 2496 through 2499 Processing helix chain 'B' and resid 2500 through 2511 Processing helix chain 'B' and resid 2519 through 2534 removed outlier: 3.630A pdb=" N LEU B2523 " --> pdb=" O LEU B2519 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASP B2524 " --> pdb=" O LEU B2520 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N VAL B2525 " --> pdb=" O HIS B2521 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU B2528 " --> pdb=" O ASP B2524 " (cutoff:3.500A) Proline residue: B2529 - end of helix removed outlier: 3.537A pdb=" N ALA B2534 " --> pdb=" O ASP B2530 " (cutoff:3.500A) Processing helix chain 'B' and resid 2549 through 2558 Processing helix chain 'B' and resid 2558 through 2566 Processing helix chain 'B' and resid 2567 through 2570 Processing helix chain 'B' and resid 2580 through 2592 removed outlier: 3.581A pdb=" N ARG B2592 " --> pdb=" O TYR B2588 " (cutoff:3.500A) Processing helix chain 'B' and resid 2600 through 2613 removed outlier: 3.784A pdb=" N GLU B2606 " --> pdb=" O ASP B2602 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG B2613 " --> pdb=" O MET B2609 " (cutoff:3.500A) Processing helix chain 'B' and resid 2621 through 2631 removed outlier: 3.774A pdb=" N ARG B2626 " --> pdb=" O HIS B2622 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N PHE B2629 " --> pdb=" O ARG B2625 " (cutoff:3.500A) Processing helix chain 'B' and resid 2642 through 2653 Processing helix chain 'B' and resid 2665 through 2683 Processing helix chain 'B' and resid 2689 through 2700 removed outlier: 3.789A pdb=" N UNK B2694 " --> pdb=" O UNK B2690 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N UNK B2695 " --> pdb=" O UNK B2691 " (cutoff:3.500A) Processing helix chain 'B' and resid 2748 through 2750 No H-bonds generated for 'chain 'B' and resid 2748 through 2750' Processing helix chain 'B' and resid 2751 through 2773 Processing helix chain 'B' and resid 2793 through 2797 Processing helix chain 'B' and resid 2798 through 2819 removed outlier: 3.617A pdb=" N ILE B2804 " --> pdb=" O LYS B2800 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N TYR B2805 " --> pdb=" O ASP B2801 " (cutoff:3.500A) Proline residue: B2808 - end of helix Processing helix chain 'B' and resid 2868 through 2897 removed outlier: 3.539A pdb=" N GLN B2877 " --> pdb=" O ALA B2873 " (cutoff:3.500A) Processing helix chain 'B' and resid 2916 through 2933 Processing helix chain 'B' and resid 2957 through 2978 Processing helix chain 'B' and resid 3000 through 3018 removed outlier: 4.347A pdb=" N UNK B3009 " --> pdb=" O UNK B3005 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N UNK B3010 " --> pdb=" O UNK B3006 " (cutoff:3.500A) Processing helix chain 'B' and resid 3033 through 3046 Processing helix chain 'B' and resid 3052 through 3062 Processing helix chain 'B' and resid 3147 through 3166 Processing helix chain 'B' and resid 3174 through 3193 Processing helix chain 'B' and resid 3203 through 3217 Processing helix chain 'B' and resid 3226 through 3238 Processing helix chain 'B' and resid 3279 through 3288 Processing helix chain 'B' and resid 3293 through 3308 Processing helix chain 'B' and resid 3322 through 3335 Processing helix chain 'B' and resid 3347 through 3352 Processing helix chain 'B' and resid 3352 through 3358 Processing helix chain 'B' and resid 3366 through 3385 Processing helix chain 'B' and resid 3412 through 3427 removed outlier: 3.589A pdb=" N TYR B3416 " --> pdb=" O LEU B3412 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP B3418 " --> pdb=" O ILE B3414 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASN B3419 " --> pdb=" O ARG B3415 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ALA B3422 " --> pdb=" O ASP B3418 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N HIS B3423 " --> pdb=" O ASN B3419 " (cutoff:3.500A) Processing helix chain 'B' and resid 3429 through 3448 removed outlier: 3.540A pdb=" N LYS B3448 " --> pdb=" O ILE B3444 " (cutoff:3.500A) Processing helix chain 'B' and resid 3510 through 3526 removed outlier: 3.581A pdb=" N UNK B3520 " --> pdb=" O UNK B3516 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N UNK B3521 " --> pdb=" O UNK B3517 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N UNK B3524 " --> pdb=" O UNK B3520 " (cutoff:3.500A) Processing helix chain 'B' and resid 3535 through 3544 Processing helix chain 'B' and resid 3549 through 3555 Processing helix chain 'B' and resid 3565 through 3574 Processing helix chain 'B' and resid 3587 through 3606 Processing helix chain 'B' and resid 3641 through 3657 removed outlier: 4.329A pdb=" N ASN B3647 " --> pdb=" O HIS B3643 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N MET B3648 " --> pdb=" O ARG B3644 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU B3651 " --> pdb=" O ASN B3647 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA B3655 " --> pdb=" O GLU B3651 " (cutoff:3.500A) Processing helix chain 'B' and resid 3664 through 3678 removed outlier: 3.986A pdb=" N ARG B3668 " --> pdb=" O SER B3664 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY B3677 " --> pdb=" O LEU B3673 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLU B3678 " --> pdb=" O SER B3674 " (cutoff:3.500A) Processing helix chain 'B' and resid 3692 through 3706 Processing helix chain 'B' and resid 3715 through 3731 removed outlier: 3.610A pdb=" N MET B3719 " --> pdb=" O ASP B3715 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU B3731 " --> pdb=" O LYS B3727 " (cutoff:3.500A) Processing helix chain 'B' and resid 3748 through 3769 removed outlier: 3.794A pdb=" N LEU B3765 " --> pdb=" O GLN B3761 " (cutoff:3.500A) Processing helix chain 'B' and resid 3769 through 3781 removed outlier: 4.012A pdb=" N LEU B3775 " --> pdb=" O ALA B3771 " (cutoff:3.500A) Processing helix chain 'B' and resid 3786 through 3800 Processing helix chain 'B' and resid 3804 through 3819 removed outlier: 3.960A pdb=" N LEU B3815 " --> pdb=" O MET B3811 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP B3817 " --> pdb=" O ASP B3813 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS B3818 " --> pdb=" O TYR B3814 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS B3819 " --> pdb=" O LEU B3815 " (cutoff:3.500A) Processing helix chain 'B' and resid 3821 through 3833 removed outlier: 3.663A pdb=" N ALA B3829 " --> pdb=" O GLN B3825 " (cutoff:3.500A) Processing helix chain 'B' and resid 3838 through 3850 Processing helix chain 'B' and resid 3872 through 3887 removed outlier: 3.754A pdb=" N GLN B3877 " --> pdb=" O ASP B3873 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE B3880 " --> pdb=" O THR B3876 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG B3881 " --> pdb=" O GLN B3877 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU B3883 " --> pdb=" O LEU B3879 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N CYS B3887 " --> pdb=" O LEU B3883 " (cutoff:3.500A) Processing helix chain 'B' and resid 3893 through 3900 Processing helix chain 'B' and resid 3909 through 3934 removed outlier: 4.265A pdb=" N CYS B3913 " --> pdb=" O ASN B3909 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL B3915 " --> pdb=" O ILE B3911 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER B3924 " --> pdb=" O ARG B3920 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TRP B3930 " --> pdb=" O SER B3926 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR B3931 " --> pdb=" O ASP B3927 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N TYR B3932 " --> pdb=" O PHE B3928 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N GLY B3934 " --> pdb=" O TRP B3930 " (cutoff:3.500A) Processing helix chain 'B' and resid 3939 through 3964 removed outlier: 4.082A pdb=" N ASN B3945 " --> pdb=" O GLN B3941 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE B3946 " --> pdb=" O GLY B3942 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER B3947 " --> pdb=" O LYS B3943 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS B3948 " --> pdb=" O ARG B3944 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE B3964 " --> pdb=" O LEU B3960 " (cutoff:3.500A) Processing helix chain 'B' and resid 3968 through 3978 Processing helix chain 'B' and resid 3979 through 3993 removed outlier: 3.745A pdb=" N ALA B3983 " --> pdb=" O ARG B3979 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL B3985 " --> pdb=" O TRP B3981 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL B3990 " --> pdb=" O GLY B3986 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N PHE B3991 " --> pdb=" O PHE B3987 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N HIS B3993 " --> pdb=" O HIS B3989 " (cutoff:3.500A) Processing helix chain 'B' and resid 3994 through 3999 removed outlier: 3.535A pdb=" N LEU B3998 " --> pdb=" O MET B3994 " (cutoff:3.500A) Processing helix chain 'B' and resid 4004 through 4026 removed outlier: 3.719A pdb=" N GLU B4010 " --> pdb=" O GLU B4006 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU B4011 " --> pdb=" O LEU B4007 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL B4019 " --> pdb=" O GLN B4015 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL B4020 " --> pdb=" O LYS B4016 " (cutoff:3.500A) Processing helix chain 'B' and resid 4033 through 4046 removed outlier: 3.566A pdb=" N ARG B4037 " --> pdb=" O GLY B4033 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP B4041 " --> pdb=" O ARG B4037 " (cutoff:3.500A) Processing helix chain 'B' and resid 4046 through 4069 removed outlier: 3.551A pdb=" N MET B4052 " --> pdb=" O SER B4048 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE B4057 " --> pdb=" O ILE B4053 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP B4058 " --> pdb=" O LEU B4054 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET B4059 " --> pdb=" O LYS B4055 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE B4060 " --> pdb=" O PHE B4056 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP B4065 " --> pdb=" O LEU B4061 " (cutoff:3.500A) Processing helix chain 'B' and resid 4069 through 4076 removed outlier: 4.071A pdb=" N GLN B4073 " --> pdb=" O SER B4069 " (cutoff:3.500A) Processing helix chain 'B' and resid 4110 through 4114 Processing helix chain 'B' and resid 4127 through 4149 removed outlier: 4.284A pdb=" N ASP B4133 " --> pdb=" O GLU B4129 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE B4134 " --> pdb=" O PRO B4130 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU B4145 " --> pdb=" O LEU B4141 " (cutoff:3.500A) Processing helix chain 'B' and resid 4152 through 4162 removed outlier: 3.927A pdb=" N ARG B4156 " --> pdb=" O ASP B4152 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASN B4157 " --> pdb=" O PRO B4153 " (cutoff:3.500A) Processing helix chain 'B' and resid 4162 through 4169 Processing helix chain 'B' and resid 4193 through 4201 Processing helix chain 'B' and resid 4202 through 4218 removed outlier: 3.773A pdb=" N ILE B4213 " --> pdb=" O LYS B4209 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N PHE B4214 " --> pdb=" O ARG B4210 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASN B4218 " --> pdb=" O PHE B4214 " (cutoff:3.500A) Processing helix chain 'B' and resid 4221 through 4245 removed outlier: 3.576A pdb=" N PHE B4238 " --> pdb=" O GLU B4234 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU B4239 " --> pdb=" O ASP B4235 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLN B4241 " --> pdb=" O ILE B4237 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE B4242 " --> pdb=" O PHE B4238 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA B4243 " --> pdb=" O GLU B4239 " (cutoff:3.500A) Processing helix chain 'B' and resid 4545 through 4556 removed outlier: 3.651A pdb=" N ASN B4556 " --> pdb=" O TYR B4552 " (cutoff:3.500A) Processing helix chain 'B' and resid 4556 through 4577 removed outlier: 3.602A pdb=" N PHE B4577 " --> pdb=" O PHE B4573 " (cutoff:3.500A) Processing helix chain 'B' and resid 4636 through 4680 removed outlier: 3.538A pdb=" N LEU B4641 " --> pdb=" O MET B4637 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ARG B4642 " --> pdb=" O GLU B4638 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N CYS B4643 " --> pdb=" O PRO B4639 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE B4656 " --> pdb=" O ALA B4652 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS B4663 " --> pdb=" O TYR B4659 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N VAL B4664 " --> pdb=" O ASN B4660 " (cutoff:3.500A) Proline residue: B4665 - end of helix removed outlier: 3.943A pdb=" N ARG B4671 " --> pdb=" O VAL B4667 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N GLU B4674 " --> pdb=" O LYS B4670 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ALA B4676 " --> pdb=" O GLU B4672 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG B4677 " --> pdb=" O LYS B4673 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU B4680 " --> pdb=" O ALA B4676 " (cutoff:3.500A) Processing helix chain 'B' and resid 4694 through 4700 removed outlier: 3.694A pdb=" N GLN B4698 " --> pdb=" O ASP B4694 " (cutoff:3.500A) Processing helix chain 'B' and resid 4708 through 4712 removed outlier: 4.132A pdb=" N ASN B4712 " --> pdb=" O PHE B4709 " (cutoff:3.500A) Processing helix chain 'B' and resid 4717 through 4726 removed outlier: 4.006A pdb=" N LEU B4723 " --> pdb=" O LYS B4719 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP B4724 " --> pdb=" O ARG B4720 " (cutoff:3.500A) Processing helix chain 'B' and resid 4731 through 4737 Processing helix chain 'B' and resid 4770 through 4784 removed outlier: 3.506A pdb=" N ILE B4781 " --> pdb=" O LYS B4777 " (cutoff:3.500A) Processing helix chain 'B' and resid 4784 through 4803 removed outlier: 3.870A pdb=" N MET B4796 " --> pdb=" O TRP B4792 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER B4797 " --> pdb=" O TYR B4793 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N HIS B4801 " --> pdb=" O SER B4797 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N TYR B4802 " --> pdb=" O LEU B4798 " (cutoff:3.500A) Processing helix chain 'B' and resid 4804 through 4812 removed outlier: 3.564A pdb=" N ALA B4809 " --> pdb=" O PHE B4806 " (cutoff:3.500A) Processing helix chain 'B' and resid 4813 through 4818 Processing helix chain 'B' and resid 4818 through 4831 removed outlier: 4.398A pdb=" N VAL B4828 " --> pdb=" O ILE B4824 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR B4829 " --> pdb=" O LEU B4825 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASN B4831 " --> pdb=" O SER B4827 " (cutoff:3.500A) Processing helix chain 'B' and resid 4831 through 4856 removed outlier: 4.365A pdb=" N MET B4837 " --> pdb=" O LYS B4833 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL B4839 " --> pdb=" O LEU B4835 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLY B4840 " --> pdb=" O VAL B4836 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL B4844 " --> pdb=" O GLY B4840 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU B4848 " --> pdb=" O VAL B4844 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL B4852 " --> pdb=" O LEU B4848 " (cutoff:3.500A) Processing helix chain 'B' and resid 4857 through 4862 removed outlier: 3.560A pdb=" N TYR B4861 " --> pdb=" O PHE B4857 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN B4862 " --> pdb=" O ARG B4858 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4857 through 4862' Processing helix chain 'B' and resid 4876 through 4886 Processing helix chain 'B' and resid 4894 through 4898 Processing helix chain 'B' and resid 4907 through 4922 removed outlier: 3.625A pdb=" N VAL B4912 " --> pdb=" O GLU B4908 " (cutoff:3.500A) Processing helix chain 'B' and resid 4924 through 4955 removed outlier: 3.711A pdb=" N GLY B4939 " --> pdb=" O ILE B4935 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ARG B4942 " --> pdb=" O PHE B4938 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN B4944 " --> pdb=" O GLU B4940 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLN B4945 " --> pdb=" O LEU B4941 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET B4952 " --> pdb=" O VAL B4948 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU B4953 " --> pdb=" O ARG B4949 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS B4955 " --> pdb=" O ASP B4951 " (cutoff:3.500A) Processing helix chain 'B' and resid 4963 through 4967 Processing helix chain 'B' and resid 4972 through 4979 removed outlier: 3.605A pdb=" N GLU B4979 " --> pdb=" O THR B4975 " (cutoff:3.500A) Processing helix chain 'B' and resid 4982 through 4996 removed outlier: 3.675A pdb=" N TYR B4986 " --> pdb=" O ASN B4982 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N MET B4987 " --> pdb=" O LEU B4983 " (cutoff:3.500A) Processing helix chain 'B' and resid 5002 through 5015 Processing helix chain 'B' and resid 5025 through 5030 Processing helix chain 'C' and resid 40 through 42 No H-bonds generated for 'chain 'C' and resid 40 through 42' Processing helix chain 'C' and resid 56 through 66 Processing helix chain 'C' and resid 78 through 81 Processing helix chain 'D' and resid 74 through 84 Processing helix chain 'D' and resid 249 through 254 removed outlier: 4.301A pdb=" N THR D 254 " --> pdb=" O GLY D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 257 No H-bonds generated for 'chain 'D' and resid 255 through 257' Processing helix chain 'D' and resid 394 through 424 removed outlier: 3.586A pdb=" N SER D 420 " --> pdb=" O LYS D 416 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE D 421 " --> pdb=" O GLY D 417 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LYS D 424 " --> pdb=" O SER D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 450 Processing helix chain 'D' and resid 460 through 480 removed outlier: 3.881A pdb=" N GLU D 480 " --> pdb=" O SER D 476 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 495 Processing helix chain 'D' and resid 508 through 513 removed outlier: 3.801A pdb=" N GLU D 513 " --> pdb=" O GLU D 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 514 through 531 removed outlier: 3.642A pdb=" N VAL D 519 " --> pdb=" O TRP D 515 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN D 520 " --> pdb=" O LYS D 516 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 540 removed outlier: 3.579A pdb=" N CYS D 537 " --> pdb=" O ASN D 533 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 552 removed outlier: 3.505A pdb=" N LYS D 550 " --> pdb=" O TRP D 546 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ASP D 552 " --> pdb=" O VAL D 548 " (cutoff:3.500A) Processing helix chain 'D' and resid 556 through 571 removed outlier: 3.676A pdb=" N ILE D 560 " --> pdb=" O ALA D 556 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU D 568 " --> pdb=" O LEU D 564 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE D 569 " --> pdb=" O TYR D 565 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLU D 570 " --> pdb=" O CYS D 566 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER D 571 " --> pdb=" O VAL D 567 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 578 removed outlier: 3.741A pdb=" N ILE D 578 " --> pdb=" O LEU D 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 579 through 593 removed outlier: 3.570A pdb=" N ILE D 583 " --> pdb=" O GLN D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 596 through 607 removed outlier: 3.658A pdb=" N LEU D 600 " --> pdb=" O ASN D 596 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU D 603 " --> pdb=" O VAL D 599 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N CYS D 604 " --> pdb=" O LEU D 600 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER D 605 " --> pdb=" O ASP D 601 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 625 removed outlier: 3.617A pdb=" N GLN D 618 " --> pdb=" O VAL D 614 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU D 623 " --> pdb=" O ASP D 619 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 678 removed outlier: 4.128A pdb=" N ALA D 677 " --> pdb=" O PHE D 674 " (cutoff:3.500A) Processing helix chain 'D' and resid 812 through 815 removed outlier: 3.681A pdb=" N VAL D 815 " --> pdb=" O HIS D 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 812 through 815' Processing helix chain 'D' and resid 867 through 889 Processing helix chain 'D' and resid 905 through 908 removed outlier: 4.022A pdb=" N VAL D 908 " --> pdb=" O PRO D 905 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 905 through 908' Processing helix chain 'D' and resid 914 through 936 removed outlier: 3.632A pdb=" N LEU D 933 " --> pdb=" O LEU D 929 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA D 934 " --> pdb=" O LYS D 930 " (cutoff:3.500A) Processing helix chain 'D' and resid 943 through 949 removed outlier: 3.990A pdb=" N GLU D 947 " --> pdb=" O ASP D 943 " (cutoff:3.500A) Processing helix chain 'D' and resid 978 through 1004 removed outlier: 3.776A pdb=" N THR D 983 " --> pdb=" O PRO D 979 " (cutoff:3.500A) Processing helix chain 'D' and resid 1018 through 1022 removed outlier: 3.973A pdb=" N LEU D1021 " --> pdb=" O ASN D1018 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N VAL D1022 " --> pdb=" O PRO D1019 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1018 through 1022' Processing helix chain 'D' and resid 1023 through 1027 Processing helix chain 'D' and resid 1028 through 1049 removed outlier: 3.531A pdb=" N ALA D1042 " --> pdb=" O SER D1038 " (cutoff:3.500A) Processing helix chain 'D' and resid 1079 through 1082 Processing helix chain 'D' and resid 1213 through 1222 removed outlier: 4.779A pdb=" N LEU D1219 " --> pdb=" O ALA D1215 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N GLN D1220 " --> pdb=" O ILE D1216 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU D1221 " --> pdb=" O CYS D1217 " (cutoff:3.500A) Processing helix chain 'D' and resid 1444 through 1446 No H-bonds generated for 'chain 'D' and resid 1444 through 1446' Processing helix chain 'D' and resid 1465 through 1469 removed outlier: 3.648A pdb=" N VAL D1469 " --> pdb=" O LEU D1466 " (cutoff:3.500A) Processing helix chain 'D' and resid 1575 through 1580 Processing helix chain 'D' and resid 1651 through 1655 removed outlier: 3.781A pdb=" N SER D1654 " --> pdb=" O LEU D1651 " (cutoff:3.500A) Processing helix chain 'D' and resid 1656 through 1673 removed outlier: 3.803A pdb=" N GLN D1661 " --> pdb=" O LEU D1657 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N PHE D1662 " --> pdb=" O ASP D1658 " (cutoff:3.500A) Processing helix chain 'D' and resid 1679 through 1689 removed outlier: 3.593A pdb=" N HIS D1683 " --> pdb=" O ASN D1679 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA D1684 " --> pdb=" O ARG D1680 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N CYS D1686 " --> pdb=" O ALA D1682 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N SER D1687 " --> pdb=" O HIS D1683 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N HIS D1688 " --> pdb=" O ALA D1684 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL D1689 " --> pdb=" O LEU D1685 " (cutoff:3.500A) Processing helix chain 'D' and resid 1690 through 1700 removed outlier: 3.728A pdb=" N GLU D1699 " --> pdb=" O LEU D1695 " (cutoff:3.500A) Processing helix chain 'D' and resid 1704 through 1720 Processing helix chain 'D' and resid 1720 through 1730 removed outlier: 3.724A pdb=" N CYS D1724 " --> pdb=" O LEU D1720 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG D1725 " --> pdb=" O GLU D1721 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N SER D1726 " --> pdb=" O SER D1722 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET D1730 " --> pdb=" O SER D1726 " (cutoff:3.500A) Processing helix chain 'D' and resid 1739 through 1744 Processing helix chain 'D' and resid 1804 through 1826 removed outlier: 3.501A pdb=" N LEU D1808 " --> pdb=" O PRO D1804 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL D1820 " --> pdb=" O LEU D1816 " (cutoff:3.500A) Processing helix chain 'D' and resid 1830 through 1833 Processing helix chain 'D' and resid 1834 through 1853 Proline residue: D1841 - end of helix removed outlier: 3.801A pdb=" N LEU D1845 " --> pdb=" O PRO D1841 " (cutoff:3.500A) Processing helix chain 'D' and resid 1856 through 1868 removed outlier: 3.506A pdb=" N LYS D1861 " --> pdb=" O ASP D1857 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU D1868 " --> pdb=" O LEU D1864 " (cutoff:3.500A) Processing helix chain 'D' and resid 1933 through 1984 removed outlier: 3.535A pdb=" N GLN D1939 " --> pdb=" O SER D1935 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE D1947 " --> pdb=" O LEU D1943 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU D1951 " --> pdb=" O PHE D1947 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU D1952 " --> pdb=" O CYS D1948 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS D1969 " --> pdb=" O ARG D1965 " (cutoff:3.500A) Processing helix chain 'D' and resid 1988 through 2000 Processing helix chain 'D' and resid 2002 through 2012 Processing helix chain 'D' and resid 2025 through 2044 removed outlier: 3.884A pdb=" N ASP D2031 " --> pdb=" O GLU D2027 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU D2032 " --> pdb=" O ILE D2028 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU D2033 " --> pdb=" O ARG D2029 " (cutoff:3.500A) Processing helix chain 'D' and resid 2094 through 2110 removed outlier: 3.538A pdb=" N VAL D2104 " --> pdb=" O SER D2100 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA D2107 " --> pdb=" O VAL D2103 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASP D2110 " --> pdb=" O TRP D2106 " (cutoff:3.500A) Processing helix chain 'D' and resid 2114 through 2128 removed outlier: 3.651A pdb=" N ARG D2119 " --> pdb=" O PRO D2115 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA D2120 " --> pdb=" O GLU D2116 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG D2127 " --> pdb=" O SER D2123 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN D2128 " --> pdb=" O LEU D2124 " (cutoff:3.500A) Processing helix chain 'D' and resid 2130 through 2139 Processing helix chain 'D' and resid 2146 through 2148 No H-bonds generated for 'chain 'D' and resid 2146 through 2148' Processing helix chain 'D' and resid 2149 through 2169 removed outlier: 3.533A pdb=" N GLN D2162 " --> pdb=" O GLU D2158 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ILE D2168 " --> pdb=" O ARG D2164 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL D2169 " --> pdb=" O SER D2165 " (cutoff:3.500A) Processing helix chain 'D' and resid 2172 through 2188 Processing helix chain 'D' and resid 2189 through 2195 removed outlier: 4.054A pdb=" N TYR D2193 " --> pdb=" O ASN D2189 " (cutoff:3.500A) Processing helix chain 'D' and resid 2195 through 2202 removed outlier: 3.694A pdb=" N MET D2199 " --> pdb=" O HIS D2195 " (cutoff:3.500A) Processing helix chain 'D' and resid 2203 through 2217 removed outlier: 3.542A pdb=" N THR D2207 " --> pdb=" O GLY D2203 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL D2215 " --> pdb=" O VAL D2211 " (cutoff:3.500A) Processing helix chain 'D' and resid 2226 through 2244 removed outlier: 3.814A pdb=" N VAL D2230 " --> pdb=" O PHE D2226 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR D2231 " --> pdb=" O PRO D2227 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER D2232 " --> pdb=" O LYS D2228 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N CYS D2234 " --> pdb=" O VAL D2230 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG D2242 " --> pdb=" O CYS D2238 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE D2243 " --> pdb=" O TYR D2239 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N SER D2244 " --> pdb=" O PHE D2240 " (cutoff:3.500A) Processing helix chain 'D' and resid 2244 through 2254 removed outlier: 3.503A pdb=" N MET D2251 " --> pdb=" O ASN D2247 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP D2253 " --> pdb=" O ARG D2249 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N HIS D2254 " --> pdb=" O SER D2250 " (cutoff:3.500A) Processing helix chain 'D' and resid 2254 through 2263 removed outlier: 3.695A pdb=" N GLY D2263 " --> pdb=" O LEU D2259 " (cutoff:3.500A) Processing helix chain 'D' and resid 2272 through 2282 removed outlier: 3.680A pdb=" N VAL D2276 " --> pdb=" O THR D2272 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL D2281 " --> pdb=" O ALA D2277 " (cutoff:3.500A) Processing helix chain 'D' and resid 2284 through 2290 removed outlier: 3.546A pdb=" N ALA D2288 " --> pdb=" O ASN D2284 " (cutoff:3.500A) Processing helix chain 'D' and resid 2292 through 2307 removed outlier: 3.507A pdb=" N LEU D2296 " --> pdb=" O GLN D2292 " (cutoff:3.500A) Processing helix chain 'D' and resid 2325 through 2340 removed outlier: 3.790A pdb=" N GLY D2329 " --> pdb=" O ASN D2325 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ARG D2331 " --> pdb=" O CYS D2327 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TYR D2332 " --> pdb=" O GLY D2328 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE D2338 " --> pdb=" O ASP D2334 " (cutoff:3.500A) Processing helix chain 'D' and resid 2347 through 2361 removed outlier: 3.573A pdb=" N LYS D2361 " --> pdb=" O LEU D2357 " (cutoff:3.500A) Processing helix chain 'D' and resid 2378 through 2383 Processing helix chain 'D' and resid 2421 through 2437 removed outlier: 3.510A pdb=" N TYR D2427 " --> pdb=" O ILE D2423 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N CYS D2437 " --> pdb=" O LEU D2433 " (cutoff:3.500A) Processing helix chain 'D' and resid 2441 through 2446 Processing helix chain 'D' and resid 2451 through 2462 Processing helix chain 'D' and resid 2463 through 2472 Processing helix chain 'D' and resid 2496 through 2499 Processing helix chain 'D' and resid 2500 through 2511 Processing helix chain 'D' and resid 2519 through 2534 removed outlier: 3.632A pdb=" N LEU D2523 " --> pdb=" O LEU D2519 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASP D2524 " --> pdb=" O LEU D2520 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N VAL D2525 " --> pdb=" O HIS D2521 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU D2528 " --> pdb=" O ASP D2524 " (cutoff:3.500A) Proline residue: D2529 - end of helix removed outlier: 3.537A pdb=" N ALA D2534 " --> pdb=" O ASP D2530 " (cutoff:3.500A) Processing helix chain 'D' and resid 2549 through 2558 Processing helix chain 'D' and resid 2558 through 2566 Processing helix chain 'D' and resid 2567 through 2570 Processing helix chain 'D' and resid 2580 through 2592 removed outlier: 3.582A pdb=" N ARG D2592 " --> pdb=" O TYR D2588 " (cutoff:3.500A) Processing helix chain 'D' and resid 2600 through 2613 removed outlier: 3.784A pdb=" N GLU D2606 " --> pdb=" O ASP D2602 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG D2613 " --> pdb=" O MET D2609 " (cutoff:3.500A) Processing helix chain 'D' and resid 2621 through 2631 removed outlier: 3.773A pdb=" N ARG D2626 " --> pdb=" O HIS D2622 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N PHE D2629 " --> pdb=" O ARG D2625 " (cutoff:3.500A) Processing helix chain 'D' and resid 2642 through 2653 Processing helix chain 'D' and resid 2665 through 2683 Processing helix chain 'D' and resid 2689 through 2700 removed outlier: 3.788A pdb=" N UNK D2694 " --> pdb=" O UNK D2690 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N UNK D2695 " --> pdb=" O UNK D2691 " (cutoff:3.500A) Processing helix chain 'D' and resid 2748 through 2750 No H-bonds generated for 'chain 'D' and resid 2748 through 2750' Processing helix chain 'D' and resid 2751 through 2773 Processing helix chain 'D' and resid 2793 through 2797 Processing helix chain 'D' and resid 2798 through 2819 removed outlier: 3.617A pdb=" N ILE D2804 " --> pdb=" O LYS D2800 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N TYR D2805 " --> pdb=" O ASP D2801 " (cutoff:3.500A) Proline residue: D2808 - end of helix Processing helix chain 'D' and resid 2868 through 2897 removed outlier: 3.539A pdb=" N GLN D2877 " --> pdb=" O ALA D2873 " (cutoff:3.500A) Processing helix chain 'D' and resid 2916 through 2933 Processing helix chain 'D' and resid 2957 through 2978 Processing helix chain 'D' and resid 3000 through 3018 removed outlier: 4.348A pdb=" N UNK D3009 " --> pdb=" O UNK D3005 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N UNK D3010 " --> pdb=" O UNK D3006 " (cutoff:3.500A) Processing helix chain 'D' and resid 3033 through 3046 Processing helix chain 'D' and resid 3052 through 3062 Processing helix chain 'D' and resid 3147 through 3166 Processing helix chain 'D' and resid 3174 through 3193 Processing helix chain 'D' and resid 3203 through 3217 Processing helix chain 'D' and resid 3226 through 3238 Processing helix chain 'D' and resid 3279 through 3288 Processing helix chain 'D' and resid 3293 through 3308 Processing helix chain 'D' and resid 3322 through 3335 Processing helix chain 'D' and resid 3347 through 3352 Processing helix chain 'D' and resid 3352 through 3358 Processing helix chain 'D' and resid 3366 through 3385 Processing helix chain 'D' and resid 3412 through 3427 removed outlier: 3.590A pdb=" N TYR D3416 " --> pdb=" O LEU D3412 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASP D3418 " --> pdb=" O ILE D3414 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASN D3419 " --> pdb=" O ARG D3415 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ALA D3422 " --> pdb=" O ASP D3418 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N HIS D3423 " --> pdb=" O ASN D3419 " (cutoff:3.500A) Processing helix chain 'D' and resid 3429 through 3448 removed outlier: 3.540A pdb=" N LYS D3448 " --> pdb=" O ILE D3444 " (cutoff:3.500A) Processing helix chain 'D' and resid 3510 through 3526 removed outlier: 3.581A pdb=" N UNK D3520 " --> pdb=" O UNK D3516 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N UNK D3521 " --> pdb=" O UNK D3517 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N UNK D3524 " --> pdb=" O UNK D3520 " (cutoff:3.500A) Processing helix chain 'D' and resid 3535 through 3544 Processing helix chain 'D' and resid 3549 through 3555 Processing helix chain 'D' and resid 3565 through 3574 Processing helix chain 'D' and resid 3587 through 3606 Processing helix chain 'D' and resid 3641 through 3657 removed outlier: 4.329A pdb=" N ASN D3647 " --> pdb=" O HIS D3643 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N MET D3648 " --> pdb=" O ARG D3644 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU D3651 " --> pdb=" O ASN D3647 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA D3655 " --> pdb=" O GLU D3651 " (cutoff:3.500A) Processing helix chain 'D' and resid 3664 through 3678 removed outlier: 3.986A pdb=" N ARG D3668 " --> pdb=" O SER D3664 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY D3677 " --> pdb=" O LEU D3673 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLU D3678 " --> pdb=" O SER D3674 " (cutoff:3.500A) Processing helix chain 'D' and resid 3692 through 3706 Processing helix chain 'D' and resid 3715 through 3731 removed outlier: 3.610A pdb=" N MET D3719 " --> pdb=" O ASP D3715 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU D3731 " --> pdb=" O LYS D3727 " (cutoff:3.500A) Processing helix chain 'D' and resid 3748 through 3769 removed outlier: 3.793A pdb=" N LEU D3765 " --> pdb=" O GLN D3761 " (cutoff:3.500A) Processing helix chain 'D' and resid 3769 through 3781 removed outlier: 4.013A pdb=" N LEU D3775 " --> pdb=" O ALA D3771 " (cutoff:3.500A) Processing helix chain 'D' and resid 3786 through 3800 Processing helix chain 'D' and resid 3804 through 3819 removed outlier: 3.961A pdb=" N LEU D3815 " --> pdb=" O MET D3811 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP D3817 " --> pdb=" O ASP D3813 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS D3818 " --> pdb=" O TYR D3814 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS D3819 " --> pdb=" O LEU D3815 " (cutoff:3.500A) Processing helix chain 'D' and resid 3821 through 3833 removed outlier: 3.663A pdb=" N ALA D3829 " --> pdb=" O GLN D3825 " (cutoff:3.500A) Processing helix chain 'D' and resid 3838 through 3850 Processing helix chain 'D' and resid 3872 through 3887 removed outlier: 3.754A pdb=" N GLN D3877 " --> pdb=" O ASP D3873 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE D3880 " --> pdb=" O THR D3876 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG D3881 " --> pdb=" O GLN D3877 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU D3883 " --> pdb=" O LEU D3879 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N CYS D3887 " --> pdb=" O LEU D3883 " (cutoff:3.500A) Processing helix chain 'D' and resid 3893 through 3900 Processing helix chain 'D' and resid 3909 through 3934 removed outlier: 4.266A pdb=" N CYS D3913 " --> pdb=" O ASN D3909 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL D3915 " --> pdb=" O ILE D3911 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER D3924 " --> pdb=" O ARG D3920 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TRP D3930 " --> pdb=" O SER D3926 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TYR D3931 " --> pdb=" O ASP D3927 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N TYR D3932 " --> pdb=" O PHE D3928 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N GLY D3934 " --> pdb=" O TRP D3930 " (cutoff:3.500A) Processing helix chain 'D' and resid 3939 through 3964 removed outlier: 4.081A pdb=" N ASN D3945 " --> pdb=" O GLN D3941 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE D3946 " --> pdb=" O GLY D3942 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER D3947 " --> pdb=" O LYS D3943 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS D3948 " --> pdb=" O ARG D3944 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE D3964 " --> pdb=" O LEU D3960 " (cutoff:3.500A) Processing helix chain 'D' and resid 3968 through 3978 Processing helix chain 'D' and resid 3979 through 3993 removed outlier: 3.745A pdb=" N ALA D3983 " --> pdb=" O ARG D3979 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL D3985 " --> pdb=" O TRP D3981 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL D3990 " --> pdb=" O GLY D3986 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N PHE D3991 " --> pdb=" O PHE D3987 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N HIS D3993 " --> pdb=" O HIS D3989 " (cutoff:3.500A) Processing helix chain 'D' and resid 3994 through 3999 removed outlier: 3.535A pdb=" N LEU D3998 " --> pdb=" O MET D3994 " (cutoff:3.500A) Processing helix chain 'D' and resid 4004 through 4026 removed outlier: 3.718A pdb=" N GLU D4010 " --> pdb=" O GLU D4006 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU D4011 " --> pdb=" O LEU D4007 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL D4019 " --> pdb=" O GLN D4015 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL D4020 " --> pdb=" O LYS D4016 " (cutoff:3.500A) Processing helix chain 'D' and resid 4033 through 4046 removed outlier: 3.566A pdb=" N ARG D4037 " --> pdb=" O GLY D4033 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP D4041 " --> pdb=" O ARG D4037 " (cutoff:3.500A) Processing helix chain 'D' and resid 4046 through 4069 removed outlier: 3.551A pdb=" N MET D4052 " --> pdb=" O SER D4048 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE D4057 " --> pdb=" O ILE D4053 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP D4058 " --> pdb=" O LEU D4054 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET D4059 " --> pdb=" O LYS D4055 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE D4060 " --> pdb=" O PHE D4056 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASP D4065 " --> pdb=" O LEU D4061 " (cutoff:3.500A) Processing helix chain 'D' and resid 4069 through 4076 removed outlier: 4.071A pdb=" N GLN D4073 " --> pdb=" O SER D4069 " (cutoff:3.500A) Processing helix chain 'D' and resid 4110 through 4114 Processing helix chain 'D' and resid 4127 through 4149 removed outlier: 4.284A pdb=" N ASP D4133 " --> pdb=" O GLU D4129 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE D4134 " --> pdb=" O PRO D4130 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU D4145 " --> pdb=" O LEU D4141 " (cutoff:3.500A) Processing helix chain 'D' and resid 4152 through 4162 removed outlier: 3.926A pdb=" N ARG D4156 " --> pdb=" O ASP D4152 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASN D4157 " --> pdb=" O PRO D4153 " (cutoff:3.500A) Processing helix chain 'D' and resid 4162 through 4169 Processing helix chain 'D' and resid 4193 through 4201 Processing helix chain 'D' and resid 4202 through 4218 removed outlier: 3.773A pdb=" N ILE D4213 " --> pdb=" O LYS D4209 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N PHE D4214 " --> pdb=" O ARG D4210 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASN D4218 " --> pdb=" O PHE D4214 " (cutoff:3.500A) Processing helix chain 'D' and resid 4221 through 4245 removed outlier: 3.576A pdb=" N PHE D4238 " --> pdb=" O GLU D4234 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU D4239 " --> pdb=" O ASP D4235 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLN D4241 " --> pdb=" O ILE D4237 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ILE D4242 " --> pdb=" O PHE D4238 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA D4243 " --> pdb=" O GLU D4239 " (cutoff:3.500A) Processing helix chain 'D' and resid 4545 through 4556 removed outlier: 3.652A pdb=" N ASN D4556 " --> pdb=" O TYR D4552 " (cutoff:3.500A) Processing helix chain 'D' and resid 4556 through 4577 removed outlier: 3.602A pdb=" N PHE D4577 " --> pdb=" O PHE D4573 " (cutoff:3.500A) Processing helix chain 'D' and resid 4636 through 4680 removed outlier: 3.538A pdb=" N LEU D4641 " --> pdb=" O MET D4637 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ARG D4642 " --> pdb=" O GLU D4638 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYS D4643 " --> pdb=" O PRO D4639 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE D4656 " --> pdb=" O ALA D4652 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS D4663 " --> pdb=" O TYR D4659 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N VAL D4664 " --> pdb=" O ASN D4660 " (cutoff:3.500A) Proline residue: D4665 - end of helix removed outlier: 3.943A pdb=" N ARG D4671 " --> pdb=" O VAL D4667 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLU D4674 " --> pdb=" O LYS D4670 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ALA D4676 " --> pdb=" O GLU D4672 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG D4677 " --> pdb=" O LYS D4673 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU D4680 " --> pdb=" O ALA D4676 " (cutoff:3.500A) Processing helix chain 'D' and resid 4694 through 4700 removed outlier: 3.694A pdb=" N GLN D4698 " --> pdb=" O ASP D4694 " (cutoff:3.500A) Processing helix chain 'D' and resid 4708 through 4712 removed outlier: 4.132A pdb=" N ASN D4712 " --> pdb=" O PHE D4709 " (cutoff:3.500A) Processing helix chain 'D' and resid 4717 through 4726 removed outlier: 4.007A pdb=" N LEU D4723 " --> pdb=" O LYS D4719 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP D4724 " --> pdb=" O ARG D4720 " (cutoff:3.500A) Processing helix chain 'D' and resid 4731 through 4737 Processing helix chain 'D' and resid 4770 through 4784 removed outlier: 3.507A pdb=" N ILE D4781 " --> pdb=" O LYS D4777 " (cutoff:3.500A) Processing helix chain 'D' and resid 4784 through 4803 removed outlier: 3.870A pdb=" N MET D4796 " --> pdb=" O TRP D4792 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER D4797 " --> pdb=" O TYR D4793 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N HIS D4801 " --> pdb=" O SER D4797 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N TYR D4802 " --> pdb=" O LEU D4798 " (cutoff:3.500A) Processing helix chain 'D' and resid 4804 through 4812 removed outlier: 3.563A pdb=" N ALA D4809 " --> pdb=" O PHE D4806 " (cutoff:3.500A) Processing helix chain 'D' and resid 4813 through 4818 Processing helix chain 'D' and resid 4818 through 4831 removed outlier: 4.398A pdb=" N VAL D4828 " --> pdb=" O ILE D4824 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR D4829 " --> pdb=" O LEU D4825 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASN D4831 " --> pdb=" O SER D4827 " (cutoff:3.500A) Processing helix chain 'D' and resid 4831 through 4856 removed outlier: 4.365A pdb=" N MET D4837 " --> pdb=" O LYS D4833 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL D4839 " --> pdb=" O LEU D4835 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLY D4840 " --> pdb=" O VAL D4836 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL D4844 " --> pdb=" O GLY D4840 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU D4848 " --> pdb=" O VAL D4844 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL D4852 " --> pdb=" O LEU D4848 " (cutoff:3.500A) Processing helix chain 'D' and resid 4857 through 4862 removed outlier: 3.559A pdb=" N TYR D4861 " --> pdb=" O PHE D4857 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN D4862 " --> pdb=" O ARG D4858 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 4857 through 4862' Processing helix chain 'D' and resid 4876 through 4886 Processing helix chain 'D' and resid 4894 through 4898 Processing helix chain 'D' and resid 4907 through 4922 removed outlier: 3.625A pdb=" N VAL D4912 " --> pdb=" O GLU D4908 " (cutoff:3.500A) Processing helix chain 'D' and resid 4924 through 4955 removed outlier: 3.711A pdb=" N GLY D4939 " --> pdb=" O ILE D4935 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ARG D4942 " --> pdb=" O PHE D4938 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN D4944 " --> pdb=" O GLU D4940 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLN D4945 " --> pdb=" O LEU D4941 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET D4952 " --> pdb=" O VAL D4948 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU D4953 " --> pdb=" O ARG D4949 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS D4955 " --> pdb=" O ASP D4951 " (cutoff:3.500A) Processing helix chain 'D' and resid 4963 through 4967 Processing helix chain 'D' and resid 4972 through 4979 removed outlier: 3.604A pdb=" N GLU D4979 " --> pdb=" O THR D4975 " (cutoff:3.500A) Processing helix chain 'D' and resid 4982 through 4996 removed outlier: 3.674A pdb=" N TYR D4986 " --> pdb=" O ASN D4982 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N MET D4987 " --> pdb=" O LEU D4983 " (cutoff:3.500A) Processing helix chain 'D' and resid 5002 through 5015 Processing helix chain 'D' and resid 5025 through 5030 Processing helix chain 'E' and resid 40 through 42 No H-bonds generated for 'chain 'E' and resid 40 through 42' Processing helix chain 'E' and resid 56 through 66 Processing helix chain 'E' and resid 78 through 81 Processing helix chain 'F' and resid 74 through 84 Processing helix chain 'F' and resid 249 through 254 removed outlier: 4.301A pdb=" N THR F 254 " --> pdb=" O GLY F 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 257 No H-bonds generated for 'chain 'F' and resid 255 through 257' Processing helix chain 'F' and resid 394 through 424 removed outlier: 3.585A pdb=" N SER F 420 " --> pdb=" O LYS F 416 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE F 421 " --> pdb=" O GLY F 417 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LYS F 424 " --> pdb=" O SER F 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 438 through 450 Processing helix chain 'F' and resid 460 through 480 removed outlier: 3.882A pdb=" N GLU F 480 " --> pdb=" O SER F 476 " (cutoff:3.500A) Processing helix chain 'F' and resid 482 through 495 Processing helix chain 'F' and resid 508 through 513 removed outlier: 3.802A pdb=" N GLU F 513 " --> pdb=" O GLU F 509 " (cutoff:3.500A) Processing helix chain 'F' and resid 514 through 531 removed outlier: 3.642A pdb=" N VAL F 519 " --> pdb=" O TRP F 515 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN F 520 " --> pdb=" O LYS F 516 " (cutoff:3.500A) Processing helix chain 'F' and resid 533 through 540 removed outlier: 3.579A pdb=" N CYS F 537 " --> pdb=" O ASN F 533 " (cutoff:3.500A) Processing helix chain 'F' and resid 543 through 552 removed outlier: 3.504A pdb=" N LYS F 550 " --> pdb=" O TRP F 546 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ASP F 552 " --> pdb=" O VAL F 548 " (cutoff:3.500A) Processing helix chain 'F' and resid 556 through 571 removed outlier: 3.675A pdb=" N ILE F 560 " --> pdb=" O ALA F 556 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU F 568 " --> pdb=" O LEU F 564 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ILE F 569 " --> pdb=" O TYR F 565 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLU F 570 " --> pdb=" O CYS F 566 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER F 571 " --> pdb=" O VAL F 567 " (cutoff:3.500A) Processing helix chain 'F' and resid 573 through 578 removed outlier: 3.742A pdb=" N ILE F 578 " --> pdb=" O LEU F 575 " (cutoff:3.500A) Processing helix chain 'F' and resid 579 through 593 removed outlier: 3.569A pdb=" N ILE F 583 " --> pdb=" O GLN F 579 " (cutoff:3.500A) Processing helix chain 'F' and resid 596 through 607 removed outlier: 3.658A pdb=" N LEU F 600 " --> pdb=" O ASN F 596 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU F 603 " --> pdb=" O VAL F 599 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N CYS F 604 " --> pdb=" O LEU F 600 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER F 605 " --> pdb=" O ASP F 601 " (cutoff:3.500A) Processing helix chain 'F' and resid 614 through 625 removed outlier: 3.617A pdb=" N GLN F 618 " --> pdb=" O VAL F 614 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU F 623 " --> pdb=" O ASP F 619 " (cutoff:3.500A) Processing helix chain 'F' and resid 674 through 678 removed outlier: 4.129A pdb=" N ALA F 677 " --> pdb=" O PHE F 674 " (cutoff:3.500A) Processing helix chain 'F' and resid 812 through 815 removed outlier: 3.681A pdb=" N VAL F 815 " --> pdb=" O HIS F 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 812 through 815' Processing helix chain 'F' and resid 867 through 890 Processing helix chain 'F' and resid 905 through 908 removed outlier: 4.023A pdb=" N VAL F 908 " --> pdb=" O PRO F 905 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 905 through 908' Processing helix chain 'F' and resid 914 through 936 removed outlier: 3.633A pdb=" N LEU F 933 " --> pdb=" O LEU F 929 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA F 934 " --> pdb=" O LYS F 930 " (cutoff:3.500A) Processing helix chain 'F' and resid 943 through 949 removed outlier: 3.989A pdb=" N GLU F 947 " --> pdb=" O ASP F 943 " (cutoff:3.500A) Processing helix chain 'F' and resid 978 through 1004 removed outlier: 3.777A pdb=" N THR F 983 " --> pdb=" O PRO F 979 " (cutoff:3.500A) Processing helix chain 'F' and resid 1018 through 1022 removed outlier: 3.971A pdb=" N LEU F1021 " --> pdb=" O ASN F1018 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N VAL F1022 " --> pdb=" O PRO F1019 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 1018 through 1022' Processing helix chain 'F' and resid 1023 through 1027 Processing helix chain 'F' and resid 1028 through 1049 removed outlier: 3.529A pdb=" N ALA F1042 " --> pdb=" O SER F1038 " (cutoff:3.500A) Processing helix chain 'F' and resid 1079 through 1082 Processing helix chain 'F' and resid 1213 through 1222 removed outlier: 4.779A pdb=" N LEU F1219 " --> pdb=" O ALA F1215 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N GLN F1220 " --> pdb=" O ILE F1216 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU F1221 " --> pdb=" O CYS F1217 " (cutoff:3.500A) Processing helix chain 'F' and resid 1444 through 1446 No H-bonds generated for 'chain 'F' and resid 1444 through 1446' Processing helix chain 'F' and resid 1465 through 1469 removed outlier: 3.648A pdb=" N VAL F1469 " --> pdb=" O LEU F1466 " (cutoff:3.500A) Processing helix chain 'F' and resid 1575 through 1580 Processing helix chain 'F' and resid 1651 through 1655 removed outlier: 3.780A pdb=" N SER F1654 " --> pdb=" O LEU F1651 " (cutoff:3.500A) Processing helix chain 'F' and resid 1656 through 1673 removed outlier: 3.804A pdb=" N GLN F1661 " --> pdb=" O LEU F1657 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N PHE F1662 " --> pdb=" O ASP F1658 " (cutoff:3.500A) Processing helix chain 'F' and resid 1679 through 1689 removed outlier: 3.593A pdb=" N HIS F1683 " --> pdb=" O ASN F1679 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA F1684 " --> pdb=" O ARG F1680 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N CYS F1686 " --> pdb=" O ALA F1682 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N SER F1687 " --> pdb=" O HIS F1683 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N HIS F1688 " --> pdb=" O ALA F1684 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL F1689 " --> pdb=" O LEU F1685 " (cutoff:3.500A) Processing helix chain 'F' and resid 1690 through 1700 removed outlier: 3.727A pdb=" N GLU F1699 " --> pdb=" O LEU F1695 " (cutoff:3.500A) Processing helix chain 'F' and resid 1704 through 1720 Processing helix chain 'F' and resid 1720 through 1730 removed outlier: 3.724A pdb=" N CYS F1724 " --> pdb=" O LEU F1720 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG F1725 " --> pdb=" O GLU F1721 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER F1726 " --> pdb=" O SER F1722 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET F1730 " --> pdb=" O SER F1726 " (cutoff:3.500A) Processing helix chain 'F' and resid 1739 through 1744 Processing helix chain 'F' and resid 1804 through 1826 removed outlier: 3.501A pdb=" N LEU F1808 " --> pdb=" O PRO F1804 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL F1820 " --> pdb=" O LEU F1816 " (cutoff:3.500A) Processing helix chain 'F' and resid 1830 through 1833 Processing helix chain 'F' and resid 1834 through 1853 Proline residue: F1841 - end of helix removed outlier: 3.801A pdb=" N LEU F1845 " --> pdb=" O PRO F1841 " (cutoff:3.500A) Processing helix chain 'F' and resid 1856 through 1868 removed outlier: 3.507A pdb=" N LYS F1861 " --> pdb=" O ASP F1857 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU F1868 " --> pdb=" O LEU F1864 " (cutoff:3.500A) Processing helix chain 'F' and resid 1933 through 1984 removed outlier: 3.534A pdb=" N GLN F1939 " --> pdb=" O SER F1935 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE F1947 " --> pdb=" O LEU F1943 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU F1951 " --> pdb=" O PHE F1947 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU F1952 " --> pdb=" O CYS F1948 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS F1969 " --> pdb=" O ARG F1965 " (cutoff:3.500A) Processing helix chain 'F' and resid 1988 through 2000 Processing helix chain 'F' and resid 2002 through 2012 Processing helix chain 'F' and resid 2025 through 2044 removed outlier: 3.884A pdb=" N ASP F2031 " --> pdb=" O GLU F2027 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU F2032 " --> pdb=" O ILE F2028 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU F2033 " --> pdb=" O ARG F2029 " (cutoff:3.500A) Processing helix chain 'F' and resid 2094 through 2110 removed outlier: 3.538A pdb=" N VAL F2104 " --> pdb=" O SER F2100 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA F2107 " --> pdb=" O VAL F2103 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASP F2110 " --> pdb=" O TRP F2106 " (cutoff:3.500A) Processing helix chain 'F' and resid 2114 through 2128 removed outlier: 3.651A pdb=" N ARG F2119 " --> pdb=" O PRO F2115 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA F2120 " --> pdb=" O GLU F2116 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG F2127 " --> pdb=" O SER F2123 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN F2128 " --> pdb=" O LEU F2124 " (cutoff:3.500A) Processing helix chain 'F' and resid 2130 through 2139 Processing helix chain 'F' and resid 2146 through 2148 No H-bonds generated for 'chain 'F' and resid 2146 through 2148' Processing helix chain 'F' and resid 2149 through 2169 removed outlier: 3.535A pdb=" N GLN F2162 " --> pdb=" O GLU F2158 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ILE F2168 " --> pdb=" O ARG F2164 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL F2169 " --> pdb=" O SER F2165 " (cutoff:3.500A) Processing helix chain 'F' and resid 2172 through 2188 Processing helix chain 'F' and resid 2189 through 2195 removed outlier: 4.055A pdb=" N TYR F2193 " --> pdb=" O ASN F2189 " (cutoff:3.500A) Processing helix chain 'F' and resid 2195 through 2202 removed outlier: 3.694A pdb=" N MET F2199 " --> pdb=" O HIS F2195 " (cutoff:3.500A) Processing helix chain 'F' and resid 2203 through 2217 removed outlier: 3.542A pdb=" N THR F2207 " --> pdb=" O GLY F2203 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL F2215 " --> pdb=" O VAL F2211 " (cutoff:3.500A) Processing helix chain 'F' and resid 2226 through 2244 removed outlier: 3.815A pdb=" N VAL F2230 " --> pdb=" O PHE F2226 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR F2231 " --> pdb=" O PRO F2227 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER F2232 " --> pdb=" O LYS F2228 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N CYS F2234 " --> pdb=" O VAL F2230 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG F2242 " --> pdb=" O CYS F2238 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE F2243 " --> pdb=" O TYR F2239 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N SER F2244 " --> pdb=" O PHE F2240 " (cutoff:3.500A) Processing helix chain 'F' and resid 2244 through 2254 removed outlier: 3.504A pdb=" N MET F2251 " --> pdb=" O ASN F2247 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP F2253 " --> pdb=" O ARG F2249 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N HIS F2254 " --> pdb=" O SER F2250 " (cutoff:3.500A) Processing helix chain 'F' and resid 2254 through 2263 removed outlier: 3.695A pdb=" N GLY F2263 " --> pdb=" O LEU F2259 " (cutoff:3.500A) Processing helix chain 'F' and resid 2272 through 2282 removed outlier: 3.679A pdb=" N VAL F2276 " --> pdb=" O THR F2272 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL F2281 " --> pdb=" O ALA F2277 " (cutoff:3.500A) Processing helix chain 'F' and resid 2284 through 2290 removed outlier: 3.546A pdb=" N ALA F2288 " --> pdb=" O ASN F2284 " (cutoff:3.500A) Processing helix chain 'F' and resid 2292 through 2307 removed outlier: 3.507A pdb=" N LEU F2296 " --> pdb=" O GLN F2292 " (cutoff:3.500A) Processing helix chain 'F' and resid 2325 through 2340 removed outlier: 3.790A pdb=" N GLY F2329 " --> pdb=" O ASN F2325 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ARG F2331 " --> pdb=" O CYS F2327 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TYR F2332 " --> pdb=" O GLY F2328 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE F2338 " --> pdb=" O ASP F2334 " (cutoff:3.500A) Processing helix chain 'F' and resid 2347 through 2361 removed outlier: 3.573A pdb=" N LYS F2361 " --> pdb=" O LEU F2357 " (cutoff:3.500A) Processing helix chain 'F' and resid 2378 through 2383 Processing helix chain 'F' and resid 2421 through 2437 removed outlier: 3.510A pdb=" N TYR F2427 " --> pdb=" O ILE F2423 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N CYS F2437 " --> pdb=" O LEU F2433 " (cutoff:3.500A) Processing helix chain 'F' and resid 2441 through 2446 Processing helix chain 'F' and resid 2451 through 2462 Processing helix chain 'F' and resid 2463 through 2472 Processing helix chain 'F' and resid 2496 through 2499 Processing helix chain 'F' and resid 2500 through 2511 Processing helix chain 'F' and resid 2519 through 2534 removed outlier: 3.632A pdb=" N LEU F2523 " --> pdb=" O LEU F2519 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASP F2524 " --> pdb=" O LEU F2520 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N VAL F2525 " --> pdb=" O HIS F2521 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU F2528 " --> pdb=" O ASP F2524 " (cutoff:3.500A) Proline residue: F2529 - end of helix removed outlier: 3.538A pdb=" N ALA F2534 " --> pdb=" O ASP F2530 " (cutoff:3.500A) Processing helix chain 'F' and resid 2549 through 2558 Processing helix chain 'F' and resid 2558 through 2566 Processing helix chain 'F' and resid 2567 through 2570 Processing helix chain 'F' and resid 2580 through 2592 removed outlier: 3.582A pdb=" N ARG F2592 " --> pdb=" O TYR F2588 " (cutoff:3.500A) Processing helix chain 'F' and resid 2600 through 2613 removed outlier: 3.784A pdb=" N GLU F2606 " --> pdb=" O ASP F2602 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG F2613 " --> pdb=" O MET F2609 " (cutoff:3.500A) Processing helix chain 'F' and resid 2621 through 2631 removed outlier: 3.773A pdb=" N ARG F2626 " --> pdb=" O HIS F2622 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N PHE F2629 " --> pdb=" O ARG F2625 " (cutoff:3.500A) Processing helix chain 'F' and resid 2642 through 2653 Processing helix chain 'F' and resid 2665 through 2683 Processing helix chain 'F' and resid 2689 through 2700 removed outlier: 3.789A pdb=" N UNK F2694 " --> pdb=" O UNK F2690 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N UNK F2695 " --> pdb=" O UNK F2691 " (cutoff:3.500A) Processing helix chain 'F' and resid 2748 through 2750 No H-bonds generated for 'chain 'F' and resid 2748 through 2750' Processing helix chain 'F' and resid 2751 through 2773 Processing helix chain 'F' and resid 2793 through 2797 Processing helix chain 'F' and resid 2798 through 2819 removed outlier: 3.618A pdb=" N ILE F2804 " --> pdb=" O LYS F2800 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N TYR F2805 " --> pdb=" O ASP F2801 " (cutoff:3.500A) Proline residue: F2808 - end of helix Processing helix chain 'F' and resid 2868 through 2897 removed outlier: 3.539A pdb=" N GLN F2877 " --> pdb=" O ALA F2873 " (cutoff:3.500A) Processing helix chain 'F' and resid 2916 through 2933 Processing helix chain 'F' and resid 2957 through 2978 Processing helix chain 'F' and resid 3000 through 3018 removed outlier: 4.349A pdb=" N UNK F3009 " --> pdb=" O UNK F3005 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N UNK F3010 " --> pdb=" O UNK F3006 " (cutoff:3.500A) Processing helix chain 'F' and resid 3033 through 3046 Processing helix chain 'F' and resid 3052 through 3062 Processing helix chain 'F' and resid 3147 through 3166 Processing helix chain 'F' and resid 3174 through 3193 Processing helix chain 'F' and resid 3203 through 3217 Processing helix chain 'F' and resid 3226 through 3238 Processing helix chain 'F' and resid 3279 through 3288 Processing helix chain 'F' and resid 3293 through 3308 Processing helix chain 'F' and resid 3322 through 3335 Processing helix chain 'F' and resid 3347 through 3352 Processing helix chain 'F' and resid 3352 through 3358 Processing helix chain 'F' and resid 3366 through 3385 Processing helix chain 'F' and resid 3412 through 3427 removed outlier: 3.589A pdb=" N TYR F3416 " --> pdb=" O LEU F3412 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASP F3418 " --> pdb=" O ILE F3414 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASN F3419 " --> pdb=" O ARG F3415 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ALA F3422 " --> pdb=" O ASP F3418 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N HIS F3423 " --> pdb=" O ASN F3419 " (cutoff:3.500A) Processing helix chain 'F' and resid 3429 through 3448 removed outlier: 3.539A pdb=" N LYS F3448 " --> pdb=" O ILE F3444 " (cutoff:3.500A) Processing helix chain 'F' and resid 3510 through 3526 removed outlier: 3.580A pdb=" N UNK F3520 " --> pdb=" O UNK F3516 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N UNK F3521 " --> pdb=" O UNK F3517 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N UNK F3524 " --> pdb=" O UNK F3520 " (cutoff:3.500A) Processing helix chain 'F' and resid 3535 through 3544 Processing helix chain 'F' and resid 3549 through 3555 Processing helix chain 'F' and resid 3565 through 3574 Processing helix chain 'F' and resid 3587 through 3606 Processing helix chain 'F' and resid 3641 through 3657 removed outlier: 4.329A pdb=" N ASN F3647 " --> pdb=" O HIS F3643 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N MET F3648 " --> pdb=" O ARG F3644 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU F3651 " --> pdb=" O ASN F3647 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA F3655 " --> pdb=" O GLU F3651 " (cutoff:3.500A) Processing helix chain 'F' and resid 3664 through 3678 removed outlier: 3.986A pdb=" N ARG F3668 " --> pdb=" O SER F3664 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY F3677 " --> pdb=" O LEU F3673 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLU F3678 " --> pdb=" O SER F3674 " (cutoff:3.500A) Processing helix chain 'F' and resid 3692 through 3706 Processing helix chain 'F' and resid 3715 through 3731 removed outlier: 3.610A pdb=" N MET F3719 " --> pdb=" O ASP F3715 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU F3731 " --> pdb=" O LYS F3727 " (cutoff:3.500A) Processing helix chain 'F' and resid 3748 through 3769 removed outlier: 3.794A pdb=" N LEU F3765 " --> pdb=" O GLN F3761 " (cutoff:3.500A) Processing helix chain 'F' and resid 3769 through 3781 removed outlier: 4.012A pdb=" N LEU F3775 " --> pdb=" O ALA F3771 " (cutoff:3.500A) Processing helix chain 'F' and resid 3786 through 3800 Processing helix chain 'F' and resid 3804 through 3819 removed outlier: 3.959A pdb=" N LEU F3815 " --> pdb=" O MET F3811 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP F3817 " --> pdb=" O ASP F3813 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS F3818 " --> pdb=" O TYR F3814 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS F3819 " --> pdb=" O LEU F3815 " (cutoff:3.500A) Processing helix chain 'F' and resid 3821 through 3833 removed outlier: 3.662A pdb=" N ALA F3829 " --> pdb=" O GLN F3825 " (cutoff:3.500A) Processing helix chain 'F' and resid 3838 through 3850 Processing helix chain 'F' and resid 3872 through 3887 removed outlier: 3.754A pdb=" N GLN F3877 " --> pdb=" O ASP F3873 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE F3880 " --> pdb=" O THR F3876 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG F3881 " --> pdb=" O GLN F3877 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU F3883 " --> pdb=" O LEU F3879 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N CYS F3887 " --> pdb=" O LEU F3883 " (cutoff:3.500A) Processing helix chain 'F' and resid 3893 through 3900 Processing helix chain 'F' and resid 3909 through 3934 removed outlier: 4.267A pdb=" N CYS F3913 " --> pdb=" O ASN F3909 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL F3915 " --> pdb=" O ILE F3911 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER F3924 " --> pdb=" O ARG F3920 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TRP F3930 " --> pdb=" O SER F3926 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TYR F3931 " --> pdb=" O ASP F3927 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N TYR F3932 " --> pdb=" O PHE F3928 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N GLY F3934 " --> pdb=" O TRP F3930 " (cutoff:3.500A) Processing helix chain 'F' and resid 3939 through 3964 removed outlier: 4.083A pdb=" N ASN F3945 " --> pdb=" O GLN F3941 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE F3946 " --> pdb=" O GLY F3942 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER F3947 " --> pdb=" O LYS F3943 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS F3948 " --> pdb=" O ARG F3944 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE F3964 " --> pdb=" O LEU F3960 " (cutoff:3.500A) Processing helix chain 'F' and resid 3968 through 3978 Processing helix chain 'F' and resid 3979 through 3993 removed outlier: 3.745A pdb=" N ALA F3983 " --> pdb=" O ARG F3979 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL F3985 " --> pdb=" O TRP F3981 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL F3990 " --> pdb=" O GLY F3986 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N PHE F3991 " --> pdb=" O PHE F3987 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N HIS F3993 " --> pdb=" O HIS F3989 " (cutoff:3.500A) Processing helix chain 'F' and resid 3994 through 3999 removed outlier: 3.535A pdb=" N LEU F3998 " --> pdb=" O MET F3994 " (cutoff:3.500A) Processing helix chain 'F' and resid 4004 through 4026 removed outlier: 3.718A pdb=" N GLU F4010 " --> pdb=" O GLU F4006 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU F4011 " --> pdb=" O LEU F4007 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL F4019 " --> pdb=" O GLN F4015 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL F4020 " --> pdb=" O LYS F4016 " (cutoff:3.500A) Processing helix chain 'F' and resid 4033 through 4046 removed outlier: 3.565A pdb=" N ARG F4037 " --> pdb=" O GLY F4033 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP F4041 " --> pdb=" O ARG F4037 " (cutoff:3.500A) Processing helix chain 'F' and resid 4046 through 4069 removed outlier: 3.550A pdb=" N MET F4052 " --> pdb=" O SER F4048 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE F4057 " --> pdb=" O ILE F4053 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASP F4058 " --> pdb=" O LEU F4054 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET F4059 " --> pdb=" O LYS F4055 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE F4060 " --> pdb=" O PHE F4056 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASP F4065 " --> pdb=" O LEU F4061 " (cutoff:3.500A) Processing helix chain 'F' and resid 4069 through 4076 removed outlier: 4.071A pdb=" N GLN F4073 " --> pdb=" O SER F4069 " (cutoff:3.500A) Processing helix chain 'F' and resid 4110 through 4114 Processing helix chain 'F' and resid 4127 through 4149 removed outlier: 4.283A pdb=" N ASP F4133 " --> pdb=" O GLU F4129 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE F4134 " --> pdb=" O PRO F4130 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU F4145 " --> pdb=" O LEU F4141 " (cutoff:3.500A) Processing helix chain 'F' and resid 4152 through 4162 removed outlier: 3.928A pdb=" N ARG F4156 " --> pdb=" O ASP F4152 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN F4157 " --> pdb=" O PRO F4153 " (cutoff:3.500A) Processing helix chain 'F' and resid 4162 through 4169 Processing helix chain 'F' and resid 4193 through 4201 Processing helix chain 'F' and resid 4202 through 4218 removed outlier: 3.773A pdb=" N ILE F4213 " --> pdb=" O LYS F4209 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N PHE F4214 " --> pdb=" O ARG F4210 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN F4218 " --> pdb=" O PHE F4214 " (cutoff:3.500A) Processing helix chain 'F' and resid 4221 through 4245 removed outlier: 3.578A pdb=" N PHE F4238 " --> pdb=" O GLU F4234 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU F4239 " --> pdb=" O ASP F4235 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLN F4241 " --> pdb=" O ILE F4237 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE F4242 " --> pdb=" O PHE F4238 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA F4243 " --> pdb=" O GLU F4239 " (cutoff:3.500A) Processing helix chain 'F' and resid 4545 through 4556 removed outlier: 3.650A pdb=" N ASN F4556 " --> pdb=" O TYR F4552 " (cutoff:3.500A) Processing helix chain 'F' and resid 4556 through 4577 removed outlier: 3.602A pdb=" N PHE F4577 " --> pdb=" O PHE F4573 " (cutoff:3.500A) Processing helix chain 'F' and resid 4636 through 4680 removed outlier: 3.538A pdb=" N LEU F4641 " --> pdb=" O MET F4637 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ARG F4642 " --> pdb=" O GLU F4638 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N CYS F4643 " --> pdb=" O PRO F4639 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE F4656 " --> pdb=" O ALA F4652 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS F4663 " --> pdb=" O TYR F4659 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N VAL F4664 " --> pdb=" O ASN F4660 " (cutoff:3.500A) Proline residue: F4665 - end of helix removed outlier: 3.943A pdb=" N ARG F4671 " --> pdb=" O VAL F4667 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N GLU F4674 " --> pdb=" O LYS F4670 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ALA F4676 " --> pdb=" O GLU F4672 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG F4677 " --> pdb=" O LYS F4673 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU F4680 " --> pdb=" O ALA F4676 " (cutoff:3.500A) Processing helix chain 'F' and resid 4694 through 4700 removed outlier: 3.693A pdb=" N GLN F4698 " --> pdb=" O ASP F4694 " (cutoff:3.500A) Processing helix chain 'F' and resid 4708 through 4712 removed outlier: 4.132A pdb=" N ASN F4712 " --> pdb=" O PHE F4709 " (cutoff:3.500A) Processing helix chain 'F' and resid 4717 through 4726 removed outlier: 4.006A pdb=" N LEU F4723 " --> pdb=" O LYS F4719 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP F4724 " --> pdb=" O ARG F4720 " (cutoff:3.500A) Processing helix chain 'F' and resid 4731 through 4737 Processing helix chain 'F' and resid 4770 through 4784 removed outlier: 3.507A pdb=" N ILE F4781 " --> pdb=" O LYS F4777 " (cutoff:3.500A) Processing helix chain 'F' and resid 4784 through 4803 removed outlier: 3.872A pdb=" N MET F4796 " --> pdb=" O TRP F4792 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER F4797 " --> pdb=" O TYR F4793 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N HIS F4801 " --> pdb=" O SER F4797 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N TYR F4802 " --> pdb=" O LEU F4798 " (cutoff:3.500A) Processing helix chain 'F' and resid 4804 through 4812 removed outlier: 3.564A pdb=" N ALA F4809 " --> pdb=" O PHE F4806 " (cutoff:3.500A) Processing helix chain 'F' and resid 4813 through 4818 Processing helix chain 'F' and resid 4818 through 4831 removed outlier: 4.397A pdb=" N VAL F4828 " --> pdb=" O ILE F4824 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR F4829 " --> pdb=" O LEU F4825 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASN F4831 " --> pdb=" O SER F4827 " (cutoff:3.500A) Processing helix chain 'F' and resid 4831 through 4856 removed outlier: 4.365A pdb=" N MET F4837 " --> pdb=" O LYS F4833 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL F4839 " --> pdb=" O LEU F4835 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLY F4840 " --> pdb=" O VAL F4836 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL F4844 " --> pdb=" O GLY F4840 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU F4848 " --> pdb=" O VAL F4844 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL F4852 " --> pdb=" O LEU F4848 " (cutoff:3.500A) Processing helix chain 'F' and resid 4857 through 4862 removed outlier: 3.558A pdb=" N TYR F4861 " --> pdb=" O PHE F4857 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN F4862 " --> pdb=" O ARG F4858 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 4857 through 4862' Processing helix chain 'F' and resid 4876 through 4886 Processing helix chain 'F' and resid 4894 through 4898 Processing helix chain 'F' and resid 4907 through 4922 removed outlier: 3.625A pdb=" N VAL F4912 " --> pdb=" O GLU F4908 " (cutoff:3.500A) Processing helix chain 'F' and resid 4924 through 4955 removed outlier: 3.710A pdb=" N GLY F4939 " --> pdb=" O ILE F4935 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ARG F4942 " --> pdb=" O PHE F4938 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN F4944 " --> pdb=" O GLU F4940 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLN F4945 " --> pdb=" O LEU F4941 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET F4952 " --> pdb=" O VAL F4948 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU F4953 " --> pdb=" O ARG F4949 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS F4955 " --> pdb=" O ASP F4951 " (cutoff:3.500A) Processing helix chain 'F' and resid 4963 through 4967 Processing helix chain 'F' and resid 4972 through 4979 removed outlier: 3.604A pdb=" N GLU F4979 " --> pdb=" O THR F4975 " (cutoff:3.500A) Processing helix chain 'F' and resid 4982 through 4996 removed outlier: 3.674A pdb=" N TYR F4986 " --> pdb=" O ASN F4982 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N MET F4987 " --> pdb=" O LEU F4983 " (cutoff:3.500A) Processing helix chain 'F' and resid 5002 through 5015 Processing helix chain 'F' and resid 5025 through 5030 Processing helix chain 'G' and resid 40 through 42 No H-bonds generated for 'chain 'G' and resid 40 through 42' Processing helix chain 'G' and resid 56 through 66 Processing helix chain 'G' and resid 78 through 81 Processing helix chain 'H' and resid 74 through 84 Processing helix chain 'H' and resid 249 through 254 removed outlier: 4.300A pdb=" N THR H 254 " --> pdb=" O GLY H 250 " (cutoff:3.500A) Processing helix chain 'H' and resid 255 through 257 No H-bonds generated for 'chain 'H' and resid 255 through 257' Processing helix chain 'H' and resid 394 through 424 removed outlier: 3.585A pdb=" N SER H 420 " --> pdb=" O LYS H 416 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE H 421 " --> pdb=" O GLY H 417 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LYS H 424 " --> pdb=" O SER H 420 " (cutoff:3.500A) Processing helix chain 'H' and resid 438 through 450 Processing helix chain 'H' and resid 460 through 480 removed outlier: 3.883A pdb=" N GLU H 480 " --> pdb=" O SER H 476 " (cutoff:3.500A) Processing helix chain 'H' and resid 482 through 495 Processing helix chain 'H' and resid 508 through 513 removed outlier: 3.802A pdb=" N GLU H 513 " --> pdb=" O GLU H 509 " (cutoff:3.500A) Processing helix chain 'H' and resid 514 through 531 removed outlier: 3.642A pdb=" N VAL H 519 " --> pdb=" O TRP H 515 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN H 520 " --> pdb=" O LYS H 516 " (cutoff:3.500A) Processing helix chain 'H' and resid 533 through 540 removed outlier: 3.580A pdb=" N CYS H 537 " --> pdb=" O ASN H 533 " (cutoff:3.500A) Processing helix chain 'H' and resid 543 through 552 removed outlier: 3.503A pdb=" N LYS H 550 " --> pdb=" O TRP H 546 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ASP H 552 " --> pdb=" O VAL H 548 " (cutoff:3.500A) Processing helix chain 'H' and resid 556 through 571 removed outlier: 3.676A pdb=" N ILE H 560 " --> pdb=" O ALA H 556 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU H 568 " --> pdb=" O LEU H 564 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ILE H 569 " --> pdb=" O TYR H 565 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU H 570 " --> pdb=" O CYS H 566 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N SER H 571 " --> pdb=" O VAL H 567 " (cutoff:3.500A) Processing helix chain 'H' and resid 573 through 578 removed outlier: 3.742A pdb=" N ILE H 578 " --> pdb=" O LEU H 575 " (cutoff:3.500A) Processing helix chain 'H' and resid 579 through 593 removed outlier: 3.569A pdb=" N ILE H 583 " --> pdb=" O GLN H 579 " (cutoff:3.500A) Processing helix chain 'H' and resid 596 through 607 removed outlier: 3.658A pdb=" N LEU H 600 " --> pdb=" O ASN H 596 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU H 603 " --> pdb=" O VAL H 599 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N CYS H 604 " --> pdb=" O LEU H 600 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER H 605 " --> pdb=" O ASP H 601 " (cutoff:3.500A) Processing helix chain 'H' and resid 614 through 625 removed outlier: 3.618A pdb=" N GLN H 618 " --> pdb=" O VAL H 614 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU H 623 " --> pdb=" O ASP H 619 " (cutoff:3.500A) Processing helix chain 'H' and resid 674 through 678 removed outlier: 4.128A pdb=" N ALA H 677 " --> pdb=" O PHE H 674 " (cutoff:3.500A) Processing helix chain 'H' and resid 812 through 815 removed outlier: 3.681A pdb=" N VAL H 815 " --> pdb=" O HIS H 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 812 through 815' Processing helix chain 'H' and resid 867 through 889 Processing helix chain 'H' and resid 905 through 908 removed outlier: 4.022A pdb=" N VAL H 908 " --> pdb=" O PRO H 905 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 905 through 908' Processing helix chain 'H' and resid 914 through 936 removed outlier: 3.633A pdb=" N LEU H 933 " --> pdb=" O LEU H 929 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA H 934 " --> pdb=" O LYS H 930 " (cutoff:3.500A) Processing helix chain 'H' and resid 943 through 949 removed outlier: 3.989A pdb=" N GLU H 947 " --> pdb=" O ASP H 943 " (cutoff:3.500A) Processing helix chain 'H' and resid 978 through 1004 removed outlier: 3.776A pdb=" N THR H 983 " --> pdb=" O PRO H 979 " (cutoff:3.500A) Processing helix chain 'H' and resid 1018 through 1022 removed outlier: 3.973A pdb=" N LEU H1021 " --> pdb=" O ASN H1018 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N VAL H1022 " --> pdb=" O PRO H1019 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 1018 through 1022' Processing helix chain 'H' and resid 1023 through 1027 Processing helix chain 'H' and resid 1028 through 1049 removed outlier: 3.531A pdb=" N ALA H1042 " --> pdb=" O SER H1038 " (cutoff:3.500A) Processing helix chain 'H' and resid 1079 through 1082 Processing helix chain 'H' and resid 1213 through 1222 removed outlier: 4.778A pdb=" N LEU H1219 " --> pdb=" O ALA H1215 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N GLN H1220 " --> pdb=" O ILE H1216 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU H1221 " --> pdb=" O CYS H1217 " (cutoff:3.500A) Processing helix chain 'H' and resid 1444 through 1446 No H-bonds generated for 'chain 'H' and resid 1444 through 1446' Processing helix chain 'H' and resid 1465 through 1469 removed outlier: 3.648A pdb=" N VAL H1469 " --> pdb=" O LEU H1466 " (cutoff:3.500A) Processing helix chain 'H' and resid 1575 through 1580 Processing helix chain 'H' and resid 1651 through 1655 removed outlier: 3.780A pdb=" N SER H1654 " --> pdb=" O LEU H1651 " (cutoff:3.500A) Processing helix chain 'H' and resid 1656 through 1673 removed outlier: 3.804A pdb=" N GLN H1661 " --> pdb=" O LEU H1657 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N PHE H1662 " --> pdb=" O ASP H1658 " (cutoff:3.500A) Processing helix chain 'H' and resid 1679 through 1689 removed outlier: 3.593A pdb=" N HIS H1683 " --> pdb=" O ASN H1679 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA H1684 " --> pdb=" O ARG H1680 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N CYS H1686 " --> pdb=" O ALA H1682 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N SER H1687 " --> pdb=" O HIS H1683 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N HIS H1688 " --> pdb=" O ALA H1684 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL H1689 " --> pdb=" O LEU H1685 " (cutoff:3.500A) Processing helix chain 'H' and resid 1690 through 1700 removed outlier: 3.728A pdb=" N GLU H1699 " --> pdb=" O LEU H1695 " (cutoff:3.500A) Processing helix chain 'H' and resid 1704 through 1720 Processing helix chain 'H' and resid 1720 through 1730 removed outlier: 3.725A pdb=" N CYS H1724 " --> pdb=" O LEU H1720 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG H1725 " --> pdb=" O GLU H1721 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER H1726 " --> pdb=" O SER H1722 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N MET H1730 " --> pdb=" O SER H1726 " (cutoff:3.500A) Processing helix chain 'H' and resid 1739 through 1744 Processing helix chain 'H' and resid 1804 through 1826 removed outlier: 3.500A pdb=" N LEU H1808 " --> pdb=" O PRO H1804 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL H1820 " --> pdb=" O LEU H1816 " (cutoff:3.500A) Processing helix chain 'H' and resid 1830 through 1833 Processing helix chain 'H' and resid 1834 through 1853 Proline residue: H1841 - end of helix removed outlier: 3.801A pdb=" N LEU H1845 " --> pdb=" O PRO H1841 " (cutoff:3.500A) Processing helix chain 'H' and resid 1856 through 1868 removed outlier: 3.506A pdb=" N LYS H1861 " --> pdb=" O ASP H1857 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU H1868 " --> pdb=" O LEU H1864 " (cutoff:3.500A) Processing helix chain 'H' and resid 1933 through 1984 removed outlier: 3.533A pdb=" N GLN H1939 " --> pdb=" O SER H1935 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE H1947 " --> pdb=" O LEU H1943 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU H1951 " --> pdb=" O PHE H1947 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU H1952 " --> pdb=" O CYS H1948 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS H1969 " --> pdb=" O ARG H1965 " (cutoff:3.500A) Processing helix chain 'H' and resid 1988 through 2000 Processing helix chain 'H' and resid 2002 through 2012 Processing helix chain 'H' and resid 2025 through 2044 removed outlier: 3.885A pdb=" N ASP H2031 " --> pdb=" O GLU H2027 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU H2032 " --> pdb=" O ILE H2028 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU H2033 " --> pdb=" O ARG H2029 " (cutoff:3.500A) Processing helix chain 'H' and resid 2094 through 2110 removed outlier: 3.538A pdb=" N VAL H2104 " --> pdb=" O SER H2100 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA H2107 " --> pdb=" O VAL H2103 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASP H2110 " --> pdb=" O TRP H2106 " (cutoff:3.500A) Processing helix chain 'H' and resid 2114 through 2128 removed outlier: 3.651A pdb=" N ARG H2119 " --> pdb=" O PRO H2115 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA H2120 " --> pdb=" O GLU H2116 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG H2127 " --> pdb=" O SER H2123 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN H2128 " --> pdb=" O LEU H2124 " (cutoff:3.500A) Processing helix chain 'H' and resid 2130 through 2139 Processing helix chain 'H' and resid 2146 through 2148 No H-bonds generated for 'chain 'H' and resid 2146 through 2148' Processing helix chain 'H' and resid 2149 through 2169 removed outlier: 3.534A pdb=" N GLN H2162 " --> pdb=" O GLU H2158 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ILE H2168 " --> pdb=" O ARG H2164 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N VAL H2169 " --> pdb=" O SER H2165 " (cutoff:3.500A) Processing helix chain 'H' and resid 2172 through 2188 Processing helix chain 'H' and resid 2189 through 2195 removed outlier: 4.055A pdb=" N TYR H2193 " --> pdb=" O ASN H2189 " (cutoff:3.500A) Processing helix chain 'H' and resid 2195 through 2202 removed outlier: 3.694A pdb=" N MET H2199 " --> pdb=" O HIS H2195 " (cutoff:3.500A) Processing helix chain 'H' and resid 2203 through 2217 removed outlier: 3.542A pdb=" N THR H2207 " --> pdb=" O GLY H2203 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL H2215 " --> pdb=" O VAL H2211 " (cutoff:3.500A) Processing helix chain 'H' and resid 2226 through 2244 removed outlier: 3.814A pdb=" N VAL H2230 " --> pdb=" O PHE H2226 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR H2231 " --> pdb=" O PRO H2227 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER H2232 " --> pdb=" O LYS H2228 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N CYS H2234 " --> pdb=" O VAL H2230 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG H2242 " --> pdb=" O CYS H2238 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE H2243 " --> pdb=" O TYR H2239 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N SER H2244 " --> pdb=" O PHE H2240 " (cutoff:3.500A) Processing helix chain 'H' and resid 2244 through 2254 removed outlier: 3.505A pdb=" N MET H2251 " --> pdb=" O ASN H2247 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP H2253 " --> pdb=" O ARG H2249 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N HIS H2254 " --> pdb=" O SER H2250 " (cutoff:3.500A) Processing helix chain 'H' and resid 2254 through 2263 removed outlier: 3.696A pdb=" N GLY H2263 " --> pdb=" O LEU H2259 " (cutoff:3.500A) Processing helix chain 'H' and resid 2272 through 2282 removed outlier: 3.680A pdb=" N VAL H2276 " --> pdb=" O THR H2272 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL H2281 " --> pdb=" O ALA H2277 " (cutoff:3.500A) Processing helix chain 'H' and resid 2284 through 2290 removed outlier: 3.546A pdb=" N ALA H2288 " --> pdb=" O ASN H2284 " (cutoff:3.500A) Processing helix chain 'H' and resid 2292 through 2307 removed outlier: 3.506A pdb=" N LEU H2296 " --> pdb=" O GLN H2292 " (cutoff:3.500A) Processing helix chain 'H' and resid 2325 through 2340 removed outlier: 3.789A pdb=" N GLY H2329 " --> pdb=" O ASN H2325 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG H2331 " --> pdb=" O CYS H2327 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TYR H2332 " --> pdb=" O GLY H2328 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE H2338 " --> pdb=" O ASP H2334 " (cutoff:3.500A) Processing helix chain 'H' and resid 2347 through 2361 removed outlier: 3.574A pdb=" N LYS H2361 " --> pdb=" O LEU H2357 " (cutoff:3.500A) Processing helix chain 'H' and resid 2378 through 2383 Processing helix chain 'H' and resid 2421 through 2437 removed outlier: 3.510A pdb=" N TYR H2427 " --> pdb=" O ILE H2423 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N CYS H2437 " --> pdb=" O LEU H2433 " (cutoff:3.500A) Processing helix chain 'H' and resid 2441 through 2446 Processing helix chain 'H' and resid 2451 through 2462 Processing helix chain 'H' and resid 2463 through 2472 Processing helix chain 'H' and resid 2496 through 2499 Processing helix chain 'H' and resid 2500 through 2511 Processing helix chain 'H' and resid 2519 through 2534 removed outlier: 3.631A pdb=" N LEU H2523 " --> pdb=" O LEU H2519 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASP H2524 " --> pdb=" O LEU H2520 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N VAL H2525 " --> pdb=" O HIS H2521 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU H2528 " --> pdb=" O ASP H2524 " (cutoff:3.500A) Proline residue: H2529 - end of helix removed outlier: 3.538A pdb=" N ALA H2534 " --> pdb=" O ASP H2530 " (cutoff:3.500A) Processing helix chain 'H' and resid 2549 through 2558 Processing helix chain 'H' and resid 2558 through 2566 Processing helix chain 'H' and resid 2567 through 2570 Processing helix chain 'H' and resid 2580 through 2592 removed outlier: 3.581A pdb=" N ARG H2592 " --> pdb=" O TYR H2588 " (cutoff:3.500A) Processing helix chain 'H' and resid 2600 through 2613 removed outlier: 3.785A pdb=" N GLU H2606 " --> pdb=" O ASP H2602 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG H2613 " --> pdb=" O MET H2609 " (cutoff:3.500A) Processing helix chain 'H' and resid 2621 through 2631 removed outlier: 3.775A pdb=" N ARG H2626 " --> pdb=" O HIS H2622 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N PHE H2629 " --> pdb=" O ARG H2625 " (cutoff:3.500A) Processing helix chain 'H' and resid 2642 through 2653 Processing helix chain 'H' and resid 2665 through 2683 Processing helix chain 'H' and resid 2689 through 2700 removed outlier: 3.789A pdb=" N UNK H2694 " --> pdb=" O UNK H2690 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N UNK H2695 " --> pdb=" O UNK H2691 " (cutoff:3.500A) Processing helix chain 'H' and resid 2748 through 2750 No H-bonds generated for 'chain 'H' and resid 2748 through 2750' Processing helix chain 'H' and resid 2751 through 2773 Processing helix chain 'H' and resid 2793 through 2797 Processing helix chain 'H' and resid 2798 through 2819 removed outlier: 3.618A pdb=" N ILE H2804 " --> pdb=" O LYS H2800 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N TYR H2805 " --> pdb=" O ASP H2801 " (cutoff:3.500A) Proline residue: H2808 - end of helix Processing helix chain 'H' and resid 2868 through 2897 removed outlier: 3.539A pdb=" N GLN H2877 " --> pdb=" O ALA H2873 " (cutoff:3.500A) Processing helix chain 'H' and resid 2916 through 2933 Processing helix chain 'H' and resid 2957 through 2978 Processing helix chain 'H' and resid 3000 through 3018 removed outlier: 4.347A pdb=" N UNK H3009 " --> pdb=" O UNK H3005 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N UNK H3010 " --> pdb=" O UNK H3006 " (cutoff:3.500A) Processing helix chain 'H' and resid 3033 through 3046 Processing helix chain 'H' and resid 3052 through 3062 Processing helix chain 'H' and resid 3147 through 3166 Processing helix chain 'H' and resid 3174 through 3193 Processing helix chain 'H' and resid 3203 through 3217 Processing helix chain 'H' and resid 3226 through 3238 Processing helix chain 'H' and resid 3279 through 3288 Processing helix chain 'H' and resid 3293 through 3308 Processing helix chain 'H' and resid 3322 through 3335 Processing helix chain 'H' and resid 3347 through 3352 Processing helix chain 'H' and resid 3352 through 3358 Processing helix chain 'H' and resid 3366 through 3385 Processing helix chain 'H' and resid 3412 through 3427 removed outlier: 3.589A pdb=" N TYR H3416 " --> pdb=" O LEU H3412 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP H3418 " --> pdb=" O ILE H3414 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASN H3419 " --> pdb=" O ARG H3415 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ALA H3422 " --> pdb=" O ASP H3418 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N HIS H3423 " --> pdb=" O ASN H3419 " (cutoff:3.500A) Processing helix chain 'H' and resid 3429 through 3448 removed outlier: 3.540A pdb=" N LYS H3448 " --> pdb=" O ILE H3444 " (cutoff:3.500A) Processing helix chain 'H' and resid 3510 through 3526 removed outlier: 3.581A pdb=" N UNK H3520 " --> pdb=" O UNK H3516 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N UNK H3521 " --> pdb=" O UNK H3517 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N UNK H3524 " --> pdb=" O UNK H3520 " (cutoff:3.500A) Processing helix chain 'H' and resid 3535 through 3544 Processing helix chain 'H' and resid 3549 through 3555 Processing helix chain 'H' and resid 3565 through 3574 Processing helix chain 'H' and resid 3587 through 3606 Processing helix chain 'H' and resid 3641 through 3657 removed outlier: 4.329A pdb=" N ASN H3647 " --> pdb=" O HIS H3643 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N MET H3648 " --> pdb=" O ARG H3644 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU H3651 " --> pdb=" O ASN H3647 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA H3655 " --> pdb=" O GLU H3651 " (cutoff:3.500A) Processing helix chain 'H' and resid 3664 through 3678 removed outlier: 3.985A pdb=" N ARG H3668 " --> pdb=" O SER H3664 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY H3677 " --> pdb=" O LEU H3673 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLU H3678 " --> pdb=" O SER H3674 " (cutoff:3.500A) Processing helix chain 'H' and resid 3692 through 3706 Processing helix chain 'H' and resid 3715 through 3731 removed outlier: 3.611A pdb=" N MET H3719 " --> pdb=" O ASP H3715 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU H3731 " --> pdb=" O LYS H3727 " (cutoff:3.500A) Processing helix chain 'H' and resid 3748 through 3769 removed outlier: 3.794A pdb=" N LEU H3765 " --> pdb=" O GLN H3761 " (cutoff:3.500A) Processing helix chain 'H' and resid 3769 through 3781 removed outlier: 4.012A pdb=" N LEU H3775 " --> pdb=" O ALA H3771 " (cutoff:3.500A) Processing helix chain 'H' and resid 3786 through 3800 Processing helix chain 'H' and resid 3804 through 3819 removed outlier: 3.960A pdb=" N LEU H3815 " --> pdb=" O MET H3811 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP H3817 " --> pdb=" O ASP H3813 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS H3818 " --> pdb=" O TYR H3814 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS H3819 " --> pdb=" O LEU H3815 " (cutoff:3.500A) Processing helix chain 'H' and resid 3821 through 3833 removed outlier: 3.663A pdb=" N ALA H3829 " --> pdb=" O GLN H3825 " (cutoff:3.500A) Processing helix chain 'H' and resid 3838 through 3850 Processing helix chain 'H' and resid 3872 through 3887 removed outlier: 3.753A pdb=" N GLN H3877 " --> pdb=" O ASP H3873 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE H3880 " --> pdb=" O THR H3876 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG H3881 " --> pdb=" O GLN H3877 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU H3883 " --> pdb=" O LEU H3879 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N CYS H3887 " --> pdb=" O LEU H3883 " (cutoff:3.500A) Processing helix chain 'H' and resid 3893 through 3900 Processing helix chain 'H' and resid 3909 through 3934 removed outlier: 4.265A pdb=" N CYS H3913 " --> pdb=" O ASN H3909 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL H3915 " --> pdb=" O ILE H3911 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER H3924 " --> pdb=" O ARG H3920 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TRP H3930 " --> pdb=" O SER H3926 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TYR H3931 " --> pdb=" O ASP H3927 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N TYR H3932 " --> pdb=" O PHE H3928 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N GLY H3934 " --> pdb=" O TRP H3930 " (cutoff:3.500A) Processing helix chain 'H' and resid 3939 through 3964 removed outlier: 4.082A pdb=" N ASN H3945 " --> pdb=" O GLN H3941 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE H3946 " --> pdb=" O GLY H3942 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER H3947 " --> pdb=" O LYS H3943 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS H3948 " --> pdb=" O ARG H3944 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE H3964 " --> pdb=" O LEU H3960 " (cutoff:3.500A) Processing helix chain 'H' and resid 3968 through 3978 Processing helix chain 'H' and resid 3979 through 3993 removed outlier: 3.745A pdb=" N ALA H3983 " --> pdb=" O ARG H3979 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL H3985 " --> pdb=" O TRP H3981 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL H3990 " --> pdb=" O GLY H3986 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N PHE H3991 " --> pdb=" O PHE H3987 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N HIS H3993 " --> pdb=" O HIS H3989 " (cutoff:3.500A) Processing helix chain 'H' and resid 3994 through 3999 removed outlier: 3.535A pdb=" N LEU H3998 " --> pdb=" O MET H3994 " (cutoff:3.500A) Processing helix chain 'H' and resid 4004 through 4026 removed outlier: 3.718A pdb=" N GLU H4010 " --> pdb=" O GLU H4006 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU H4011 " --> pdb=" O LEU H4007 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL H4019 " --> pdb=" O GLN H4015 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL H4020 " --> pdb=" O LYS H4016 " (cutoff:3.500A) Processing helix chain 'H' and resid 4033 through 4046 removed outlier: 3.565A pdb=" N ARG H4037 " --> pdb=" O GLY H4033 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP H4041 " --> pdb=" O ARG H4037 " (cutoff:3.500A) Processing helix chain 'H' and resid 4046 through 4069 removed outlier: 3.550A pdb=" N MET H4052 " --> pdb=" O SER H4048 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE H4057 " --> pdb=" O ILE H4053 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP H4058 " --> pdb=" O LEU H4054 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET H4059 " --> pdb=" O LYS H4055 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE H4060 " --> pdb=" O PHE H4056 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP H4065 " --> pdb=" O LEU H4061 " (cutoff:3.500A) Processing helix chain 'H' and resid 4069 through 4076 removed outlier: 4.071A pdb=" N GLN H4073 " --> pdb=" O SER H4069 " (cutoff:3.500A) Processing helix chain 'H' and resid 4110 through 4114 Processing helix chain 'H' and resid 4127 through 4149 removed outlier: 4.284A pdb=" N ASP H4133 " --> pdb=" O GLU H4129 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE H4134 " --> pdb=" O PRO H4130 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU H4145 " --> pdb=" O LEU H4141 " (cutoff:3.500A) Processing helix chain 'H' and resid 4152 through 4162 removed outlier: 3.927A pdb=" N ARG H4156 " --> pdb=" O ASP H4152 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASN H4157 " --> pdb=" O PRO H4153 " (cutoff:3.500A) Processing helix chain 'H' and resid 4162 through 4169 Processing helix chain 'H' and resid 4193 through 4201 Processing helix chain 'H' and resid 4202 through 4218 removed outlier: 3.772A pdb=" N ILE H4213 " --> pdb=" O LYS H4209 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N PHE H4214 " --> pdb=" O ARG H4210 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN H4218 " --> pdb=" O PHE H4214 " (cutoff:3.500A) Processing helix chain 'H' and resid 4221 through 4245 removed outlier: 3.577A pdb=" N PHE H4238 " --> pdb=" O GLU H4234 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU H4239 " --> pdb=" O ASP H4235 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLN H4241 " --> pdb=" O ILE H4237 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE H4242 " --> pdb=" O PHE H4238 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA H4243 " --> pdb=" O GLU H4239 " (cutoff:3.500A) Processing helix chain 'H' and resid 4545 through 4556 removed outlier: 3.652A pdb=" N ASN H4556 " --> pdb=" O TYR H4552 " (cutoff:3.500A) Processing helix chain 'H' and resid 4556 through 4577 removed outlier: 3.602A pdb=" N PHE H4577 " --> pdb=" O PHE H4573 " (cutoff:3.500A) Processing helix chain 'H' and resid 4636 through 4680 removed outlier: 3.538A pdb=" N LEU H4641 " --> pdb=" O MET H4637 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ARG H4642 " --> pdb=" O GLU H4638 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N CYS H4643 " --> pdb=" O PRO H4639 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE H4656 " --> pdb=" O ALA H4652 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS H4663 " --> pdb=" O TYR H4659 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N VAL H4664 " --> pdb=" O ASN H4660 " (cutoff:3.500A) Proline residue: H4665 - end of helix removed outlier: 3.942A pdb=" N ARG H4671 " --> pdb=" O VAL H4667 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N GLU H4674 " --> pdb=" O LYS H4670 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ALA H4676 " --> pdb=" O GLU H4672 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG H4677 " --> pdb=" O LYS H4673 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU H4680 " --> pdb=" O ALA H4676 " (cutoff:3.500A) Processing helix chain 'H' and resid 4694 through 4700 removed outlier: 3.694A pdb=" N GLN H4698 " --> pdb=" O ASP H4694 " (cutoff:3.500A) Processing helix chain 'H' and resid 4708 through 4712 removed outlier: 4.132A pdb=" N ASN H4712 " --> pdb=" O PHE H4709 " (cutoff:3.500A) Processing helix chain 'H' and resid 4717 through 4726 removed outlier: 4.006A pdb=" N LEU H4723 " --> pdb=" O LYS H4719 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP H4724 " --> pdb=" O ARG H4720 " (cutoff:3.500A) Processing helix chain 'H' and resid 4731 through 4737 Processing helix chain 'H' and resid 4770 through 4784 removed outlier: 3.506A pdb=" N ILE H4781 " --> pdb=" O LYS H4777 " (cutoff:3.500A) Processing helix chain 'H' and resid 4784 through 4803 removed outlier: 3.870A pdb=" N MET H4796 " --> pdb=" O TRP H4792 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER H4797 " --> pdb=" O TYR H4793 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N HIS H4801 " --> pdb=" O SER H4797 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N TYR H4802 " --> pdb=" O LEU H4798 " (cutoff:3.500A) Processing helix chain 'H' and resid 4804 through 4812 removed outlier: 3.565A pdb=" N ALA H4809 " --> pdb=" O PHE H4806 " (cutoff:3.500A) Processing helix chain 'H' and resid 4813 through 4818 Processing helix chain 'H' and resid 4818 through 4831 removed outlier: 4.398A pdb=" N VAL H4828 " --> pdb=" O ILE H4824 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR H4829 " --> pdb=" O LEU H4825 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN H4831 " --> pdb=" O SER H4827 " (cutoff:3.500A) Processing helix chain 'H' and resid 4831 through 4856 removed outlier: 4.365A pdb=" N MET H4837 " --> pdb=" O LYS H4833 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL H4839 " --> pdb=" O LEU H4835 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLY H4840 " --> pdb=" O VAL H4836 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL H4844 " --> pdb=" O GLY H4840 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU H4848 " --> pdb=" O VAL H4844 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL H4852 " --> pdb=" O LEU H4848 " (cutoff:3.500A) Processing helix chain 'H' and resid 4857 through 4862 removed outlier: 3.557A pdb=" N TYR H4861 " --> pdb=" O PHE H4857 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN H4862 " --> pdb=" O ARG H4858 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 4857 through 4862' Processing helix chain 'H' and resid 4876 through 4886 Processing helix chain 'H' and resid 4894 through 4898 Processing helix chain 'H' and resid 4907 through 4922 removed outlier: 3.626A pdb=" N VAL H4912 " --> pdb=" O GLU H4908 " (cutoff:3.500A) Processing helix chain 'H' and resid 4924 through 4955 removed outlier: 3.711A pdb=" N GLY H4939 " --> pdb=" O ILE H4935 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ARG H4942 " --> pdb=" O PHE H4938 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN H4944 " --> pdb=" O GLU H4940 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLN H4945 " --> pdb=" O LEU H4941 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET H4952 " --> pdb=" O VAL H4948 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU H4953 " --> pdb=" O ARG H4949 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS H4955 " --> pdb=" O ASP H4951 " (cutoff:3.500A) Processing helix chain 'H' and resid 4963 through 4967 Processing helix chain 'H' and resid 4972 through 4979 removed outlier: 3.604A pdb=" N GLU H4979 " --> pdb=" O THR H4975 " (cutoff:3.500A) Processing helix chain 'H' and resid 4982 through 4996 removed outlier: 3.674A pdb=" N TYR H4986 " --> pdb=" O ASN H4982 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N MET H4987 " --> pdb=" O LEU H4983 " (cutoff:3.500A) Processing helix chain 'H' and resid 5002 through 5015 Processing helix chain 'H' and resid 5025 through 5030 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 6 removed outlier: 3.770A pdb=" N GLU A 3 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU A 5 " --> pdb=" O LYS A 73 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS A 73 " --> pdb=" O GLU A 5 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASP A 37 " --> pdb=" O GLY A 28 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N LEU A 30 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N LYS A 35 " --> pdb=" O LEU A 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 21 through 24 Processing sheet with id=AA3, first strand: chain 'B' and resid 48 through 51 removed outlier: 3.513A pdb=" N GLU B 50 " --> pdb=" O CYS B 36 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU B 37 " --> pdb=" O LEU B 22 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N LEU B 22 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N GLU B 19 " --> pdb=" O ILE B 205 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE B 170 " --> pdb=" O HIS B 151 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N GLN B 71 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N ARG B 110 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N LEU B 69 " --> pdb=" O ARG B 110 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 117 through 120 removed outlier: 4.596A pdb=" N VAL B 135 " --> pdb=" O VAL B 191 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N VAL B 191 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLN B 190 " --> pdb=" O SER B 183 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 282 through 283 removed outlier: 3.597A pdb=" N THR B 391 " --> pdb=" O ARG B 221 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N CYS B 346 " --> pdb=" O LEU B 388 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 230 through 233 removed outlier: 6.050A pdb=" N VAL B 245 " --> pdb=" O ALA B 376 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA B 376 " --> pdb=" O VAL B 245 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LYS B 374 " --> pdb=" O TYR B 247 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE B 377 " --> pdb=" O THR B 358 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR B 358 " --> pdb=" O ILE B 377 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 293 through 294 Processing sheet with id=AA8, first strand: chain 'B' and resid 608 through 609 Processing sheet with id=AA9, first strand: chain 'B' and resid 634 through 639 removed outlier: 3.942A pdb=" N GLN B 634 " --> pdb=" O HIS B1640 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N MET B1648 " --> pdb=" O LEU B1639 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG B1646 " --> pdb=" O ILE B1641 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 650 through 651 removed outlier: 3.508A pdb=" N PHE B 778 " --> pdb=" O ALA B 687 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLY B 715 " --> pdb=" O TRP B 722 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 650 through 651 removed outlier: 3.833A pdb=" N THR B 642 " --> pdb=" O PHE B 783 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 762 through 763 removed outlier: 3.780A pdb=" N SER B 754 " --> pdb=" O ASP B 749 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 762 through 763 removed outlier: 3.780A pdb=" N SER B 754 " --> pdb=" O ASP B 749 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N LYS B 788 " --> pdb=" O ASP B 669 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ARG B1618 " --> pdb=" O ALA B1627 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLN B1629 " --> pdb=" O GLU B1616 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLU B1616 " --> pdb=" O GLN B1629 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 766 through 769 Processing sheet with id=AB6, first strand: chain 'B' and resid 830 through 831 Processing sheet with id=AB7, first strand: chain 'B' and resid 892 through 893 removed outlier: 6.014A pdb=" N THR B 892 " --> pdb=" O HIS B 904 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 940 through 941 removed outlier: 3.784A pdb=" N GLY B 940 " --> pdb=" O ASN B1052 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 1121 through 1125 removed outlier: 3.542A pdb=" N ALA B1077 " --> pdb=" O PRO B1190 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG B1073 " --> pdb=" O LEU B1194 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N ILE B1074 " --> pdb=" O SER B1239 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 1130 through 1131 Processing sheet with id=AC2, first strand: chain 'B' and resid 1149 through 1151 Processing sheet with id=AC3, first strand: chain 'B' and resid 1159 through 1160 removed outlier: 3.686A pdb=" N PHE B1179 " --> pdb=" O ILE B1160 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 1244 through 1247 Processing sheet with id=AC5, first strand: chain 'B' and resid 1255 through 1260 removed outlier: 3.692A pdb=" N ILE B1562 " --> pdb=" O LEU B1272 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N HIS B1274 " --> pdb=" O ASN B1560 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N ASN B1560 " --> pdb=" O HIS B1274 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU B1514 " --> pdb=" O VAL B1439 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR B1528 " --> pdb=" O LEU B1519 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 1255 through 1260 removed outlier: 3.692A pdb=" N ILE B1562 " --> pdb=" O LEU B1272 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N HIS B1274 " --> pdb=" O ASN B1560 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N ASN B1560 " --> pdb=" O HIS B1274 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 1287 through 1290 removed outlier: 3.637A pdb=" N TYR B1493 " --> pdb=" O TRP B1452 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 1734 through 1737 Processing sheet with id=AC9, first strand: chain 'B' and resid 2341 through 2342 Processing sheet with id=AD1, first strand: chain 'B' and resid 2776 through 2777 removed outlier: 6.534A pdb=" N SER B2776 " --> pdb=" O HIS B2788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 2822 through 2825 Processing sheet with id=AD3, first strand: chain 'B' and resid 4173 through 4177 removed outlier: 4.013A pdb=" N PHE B4190 " --> pdb=" O GLY B4174 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 4579 through 4581 removed outlier: 3.616A pdb=" N LYS B4579 " --> pdb=" O LEU B4630 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU B4630 " --> pdb=" O LYS B4579 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 2 through 6 removed outlier: 3.771A pdb=" N GLU C 3 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU C 5 " --> pdb=" O LYS C 73 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS C 73 " --> pdb=" O GLU C 5 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASP C 37 " --> pdb=" O GLY C 28 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N LEU C 30 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N LYS C 35 " --> pdb=" O LEU C 30 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 21 through 24 Processing sheet with id=AD7, first strand: chain 'D' and resid 48 through 51 removed outlier: 3.513A pdb=" N GLU D 50 " --> pdb=" O CYS D 36 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU D 37 " --> pdb=" O LEU D 22 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N LEU D 22 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N GLU D 19 " --> pdb=" O ILE D 205 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE D 170 " --> pdb=" O HIS D 151 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N GLN D 71 " --> pdb=" O LEU D 108 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N ARG D 110 " --> pdb=" O LEU D 69 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N LEU D 69 " --> pdb=" O ARG D 110 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 117 through 120 removed outlier: 4.595A pdb=" N VAL D 135 " --> pdb=" O VAL D 191 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N VAL D 191 " --> pdb=" O VAL D 135 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLN D 190 " --> pdb=" O SER D 183 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 282 through 283 removed outlier: 3.597A pdb=" N THR D 391 " --> pdb=" O ARG D 221 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N CYS D 346 " --> pdb=" O LEU D 388 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 230 through 233 removed outlier: 6.050A pdb=" N VAL D 245 " --> pdb=" O ALA D 376 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA D 376 " --> pdb=" O VAL D 245 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LYS D 374 " --> pdb=" O TYR D 247 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE D 377 " --> pdb=" O THR D 358 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR D 358 " --> pdb=" O ILE D 377 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 293 through 294 Processing sheet with id=AE3, first strand: chain 'D' and resid 608 through 609 Processing sheet with id=AE4, first strand: chain 'D' and resid 634 through 639 removed outlier: 3.942A pdb=" N GLN D 634 " --> pdb=" O HIS D1640 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N MET D1648 " --> pdb=" O LEU D1639 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG D1646 " --> pdb=" O ILE D1641 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 650 through 651 removed outlier: 3.508A pdb=" N PHE D 778 " --> pdb=" O ALA D 687 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLY D 715 " --> pdb=" O TRP D 722 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 650 through 651 removed outlier: 3.832A pdb=" N THR D 642 " --> pdb=" O PHE D 783 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 762 through 763 removed outlier: 3.779A pdb=" N SER D 754 " --> pdb=" O ASP D 749 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 762 through 763 removed outlier: 3.779A pdb=" N SER D 754 " --> pdb=" O ASP D 749 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N LYS D 788 " --> pdb=" O ASP D 669 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ARG D1618 " --> pdb=" O ALA D1627 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLN D1629 " --> pdb=" O GLU D1616 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLU D1616 " --> pdb=" O GLN D1629 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 766 through 769 Processing sheet with id=AF1, first strand: chain 'D' and resid 830 through 831 Processing sheet with id=AF2, first strand: chain 'D' and resid 892 through 893 removed outlier: 6.014A pdb=" N THR D 892 " --> pdb=" O HIS D 904 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'D' and resid 940 through 941 removed outlier: 3.784A pdb=" N GLY D 940 " --> pdb=" O ASN D1052 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 1121 through 1125 removed outlier: 3.543A pdb=" N ALA D1077 " --> pdb=" O PRO D1190 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG D1073 " --> pdb=" O LEU D1194 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ILE D1074 " --> pdb=" O SER D1239 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 1130 through 1131 Processing sheet with id=AF6, first strand: chain 'D' and resid 1149 through 1151 Processing sheet with id=AF7, first strand: chain 'D' and resid 1159 through 1160 removed outlier: 3.686A pdb=" N PHE D1179 " --> pdb=" O ILE D1160 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 1244 through 1247 Processing sheet with id=AF9, first strand: chain 'D' and resid 1255 through 1260 removed outlier: 3.692A pdb=" N ILE D1562 " --> pdb=" O LEU D1272 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N HIS D1274 " --> pdb=" O ASN D1560 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N ASN D1560 " --> pdb=" O HIS D1274 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU D1514 " --> pdb=" O VAL D1439 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR D1528 " --> pdb=" O LEU D1519 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 1255 through 1260 removed outlier: 3.692A pdb=" N ILE D1562 " --> pdb=" O LEU D1272 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N HIS D1274 " --> pdb=" O ASN D1560 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N ASN D1560 " --> pdb=" O HIS D1274 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'D' and resid 1287 through 1290 removed outlier: 3.637A pdb=" N TYR D1493 " --> pdb=" O TRP D1452 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'D' and resid 1734 through 1737 Processing sheet with id=AG4, first strand: chain 'D' and resid 2341 through 2342 Processing sheet with id=AG5, first strand: chain 'D' and resid 2776 through 2777 removed outlier: 6.534A pdb=" N SER D2776 " --> pdb=" O HIS D2788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG5 Processing sheet with id=AG6, first strand: chain 'D' and resid 2822 through 2825 Processing sheet with id=AG7, first strand: chain 'D' and resid 4176 through 4177 Processing sheet with id=AG8, first strand: chain 'D' and resid 4579 through 4581 removed outlier: 3.616A pdb=" N LYS D4579 " --> pdb=" O LEU D4630 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU D4630 " --> pdb=" O LYS D4579 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'E' and resid 2 through 6 removed outlier: 3.771A pdb=" N GLU E 3 " --> pdb=" O THR E 75 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLU E 5 " --> pdb=" O LYS E 73 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS E 73 " --> pdb=" O GLU E 5 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP E 37 " --> pdb=" O GLY E 28 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N LEU E 30 " --> pdb=" O LYS E 35 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N LYS E 35 " --> pdb=" O LEU E 30 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'E' and resid 21 through 24 Processing sheet with id=AH2, first strand: chain 'F' and resid 48 through 51 removed outlier: 3.514A pdb=" N GLU F 50 " --> pdb=" O CYS F 36 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU F 37 " --> pdb=" O LEU F 22 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N LEU F 22 " --> pdb=" O LEU F 37 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N GLU F 19 " --> pdb=" O ILE F 205 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE F 170 " --> pdb=" O HIS F 151 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N GLN F 71 " --> pdb=" O LEU F 108 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N ARG F 110 " --> pdb=" O LEU F 69 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N LEU F 69 " --> pdb=" O ARG F 110 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'F' and resid 117 through 120 removed outlier: 4.596A pdb=" N VAL F 135 " --> pdb=" O VAL F 191 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N VAL F 191 " --> pdb=" O VAL F 135 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLN F 190 " --> pdb=" O SER F 183 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'F' and resid 282 through 283 removed outlier: 3.597A pdb=" N THR F 391 " --> pdb=" O ARG F 221 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N CYS F 346 " --> pdb=" O LEU F 388 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'F' and resid 230 through 233 removed outlier: 6.049A pdb=" N VAL F 245 " --> pdb=" O ALA F 376 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA F 376 " --> pdb=" O VAL F 245 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LYS F 374 " --> pdb=" O TYR F 247 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE F 377 " --> pdb=" O THR F 358 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR F 358 " --> pdb=" O ILE F 377 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'F' and resid 293 through 294 Processing sheet with id=AH7, first strand: chain 'F' and resid 608 through 609 Processing sheet with id=AH8, first strand: chain 'F' and resid 634 through 639 removed outlier: 3.943A pdb=" N GLN F 634 " --> pdb=" O HIS F1640 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N MET F1648 " --> pdb=" O LEU F1639 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG F1646 " --> pdb=" O ILE F1641 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'F' and resid 650 through 651 removed outlier: 3.508A pdb=" N PHE F 778 " --> pdb=" O ALA F 687 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLY F 715 " --> pdb=" O TRP F 722 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'F' and resid 650 through 651 removed outlier: 3.833A pdb=" N THR F 642 " --> pdb=" O PHE F 783 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'F' and resid 762 through 763 removed outlier: 3.778A pdb=" N SER F 754 " --> pdb=" O ASP F 749 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'F' and resid 762 through 763 removed outlier: 3.778A pdb=" N SER F 754 " --> pdb=" O ASP F 749 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N LYS F 788 " --> pdb=" O ASP F 669 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ARG F1618 " --> pdb=" O ALA F1627 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLN F1629 " --> pdb=" O GLU F1616 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLU F1616 " --> pdb=" O GLN F1629 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'F' and resid 766 through 769 Processing sheet with id=AI5, first strand: chain 'F' and resid 830 through 831 Processing sheet with id=AI6, first strand: chain 'F' and resid 892 through 893 removed outlier: 6.012A pdb=" N THR F 892 " --> pdb=" O HIS F 904 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI6 Processing sheet with id=AI7, first strand: chain 'F' and resid 940 through 941 removed outlier: 3.785A pdb=" N GLY F 940 " --> pdb=" O ASN F1052 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'F' and resid 1121 through 1125 removed outlier: 3.543A pdb=" N ALA F1077 " --> pdb=" O PRO F1190 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG F1073 " --> pdb=" O LEU F1194 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N ILE F1074 " --> pdb=" O SER F1239 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'F' and resid 1130 through 1131 Processing sheet with id=AJ1, first strand: chain 'F' and resid 1149 through 1151 Processing sheet with id=AJ2, first strand: chain 'F' and resid 1159 through 1160 removed outlier: 3.685A pdb=" N PHE F1179 " --> pdb=" O ILE F1160 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'F' and resid 1244 through 1247 Processing sheet with id=AJ4, first strand: chain 'F' and resid 1255 through 1260 removed outlier: 3.692A pdb=" N ILE F1562 " --> pdb=" O LEU F1272 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N HIS F1274 " --> pdb=" O ASN F1560 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N ASN F1560 " --> pdb=" O HIS F1274 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU F1514 " --> pdb=" O VAL F1439 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR F1528 " --> pdb=" O LEU F1519 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'F' and resid 1255 through 1260 removed outlier: 3.692A pdb=" N ILE F1562 " --> pdb=" O LEU F1272 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N HIS F1274 " --> pdb=" O ASN F1560 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N ASN F1560 " --> pdb=" O HIS F1274 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'F' and resid 1287 through 1290 removed outlier: 3.637A pdb=" N TYR F1493 " --> pdb=" O TRP F1452 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'F' and resid 1734 through 1737 Processing sheet with id=AJ8, first strand: chain 'F' and resid 2341 through 2342 Processing sheet with id=AJ9, first strand: chain 'F' and resid 2776 through 2777 removed outlier: 6.533A pdb=" N SER F2776 " --> pdb=" O HIS F2788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ9 Processing sheet with id=AK1, first strand: chain 'F' and resid 2822 through 2825 Processing sheet with id=AK2, first strand: chain 'F' and resid 4173 through 4177 removed outlier: 4.013A pdb=" N PHE F4190 " --> pdb=" O GLY F4174 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'F' and resid 4579 through 4581 removed outlier: 3.616A pdb=" N LYS F4579 " --> pdb=" O LEU F4630 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU F4630 " --> pdb=" O LYS F4579 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'G' and resid 2 through 6 removed outlier: 3.771A pdb=" N GLU G 3 " --> pdb=" O THR G 75 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU G 5 " --> pdb=" O LYS G 73 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS G 73 " --> pdb=" O GLU G 5 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP G 37 " --> pdb=" O GLY G 28 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N LEU G 30 " --> pdb=" O LYS G 35 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N LYS G 35 " --> pdb=" O LEU G 30 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'G' and resid 21 through 24 Processing sheet with id=AK6, first strand: chain 'H' and resid 48 through 51 removed outlier: 3.514A pdb=" N GLU H 50 " --> pdb=" O CYS H 36 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU H 37 " --> pdb=" O LEU H 22 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N LEU H 22 " --> pdb=" O LEU H 37 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N GLU H 19 " --> pdb=" O ILE H 205 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE H 170 " --> pdb=" O HIS H 151 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N GLN H 71 " --> pdb=" O LEU H 108 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N ARG H 110 " --> pdb=" O LEU H 69 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N LEU H 69 " --> pdb=" O ARG H 110 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'H' and resid 117 through 120 removed outlier: 4.596A pdb=" N VAL H 135 " --> pdb=" O VAL H 191 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N VAL H 191 " --> pdb=" O VAL H 135 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLN H 190 " --> pdb=" O SER H 183 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'H' and resid 282 through 283 removed outlier: 3.596A pdb=" N THR H 391 " --> pdb=" O ARG H 221 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N CYS H 346 " --> pdb=" O LEU H 388 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'H' and resid 230 through 233 removed outlier: 6.050A pdb=" N VAL H 245 " --> pdb=" O ALA H 376 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA H 376 " --> pdb=" O VAL H 245 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LYS H 374 " --> pdb=" O TYR H 247 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE H 377 " --> pdb=" O THR H 358 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR H 358 " --> pdb=" O ILE H 377 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'H' and resid 293 through 294 Processing sheet with id=AL2, first strand: chain 'H' and resid 608 through 609 Processing sheet with id=AL3, first strand: chain 'H' and resid 634 through 639 removed outlier: 3.943A pdb=" N GLN H 634 " --> pdb=" O HIS H1640 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N MET H1648 " --> pdb=" O LEU H1639 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG H1646 " --> pdb=" O ILE H1641 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'H' and resid 650 through 651 removed outlier: 3.509A pdb=" N PHE H 778 " --> pdb=" O ALA H 687 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY H 715 " --> pdb=" O TRP H 722 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'H' and resid 650 through 651 removed outlier: 3.833A pdb=" N THR H 642 " --> pdb=" O PHE H 783 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'H' and resid 762 through 763 removed outlier: 3.779A pdb=" N SER H 754 " --> pdb=" O ASP H 749 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 'H' and resid 762 through 763 removed outlier: 3.779A pdb=" N SER H 754 " --> pdb=" O ASP H 749 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N LYS H 788 " --> pdb=" O ASP H 669 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ARG H1618 " --> pdb=" O ALA H1627 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLN H1629 " --> pdb=" O GLU H1616 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLU H1616 " --> pdb=" O GLN H1629 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'H' and resid 766 through 769 Processing sheet with id=AL9, first strand: chain 'H' and resid 830 through 831 Processing sheet with id=AM1, first strand: chain 'H' and resid 892 through 893 removed outlier: 6.014A pdb=" N THR H 892 " --> pdb=" O HIS H 904 " (cutoff:3.500A) No H-bonds generated for sheet with id=AM1 Processing sheet with id=AM2, first strand: chain 'H' and resid 940 through 941 removed outlier: 3.785A pdb=" N GLY H 940 " --> pdb=" O ASN H1052 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain 'H' and resid 1121 through 1125 removed outlier: 3.542A pdb=" N ALA H1077 " --> pdb=" O PRO H1190 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG H1073 " --> pdb=" O LEU H1194 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N ILE H1074 " --> pdb=" O SER H1239 " (cutoff:3.500A) Processing sheet with id=AM4, first strand: chain 'H' and resid 1130 through 1131 Processing sheet with id=AM5, first strand: chain 'H' and resid 1149 through 1151 Processing sheet with id=AM6, first strand: chain 'H' and resid 1159 through 1160 removed outlier: 3.685A pdb=" N PHE H1179 " --> pdb=" O ILE H1160 " (cutoff:3.500A) Processing sheet with id=AM7, first strand: chain 'H' and resid 1244 through 1247 Processing sheet with id=AM8, first strand: chain 'H' and resid 1255 through 1260 removed outlier: 3.692A pdb=" N ILE H1562 " --> pdb=" O LEU H1272 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N HIS H1274 " --> pdb=" O ASN H1560 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N ASN H1560 " --> pdb=" O HIS H1274 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU H1514 " --> pdb=" O VAL H1439 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR H1528 " --> pdb=" O LEU H1519 " (cutoff:3.500A) Processing sheet with id=AM9, first strand: chain 'H' and resid 1255 through 1260 removed outlier: 3.692A pdb=" N ILE H1562 " --> pdb=" O LEU H1272 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N HIS H1274 " --> pdb=" O ASN H1560 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N ASN H1560 " --> pdb=" O HIS H1274 " (cutoff:3.500A) Processing sheet with id=AN1, first strand: chain 'H' and resid 1287 through 1290 removed outlier: 3.636A pdb=" N TYR H1493 " --> pdb=" O TRP H1452 " (cutoff:3.500A) Processing sheet with id=AN2, first strand: chain 'H' and resid 1734 through 1737 Processing sheet with id=AN3, first strand: chain 'H' and resid 2341 through 2342 Processing sheet with id=AN4, first strand: chain 'H' and resid 2776 through 2777 removed outlier: 6.533A pdb=" N SER H2776 " --> pdb=" O HIS H2788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AN4 Processing sheet with id=AN5, first strand: chain 'H' and resid 2822 through 2825 Processing sheet with id=AN6, first strand: chain 'H' and resid 4173 through 4177 removed outlier: 4.014A pdb=" N PHE H4190 " --> pdb=" O GLY H4174 " (cutoff:3.500A) Processing sheet with id=AN7, first strand: chain 'H' and resid 4579 through 4581 removed outlier: 3.616A pdb=" N LYS H4579 " --> pdb=" O LEU H4630 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU H4630 " --> pdb=" O LYS H4579 " (cutoff:3.500A) 6184 hydrogen bonds defined for protein. 17789 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: 101.17 Time building geometry restraints manager: 32.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 34932 1.34 - 1.46: 25309 1.46 - 1.58: 46127 1.58 - 1.70: 4 1.70 - 1.83: 956 Bond restraints: 107328 Sorted by residual: bond pdb=" CB PRO B 727 " pdb=" CG PRO B 727 " ideal model delta sigma weight residual 1.492 1.599 -0.107 5.00e-02 4.00e+02 4.56e+00 bond pdb=" CB PRO D 727 " pdb=" CG PRO D 727 " ideal model delta sigma weight residual 1.492 1.599 -0.107 5.00e-02 4.00e+02 4.56e+00 bond pdb=" CB PRO F 727 " pdb=" CG PRO F 727 " ideal model delta sigma weight residual 1.492 1.599 -0.107 5.00e-02 4.00e+02 4.56e+00 bond pdb=" CB PRO H 727 " pdb=" CG PRO H 727 " ideal model delta sigma weight residual 1.492 1.599 -0.107 5.00e-02 4.00e+02 4.54e+00 bond pdb=" CG GLU H 480 " pdb=" CD GLU H 480 " ideal model delta sigma weight residual 1.516 1.468 0.048 2.50e-02 1.60e+03 3.62e+00 ... (remaining 107323 not shown) Histogram of bond angle deviations from ideal: 98.18 - 105.69: 2337 105.69 - 113.20: 59426 113.20 - 120.72: 47460 120.72 - 128.23: 36965 128.23 - 135.74: 784 Bond angle restraints: 146972 Sorted by residual: angle pdb=" CA GLN E 31 " pdb=" CB GLN E 31 " pdb=" CG GLN E 31 " ideal model delta sigma weight residual 114.10 126.15 -12.05 2.00e+00 2.50e-01 3.63e+01 angle pdb=" CA GLN C 31 " pdb=" CB GLN C 31 " pdb=" CG GLN C 31 " ideal model delta sigma weight residual 114.10 126.11 -12.01 2.00e+00 2.50e-01 3.60e+01 angle pdb=" CA GLN A 31 " pdb=" CB GLN A 31 " pdb=" CG GLN A 31 " ideal model delta sigma weight residual 114.10 126.10 -12.00 2.00e+00 2.50e-01 3.60e+01 angle pdb=" CA GLN G 31 " pdb=" CB GLN G 31 " pdb=" CG GLN G 31 " ideal model delta sigma weight residual 114.10 126.09 -11.99 2.00e+00 2.50e-01 3.59e+01 angle pdb=" CA PRO F 727 " pdb=" N PRO F 727 " pdb=" CD PRO F 727 " ideal model delta sigma weight residual 112.00 104.80 7.20 1.40e+00 5.10e-01 2.64e+01 ... (remaining 146967 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 58369 17.99 - 35.98: 3411 35.98 - 53.98: 488 53.98 - 71.97: 144 71.97 - 89.96: 48 Dihedral angle restraints: 62460 sinusoidal: 18120 harmonic: 44340 Sorted by residual: dihedral pdb=" CA THR B 254 " pdb=" C THR B 254 " pdb=" N HIS B 255 " pdb=" CA HIS B 255 " ideal model delta harmonic sigma weight residual -180.00 -154.63 -25.37 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA THR H 254 " pdb=" C THR H 254 " pdb=" N HIS H 255 " pdb=" CA HIS H 255 " ideal model delta harmonic sigma weight residual -180.00 -154.63 -25.37 0 5.00e+00 4.00e-02 2.57e+01 dihedral pdb=" CA THR F 254 " pdb=" C THR F 254 " pdb=" N HIS F 255 " pdb=" CA HIS F 255 " ideal model delta harmonic sigma weight residual -180.00 -154.63 -25.37 0 5.00e+00 4.00e-02 2.57e+01 ... (remaining 62457 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 13097 0.036 - 0.071: 3623 0.071 - 0.107: 850 0.107 - 0.143: 209 0.143 - 0.178: 5 Chirality restraints: 17784 Sorted by residual: chirality pdb=" CG LEU C 103 " pdb=" CB LEU C 103 " pdb=" CD1 LEU C 103 " pdb=" CD2 LEU C 103 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.96e-01 chirality pdb=" CG LEU G 103 " pdb=" CB LEU G 103 " pdb=" CD1 LEU G 103 " pdb=" CD2 LEU G 103 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.67e-01 chirality pdb=" CG LEU A 103 " pdb=" CB LEU A 103 " pdb=" CD1 LEU A 103 " pdb=" CD2 LEU A 103 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.46e-01 ... (remaining 17781 not shown) Planarity restraints: 19000 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL F 726 " 0.071 5.00e-02 4.00e+02 1.04e-01 1.73e+01 pdb=" N PRO F 727 " -0.180 5.00e-02 4.00e+02 pdb=" CA PRO F 727 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO F 727 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 726 " -0.071 5.00e-02 4.00e+02 1.04e-01 1.73e+01 pdb=" N PRO B 727 " 0.180 5.00e-02 4.00e+02 pdb=" CA PRO B 727 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO B 727 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 726 " -0.071 5.00e-02 4.00e+02 1.04e-01 1.73e+01 pdb=" N PRO D 727 " 0.180 5.00e-02 4.00e+02 pdb=" CA PRO D 727 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO D 727 " -0.056 5.00e-02 4.00e+02 ... (remaining 18997 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 16870 2.76 - 3.30: 103577 3.30 - 3.83: 166553 3.83 - 4.37: 181089 4.37 - 4.90: 312913 Nonbonded interactions: 781002 Sorted by model distance: nonbonded pdb=" OG1 THR B 215 " pdb=" O GLY B 271 " model vdw 2.226 2.440 nonbonded pdb=" OG1 THR D 215 " pdb=" O GLY D 271 " model vdw 2.226 2.440 nonbonded pdb=" OG1 THR F 215 " pdb=" O GLY F 271 " model vdw 2.226 2.440 nonbonded pdb=" OG1 THR H 215 " pdb=" O GLY H 271 " model vdw 2.226 2.440 nonbonded pdb=" OD1 ASP B4784 " pdb=" OG SER B4786 " model vdw 2.232 2.440 ... (remaining 780997 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 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = (chain 'B' and (resid 12 through 2761 or resid 2763 through 5035 or resid 5101)) \ selection = (chain 'D' and (resid 12 through 2761 or resid 2763 through 5035 or resid 5101)) \ selection = (chain 'F' and (resid 12 through 2761 or resid 2763 through 5035 or resid 5101)) \ selection = (chain 'H' and (resid 12 through 2761 or resid 2763 through 5035 or resid 5101)) \ } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.900 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: 24.300 Check model and map are aligned: 1.140 Set scattering table: 0.730 Process input model: 341.290 Find NCS groups from input model: 5.700 Set up NCS constraints: 0.640 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:2.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 380.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 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 : 0.002 0.107 107328 Z= 0.150 Angle : 0.547 14.474 146972 Z= 0.298 Chirality : 0.036 0.178 17784 Planarity : 0.004 0.104 19000 Dihedral : 12.170 89.961 33620 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.41 % Allowed : 0.52 % Favored : 99.07 % 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: -0.42 (0.07), residues: 13692 helix: 0.02 (0.06), residues: 6272 sheet: -0.08 (0.14), residues: 1596 loop : -0.51 (0.08), residues: 5824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP B 722 HIS 0.026 0.001 HIS D 255 PHE 0.027 0.001 PHE F3991 TYR 0.010 0.001 TYR F1007 ARG 0.023 0.001 ARG H 683 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27384 Ramachandran restraints generated. 13692 Oldfield, 0 Emsley, 13692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27384 Ramachandran restraints generated. 13692 Oldfield, 0 Emsley, 13692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2439 residues out of total 12212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 2403 time to evaluate : 8.446 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: A 46 PHE cc_start: 0.7823 (t80) cc_final: 0.7581 (t80) REVERT: B 384 MET cc_start: 0.8096 (tmm) cc_final: 0.7849 (tmm) REVERT: B 471 LEU cc_start: 0.9385 (tp) cc_final: 0.9082 (tp) REVERT: B 589 LEU cc_start: 0.9343 (tp) cc_final: 0.9096 (tp) REVERT: B 636 ASN cc_start: 0.8118 (t0) cc_final: 0.7642 (t0) REVERT: B 1132 TRP cc_start: 0.6752 (t-100) cc_final: 0.6512 (t-100) REVERT: B 1286 MET cc_start: 0.8053 (tpp) cc_final: 0.7709 (mmm) REVERT: B 1452 TRP cc_start: 0.8303 (m100) cc_final: 0.8080 (m100) REVERT: B 2166 LEU cc_start: 0.8499 (tp) cc_final: 0.7245 (tp) REVERT: B 2168 ILE cc_start: 0.9346 (pt) cc_final: 0.9071 (mt) REVERT: B 2214 ASN cc_start: 0.8715 (m-40) cc_final: 0.8467 (m110) REVERT: B 2527 PHE cc_start: 0.7841 (m-10) cc_final: 0.7384 (m-80) REVERT: B 3436 PHE cc_start: 0.8372 (t80) cc_final: 0.8057 (t80) REVERT: B 3648 MET cc_start: 0.8832 (mpp) cc_final: 0.8541 (mpp) REVERT: B 3910 ILE cc_start: 0.8997 (mt) cc_final: 0.8755 (mt) REVERT: B 3922 GLN cc_start: 0.8751 (tm-30) cc_final: 0.8427 (tm-30) REVERT: B 3965 GLN cc_start: 0.8529 (tp-100) cc_final: 0.8311 (tm-30) REVERT: B 3991 PHE cc_start: 0.6057 (m-80) cc_final: 0.5151 (m-10) REVERT: B 4040 VAL cc_start: 0.9728 (m) cc_final: 0.9499 (p) REVERT: B 4052 MET cc_start: 0.9007 (mmm) cc_final: 0.8641 (tpp) REVERT: B 4056 PHE cc_start: 0.8014 (t80) cc_final: 0.7549 (t80) REVERT: B 4059 MET cc_start: 0.9211 (ppp) cc_final: 0.8756 (ppp) REVERT: B 4202 MET cc_start: 0.7952 (ttp) cc_final: 0.7659 (tpp) REVERT: B 4794 MET cc_start: 0.8498 (tpt) cc_final: 0.8132 (tpt) REVERT: B 4847 TYR cc_start: 0.8314 (t80) cc_final: 0.7842 (t80) REVERT: B 4857 PHE cc_start: 0.7507 (m-80) cc_final: 0.7121 (m-80) REVERT: B 4909 LEU cc_start: 0.9038 (tp) cc_final: 0.8808 (pp) REVERT: D 384 MET cc_start: 0.8013 (tmm) cc_final: 0.7788 (tmm) REVERT: D 471 LEU cc_start: 0.9384 (tp) cc_final: 0.9102 (tp) REVERT: D 589 LEU cc_start: 0.9323 (tp) cc_final: 0.9072 (tp) REVERT: D 636 ASN cc_start: 0.8033 (t0) cc_final: 0.7564 (t0) REVERT: D 1132 TRP cc_start: 0.6706 (t-100) cc_final: 0.6454 (t-100) REVERT: D 1286 MET cc_start: 0.8078 (tpp) cc_final: 0.7780 (mmm) REVERT: D 1289 LEU cc_start: 0.8648 (mt) cc_final: 0.8446 (mp) REVERT: D 1452 TRP cc_start: 0.8210 (m100) cc_final: 0.7998 (m100) REVERT: D 2214 ASN cc_start: 0.8716 (m-40) cc_final: 0.8479 (m110) REVERT: D 2527 PHE cc_start: 0.7882 (m-10) cc_final: 0.7417 (m-80) REVERT: D 3436 PHE cc_start: 0.8423 (t80) cc_final: 0.8109 (t80) REVERT: D 3648 MET cc_start: 0.8811 (mpp) cc_final: 0.8496 (mpp) REVERT: D 3775 LEU cc_start: 0.9052 (mp) cc_final: 0.8848 (mp) REVERT: D 3910 ILE cc_start: 0.9056 (mt) cc_final: 0.8776 (mt) REVERT: D 3922 GLN cc_start: 0.8747 (tm-30) cc_final: 0.8416 (tm-30) REVERT: D 3965 GLN cc_start: 0.8552 (tp-100) cc_final: 0.8317 (tm-30) REVERT: D 3991 PHE cc_start: 0.6100 (m-80) cc_final: 0.5163 (m-10) REVERT: D 4038 GLN cc_start: 0.9067 (mm-40) cc_final: 0.8828 (mp10) REVERT: D 4040 VAL cc_start: 0.9724 (m) cc_final: 0.9505 (p) REVERT: D 4052 MET cc_start: 0.8998 (mmm) cc_final: 0.8688 (tpp) REVERT: D 4056 PHE cc_start: 0.8047 (t80) cc_final: 0.7573 (t80) REVERT: D 4059 MET cc_start: 0.9224 (ppp) cc_final: 0.8779 (ppp) REVERT: D 4202 MET cc_start: 0.7903 (ttp) cc_final: 0.7648 (tpp) REVERT: D 4794 MET cc_start: 0.8505 (tpt) cc_final: 0.8199 (tpt) REVERT: D 4847 TYR cc_start: 0.8301 (t80) cc_final: 0.7826 (t80) REVERT: D 4857 PHE cc_start: 0.7623 (m-80) cc_final: 0.7223 (m-80) REVERT: D 4909 LEU cc_start: 0.9014 (tp) cc_final: 0.8768 (pp) REVERT: F 384 MET cc_start: 0.8016 (tmm) cc_final: 0.7792 (tmm) REVERT: F 471 LEU cc_start: 0.9380 (tp) cc_final: 0.9101 (tp) REVERT: F 636 ASN cc_start: 0.8025 (t0) cc_final: 0.7613 (t0) REVERT: F 1132 TRP cc_start: 0.6709 (t-100) cc_final: 0.6448 (t-100) REVERT: F 1286 MET cc_start: 0.8077 (tpp) cc_final: 0.7779 (mmm) REVERT: F 1289 LEU cc_start: 0.8634 (mt) cc_final: 0.8432 (mp) REVERT: F 1452 TRP cc_start: 0.8214 (m100) cc_final: 0.8010 (m100) REVERT: F 1717 SER cc_start: 0.8740 (t) cc_final: 0.8525 (p) REVERT: F 2166 LEU cc_start: 0.8514 (tp) cc_final: 0.7325 (tp) REVERT: F 2168 ILE cc_start: 0.9340 (pt) cc_final: 0.8993 (tp) REVERT: F 2214 ASN cc_start: 0.8705 (m-40) cc_final: 0.8455 (m110) REVERT: F 2527 PHE cc_start: 0.7867 (m-10) cc_final: 0.7401 (m-80) REVERT: F 3436 PHE cc_start: 0.8477 (t80) cc_final: 0.8158 (t80) REVERT: F 3648 MET cc_start: 0.8763 (mpp) cc_final: 0.8513 (mpp) REVERT: F 3775 LEU cc_start: 0.9032 (mp) cc_final: 0.8827 (mp) REVERT: F 3910 ILE cc_start: 0.9046 (mt) cc_final: 0.8771 (mt) REVERT: F 3922 GLN cc_start: 0.8687 (tm-30) cc_final: 0.8386 (tm-30) REVERT: F 3965 GLN cc_start: 0.8551 (tp-100) cc_final: 0.8314 (tm-30) REVERT: F 3991 PHE cc_start: 0.6109 (m-80) cc_final: 0.5176 (m-10) REVERT: F 4038 GLN cc_start: 0.9049 (mm-40) cc_final: 0.8817 (mp10) REVERT: F 4040 VAL cc_start: 0.9713 (m) cc_final: 0.9511 (p) REVERT: F 4052 MET cc_start: 0.8989 (mmm) cc_final: 0.8617 (tpp) REVERT: F 4056 PHE cc_start: 0.8060 (t80) cc_final: 0.7580 (t80) REVERT: F 4059 MET cc_start: 0.9223 (ppp) cc_final: 0.8766 (ppp) REVERT: F 4202 MET cc_start: 0.7865 (ttp) cc_final: 0.7575 (tpp) REVERT: F 4794 MET cc_start: 0.8505 (tpt) cc_final: 0.8185 (tpt) REVERT: F 4847 TYR cc_start: 0.8357 (t80) cc_final: 0.7935 (t80) REVERT: F 4909 LEU cc_start: 0.9028 (tp) cc_final: 0.8783 (pp) REVERT: H 384 MET cc_start: 0.8095 (tmm) cc_final: 0.7833 (tmm) REVERT: H 471 LEU cc_start: 0.9382 (tp) cc_final: 0.9076 (tp) REVERT: H 589 LEU cc_start: 0.9338 (tp) cc_final: 0.9086 (tp) REVERT: H 636 ASN cc_start: 0.8097 (t0) cc_final: 0.7644 (t0) REVERT: H 1132 TRP cc_start: 0.6733 (t-100) cc_final: 0.6485 (t-100) REVERT: H 1286 MET cc_start: 0.8061 (tpp) cc_final: 0.7772 (mmm) REVERT: H 1452 TRP cc_start: 0.8240 (m100) cc_final: 0.8003 (m100) REVERT: H 1674 CYS cc_start: 0.6816 (m) cc_final: 0.6593 (t) REVERT: H 1717 SER cc_start: 0.8727 (t) cc_final: 0.8510 (p) REVERT: H 2166 LEU cc_start: 0.8456 (tp) cc_final: 0.7315 (tp) REVERT: H 2168 ILE cc_start: 0.9329 (pt) cc_final: 0.9093 (mt) REVERT: H 2214 ASN cc_start: 0.8694 (m-40) cc_final: 0.8432 (m110) REVERT: H 2527 PHE cc_start: 0.7806 (m-10) cc_final: 0.7353 (m-80) REVERT: H 3436 PHE cc_start: 0.8491 (t80) cc_final: 0.8171 (t80) REVERT: H 3648 MET cc_start: 0.8827 (mpp) cc_final: 0.8546 (mpp) REVERT: H 3910 ILE cc_start: 0.8994 (mt) cc_final: 0.8760 (mt) REVERT: H 3922 GLN cc_start: 0.8762 (tm-30) cc_final: 0.8441 (tm-30) REVERT: H 3965 GLN cc_start: 0.8577 (tp-100) cc_final: 0.8332 (tm-30) REVERT: H 3991 PHE cc_start: 0.6134 (m-80) cc_final: 0.5226 (m-10) REVERT: H 4038 GLN cc_start: 0.9045 (mm-40) cc_final: 0.8827 (mp10) REVERT: H 4052 MET cc_start: 0.8998 (mmm) cc_final: 0.8630 (tpp) REVERT: H 4056 PHE cc_start: 0.8015 (t80) cc_final: 0.7303 (t80) REVERT: H 4059 MET cc_start: 0.9217 (ppp) cc_final: 0.8701 (ppp) REVERT: H 4202 MET cc_start: 0.7916 (ttp) cc_final: 0.7619 (tpp) REVERT: H 4794 MET cc_start: 0.8481 (tpt) cc_final: 0.8223 (tpt) REVERT: H 4847 TYR cc_start: 0.8367 (t80) cc_final: 0.7948 (t80) REVERT: H 4909 LEU cc_start: 0.9038 (tp) cc_final: 0.8794 (pp) outliers start: 36 outliers final: 16 residues processed: 2424 average time/residue: 0.8005 time to fit residues: 3511.8573 Evaluate side-chains 1595 residues out of total 12212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 1579 time to evaluate : 8.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 2128 GLN Chi-restraints excluded: chain B residue 2628 VAL Chi-restraints excluded: chain C residue 31 GLN Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 2128 GLN Chi-restraints excluded: chain D residue 2628 VAL Chi-restraints excluded: chain E residue 31 GLN Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 2128 GLN Chi-restraints excluded: chain F residue 2628 VAL Chi-restraints excluded: chain G residue 31 GLN Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain H residue 2128 GLN Chi-restraints excluded: chain H residue 2628 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1524 random chunks: chunk 1286 optimal weight: 10.0000 chunk 1155 optimal weight: 9.9990 chunk 640 optimal weight: 20.0000 chunk 394 optimal weight: 8.9990 chunk 779 optimal weight: 7.9990 chunk 617 optimal weight: 8.9990 chunk 1194 optimal weight: 3.9990 chunk 462 optimal weight: 6.9990 chunk 726 optimal weight: 8.9990 chunk 889 optimal weight: 9.9990 chunk 1383 optimal weight: 6.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 HIS ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 383 HIS ** B 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1052 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1198 GLN ** B1459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1460 HIS B1463 ASN ** B1598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1974 GLN B2248 GLN ** B2261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3993 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4801 HIS C 25 HIS ** D 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 383 HIS ** D 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1052 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1198 GLN ** D1459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1460 HIS D1463 ASN ** D1598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1974 GLN D2248 GLN ** D2261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3993 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4151 HIS ** D4157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4801 HIS E 25 HIS ** F 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 383 HIS ** F 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1052 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1198 GLN ** F1459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1460 HIS F1463 ASN ** F1598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1974 GLN F2248 GLN ** F3993 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F4157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F4204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F4712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F4801 HIS G 25 HIS ** H 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 383 HIS ** H 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1052 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H1198 GLN ** H1459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1460 HIS H1463 ASN ** H1598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1974 GLN H2248 GLN ** H2261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H3973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H3993 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H4157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H4204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H4712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H4801 HIS Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.091 107328 Z= 0.569 Angle : 0.909 13.307 146972 Z= 0.472 Chirality : 0.047 0.210 17784 Planarity : 0.006 0.068 19000 Dihedral : 4.562 59.938 15900 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 18.17 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.08 % Favored : 96.91 % Rotamer: Outliers : 3.87 % Allowed : 16.09 % Favored : 80.04 % 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: -0.26 (0.07), residues: 13692 helix: 0.40 (0.06), residues: 6636 sheet: -0.68 (0.13), residues: 1576 loop : -0.57 (0.08), residues: 5480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.004 TRP B3930 HIS 0.012 0.003 HIS H 597 PHE 0.033 0.004 PHE D3987 TYR 0.031 0.003 TYR D3721 ARG 0.016 0.001 ARG D 683 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27384 Ramachandran restraints generated. 13692 Oldfield, 0 Emsley, 13692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27384 Ramachandran restraints generated. 13692 Oldfield, 0 Emsley, 13692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1686 residues out of total 12212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 338 poor density : 1348 time to evaluate : 8.183 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: A 90 VAL cc_start: 0.8131 (OUTLIER) cc_final: 0.7695 (p) REVERT: A 99 PHE cc_start: 0.7579 (m-80) cc_final: 0.7312 (m-80) REVERT: B 384 MET cc_start: 0.8121 (tmm) cc_final: 0.7895 (tmm) REVERT: B 480 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.8027 (pt0) REVERT: B 791 PHE cc_start: 0.8296 (OUTLIER) cc_final: 0.7957 (m-10) REVERT: B 1132 TRP cc_start: 0.7433 (t-100) cc_final: 0.7037 (t-100) REVERT: B 1652 GLU cc_start: 0.7065 (pp20) cc_final: 0.6835 (pp20) REVERT: B 1852 MET cc_start: 0.8583 (mmm) cc_final: 0.8127 (mmm) REVERT: B 2527 PHE cc_start: 0.8231 (m-10) cc_final: 0.7810 (m-80) REVERT: B 3436 PHE cc_start: 0.8307 (t80) cc_final: 0.7991 (t80) REVERT: B 3445 TYR cc_start: 0.8801 (m-80) cc_final: 0.8555 (t80) REVERT: B 4056 PHE cc_start: 0.8412 (t80) cc_final: 0.7915 (t80) REVERT: B 4186 GLU cc_start: 0.7563 (tp30) cc_final: 0.6886 (tp30) REVERT: B 4700 ASP cc_start: 0.8801 (m-30) cc_final: 0.8598 (m-30) REVERT: B 4794 MET cc_start: 0.8671 (tpt) cc_final: 0.8325 (tpt) REVERT: B 4825 LEU cc_start: 0.9424 (OUTLIER) cc_final: 0.9218 (mm) REVERT: B 4878 MET cc_start: 0.7517 (tpp) cc_final: 0.6980 (tpp) REVERT: B 4965 TYR cc_start: 0.8675 (t80) cc_final: 0.8361 (t80) REVERT: B 4993 LEU cc_start: 0.9629 (mm) cc_final: 0.9424 (tp) REVERT: D 384 MET cc_start: 0.8171 (tmm) cc_final: 0.7889 (tmm) REVERT: D 480 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.8014 (pt0) REVERT: D 791 PHE cc_start: 0.8287 (OUTLIER) cc_final: 0.7962 (m-10) REVERT: D 1132 TRP cc_start: 0.7368 (t-100) cc_final: 0.7012 (t-100) REVERT: D 1652 GLU cc_start: 0.7066 (pp20) cc_final: 0.6858 (pp20) REVERT: D 1852 MET cc_start: 0.8587 (mmm) cc_final: 0.8140 (mmm) REVERT: D 2527 PHE cc_start: 0.8258 (m-10) cc_final: 0.7845 (m-80) REVERT: D 3436 PHE cc_start: 0.8307 (t80) cc_final: 0.7965 (t80) REVERT: D 3445 TYR cc_start: 0.8766 (m-80) cc_final: 0.8535 (t80) REVERT: D 3640 LEU cc_start: 0.8395 (tp) cc_final: 0.8189 (tp) REVERT: D 3811 MET cc_start: 0.8353 (mmm) cc_final: 0.7867 (mmm) REVERT: D 4056 PHE cc_start: 0.8426 (t80) cc_final: 0.7917 (t80) REVERT: D 4186 GLU cc_start: 0.7540 (tp30) cc_final: 0.6877 (tp30) REVERT: D 4794 MET cc_start: 0.8664 (tpt) cc_final: 0.8318 (tpt) REVERT: D 4878 MET cc_start: 0.7660 (tpp) cc_final: 0.7241 (tpp) REVERT: D 4965 TYR cc_start: 0.8642 (t80) cc_final: 0.8330 (t80) REVERT: D 4993 LEU cc_start: 0.9626 (mm) cc_final: 0.9413 (tp) REVERT: E 90 VAL cc_start: 0.8293 (OUTLIER) cc_final: 0.7869 (p) REVERT: F 384 MET cc_start: 0.8210 (tmm) cc_final: 0.7935 (tmm) REVERT: F 791 PHE cc_start: 0.8266 (OUTLIER) cc_final: 0.7947 (m-10) REVERT: F 1132 TRP cc_start: 0.7352 (t-100) cc_final: 0.6969 (t-100) REVERT: F 1652 GLU cc_start: 0.7091 (pp20) cc_final: 0.6839 (pp20) REVERT: F 1852 MET cc_start: 0.8581 (mmm) cc_final: 0.8118 (mmm) REVERT: F 2527 PHE cc_start: 0.8247 (m-10) cc_final: 0.7832 (m-80) REVERT: F 3436 PHE cc_start: 0.8345 (t80) cc_final: 0.8030 (t80) REVERT: F 3445 TYR cc_start: 0.8806 (m-80) cc_final: 0.8564 (t80) REVERT: F 3640 LEU cc_start: 0.8379 (tp) cc_final: 0.8171 (tp) REVERT: F 3648 MET cc_start: 0.8776 (mpp) cc_final: 0.8394 (mpp) REVERT: F 3716 TYR cc_start: 0.7993 (p90) cc_final: 0.7772 (p90) REVERT: F 3811 MET cc_start: 0.8356 (mmm) cc_final: 0.7869 (mmm) REVERT: F 3973 GLN cc_start: 0.7212 (tm-30) cc_final: 0.6536 (tp40) REVERT: F 4056 PHE cc_start: 0.8422 (t80) cc_final: 0.7886 (t80) REVERT: F 4186 GLU cc_start: 0.7522 (tp30) cc_final: 0.6838 (tp30) REVERT: F 4700 ASP cc_start: 0.8797 (m-30) cc_final: 0.8596 (m-30) REVERT: F 4794 MET cc_start: 0.8679 (tpt) cc_final: 0.8327 (tpt) REVERT: F 4878 MET cc_start: 0.7687 (tpp) cc_final: 0.7274 (tpp) REVERT: F 4965 TYR cc_start: 0.8635 (t80) cc_final: 0.8301 (t80) REVERT: F 4993 LEU cc_start: 0.9629 (mm) cc_final: 0.9412 (tp) REVERT: H 169 LEU cc_start: 0.8639 (mm) cc_final: 0.8429 (mm) REVERT: H 384 MET cc_start: 0.8136 (tmm) cc_final: 0.7878 (tmm) REVERT: H 480 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7921 (pt0) REVERT: H 791 PHE cc_start: 0.8250 (OUTLIER) cc_final: 0.7836 (m-10) REVERT: H 1132 TRP cc_start: 0.7408 (t-100) cc_final: 0.6994 (t-100) REVERT: H 1652 GLU cc_start: 0.7092 (pp20) cc_final: 0.6852 (pp20) REVERT: H 1852 MET cc_start: 0.8576 (mmm) cc_final: 0.8131 (mmm) REVERT: H 2527 PHE cc_start: 0.8223 (m-10) cc_final: 0.7798 (m-80) REVERT: H 3436 PHE cc_start: 0.8318 (t80) cc_final: 0.8000 (t80) REVERT: H 3445 TYR cc_start: 0.8815 (m-80) cc_final: 0.8562 (t80) REVERT: H 3640 LEU cc_start: 0.8383 (tp) cc_final: 0.8171 (tp) REVERT: H 3648 MET cc_start: 0.8801 (mpp) cc_final: 0.8414 (mpp) REVERT: H 3716 TYR cc_start: 0.7912 (p90) cc_final: 0.7701 (p90) REVERT: H 4038 GLN cc_start: 0.9105 (mm-40) cc_final: 0.8903 (mm-40) REVERT: H 4186 GLU cc_start: 0.7546 (tp30) cc_final: 0.6856 (tp30) REVERT: H 4700 ASP cc_start: 0.8794 (m-30) cc_final: 0.8586 (m-30) REVERT: H 4794 MET cc_start: 0.8689 (tpt) cc_final: 0.8337 (tpt) REVERT: H 4825 LEU cc_start: 0.9425 (OUTLIER) cc_final: 0.9221 (mm) REVERT: H 4878 MET cc_start: 0.7610 (tpp) cc_final: 0.7146 (tpp) REVERT: H 4965 TYR cc_start: 0.8670 (t80) cc_final: 0.8348 (t80) REVERT: H 4993 LEU cc_start: 0.9619 (mm) cc_final: 0.9406 (tp) outliers start: 338 outliers final: 209 residues processed: 1568 average time/residue: 0.7893 time to fit residues: 2244.0134 Evaluate side-chains 1377 residues out of total 12212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 1157 time to evaluate : 7.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 586 ILE Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 744 VAL Chi-restraints excluded: chain B residue 746 CYS Chi-restraints excluded: chain B residue 791 PHE Chi-restraints excluded: chain B residue 1113 VAL Chi-restraints excluded: chain B residue 1143 TRP Chi-restraints excluded: chain B residue 1450 VAL Chi-restraints excluded: chain B residue 1542 VAL Chi-restraints excluded: chain B residue 1659 LEU Chi-restraints excluded: chain B residue 1685 LEU Chi-restraints excluded: chain B residue 1784 VAL Chi-restraints excluded: chain B residue 1840 VAL Chi-restraints excluded: chain B residue 1851 VAL Chi-restraints excluded: chain B residue 2127 ARG Chi-restraints excluded: chain B residue 2186 ILE Chi-restraints excluded: chain B residue 2229 MET Chi-restraints excluded: chain B residue 2504 VAL Chi-restraints excluded: chain B residue 3665 PHE Chi-restraints excluded: chain B residue 3766 HIS Chi-restraints excluded: chain B residue 3952 VAL Chi-restraints excluded: chain B residue 3985 VAL Chi-restraints excluded: chain B residue 3990 VAL Chi-restraints excluded: chain B residue 3996 MET Chi-restraints excluded: chain B residue 4019 VAL Chi-restraints excluded: chain B residue 4026 LEU Chi-restraints excluded: chain B residue 4065 ASP Chi-restraints excluded: chain B residue 4134 ILE Chi-restraints excluded: chain B residue 4157 ASN Chi-restraints excluded: chain B residue 4790 LEU Chi-restraints excluded: chain B residue 4792 TRP Chi-restraints excluded: chain B residue 4818 VAL Chi-restraints excluded: chain B residue 4825 LEU Chi-restraints excluded: chain B residue 4839 VAL Chi-restraints excluded: chain B residue 4842 LEU Chi-restraints excluded: chain B residue 4844 VAL Chi-restraints excluded: chain B residue 4912 VAL Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain C residue 41 ASP Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain D residue 65 CYS Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 158 SER Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 480 GLU Chi-restraints excluded: chain D residue 586 ILE Chi-restraints excluded: chain D residue 648 ILE Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain D residue 723 THR Chi-restraints excluded: chain D residue 744 VAL Chi-restraints excluded: chain D residue 746 CYS Chi-restraints excluded: chain D residue 791 PHE Chi-restraints excluded: chain D residue 1113 VAL Chi-restraints excluded: chain D residue 1143 TRP Chi-restraints excluded: chain D residue 1450 VAL Chi-restraints excluded: chain D residue 1542 VAL Chi-restraints excluded: chain D residue 1659 LEU Chi-restraints excluded: chain D residue 1685 LEU Chi-restraints excluded: chain D residue 1784 VAL Chi-restraints excluded: chain D residue 1840 VAL Chi-restraints excluded: chain D residue 1851 VAL Chi-restraints excluded: chain D residue 2127 ARG Chi-restraints excluded: chain D residue 2167 LEU Chi-restraints excluded: chain D residue 2171 MET Chi-restraints excluded: chain D residue 2186 ILE Chi-restraints excluded: chain D residue 2229 MET Chi-restraints excluded: chain D residue 2503 MET Chi-restraints excluded: chain D residue 2504 VAL Chi-restraints excluded: chain D residue 3665 PHE Chi-restraints excluded: chain D residue 3766 HIS Chi-restraints excluded: chain D residue 3952 VAL Chi-restraints excluded: chain D residue 3985 VAL Chi-restraints excluded: chain D residue 3990 VAL Chi-restraints excluded: chain D residue 3996 MET Chi-restraints excluded: chain D residue 4019 VAL Chi-restraints excluded: chain D residue 4026 LEU Chi-restraints excluded: chain D residue 4065 ASP Chi-restraints excluded: chain D residue 4134 ILE Chi-restraints excluded: chain D residue 4157 ASN Chi-restraints excluded: chain D residue 4790 LEU Chi-restraints excluded: chain D residue 4792 TRP Chi-restraints excluded: chain D residue 4818 VAL Chi-restraints excluded: chain D residue 4839 VAL Chi-restraints excluded: chain D residue 4842 LEU Chi-restraints excluded: chain D residue 4844 VAL Chi-restraints excluded: chain E residue 35 LYS Chi-restraints excluded: chain E residue 43 ASN Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain F residue 17 ASP Chi-restraints excluded: chain F residue 18 ASP Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 245 VAL Chi-restraints excluded: chain F residue 448 LEU Chi-restraints excluded: chain F residue 480 GLU Chi-restraints excluded: chain F residue 586 ILE Chi-restraints excluded: chain F residue 648 ILE Chi-restraints excluded: chain F residue 707 VAL Chi-restraints excluded: chain F residue 723 THR Chi-restraints excluded: chain F residue 744 VAL Chi-restraints excluded: chain F residue 746 CYS Chi-restraints excluded: chain F residue 791 PHE Chi-restraints excluded: chain F residue 1113 VAL Chi-restraints excluded: chain F residue 1143 TRP Chi-restraints excluded: chain F residue 1450 VAL Chi-restraints excluded: chain F residue 1542 VAL Chi-restraints excluded: chain F residue 1659 LEU Chi-restraints excluded: chain F residue 1685 LEU Chi-restraints excluded: chain F residue 1784 VAL Chi-restraints excluded: chain F residue 1840 VAL Chi-restraints excluded: chain F residue 1851 VAL Chi-restraints excluded: chain F residue 2127 ARG Chi-restraints excluded: chain F residue 2167 LEU Chi-restraints excluded: chain F residue 2186 ILE Chi-restraints excluded: chain F residue 2229 MET Chi-restraints excluded: chain F residue 2503 MET Chi-restraints excluded: chain F residue 2504 VAL Chi-restraints excluded: chain F residue 3665 PHE Chi-restraints excluded: chain F residue 3766 HIS Chi-restraints excluded: chain F residue 3952 VAL Chi-restraints excluded: chain F residue 3985 VAL Chi-restraints excluded: chain F residue 3990 VAL Chi-restraints excluded: chain F residue 3996 MET Chi-restraints excluded: chain F residue 4019 VAL Chi-restraints excluded: chain F residue 4026 LEU Chi-restraints excluded: chain F residue 4065 ASP Chi-restraints excluded: chain F residue 4134 ILE Chi-restraints excluded: chain F residue 4157 ASN Chi-restraints excluded: chain F residue 4790 LEU Chi-restraints excluded: chain F residue 4792 TRP Chi-restraints excluded: chain F residue 4818 VAL Chi-restraints excluded: chain F residue 4839 VAL Chi-restraints excluded: chain F residue 4842 LEU Chi-restraints excluded: chain F residue 4844 VAL Chi-restraints excluded: chain H residue 17 ASP Chi-restraints excluded: chain H residue 18 ASP Chi-restraints excluded: chain H residue 25 ASN Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 232 THR Chi-restraints excluded: chain H residue 245 VAL Chi-restraints excluded: chain H residue 404 ILE Chi-restraints excluded: chain H residue 448 LEU Chi-restraints excluded: chain H residue 480 GLU Chi-restraints excluded: chain H residue 586 ILE Chi-restraints excluded: chain H residue 648 ILE Chi-restraints excluded: chain H residue 707 VAL Chi-restraints excluded: chain H residue 723 THR Chi-restraints excluded: chain H residue 744 VAL Chi-restraints excluded: chain H residue 746 CYS Chi-restraints excluded: chain H residue 791 PHE Chi-restraints excluded: chain H residue 1113 VAL Chi-restraints excluded: chain H residue 1143 TRP Chi-restraints excluded: chain H residue 1450 VAL Chi-restraints excluded: chain H residue 1542 VAL Chi-restraints excluded: chain H residue 1659 LEU Chi-restraints excluded: chain H residue 1685 LEU Chi-restraints excluded: chain H residue 1721 GLU Chi-restraints excluded: chain H residue 1840 VAL Chi-restraints excluded: chain H residue 1851 VAL Chi-restraints excluded: chain H residue 2127 ARG Chi-restraints excluded: chain H residue 2186 ILE Chi-restraints excluded: chain H residue 2229 MET Chi-restraints excluded: chain H residue 2503 MET Chi-restraints excluded: chain H residue 2504 VAL Chi-restraints excluded: chain H residue 3665 PHE Chi-restraints excluded: chain H residue 3766 HIS Chi-restraints excluded: chain H residue 3952 VAL Chi-restraints excluded: chain H residue 3985 VAL Chi-restraints excluded: chain H residue 3990 VAL Chi-restraints excluded: chain H residue 3996 MET Chi-restraints excluded: chain H residue 4019 VAL Chi-restraints excluded: chain H residue 4026 LEU Chi-restraints excluded: chain H residue 4065 ASP Chi-restraints excluded: chain H residue 4134 ILE Chi-restraints excluded: chain H residue 4157 ASN Chi-restraints excluded: chain H residue 4790 LEU Chi-restraints excluded: chain H residue 4792 TRP Chi-restraints excluded: chain H residue 4818 VAL Chi-restraints excluded: chain H residue 4825 LEU Chi-restraints excluded: chain H residue 4839 VAL Chi-restraints excluded: chain H residue 4842 LEU Chi-restraints excluded: chain H residue 4844 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1524 random chunks: chunk 769 optimal weight: 10.0000 chunk 429 optimal weight: 6.9990 chunk 1151 optimal weight: 0.4980 chunk 942 optimal weight: 6.9990 chunk 381 optimal weight: 10.0000 chunk 1386 optimal weight: 30.0000 chunk 1497 optimal weight: 0.7980 chunk 1234 optimal weight: 20.0000 chunk 1374 optimal weight: 10.0000 chunk 472 optimal weight: 20.0000 chunk 1112 optimal weight: 0.7980 overall best weight: 3.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 181 HIS B 255 HIS ** B 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 610 ASN B1203 ASN ** B1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1459 GLN B1598 GLN ** B1688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2162 GLN ** B3804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3945 ASN ** B3973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3993 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4157 ASN ** B4712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 HIS D 255 HIS ** D 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 610 ASN D1203 ASN ** D1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1459 GLN D1598 GLN D3945 ASN ** D3973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3993 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4157 ASN D4204 GLN ** D4712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 181 HIS F 255 HIS ** F 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 610 ASN F1203 ASN ** F1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1459 GLN F1598 GLN F3945 ASN ** F3993 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F4157 ASN ** F4204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F4712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 181 HIS H 255 HIS ** H 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 610 ASN H1203 ASN ** H1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1459 GLN H1598 GLN ** H1688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H3973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H3993 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H4157 ASN H4204 GLN ** H4712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 107328 Z= 0.287 Angle : 0.667 11.554 146972 Z= 0.334 Chirality : 0.040 0.298 17784 Planarity : 0.004 0.055 19000 Dihedral : 4.115 47.921 15872 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.02 % Allowed : 18.82 % Favored : 78.15 % 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: 0.26 (0.07), residues: 13692 helix: 1.04 (0.06), residues: 6604 sheet: -0.63 (0.13), residues: 1608 loop : -0.53 (0.08), residues: 5480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP D3930 HIS 0.008 0.001 HIS B3993 PHE 0.027 0.002 PHE D3987 TYR 0.024 0.002 TYR D3721 ARG 0.010 0.001 ARG H4132 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27384 Ramachandran restraints generated. 13692 Oldfield, 0 Emsley, 13692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27384 Ramachandran restraints generated. 13692 Oldfield, 0 Emsley, 13692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1593 residues out of total 12212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 264 poor density : 1329 time to evaluate : 8.161 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: B 197 GLN cc_start: 0.7591 (pp30) cc_final: 0.7280 (pp30) REVERT: B 384 MET cc_start: 0.8199 (tmm) cc_final: 0.7936 (tmm) REVERT: B 791 PHE cc_start: 0.8301 (OUTLIER) cc_final: 0.7869 (m-10) REVERT: B 1132 TRP cc_start: 0.7445 (t-100) cc_final: 0.7016 (t-100) REVERT: B 1143 TRP cc_start: 0.6306 (OUTLIER) cc_final: 0.4881 (p-90) REVERT: B 1562 ILE cc_start: 0.9432 (mm) cc_final: 0.9111 (mm) REVERT: B 1852 MET cc_start: 0.8564 (mmm) cc_final: 0.8087 (mmm) REVERT: B 1945 GLU cc_start: 0.8375 (tp30) cc_final: 0.7885 (tp30) REVERT: B 2121 MET cc_start: 0.8055 (mtp) cc_final: 0.7780 (ttm) REVERT: B 2214 ASN cc_start: 0.8781 (m-40) cc_final: 0.8546 (m110) REVERT: B 2507 LEU cc_start: 0.9340 (tp) cc_final: 0.9119 (tt) REVERT: B 2527 PHE cc_start: 0.8248 (m-10) cc_final: 0.7886 (m-80) REVERT: B 3436 PHE cc_start: 0.8233 (t80) cc_final: 0.7916 (t80) REVERT: B 3445 TYR cc_start: 0.8813 (m-80) cc_final: 0.8477 (t80) REVERT: B 4040 VAL cc_start: 0.9630 (m) cc_final: 0.9411 (p) REVERT: B 4052 MET cc_start: 0.8944 (tpp) cc_final: 0.8714 (tpp) REVERT: B 4056 PHE cc_start: 0.8613 (t80) cc_final: 0.8393 (t80) REVERT: B 4186 GLU cc_start: 0.7450 (tp30) cc_final: 0.7005 (tp30) REVERT: B 4202 MET cc_start: 0.8277 (tpp) cc_final: 0.7950 (ttp) REVERT: B 4576 LEU cc_start: 0.8960 (tp) cc_final: 0.8732 (tp) REVERT: B 4794 MET cc_start: 0.8802 (tpt) cc_final: 0.8354 (tpt) REVERT: B 4878 MET cc_start: 0.7840 (tpp) cc_final: 0.7627 (tpp) REVERT: B 4965 TYR cc_start: 0.8635 (t80) cc_final: 0.8388 (t80) REVERT: B 5000 GLU cc_start: 0.8500 (tp30) cc_final: 0.8270 (tm-30) REVERT: D 177 GLU cc_start: 0.7129 (tm-30) cc_final: 0.6921 (tm-30) REVERT: D 197 GLN cc_start: 0.7562 (pp30) cc_final: 0.7350 (pp30) REVERT: D 384 MET cc_start: 0.8230 (tmm) cc_final: 0.7943 (tmm) REVERT: D 791 PHE cc_start: 0.8291 (OUTLIER) cc_final: 0.7872 (m-10) REVERT: D 1100 MET cc_start: 0.8348 (mmm) cc_final: 0.7992 (mmt) REVERT: D 1132 TRP cc_start: 0.7341 (t-100) cc_final: 0.6973 (t-100) REVERT: D 1143 TRP cc_start: 0.6291 (OUTLIER) cc_final: 0.4831 (p-90) REVERT: D 1562 ILE cc_start: 0.9441 (mm) cc_final: 0.9115 (mm) REVERT: D 1852 MET cc_start: 0.8570 (mmm) cc_final: 0.8111 (mmm) REVERT: D 2121 MET cc_start: 0.8051 (mtp) cc_final: 0.7760 (ttm) REVERT: D 2214 ASN cc_start: 0.8761 (m-40) cc_final: 0.8534 (m110) REVERT: D 2507 LEU cc_start: 0.9332 (tp) cc_final: 0.9118 (tt) REVERT: D 2527 PHE cc_start: 0.8248 (m-10) cc_final: 0.7905 (m-80) REVERT: D 3436 PHE cc_start: 0.8237 (t80) cc_final: 0.7916 (t80) REVERT: D 3445 TYR cc_start: 0.8792 (m-80) cc_final: 0.8451 (t80) REVERT: D 3775 LEU cc_start: 0.9372 (mp) cc_final: 0.9122 (mt) REVERT: D 4040 VAL cc_start: 0.9630 (m) cc_final: 0.9414 (p) REVERT: D 4052 MET cc_start: 0.8942 (tpp) cc_final: 0.8709 (tpp) REVERT: D 4056 PHE cc_start: 0.8628 (t80) cc_final: 0.8385 (t80) REVERT: D 4186 GLU cc_start: 0.7438 (tp30) cc_final: 0.6975 (tp30) REVERT: D 4202 MET cc_start: 0.8260 (tpp) cc_final: 0.7944 (ttp) REVERT: D 4576 LEU cc_start: 0.8947 (tp) cc_final: 0.8719 (tp) REVERT: D 4794 MET cc_start: 0.8798 (tpt) cc_final: 0.8358 (tpt) REVERT: D 4878 MET cc_start: 0.8046 (tpp) cc_final: 0.7815 (tpp) REVERT: D 4946 GLU cc_start: 0.8836 (tp30) cc_final: 0.8229 (tp30) REVERT: D 4965 TYR cc_start: 0.8617 (t80) cc_final: 0.8356 (t80) REVERT: D 5000 GLU cc_start: 0.8500 (tp30) cc_final: 0.8271 (tm-30) REVERT: F 179 TYR cc_start: 0.8455 (m-80) cc_final: 0.8237 (m-80) REVERT: F 384 MET cc_start: 0.8284 (tmm) cc_final: 0.7979 (tmm) REVERT: F 791 PHE cc_start: 0.8274 (OUTLIER) cc_final: 0.7858 (m-10) REVERT: F 1100 MET cc_start: 0.8336 (mmm) cc_final: 0.7963 (mmt) REVERT: F 1132 TRP cc_start: 0.7328 (t-100) cc_final: 0.6954 (t-100) REVERT: F 1143 TRP cc_start: 0.6275 (OUTLIER) cc_final: 0.4835 (p-90) REVERT: F 1562 ILE cc_start: 0.9430 (mm) cc_final: 0.9100 (mm) REVERT: F 1852 MET cc_start: 0.8632 (mmm) cc_final: 0.8118 (mmm) REVERT: F 1945 GLU cc_start: 0.8342 (tp30) cc_final: 0.7617 (tp30) REVERT: F 2121 MET cc_start: 0.8042 (mtp) cc_final: 0.7775 (ttm) REVERT: F 2214 ASN cc_start: 0.8755 (m-40) cc_final: 0.8523 (m110) REVERT: F 2507 LEU cc_start: 0.9368 (tp) cc_final: 0.9149 (tt) REVERT: F 2527 PHE cc_start: 0.8272 (m-10) cc_final: 0.7924 (m-80) REVERT: F 3436 PHE cc_start: 0.8254 (t80) cc_final: 0.7934 (t80) REVERT: F 3445 TYR cc_start: 0.8851 (m-80) cc_final: 0.8486 (t80) REVERT: F 3775 LEU cc_start: 0.9360 (mp) cc_final: 0.9106 (mt) REVERT: F 3973 GLN cc_start: 0.7387 (tm-30) cc_final: 0.6210 (tm-30) REVERT: F 3977 HIS cc_start: 0.6937 (m170) cc_final: 0.6639 (m-70) REVERT: F 4040 VAL cc_start: 0.9633 (m) cc_final: 0.9411 (p) REVERT: F 4052 MET cc_start: 0.8932 (tpp) cc_final: 0.8707 (tpp) REVERT: F 4056 PHE cc_start: 0.8602 (t80) cc_final: 0.8360 (t80) REVERT: F 4186 GLU cc_start: 0.7418 (tp30) cc_final: 0.6956 (tp30) REVERT: F 4202 MET cc_start: 0.8250 (tpp) cc_final: 0.7929 (ttp) REVERT: F 4576 LEU cc_start: 0.8963 (tp) cc_final: 0.8752 (tp) REVERT: F 4794 MET cc_start: 0.8801 (tpt) cc_final: 0.8353 (tpt) REVERT: F 4878 MET cc_start: 0.8064 (tpp) cc_final: 0.7818 (tpp) REVERT: F 4946 GLU cc_start: 0.8837 (tp30) cc_final: 0.8233 (tp30) REVERT: F 4965 TYR cc_start: 0.8573 (t80) cc_final: 0.8358 (t80) REVERT: F 5000 GLU cc_start: 0.8492 (tp30) cc_final: 0.8283 (tm-30) REVERT: H 197 GLN cc_start: 0.7638 (pp30) cc_final: 0.7294 (pp30) REVERT: H 384 MET cc_start: 0.8188 (tmm) cc_final: 0.7908 (tmm) REVERT: H 791 PHE cc_start: 0.8317 (OUTLIER) cc_final: 0.7842 (m-10) REVERT: H 1132 TRP cc_start: 0.7438 (t-100) cc_final: 0.7024 (t-100) REVERT: H 1143 TRP cc_start: 0.6286 (OUTLIER) cc_final: 0.4878 (p-90) REVERT: H 1562 ILE cc_start: 0.9435 (mm) cc_final: 0.9101 (mm) REVERT: H 1852 MET cc_start: 0.8641 (mmm) cc_final: 0.8157 (mmm) REVERT: H 1945 GLU cc_start: 0.8069 (tp30) cc_final: 0.7826 (tp30) REVERT: H 2121 MET cc_start: 0.7998 (mtp) cc_final: 0.7700 (ttm) REVERT: H 2214 ASN cc_start: 0.8751 (m-40) cc_final: 0.8528 (m110) REVERT: H 2507 LEU cc_start: 0.9356 (tp) cc_final: 0.9132 (tt) REVERT: H 2527 PHE cc_start: 0.8226 (m-10) cc_final: 0.7859 (m-80) REVERT: H 3436 PHE cc_start: 0.8244 (t80) cc_final: 0.7935 (t80) REVERT: H 3445 TYR cc_start: 0.8811 (m-80) cc_final: 0.8481 (t80) REVERT: H 4052 MET cc_start: 0.8898 (tpp) cc_final: 0.8676 (tpp) REVERT: H 4186 GLU cc_start: 0.7448 (tp30) cc_final: 0.6994 (tp30) REVERT: H 4202 MET cc_start: 0.8253 (tpp) cc_final: 0.7935 (ttp) REVERT: H 4576 LEU cc_start: 0.8970 (tp) cc_final: 0.8736 (tp) REVERT: H 4794 MET cc_start: 0.8812 (tpt) cc_final: 0.8354 (tpt) REVERT: H 4878 MET cc_start: 0.8020 (tpp) cc_final: 0.7804 (tpp) REVERT: H 4965 TYR cc_start: 0.8630 (t80) cc_final: 0.8382 (t80) REVERT: H 5000 GLU cc_start: 0.8492 (tp30) cc_final: 0.8273 (tm-30) outliers start: 264 outliers final: 172 residues processed: 1488 average time/residue: 0.7495 time to fit residues: 2050.8758 Evaluate side-chains 1387 residues out of total 12212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 1207 time to evaluate : 8.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 113 HIS Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 537 CYS Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 586 ILE Chi-restraints excluded: chain B residue 791 PHE Chi-restraints excluded: chain B residue 1143 TRP Chi-restraints excluded: chain B residue 1236 THR Chi-restraints excluded: chain B residue 1450 VAL Chi-restraints excluded: chain B residue 1659 LEU Chi-restraints excluded: chain B residue 1685 LEU Chi-restraints excluded: chain B residue 1840 VAL Chi-restraints excluded: chain B residue 1851 VAL Chi-restraints excluded: chain B residue 1959 LEU Chi-restraints excluded: chain B residue 2124 LEU Chi-restraints excluded: chain B residue 2229 MET Chi-restraints excluded: chain B residue 2241 CYS Chi-restraints excluded: chain B residue 2281 VAL Chi-restraints excluded: chain B residue 2303 LEU Chi-restraints excluded: chain B residue 2496 VAL Chi-restraints excluded: chain B residue 3964 ILE Chi-restraints excluded: chain B residue 3996 MET Chi-restraints excluded: chain B residue 3998 LEU Chi-restraints excluded: chain B residue 4026 LEU Chi-restraints excluded: chain B residue 4065 ASP Chi-restraints excluded: chain B residue 4134 ILE Chi-restraints excluded: chain B residue 4157 ASN Chi-restraints excluded: chain B residue 4574 ILE Chi-restraints excluded: chain B residue 4790 LEU Chi-restraints excluded: chain B residue 4792 TRP Chi-restraints excluded: chain B residue 4839 VAL Chi-restraints excluded: chain B residue 4842 LEU Chi-restraints excluded: chain B residue 4844 VAL Chi-restraints excluded: chain B residue 5006 SER Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 113 HIS Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 586 ILE Chi-restraints excluded: chain D residue 791 PHE Chi-restraints excluded: chain D residue 1143 TRP Chi-restraints excluded: chain D residue 1236 THR Chi-restraints excluded: chain D residue 1450 VAL Chi-restraints excluded: chain D residue 1659 LEU Chi-restraints excluded: chain D residue 1685 LEU Chi-restraints excluded: chain D residue 1840 VAL Chi-restraints excluded: chain D residue 1851 VAL Chi-restraints excluded: chain D residue 1959 LEU Chi-restraints excluded: chain D residue 2124 LEU Chi-restraints excluded: chain D residue 2229 MET Chi-restraints excluded: chain D residue 2241 CYS Chi-restraints excluded: chain D residue 2281 VAL Chi-restraints excluded: chain D residue 2303 LEU Chi-restraints excluded: chain D residue 2496 VAL Chi-restraints excluded: chain D residue 3964 ILE Chi-restraints excluded: chain D residue 3996 MET Chi-restraints excluded: chain D residue 3998 LEU Chi-restraints excluded: chain D residue 4026 LEU Chi-restraints excluded: chain D residue 4065 ASP Chi-restraints excluded: chain D residue 4134 ILE Chi-restraints excluded: chain D residue 4157 ASN Chi-restraints excluded: chain D residue 4574 ILE Chi-restraints excluded: chain D residue 4790 LEU Chi-restraints excluded: chain D residue 4792 TRP Chi-restraints excluded: chain D residue 4839 VAL Chi-restraints excluded: chain D residue 4842 LEU Chi-restraints excluded: chain D residue 4844 VAL Chi-restraints excluded: chain D residue 4948 VAL Chi-restraints excluded: chain D residue 5006 SER Chi-restraints excluded: chain E residue 35 LYS Chi-restraints excluded: chain F residue 17 ASP Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 113 HIS Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 191 VAL Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 448 LEU Chi-restraints excluded: chain F residue 564 LEU Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain F residue 586 ILE Chi-restraints excluded: chain F residue 791 PHE Chi-restraints excluded: chain F residue 1143 TRP Chi-restraints excluded: chain F residue 1159 THR Chi-restraints excluded: chain F residue 1236 THR Chi-restraints excluded: chain F residue 1450 VAL Chi-restraints excluded: chain F residue 1659 LEU Chi-restraints excluded: chain F residue 1685 LEU Chi-restraints excluded: chain F residue 1717 SER Chi-restraints excluded: chain F residue 1840 VAL Chi-restraints excluded: chain F residue 1851 VAL Chi-restraints excluded: chain F residue 1959 LEU Chi-restraints excluded: chain F residue 2124 LEU Chi-restraints excluded: chain F residue 2229 MET Chi-restraints excluded: chain F residue 2241 CYS Chi-restraints excluded: chain F residue 2281 VAL Chi-restraints excluded: chain F residue 2303 LEU Chi-restraints excluded: chain F residue 2496 VAL Chi-restraints excluded: chain F residue 3792 THR Chi-restraints excluded: chain F residue 3964 ILE Chi-restraints excluded: chain F residue 3996 MET Chi-restraints excluded: chain F residue 3998 LEU Chi-restraints excluded: chain F residue 4026 LEU Chi-restraints excluded: chain F residue 4065 ASP Chi-restraints excluded: chain F residue 4134 ILE Chi-restraints excluded: chain F residue 4157 ASN Chi-restraints excluded: chain F residue 4574 ILE Chi-restraints excluded: chain F residue 4778 PHE Chi-restraints excluded: chain F residue 4790 LEU Chi-restraints excluded: chain F residue 4792 TRP Chi-restraints excluded: chain F residue 4839 VAL Chi-restraints excluded: chain F residue 4842 LEU Chi-restraints excluded: chain F residue 4844 VAL Chi-restraints excluded: chain F residue 4948 VAL Chi-restraints excluded: chain F residue 5006 SER Chi-restraints excluded: chain H residue 17 ASP Chi-restraints excluded: chain H residue 25 ASN Chi-restraints excluded: chain H residue 65 CYS Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 113 HIS Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 232 THR Chi-restraints excluded: chain H residue 357 LEU Chi-restraints excluded: chain H residue 448 LEU Chi-restraints excluded: chain H residue 564 LEU Chi-restraints excluded: chain H residue 569 ILE Chi-restraints excluded: chain H residue 586 ILE Chi-restraints excluded: chain H residue 791 PHE Chi-restraints excluded: chain H residue 1143 TRP Chi-restraints excluded: chain H residue 1236 THR Chi-restraints excluded: chain H residue 1450 VAL Chi-restraints excluded: chain H residue 1600 LEU Chi-restraints excluded: chain H residue 1659 LEU Chi-restraints excluded: chain H residue 1685 LEU Chi-restraints excluded: chain H residue 1717 SER Chi-restraints excluded: chain H residue 1851 VAL Chi-restraints excluded: chain H residue 1959 LEU Chi-restraints excluded: chain H residue 2124 LEU Chi-restraints excluded: chain H residue 2127 ARG Chi-restraints excluded: chain H residue 2229 MET Chi-restraints excluded: chain H residue 2241 CYS Chi-restraints excluded: chain H residue 2281 VAL Chi-restraints excluded: chain H residue 2303 LEU Chi-restraints excluded: chain H residue 2496 VAL Chi-restraints excluded: chain H residue 3964 ILE Chi-restraints excluded: chain H residue 3996 MET Chi-restraints excluded: chain H residue 3998 LEU Chi-restraints excluded: chain H residue 4026 LEU Chi-restraints excluded: chain H residue 4065 ASP Chi-restraints excluded: chain H residue 4134 ILE Chi-restraints excluded: chain H residue 4157 ASN Chi-restraints excluded: chain H residue 4574 ILE Chi-restraints excluded: chain H residue 4778 PHE Chi-restraints excluded: chain H residue 4790 LEU Chi-restraints excluded: chain H residue 4792 TRP Chi-restraints excluded: chain H residue 4825 LEU Chi-restraints excluded: chain H residue 4839 VAL Chi-restraints excluded: chain H residue 4842 LEU Chi-restraints excluded: chain H residue 4844 VAL Chi-restraints excluded: chain H residue 5006 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1524 random chunks: chunk 1369 optimal weight: 2.9990 chunk 1042 optimal weight: 30.0000 chunk 719 optimal weight: 0.6980 chunk 153 optimal weight: 2.9990 chunk 661 optimal weight: 30.0000 chunk 930 optimal weight: 0.7980 chunk 1391 optimal weight: 7.9990 chunk 1473 optimal weight: 4.9990 chunk 726 optimal weight: 1.9990 chunk 1318 optimal weight: 0.7980 chunk 396 optimal weight: 0.1980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B2128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2261 ASN B3776 GLN B3804 ASN B3973 GLN ** B3993 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4151 HIS ** B4712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1052 ASN ** D2128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2261 ASN D3776 GLN ** D3973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3993 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F2261 ASN F3776 GLN ** F3993 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F4148 HIS F4151 HIS F4204 GLN ** F4712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H2261 ASN H3776 GLN H3945 ASN H3973 GLN ** H3993 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H4151 HIS H4204 GLN ** H4712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.3962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 107328 Z= 0.168 Angle : 0.645 15.352 146972 Z= 0.304 Chirality : 0.039 0.278 17784 Planarity : 0.004 0.055 19000 Dihedral : 3.857 39.867 15872 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.45 % Allowed : 19.58 % Favored : 77.97 % 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: 0.59 (0.07), residues: 13692 helix: 1.32 (0.06), residues: 6572 sheet: -0.35 (0.13), residues: 1616 loop : -0.43 (0.08), residues: 5504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B3930 HIS 0.005 0.001 HIS H1688 PHE 0.027 0.001 PHE F1223 TYR 0.022 0.001 TYR D4793 ARG 0.028 0.001 ARG B2141 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27384 Ramachandran restraints generated. 13692 Oldfield, 0 Emsley, 13692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27384 Ramachandran restraints generated. 13692 Oldfield, 0 Emsley, 13692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1548 residues out of total 12212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 1334 time to evaluate : 8.148 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: B 197 GLN cc_start: 0.7706 (pp30) cc_final: 0.7494 (pp30) REVERT: B 202 MET cc_start: 0.7866 (ptp) cc_final: 0.7126 (mtm) REVERT: B 1132 TRP cc_start: 0.7358 (t-100) cc_final: 0.6965 (t-100) REVERT: B 1143 TRP cc_start: 0.6121 (OUTLIER) cc_final: 0.5398 (p-90) REVERT: B 1286 MET cc_start: 0.8299 (tpp) cc_final: 0.8011 (tpp) REVERT: B 1562 ILE cc_start: 0.9415 (mm) cc_final: 0.9078 (mm) REVERT: B 1852 MET cc_start: 0.8557 (mmm) cc_final: 0.8156 (mmm) REVERT: B 1940 MET cc_start: 0.7711 (tpp) cc_final: 0.7457 (tpp) REVERT: B 1941 CYS cc_start: 0.8451 (m) cc_final: 0.8245 (m) REVERT: B 2121 MET cc_start: 0.7976 (mtp) cc_final: 0.7642 (ttm) REVERT: B 2507 LEU cc_start: 0.9328 (tp) cc_final: 0.9103 (tt) REVERT: B 2527 PHE cc_start: 0.8224 (m-10) cc_final: 0.7908 (m-80) REVERT: B 3436 PHE cc_start: 0.8165 (t80) cc_final: 0.7888 (t80) REVERT: B 3718 TYR cc_start: 0.8668 (t80) cc_final: 0.8133 (t80) REVERT: B 3775 LEU cc_start: 0.9349 (mp) cc_final: 0.9008 (mt) REVERT: B 3776 GLN cc_start: 0.9073 (mt0) cc_final: 0.8452 (mt0) REVERT: B 4040 VAL cc_start: 0.9626 (m) cc_final: 0.9398 (p) REVERT: B 4056 PHE cc_start: 0.8549 (t80) cc_final: 0.8320 (t80) REVERT: B 4072 PHE cc_start: 0.6816 (OUTLIER) cc_final: 0.6477 (m-80) REVERT: B 4186 GLU cc_start: 0.7344 (tp30) cc_final: 0.6868 (tp30) REVERT: B 4656 ILE cc_start: 0.9276 (mt) cc_final: 0.9026 (mt) REVERT: B 4700 ASP cc_start: 0.8615 (m-30) cc_final: 0.8259 (p0) REVERT: B 4794 MET cc_start: 0.8757 (tpt) cc_final: 0.8426 (tpt) REVERT: B 4847 TYR cc_start: 0.8873 (t80) cc_final: 0.8438 (t80) REVERT: B 4878 MET cc_start: 0.7973 (tpp) cc_final: 0.7645 (tpp) REVERT: B 4946 GLU cc_start: 0.8809 (tp30) cc_final: 0.7374 (tp30) REVERT: B 4950 GLU cc_start: 0.8759 (mm-30) cc_final: 0.8101 (mm-30) REVERT: B 4965 TYR cc_start: 0.8594 (t80) cc_final: 0.8380 (t80) REVERT: D 179 TYR cc_start: 0.8416 (m-80) cc_final: 0.8152 (m-80) REVERT: D 197 GLN cc_start: 0.7670 (pp30) cc_final: 0.7380 (pp30) REVERT: D 202 MET cc_start: 0.7840 (ptp) cc_final: 0.7085 (mtm) REVERT: D 1100 MET cc_start: 0.8459 (mmm) cc_final: 0.8073 (mmt) REVERT: D 1132 TRP cc_start: 0.7253 (t-100) cc_final: 0.6855 (t-100) REVERT: D 1143 TRP cc_start: 0.6084 (OUTLIER) cc_final: 0.5310 (p-90) REVERT: D 1562 ILE cc_start: 0.9422 (mm) cc_final: 0.9079 (mm) REVERT: D 1852 MET cc_start: 0.8564 (mmm) cc_final: 0.8166 (mmm) REVERT: D 1945 GLU cc_start: 0.8054 (tp30) cc_final: 0.7797 (tp30) REVERT: D 2121 MET cc_start: 0.7968 (mtp) cc_final: 0.7604 (ttm) REVERT: D 2507 LEU cc_start: 0.9309 (tp) cc_final: 0.9085 (tt) REVERT: D 2527 PHE cc_start: 0.8231 (m-10) cc_final: 0.7926 (m-80) REVERT: D 3436 PHE cc_start: 0.8165 (t80) cc_final: 0.7865 (t80) REVERT: D 4040 VAL cc_start: 0.9637 (m) cc_final: 0.9411 (p) REVERT: D 4186 GLU cc_start: 0.7300 (tp30) cc_final: 0.6836 (tp30) REVERT: D 4576 LEU cc_start: 0.8840 (tp) cc_final: 0.8593 (tp) REVERT: D 4656 ILE cc_start: 0.9304 (mt) cc_final: 0.9063 (mt) REVERT: D 4700 ASP cc_start: 0.8631 (m-30) cc_final: 0.8260 (p0) REVERT: D 4847 TYR cc_start: 0.8872 (t80) cc_final: 0.8429 (t80) REVERT: D 4965 TYR cc_start: 0.8568 (t80) cc_final: 0.8341 (t80) REVERT: F 177 GLU cc_start: 0.7238 (tm-30) cc_final: 0.7026 (tm-30) REVERT: F 202 MET cc_start: 0.7896 (ptp) cc_final: 0.7156 (mtm) REVERT: F 619 ASP cc_start: 0.7954 (m-30) cc_final: 0.7651 (m-30) REVERT: F 791 PHE cc_start: 0.8242 (OUTLIER) cc_final: 0.7756 (m-80) REVERT: F 1100 MET cc_start: 0.8449 (mmm) cc_final: 0.8064 (mmt) REVERT: F 1132 TRP cc_start: 0.7243 (t-100) cc_final: 0.6844 (t-100) REVERT: F 1143 TRP cc_start: 0.6084 (OUTLIER) cc_final: 0.5326 (p-90) REVERT: F 1286 MET cc_start: 0.8277 (tpp) cc_final: 0.8006 (tpp) REVERT: F 1562 ILE cc_start: 0.9413 (mm) cc_final: 0.9071 (mm) REVERT: F 1730 MET cc_start: 0.8133 (mmm) cc_final: 0.7714 (mmp) REVERT: F 1852 MET cc_start: 0.8587 (mmm) cc_final: 0.8161 (mmm) REVERT: F 2121 MET cc_start: 0.7966 (mtp) cc_final: 0.7610 (ttm) REVERT: F 2507 LEU cc_start: 0.9335 (tp) cc_final: 0.9106 (tt) REVERT: F 2527 PHE cc_start: 0.8221 (m-10) cc_final: 0.7908 (m-80) REVERT: F 3436 PHE cc_start: 0.8174 (t80) cc_final: 0.7892 (t80) REVERT: F 3648 MET cc_start: 0.8743 (OUTLIER) cc_final: 0.8522 (pmm) REVERT: F 3973 GLN cc_start: 0.7454 (mm-40) cc_final: 0.7240 (tm-30) REVERT: F 4040 VAL cc_start: 0.9633 (m) cc_final: 0.9409 (p) REVERT: F 4186 GLU cc_start: 0.7292 (tp30) cc_final: 0.6815 (tp30) REVERT: F 4656 ILE cc_start: 0.9284 (mt) cc_final: 0.9042 (mt) REVERT: F 4700 ASP cc_start: 0.8618 (m-30) cc_final: 0.8268 (p0) REVERT: F 4847 TYR cc_start: 0.8880 (t80) cc_final: 0.8451 (t80) REVERT: F 4965 TYR cc_start: 0.8556 (t80) cc_final: 0.8325 (t80) REVERT: H 197 GLN cc_start: 0.7719 (pp30) cc_final: 0.7293 (pp30) REVERT: H 202 MET cc_start: 0.7883 (ptp) cc_final: 0.7174 (mtm) REVERT: H 619 ASP cc_start: 0.8004 (m-30) cc_final: 0.7750 (m-30) REVERT: H 1132 TRP cc_start: 0.7345 (t-100) cc_final: 0.6963 (t-100) REVERT: H 1143 TRP cc_start: 0.6144 (OUTLIER) cc_final: 0.5310 (p-90) REVERT: H 1562 ILE cc_start: 0.9405 (mm) cc_final: 0.9073 (mm) REVERT: H 1852 MET cc_start: 0.8609 (mmm) cc_final: 0.8223 (mmm) REVERT: H 2121 MET cc_start: 0.8040 (mtp) cc_final: 0.7714 (ttm) REVERT: H 2507 LEU cc_start: 0.9322 (tp) cc_final: 0.9093 (tt) REVERT: H 2527 PHE cc_start: 0.8187 (m-10) cc_final: 0.7866 (m-80) REVERT: H 3436 PHE cc_start: 0.8163 (t80) cc_final: 0.7884 (t80) REVERT: H 3648 MET cc_start: 0.8749 (mpp) cc_final: 0.8483 (pmm) REVERT: H 4056 PHE cc_start: 0.8012 (t80) cc_final: 0.7684 (t80) REVERT: H 4186 GLU cc_start: 0.7332 (tp30) cc_final: 0.6845 (tp30) REVERT: H 4656 ILE cc_start: 0.9288 (mt) cc_final: 0.9039 (mt) REVERT: H 4700 ASP cc_start: 0.8555 (m-30) cc_final: 0.8219 (p0) REVERT: H 4847 TYR cc_start: 0.8884 (t80) cc_final: 0.8440 (t80) REVERT: H 4878 MET cc_start: 0.8153 (tpp) cc_final: 0.7664 (tpp) REVERT: H 4946 GLU cc_start: 0.8809 (tp30) cc_final: 0.7393 (tp30) REVERT: H 4950 GLU cc_start: 0.8751 (mm-30) cc_final: 0.8096 (mm-30) REVERT: H 4965 TYR cc_start: 0.8535 (t80) cc_final: 0.8319 (t80) outliers start: 214 outliers final: 128 residues processed: 1453 average time/residue: 0.7654 time to fit residues: 2051.3316 Evaluate side-chains 1374 residues out of total 12212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 1239 time to evaluate : 8.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 537 CYS Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 607 CYS Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 1143 TRP Chi-restraints excluded: chain B residue 1450 VAL Chi-restraints excluded: chain B residue 1685 LEU Chi-restraints excluded: chain B residue 2136 LEU Chi-restraints excluded: chain B residue 2303 LEU Chi-restraints excluded: chain B residue 2496 VAL Chi-restraints excluded: chain B residue 3946 PHE Chi-restraints excluded: chain B residue 3964 ILE Chi-restraints excluded: chain B residue 4026 LEU Chi-restraints excluded: chain B residue 4049 ASN Chi-restraints excluded: chain B residue 4065 ASP Chi-restraints excluded: chain B residue 4072 PHE Chi-restraints excluded: chain B residue 4200 TRP Chi-restraints excluded: chain B residue 4842 LEU Chi-restraints excluded: chain B residue 4948 VAL Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain D residue 65 CYS Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 537 CYS Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 607 CYS Chi-restraints excluded: chain D residue 668 VAL Chi-restraints excluded: chain D residue 1143 TRP Chi-restraints excluded: chain D residue 1450 VAL Chi-restraints excluded: chain D residue 1659 LEU Chi-restraints excluded: chain D residue 1685 LEU Chi-restraints excluded: chain D residue 1707 LEU Chi-restraints excluded: chain D residue 1959 LEU Chi-restraints excluded: chain D residue 2136 LEU Chi-restraints excluded: chain D residue 2178 LEU Chi-restraints excluded: chain D residue 2303 LEU Chi-restraints excluded: chain D residue 2496 VAL Chi-restraints excluded: chain D residue 2503 MET Chi-restraints excluded: chain D residue 3776 GLN Chi-restraints excluded: chain D residue 3946 PHE Chi-restraints excluded: chain D residue 3964 ILE Chi-restraints excluded: chain D residue 4026 LEU Chi-restraints excluded: chain D residue 4065 ASP Chi-restraints excluded: chain D residue 4200 TRP Chi-restraints excluded: chain D residue 4842 LEU Chi-restraints excluded: chain D residue 4948 VAL Chi-restraints excluded: chain E residue 35 LYS Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 191 VAL Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain F residue 448 LEU Chi-restraints excluded: chain F residue 537 CYS Chi-restraints excluded: chain F residue 564 LEU Chi-restraints excluded: chain F residue 607 CYS Chi-restraints excluded: chain F residue 791 PHE Chi-restraints excluded: chain F residue 1143 TRP Chi-restraints excluded: chain F residue 1450 VAL Chi-restraints excluded: chain F residue 1659 LEU Chi-restraints excluded: chain F residue 1685 LEU Chi-restraints excluded: chain F residue 1707 LEU Chi-restraints excluded: chain F residue 1959 LEU Chi-restraints excluded: chain F residue 2136 LEU Chi-restraints excluded: chain F residue 2303 LEU Chi-restraints excluded: chain F residue 2496 VAL Chi-restraints excluded: chain F residue 2503 MET Chi-restraints excluded: chain F residue 3648 MET Chi-restraints excluded: chain F residue 3776 GLN Chi-restraints excluded: chain F residue 3946 PHE Chi-restraints excluded: chain F residue 3964 ILE Chi-restraints excluded: chain F residue 4026 LEU Chi-restraints excluded: chain F residue 4049 ASN Chi-restraints excluded: chain F residue 4065 ASP Chi-restraints excluded: chain F residue 4148 HIS Chi-restraints excluded: chain F residue 4200 TRP Chi-restraints excluded: chain F residue 4204 GLN Chi-restraints excluded: chain F residue 4778 PHE Chi-restraints excluded: chain F residue 4842 LEU Chi-restraints excluded: chain F residue 4948 VAL Chi-restraints excluded: chain F residue 4991 MET Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain H residue 25 ASN Chi-restraints excluded: chain H residue 65 CYS Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain H residue 232 THR Chi-restraints excluded: chain H residue 285 VAL Chi-restraints excluded: chain H residue 448 LEU Chi-restraints excluded: chain H residue 537 CYS Chi-restraints excluded: chain H residue 564 LEU Chi-restraints excluded: chain H residue 569 ILE Chi-restraints excluded: chain H residue 607 CYS Chi-restraints excluded: chain H residue 1143 TRP Chi-restraints excluded: chain H residue 1450 VAL Chi-restraints excluded: chain H residue 1685 LEU Chi-restraints excluded: chain H residue 2127 ARG Chi-restraints excluded: chain H residue 2136 LEU Chi-restraints excluded: chain H residue 2303 LEU Chi-restraints excluded: chain H residue 2496 VAL Chi-restraints excluded: chain H residue 2503 MET Chi-restraints excluded: chain H residue 3776 GLN Chi-restraints excluded: chain H residue 3964 ILE Chi-restraints excluded: chain H residue 4026 LEU Chi-restraints excluded: chain H residue 4049 ASN Chi-restraints excluded: chain H residue 4065 ASP Chi-restraints excluded: chain H residue 4072 PHE Chi-restraints excluded: chain H residue 4200 TRP Chi-restraints excluded: chain H residue 4778 PHE Chi-restraints excluded: chain H residue 4825 LEU Chi-restraints excluded: chain H residue 4842 LEU Chi-restraints excluded: chain H residue 4948 VAL Chi-restraints excluded: chain H residue 4991 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1524 random chunks: chunk 1226 optimal weight: 10.0000 chunk 836 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 1096 optimal weight: 3.9990 chunk 607 optimal weight: 3.9990 chunk 1257 optimal weight: 8.9990 chunk 1018 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 752 optimal weight: 0.8980 chunk 1322 optimal weight: 20.0000 chunk 371 optimal weight: 0.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1691 GLN ** B2128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2261 ASN ** B3993 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4148 HIS ** B4712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B5001 HIS ** D 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2261 ASN D3776 GLN ** D3804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3993 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4148 HIS ** D4712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4831 ASN D5001 HIS ** F 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F2261 ASN ** F3776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F3993 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F4712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F5001 HIS ** H 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H2261 ASN ** H3776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H3993 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H4148 HIS ** H4712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H4831 ASN H5001 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.4383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 107328 Z= 0.288 Angle : 0.671 13.090 146972 Z= 0.330 Chirality : 0.040 0.249 17784 Planarity : 0.004 0.068 19000 Dihedral : 3.967 33.608 15872 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.80 % Allowed : 20.54 % Favored : 76.66 % 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: 0.51 (0.07), residues: 13692 helix: 1.27 (0.06), residues: 6668 sheet: -0.47 (0.13), residues: 1656 loop : -0.49 (0.08), residues: 5368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 882 HIS 0.034 0.001 HIS F4148 PHE 0.032 0.002 PHE D 478 TYR 0.021 0.002 TYR D3721 ARG 0.009 0.001 ARG F1087 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27384 Ramachandran restraints generated. 13692 Oldfield, 0 Emsley, 13692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27384 Ramachandran restraints generated. 13692 Oldfield, 0 Emsley, 13692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1475 residues out of total 12212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 244 poor density : 1231 time to evaluate : 8.285 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: B 197 GLN cc_start: 0.7787 (pp30) cc_final: 0.7378 (pp30) REVERT: B 202 MET cc_start: 0.8021 (ptp) cc_final: 0.7262 (mtm) REVERT: B 667 MET cc_start: 0.7963 (ppp) cc_final: 0.7502 (ppp) REVERT: B 791 PHE cc_start: 0.8325 (OUTLIER) cc_final: 0.7709 (m-80) REVERT: B 1132 TRP cc_start: 0.7538 (t-100) cc_final: 0.7144 (t-100) REVERT: B 1143 TRP cc_start: 0.6263 (OUTLIER) cc_final: 0.5667 (p-90) REVERT: B 1562 ILE cc_start: 0.9561 (mm) cc_final: 0.9356 (mm) REVERT: B 1730 MET cc_start: 0.8271 (mmm) cc_final: 0.7657 (mmp) REVERT: B 1852 MET cc_start: 0.8689 (mmm) cc_final: 0.8252 (mmm) REVERT: B 2527 PHE cc_start: 0.8286 (m-10) cc_final: 0.7952 (m-80) REVERT: B 3436 PHE cc_start: 0.8138 (t80) cc_final: 0.7871 (t80) REVERT: B 3648 MET cc_start: 0.8520 (pmm) cc_final: 0.8222 (pmm) REVERT: B 4040 VAL cc_start: 0.9630 (m) cc_final: 0.9380 (p) REVERT: B 4056 PHE cc_start: 0.8407 (t80) cc_final: 0.8184 (t80) REVERT: B 4186 GLU cc_start: 0.7521 (tp30) cc_final: 0.7066 (tp30) REVERT: B 4572 ASN cc_start: 0.8585 (m110) cc_final: 0.8313 (m110) REVERT: B 4650 LEU cc_start: 0.9336 (mm) cc_final: 0.9101 (mm) REVERT: B 4656 ILE cc_start: 0.9266 (mt) cc_final: 0.9028 (mt) REVERT: B 4700 ASP cc_start: 0.8495 (m-30) cc_final: 0.8171 (p0) REVERT: B 4788 LEU cc_start: 0.9181 (mm) cc_final: 0.8962 (tp) REVERT: B 4794 MET cc_start: 0.8724 (tpt) cc_final: 0.8302 (tpt) REVERT: B 4847 TYR cc_start: 0.8981 (t80) cc_final: 0.8719 (t80) REVERT: D 179 TYR cc_start: 0.8422 (m-80) cc_final: 0.8081 (m-80) REVERT: D 197 GLN cc_start: 0.7823 (pp30) cc_final: 0.7568 (pp30) REVERT: D 667 MET cc_start: 0.7972 (ppp) cc_final: 0.7507 (ppp) REVERT: D 791 PHE cc_start: 0.8388 (OUTLIER) cc_final: 0.7874 (m-80) REVERT: D 1100 MET cc_start: 0.8425 (mmm) cc_final: 0.8054 (mmt) REVERT: D 1132 TRP cc_start: 0.7572 (t-100) cc_final: 0.7171 (t-100) REVERT: D 1143 TRP cc_start: 0.6226 (OUTLIER) cc_final: 0.5604 (p-90) REVERT: D 1562 ILE cc_start: 0.9567 (mm) cc_final: 0.9353 (mm) REVERT: D 1852 MET cc_start: 0.8696 (mmm) cc_final: 0.8260 (mmm) REVERT: D 2121 MET cc_start: 0.8044 (mtp) cc_final: 0.7604 (ttm) REVERT: D 2527 PHE cc_start: 0.8351 (m-10) cc_final: 0.8028 (m-80) REVERT: D 3436 PHE cc_start: 0.8138 (t80) cc_final: 0.7852 (t80) REVERT: D 3648 MET cc_start: 0.8472 (pmm) cc_final: 0.8230 (pmm) REVERT: D 3775 LEU cc_start: 0.9490 (mp) cc_final: 0.9157 (mt) REVERT: D 4040 VAL cc_start: 0.9651 (m) cc_final: 0.9439 (p) REVERT: D 4186 GLU cc_start: 0.7510 (tp30) cc_final: 0.7064 (tp30) REVERT: D 4572 ASN cc_start: 0.8613 (m110) cc_final: 0.8328 (m110) REVERT: D 4656 ILE cc_start: 0.9282 (mt) cc_final: 0.9017 (mt) REVERT: D 4700 ASP cc_start: 0.8588 (m-30) cc_final: 0.8243 (p0) REVERT: D 4788 LEU cc_start: 0.9181 (mm) cc_final: 0.8957 (tp) REVERT: D 4794 MET cc_start: 0.8796 (tpt) cc_final: 0.8566 (tpt) REVERT: D 4847 TYR cc_start: 0.8975 (t80) cc_final: 0.8719 (t80) REVERT: D 4965 TYR cc_start: 0.8705 (t80) cc_final: 0.8445 (t80) REVERT: F 177 GLU cc_start: 0.7337 (tm-30) cc_final: 0.7080 (tm-30) REVERT: F 197 GLN cc_start: 0.8244 (pp30) cc_final: 0.7791 (pp30) REVERT: F 202 MET cc_start: 0.8023 (ptp) cc_final: 0.7260 (mtm) REVERT: F 667 MET cc_start: 0.7934 (ppp) cc_final: 0.7474 (ppp) REVERT: F 791 PHE cc_start: 0.8374 (OUTLIER) cc_final: 0.7805 (m-80) REVERT: F 1100 MET cc_start: 0.8421 (mmm) cc_final: 0.8055 (mmt) REVERT: F 1132 TRP cc_start: 0.7515 (t-100) cc_final: 0.7097 (t-100) REVERT: F 1143 TRP cc_start: 0.6286 (OUTLIER) cc_final: 0.5558 (p-90) REVERT: F 1562 ILE cc_start: 0.9558 (mm) cc_final: 0.9344 (mm) REVERT: F 1852 MET cc_start: 0.8694 (mmm) cc_final: 0.8248 (mmm) REVERT: F 1941 CYS cc_start: 0.8559 (m) cc_final: 0.8343 (m) REVERT: F 2121 MET cc_start: 0.8041 (mtp) cc_final: 0.7627 (ttm) REVERT: F 2527 PHE cc_start: 0.8311 (m-10) cc_final: 0.7982 (m-80) REVERT: F 3436 PHE cc_start: 0.8163 (t80) cc_final: 0.7884 (t80) REVERT: F 3775 LEU cc_start: 0.9499 (mp) cc_final: 0.9189 (mt) REVERT: F 4040 VAL cc_start: 0.9648 (m) cc_final: 0.9430 (p) REVERT: F 4186 GLU cc_start: 0.7489 (tp30) cc_final: 0.7050 (tp30) REVERT: F 4572 ASN cc_start: 0.8576 (m110) cc_final: 0.8300 (m110) REVERT: F 4656 ILE cc_start: 0.9288 (mt) cc_final: 0.9025 (mt) REVERT: F 4700 ASP cc_start: 0.8594 (m-30) cc_final: 0.8249 (p0) REVERT: F 4788 LEU cc_start: 0.9209 (mm) cc_final: 0.9001 (tp) REVERT: H 197 GLN cc_start: 0.7910 (pp30) cc_final: 0.7592 (pp30) REVERT: H 202 MET cc_start: 0.8032 (ptp) cc_final: 0.7292 (mtm) REVERT: H 667 MET cc_start: 0.7936 (ppp) cc_final: 0.7456 (ppp) REVERT: H 1132 TRP cc_start: 0.7519 (t-100) cc_final: 0.7174 (t-100) REVERT: H 1143 TRP cc_start: 0.6316 (OUTLIER) cc_final: 0.5619 (p-90) REVERT: H 1286 MET cc_start: 0.8475 (tpp) cc_final: 0.8121 (tpp) REVERT: H 1562 ILE cc_start: 0.9549 (mm) cc_final: 0.9338 (mm) REVERT: H 1730 MET cc_start: 0.8281 (mmm) cc_final: 0.7668 (mmp) REVERT: H 1852 MET cc_start: 0.8707 (mmm) cc_final: 0.8263 (mmm) REVERT: H 1941 CYS cc_start: 0.8546 (m) cc_final: 0.8336 (m) REVERT: H 2121 MET cc_start: 0.8038 (mtp) cc_final: 0.7625 (ttm) REVERT: H 2527 PHE cc_start: 0.8269 (m-10) cc_final: 0.7929 (m-80) REVERT: H 3436 PHE cc_start: 0.8130 (t80) cc_final: 0.7878 (t80) REVERT: H 4144 ASN cc_start: 0.8924 (t0) cc_final: 0.8682 (m-40) REVERT: H 4186 GLU cc_start: 0.7495 (tp30) cc_final: 0.7029 (tp30) REVERT: H 4572 ASN cc_start: 0.8575 (m110) cc_final: 0.8306 (m110) REVERT: H 4576 LEU cc_start: 0.8978 (tp) cc_final: 0.8745 (tp) REVERT: H 4656 ILE cc_start: 0.9294 (mt) cc_final: 0.9031 (mt) REVERT: H 4700 ASP cc_start: 0.8501 (m-30) cc_final: 0.8190 (p0) REVERT: H 4788 LEU cc_start: 0.9186 (mm) cc_final: 0.8958 (tp) REVERT: H 4794 MET cc_start: 0.8786 (tpt) cc_final: 0.8559 (tpt) outliers start: 244 outliers final: 191 residues processed: 1383 average time/residue: 0.7674 time to fit residues: 1958.4290 Evaluate side-chains 1392 residues out of total 12212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 1194 time to evaluate : 8.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 113 HIS Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 586 ILE Chi-restraints excluded: chain B residue 607 CYS Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 791 PHE Chi-restraints excluded: chain B residue 1143 TRP Chi-restraints excluded: chain B residue 1450 VAL Chi-restraints excluded: chain B residue 1659 LEU Chi-restraints excluded: chain B residue 1685 LEU Chi-restraints excluded: chain B residue 1769 THR Chi-restraints excluded: chain B residue 1851 VAL Chi-restraints excluded: chain B residue 1959 LEU Chi-restraints excluded: chain B residue 2124 LEU Chi-restraints excluded: chain B residue 2127 ARG Chi-restraints excluded: chain B residue 2186 ILE Chi-restraints excluded: chain B residue 2281 VAL Chi-restraints excluded: chain B residue 2496 VAL Chi-restraints excluded: chain B residue 3946 PHE Chi-restraints excluded: chain B residue 3964 ILE Chi-restraints excluded: chain B residue 3990 VAL Chi-restraints excluded: chain B residue 3996 MET Chi-restraints excluded: chain B residue 4026 LEU Chi-restraints excluded: chain B residue 4049 ASN Chi-restraints excluded: chain B residue 4065 ASP Chi-restraints excluded: chain B residue 4148 HIS Chi-restraints excluded: chain B residue 4200 TRP Chi-restraints excluded: chain B residue 4790 LEU Chi-restraints excluded: chain B residue 4842 LEU Chi-restraints excluded: chain B residue 4844 VAL Chi-restraints excluded: chain B residue 4948 VAL Chi-restraints excluded: chain B residue 4991 MET Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 113 HIS Chi-restraints excluded: chain D residue 158 SER Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 346 CYS Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 586 ILE Chi-restraints excluded: chain D residue 607 CYS Chi-restraints excluded: chain D residue 668 VAL Chi-restraints excluded: chain D residue 672 VAL Chi-restraints excluded: chain D residue 791 PHE Chi-restraints excluded: chain D residue 1113 VAL Chi-restraints excluded: chain D residue 1143 TRP Chi-restraints excluded: chain D residue 1450 VAL Chi-restraints excluded: chain D residue 1659 LEU Chi-restraints excluded: chain D residue 1685 LEU Chi-restraints excluded: chain D residue 1707 LEU Chi-restraints excluded: chain D residue 1769 THR Chi-restraints excluded: chain D residue 1851 VAL Chi-restraints excluded: chain D residue 2124 LEU Chi-restraints excluded: chain D residue 2178 LEU Chi-restraints excluded: chain D residue 2281 VAL Chi-restraints excluded: chain D residue 2303 LEU Chi-restraints excluded: chain D residue 2496 VAL Chi-restraints excluded: chain D residue 2503 MET Chi-restraints excluded: chain D residue 3946 PHE Chi-restraints excluded: chain D residue 3964 ILE Chi-restraints excluded: chain D residue 3990 VAL Chi-restraints excluded: chain D residue 4026 LEU Chi-restraints excluded: chain D residue 4049 ASN Chi-restraints excluded: chain D residue 4065 ASP Chi-restraints excluded: chain D residue 4072 PHE Chi-restraints excluded: chain D residue 4148 HIS Chi-restraints excluded: chain D residue 4200 TRP Chi-restraints excluded: chain D residue 4790 LEU Chi-restraints excluded: chain D residue 4842 LEU Chi-restraints excluded: chain D residue 4844 VAL Chi-restraints excluded: chain D residue 4877 MET Chi-restraints excluded: chain D residue 4948 VAL Chi-restraints excluded: chain D residue 4991 MET Chi-restraints excluded: chain E residue 35 LYS Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain F residue 17 ASP Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 113 HIS Chi-restraints excluded: chain F residue 191 VAL Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 346 CYS Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain F residue 448 LEU Chi-restraints excluded: chain F residue 491 ILE Chi-restraints excluded: chain F residue 564 LEU Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain F residue 586 ILE Chi-restraints excluded: chain F residue 607 CYS Chi-restraints excluded: chain F residue 668 VAL Chi-restraints excluded: chain F residue 672 VAL Chi-restraints excluded: chain F residue 723 THR Chi-restraints excluded: chain F residue 791 PHE Chi-restraints excluded: chain F residue 1113 VAL Chi-restraints excluded: chain F residue 1143 TRP Chi-restraints excluded: chain F residue 1450 VAL Chi-restraints excluded: chain F residue 1659 LEU Chi-restraints excluded: chain F residue 1685 LEU Chi-restraints excluded: chain F residue 1707 LEU Chi-restraints excluded: chain F residue 1769 THR Chi-restraints excluded: chain F residue 1851 VAL Chi-restraints excluded: chain F residue 1959 LEU Chi-restraints excluded: chain F residue 2127 ARG Chi-restraints excluded: chain F residue 2281 VAL Chi-restraints excluded: chain F residue 2303 LEU Chi-restraints excluded: chain F residue 2496 VAL Chi-restraints excluded: chain F residue 2503 MET Chi-restraints excluded: chain F residue 3946 PHE Chi-restraints excluded: chain F residue 3964 ILE Chi-restraints excluded: chain F residue 4026 LEU Chi-restraints excluded: chain F residue 4065 ASP Chi-restraints excluded: chain F residue 4072 PHE Chi-restraints excluded: chain F residue 4200 TRP Chi-restraints excluded: chain F residue 4790 LEU Chi-restraints excluded: chain F residue 4842 LEU Chi-restraints excluded: chain F residue 4844 VAL Chi-restraints excluded: chain F residue 4877 MET Chi-restraints excluded: chain F residue 4948 VAL Chi-restraints excluded: chain F residue 4991 MET Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain H residue 17 ASP Chi-restraints excluded: chain H residue 25 ASN Chi-restraints excluded: chain H residue 65 CYS Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 113 HIS Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 232 THR Chi-restraints excluded: chain H residue 285 VAL Chi-restraints excluded: chain H residue 346 CYS Chi-restraints excluded: chain H residue 357 LEU Chi-restraints excluded: chain H residue 448 LEU Chi-restraints excluded: chain H residue 480 GLU Chi-restraints excluded: chain H residue 564 LEU Chi-restraints excluded: chain H residue 569 ILE Chi-restraints excluded: chain H residue 586 ILE Chi-restraints excluded: chain H residue 607 CYS Chi-restraints excluded: chain H residue 668 VAL Chi-restraints excluded: chain H residue 672 VAL Chi-restraints excluded: chain H residue 723 THR Chi-restraints excluded: chain H residue 1143 TRP Chi-restraints excluded: chain H residue 1450 VAL Chi-restraints excluded: chain H residue 1659 LEU Chi-restraints excluded: chain H residue 1685 LEU Chi-restraints excluded: chain H residue 1769 THR Chi-restraints excluded: chain H residue 1840 VAL Chi-restraints excluded: chain H residue 1851 VAL Chi-restraints excluded: chain H residue 1959 LEU Chi-restraints excluded: chain H residue 2124 LEU Chi-restraints excluded: chain H residue 2127 ARG Chi-restraints excluded: chain H residue 2281 VAL Chi-restraints excluded: chain H residue 2303 LEU Chi-restraints excluded: chain H residue 2496 VAL Chi-restraints excluded: chain H residue 2503 MET Chi-restraints excluded: chain H residue 3964 ILE Chi-restraints excluded: chain H residue 3990 VAL Chi-restraints excluded: chain H residue 4026 LEU Chi-restraints excluded: chain H residue 4049 ASN Chi-restraints excluded: chain H residue 4065 ASP Chi-restraints excluded: chain H residue 4148 HIS Chi-restraints excluded: chain H residue 4200 TRP Chi-restraints excluded: chain H residue 4778 PHE Chi-restraints excluded: chain H residue 4790 LEU Chi-restraints excluded: chain H residue 4825 LEU Chi-restraints excluded: chain H residue 4842 LEU Chi-restraints excluded: chain H residue 4844 VAL Chi-restraints excluded: chain H residue 4877 MET Chi-restraints excluded: chain H residue 4938 PHE Chi-restraints excluded: chain H residue 4948 VAL Chi-restraints excluded: chain H residue 4991 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1524 random chunks: chunk 495 optimal weight: 0.0040 chunk 1326 optimal weight: 4.9990 chunk 291 optimal weight: 4.9990 chunk 864 optimal weight: 4.9990 chunk 363 optimal weight: 3.9990 chunk 1474 optimal weight: 0.5980 chunk 1224 optimal weight: 7.9990 chunk 682 optimal weight: 0.9990 chunk 122 optimal weight: 9.9990 chunk 487 optimal weight: 3.9990 chunk 774 optimal weight: 9.9990 overall best weight: 1.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B2128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3776 GLN ** B3993 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3804 ASN D3973 GLN ** D3993 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F3776 GLN F3804 ASN ** F3977 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F3993 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F4148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F4204 GLN ** F4712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H1691 GLN ** H2128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H3776 GLN ** H3993 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H4712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.4524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 107328 Z= 0.201 Angle : 0.663 14.230 146972 Z= 0.312 Chirality : 0.039 0.254 17784 Planarity : 0.004 0.064 19000 Dihedral : 3.886 24.255 15870 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.77 % Allowed : 21.77 % Favored : 75.46 % 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: 0.67 (0.07), residues: 13692 helix: 1.42 (0.06), residues: 6648 sheet: -0.36 (0.13), residues: 1644 loop : -0.43 (0.08), residues: 5400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 882 HIS 0.022 0.001 HIS H4148 PHE 0.026 0.001 PHE D 478 TYR 0.029 0.001 TYR B4965 ARG 0.007 0.001 ARG F1087 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27384 Ramachandran restraints generated. 13692 Oldfield, 0 Emsley, 13692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27384 Ramachandran restraints generated. 13692 Oldfield, 0 Emsley, 13692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1507 residues out of total 12212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 242 poor density : 1265 time to evaluate : 8.130 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: B 202 MET cc_start: 0.7993 (ptp) cc_final: 0.7181 (mtm) REVERT: B 667 MET cc_start: 0.7753 (ppp) cc_final: 0.7403 (ppp) REVERT: B 1132 TRP cc_start: 0.7560 (t-100) cc_final: 0.7189 (t-100) REVERT: B 1143 TRP cc_start: 0.6387 (OUTLIER) cc_final: 0.5789 (p-90) REVERT: B 1852 MET cc_start: 0.8659 (mmm) cc_final: 0.8207 (mmm) REVERT: B 2527 PHE cc_start: 0.8301 (m-10) cc_final: 0.8020 (m-80) REVERT: B 3436 PHE cc_start: 0.8106 (t80) cc_final: 0.7810 (t80) REVERT: B 3648 MET cc_start: 0.8556 (pmm) cc_final: 0.8256 (pmm) REVERT: B 4040 VAL cc_start: 0.9613 (m) cc_final: 0.9360 (p) REVERT: B 4572 ASN cc_start: 0.8428 (m110) cc_final: 0.8206 (m110) REVERT: B 4656 ILE cc_start: 0.9242 (mt) cc_final: 0.8986 (mt) REVERT: B 4700 ASP cc_start: 0.8570 (m-30) cc_final: 0.8211 (p0) REVERT: B 4788 LEU cc_start: 0.9193 (mm) cc_final: 0.8935 (tp) REVERT: B 4794 MET cc_start: 0.8675 (tpt) cc_final: 0.8251 (tpt) REVERT: B 4847 TYR cc_start: 0.8969 (t80) cc_final: 0.8651 (t80) REVERT: B 4946 GLU cc_start: 0.8752 (tp30) cc_final: 0.7356 (tp30) REVERT: B 4950 GLU cc_start: 0.8692 (mm-30) cc_final: 0.8056 (mm-30) REVERT: D 179 TYR cc_start: 0.8432 (m-80) cc_final: 0.8136 (m-80) REVERT: D 202 MET cc_start: 0.7949 (ptp) cc_final: 0.7109 (mtm) REVERT: D 667 MET cc_start: 0.7760 (ppp) cc_final: 0.7416 (ppp) REVERT: D 791 PHE cc_start: 0.8365 (OUTLIER) cc_final: 0.7766 (m-80) REVERT: D 1100 MET cc_start: 0.8615 (mmm) cc_final: 0.8157 (mmt) REVERT: D 1132 TRP cc_start: 0.7515 (t-100) cc_final: 0.7157 (t-100) REVERT: D 1143 TRP cc_start: 0.6334 (OUTLIER) cc_final: 0.5698 (p-90) REVERT: D 1852 MET cc_start: 0.8691 (mmm) cc_final: 0.8222 (mmm) REVERT: D 2527 PHE cc_start: 0.8362 (m-10) cc_final: 0.8098 (m-80) REVERT: D 3436 PHE cc_start: 0.8110 (t80) cc_final: 0.7813 (t80) REVERT: D 3648 MET cc_start: 0.8498 (pmm) cc_final: 0.8180 (pmm) REVERT: D 3718 TYR cc_start: 0.8559 (t80) cc_final: 0.7980 (t80) REVERT: D 4040 VAL cc_start: 0.9618 (m) cc_final: 0.9370 (p) REVERT: D 4186 GLU cc_start: 0.7575 (tp30) cc_final: 0.7114 (tp30) REVERT: D 4572 ASN cc_start: 0.8448 (m110) cc_final: 0.8155 (m110) REVERT: D 4656 ILE cc_start: 0.9237 (mt) cc_final: 0.8848 (mt) REVERT: D 4700 ASP cc_start: 0.8594 (m-30) cc_final: 0.8227 (p0) REVERT: D 4788 LEU cc_start: 0.9199 (mm) cc_final: 0.8946 (tp) REVERT: D 4794 MET cc_start: 0.8742 (tpt) cc_final: 0.8508 (tpt) REVERT: D 4847 TYR cc_start: 0.8939 (t80) cc_final: 0.8623 (t80) REVERT: D 4885 MET cc_start: 0.8662 (mmm) cc_final: 0.8398 (tpp) REVERT: E 47 LYS cc_start: 0.8664 (mppt) cc_final: 0.8337 (mptt) REVERT: E 102 GLU cc_start: 0.8079 (pp20) cc_final: 0.7698 (pp20) REVERT: F 101 LEU cc_start: 0.8406 (tt) cc_final: 0.8072 (tp) REVERT: F 177 GLU cc_start: 0.7243 (tm-30) cc_final: 0.6968 (tm-30) REVERT: F 197 GLN cc_start: 0.8203 (pp30) cc_final: 0.7773 (pp30) REVERT: F 202 MET cc_start: 0.7996 (ptp) cc_final: 0.7174 (mtm) REVERT: F 667 MET cc_start: 0.7726 (ppp) cc_final: 0.7315 (ppp) REVERT: F 791 PHE cc_start: 0.8398 (OUTLIER) cc_final: 0.7781 (m-80) REVERT: F 1100 MET cc_start: 0.8544 (mmm) cc_final: 0.8089 (mmt) REVERT: F 1132 TRP cc_start: 0.7512 (t-100) cc_final: 0.7150 (t-100) REVERT: F 1143 TRP cc_start: 0.6325 (OUTLIER) cc_final: 0.5701 (p-90) REVERT: F 1152 MET cc_start: 0.7978 (mmm) cc_final: 0.7373 (mmm) REVERT: F 1730 MET cc_start: 0.8220 (mmm) cc_final: 0.7568 (mmp) REVERT: F 1852 MET cc_start: 0.8688 (mmm) cc_final: 0.8213 (mmm) REVERT: F 2527 PHE cc_start: 0.8356 (m-10) cc_final: 0.8081 (m-80) REVERT: F 3436 PHE cc_start: 0.8121 (t80) cc_final: 0.7818 (t80) REVERT: F 3718 TYR cc_start: 0.8589 (t80) cc_final: 0.8230 (t80) REVERT: F 3973 GLN cc_start: 0.7530 (tm-30) cc_final: 0.6157 (tp-100) REVERT: F 3977 HIS cc_start: 0.7431 (m170) cc_final: 0.7208 (m170) REVERT: F 4040 VAL cc_start: 0.9613 (m) cc_final: 0.9360 (p) REVERT: F 4204 GLN cc_start: 0.9198 (OUTLIER) cc_final: 0.8900 (mp10) REVERT: F 4572 ASN cc_start: 0.8419 (m110) cc_final: 0.8195 (m110) REVERT: F 4656 ILE cc_start: 0.9254 (mt) cc_final: 0.9045 (mt) REVERT: F 4700 ASP cc_start: 0.8572 (m-30) cc_final: 0.8217 (p0) REVERT: F 4788 LEU cc_start: 0.9207 (mm) cc_final: 0.8961 (tp) REVERT: F 4847 TYR cc_start: 0.8953 (t80) cc_final: 0.8630 (t80) REVERT: H 101 LEU cc_start: 0.8380 (tt) cc_final: 0.8043 (tp) REVERT: H 197 GLN cc_start: 0.7923 (pp30) cc_final: 0.7606 (pp30) REVERT: H 202 MET cc_start: 0.8007 (ptp) cc_final: 0.7228 (mtm) REVERT: H 667 MET cc_start: 0.7725 (ppp) cc_final: 0.7294 (ppp) REVERT: H 1132 TRP cc_start: 0.7533 (t-100) cc_final: 0.7196 (t-100) REVERT: H 1143 TRP cc_start: 0.6374 (OUTLIER) cc_final: 0.5675 (p-90) REVERT: H 1286 MET cc_start: 0.8405 (tpp) cc_final: 0.8116 (tpp) REVERT: H 1852 MET cc_start: 0.8683 (mmm) cc_final: 0.8208 (mmm) REVERT: H 2527 PHE cc_start: 0.8292 (m-10) cc_final: 0.8002 (m-80) REVERT: H 3436 PHE cc_start: 0.8113 (t80) cc_final: 0.7835 (t80) REVERT: H 4572 ASN cc_start: 0.8451 (m110) cc_final: 0.8228 (m110) REVERT: H 4656 ILE cc_start: 0.9239 (mt) cc_final: 0.8861 (mt) REVERT: H 4700 ASP cc_start: 0.8585 (m-30) cc_final: 0.8242 (p0) REVERT: H 4788 LEU cc_start: 0.9182 (mm) cc_final: 0.8914 (tp) REVERT: H 4794 MET cc_start: 0.8730 (tpt) cc_final: 0.8482 (tpt) REVERT: H 4847 TYR cc_start: 0.8899 (t80) cc_final: 0.8610 (t80) REVERT: H 4946 GLU cc_start: 0.8754 (tp30) cc_final: 0.7367 (tp30) REVERT: H 4950 GLU cc_start: 0.8665 (mm-30) cc_final: 0.8040 (mm-30) outliers start: 242 outliers final: 190 residues processed: 1426 average time/residue: 0.7570 time to fit residues: 1989.9476 Evaluate side-chains 1398 residues out of total 12212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 1201 time to evaluate : 8.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 522 LEU Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 607 CYS Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 1143 TRP Chi-restraints excluded: chain B residue 1236 THR Chi-restraints excluded: chain B residue 1450 VAL Chi-restraints excluded: chain B residue 1659 LEU Chi-restraints excluded: chain B residue 1685 LEU Chi-restraints excluded: chain B residue 1717 SER Chi-restraints excluded: chain B residue 1851 VAL Chi-restraints excluded: chain B residue 1959 LEU Chi-restraints excluded: chain B residue 2124 LEU Chi-restraints excluded: chain B residue 2127 ARG Chi-restraints excluded: chain B residue 2136 LEU Chi-restraints excluded: chain B residue 2281 VAL Chi-restraints excluded: chain B residue 2303 LEU Chi-restraints excluded: chain B residue 2496 VAL Chi-restraints excluded: chain B residue 3776 GLN Chi-restraints excluded: chain B residue 3946 PHE Chi-restraints excluded: chain B residue 3964 ILE Chi-restraints excluded: chain B residue 4026 LEU Chi-restraints excluded: chain B residue 4065 ASP Chi-restraints excluded: chain B residue 4148 HIS Chi-restraints excluded: chain B residue 4200 TRP Chi-restraints excluded: chain B residue 4790 LEU Chi-restraints excluded: chain B residue 4839 VAL Chi-restraints excluded: chain B residue 4842 LEU Chi-restraints excluded: chain B residue 4926 LEU Chi-restraints excluded: chain B residue 4948 VAL Chi-restraints excluded: chain C residue 25 HIS Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 158 SER Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 346 CYS Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 522 LEU Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 607 CYS Chi-restraints excluded: chain D residue 668 VAL Chi-restraints excluded: chain D residue 672 VAL Chi-restraints excluded: chain D residue 791 PHE Chi-restraints excluded: chain D residue 1143 TRP Chi-restraints excluded: chain D residue 1236 THR Chi-restraints excluded: chain D residue 1450 VAL Chi-restraints excluded: chain D residue 1659 LEU Chi-restraints excluded: chain D residue 1685 LEU Chi-restraints excluded: chain D residue 1707 LEU Chi-restraints excluded: chain D residue 1717 SER Chi-restraints excluded: chain D residue 1851 VAL Chi-restraints excluded: chain D residue 1959 LEU Chi-restraints excluded: chain D residue 2136 LEU Chi-restraints excluded: chain D residue 2186 ILE Chi-restraints excluded: chain D residue 2281 VAL Chi-restraints excluded: chain D residue 2303 LEU Chi-restraints excluded: chain D residue 2496 VAL Chi-restraints excluded: chain D residue 3946 PHE Chi-restraints excluded: chain D residue 3964 ILE Chi-restraints excluded: chain D residue 4026 LEU Chi-restraints excluded: chain D residue 4049 ASN Chi-restraints excluded: chain D residue 4065 ASP Chi-restraints excluded: chain D residue 4072 PHE Chi-restraints excluded: chain D residue 4148 HIS Chi-restraints excluded: chain D residue 4200 TRP Chi-restraints excluded: chain D residue 4790 LEU Chi-restraints excluded: chain D residue 4839 VAL Chi-restraints excluded: chain D residue 4842 LEU Chi-restraints excluded: chain D residue 4877 MET Chi-restraints excluded: chain D residue 4948 VAL Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 25 HIS Chi-restraints excluded: chain E residue 35 LYS Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain F residue 17 ASP Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 191 VAL Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain F residue 448 LEU Chi-restraints excluded: chain F residue 564 LEU Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain F residue 607 CYS Chi-restraints excluded: chain F residue 723 THR Chi-restraints excluded: chain F residue 791 PHE Chi-restraints excluded: chain F residue 1113 VAL Chi-restraints excluded: chain F residue 1143 TRP Chi-restraints excluded: chain F residue 1236 THR Chi-restraints excluded: chain F residue 1450 VAL Chi-restraints excluded: chain F residue 1659 LEU Chi-restraints excluded: chain F residue 1685 LEU Chi-restraints excluded: chain F residue 1707 LEU Chi-restraints excluded: chain F residue 1717 SER Chi-restraints excluded: chain F residue 1851 VAL Chi-restraints excluded: chain F residue 1959 LEU Chi-restraints excluded: chain F residue 2124 LEU Chi-restraints excluded: chain F residue 2127 ARG Chi-restraints excluded: chain F residue 2136 LEU Chi-restraints excluded: chain F residue 2281 VAL Chi-restraints excluded: chain F residue 2303 LEU Chi-restraints excluded: chain F residue 2496 VAL Chi-restraints excluded: chain F residue 3946 PHE Chi-restraints excluded: chain F residue 3964 ILE Chi-restraints excluded: chain F residue 4026 LEU Chi-restraints excluded: chain F residue 4049 ASN Chi-restraints excluded: chain F residue 4065 ASP Chi-restraints excluded: chain F residue 4072 PHE Chi-restraints excluded: chain F residue 4148 HIS Chi-restraints excluded: chain F residue 4200 TRP Chi-restraints excluded: chain F residue 4204 GLN Chi-restraints excluded: chain F residue 4790 LEU Chi-restraints excluded: chain F residue 4839 VAL Chi-restraints excluded: chain F residue 4842 LEU Chi-restraints excluded: chain F residue 4877 MET Chi-restraints excluded: chain F residue 4948 VAL Chi-restraints excluded: chain F residue 4991 MET Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 25 HIS Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain H residue 17 ASP Chi-restraints excluded: chain H residue 25 ASN Chi-restraints excluded: chain H residue 65 CYS Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 135 VAL Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 232 THR Chi-restraints excluded: chain H residue 285 VAL Chi-restraints excluded: chain H residue 357 LEU Chi-restraints excluded: chain H residue 448 LEU Chi-restraints excluded: chain H residue 522 LEU Chi-restraints excluded: chain H residue 564 LEU Chi-restraints excluded: chain H residue 569 ILE Chi-restraints excluded: chain H residue 607 CYS Chi-restraints excluded: chain H residue 672 VAL Chi-restraints excluded: chain H residue 723 THR Chi-restraints excluded: chain H residue 1143 TRP Chi-restraints excluded: chain H residue 1236 THR Chi-restraints excluded: chain H residue 1450 VAL Chi-restraints excluded: chain H residue 1659 LEU Chi-restraints excluded: chain H residue 1685 LEU Chi-restraints excluded: chain H residue 1851 VAL Chi-restraints excluded: chain H residue 1959 LEU Chi-restraints excluded: chain H residue 2124 LEU Chi-restraints excluded: chain H residue 2136 LEU Chi-restraints excluded: chain H residue 2281 VAL Chi-restraints excluded: chain H residue 2303 LEU Chi-restraints excluded: chain H residue 2496 VAL Chi-restraints excluded: chain H residue 3964 ILE Chi-restraints excluded: chain H residue 4026 LEU Chi-restraints excluded: chain H residue 4049 ASN Chi-restraints excluded: chain H residue 4065 ASP Chi-restraints excluded: chain H residue 4134 ILE Chi-restraints excluded: chain H residue 4200 TRP Chi-restraints excluded: chain H residue 4790 LEU Chi-restraints excluded: chain H residue 4825 LEU Chi-restraints excluded: chain H residue 4839 VAL Chi-restraints excluded: chain H residue 4842 LEU Chi-restraints excluded: chain H residue 4877 MET Chi-restraints excluded: chain H residue 4926 LEU Chi-restraints excluded: chain H residue 4938 PHE Chi-restraints excluded: chain H residue 4948 VAL Chi-restraints excluded: chain H residue 4991 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1524 random chunks: chunk 1421 optimal weight: 20.0000 chunk 166 optimal weight: 0.8980 chunk 840 optimal weight: 6.9990 chunk 1076 optimal weight: 4.9990 chunk 834 optimal weight: 4.9990 chunk 1241 optimal weight: 5.9990 chunk 823 optimal weight: 0.9990 chunk 1468 optimal weight: 20.0000 chunk 919 optimal weight: 3.9990 chunk 895 optimal weight: 7.9990 chunk 678 optimal weight: 1.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2101 HIS ** B2128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2261 ASN ** B3762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3776 GLN ** B3989 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3993 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2101 HIS ** D2128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2261 ASN D3776 GLN ** D3973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3993 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4831 ASN ** F 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F2101 HIS ** F2128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F3973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F3993 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F4148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F4712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H2101 HIS ** H2128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H3993 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H4712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H4831 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.4794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 107328 Z= 0.242 Angle : 0.670 12.761 146972 Z= 0.321 Chirality : 0.039 0.304 17784 Planarity : 0.004 0.067 19000 Dihedral : 3.934 25.553 15870 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.00 % Allowed : 21.75 % Favored : 75.25 % 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: 0.65 (0.07), residues: 13692 helix: 1.40 (0.06), residues: 6684 sheet: -0.38 (0.13), residues: 1648 loop : -0.45 (0.09), residues: 5360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 882 HIS 0.010 0.001 HIS D4148 PHE 0.028 0.002 PHE D 478 TYR 0.032 0.001 TYR D4965 ARG 0.006 0.001 ARG H2141 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27384 Ramachandran restraints generated. 13692 Oldfield, 0 Emsley, 13692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27384 Ramachandran restraints generated. 13692 Oldfield, 0 Emsley, 13692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1496 residues out of total 12212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 262 poor density : 1234 time to evaluate : 8.232 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: B 202 MET cc_start: 0.8002 (ptp) cc_final: 0.7252 (mtm) REVERT: B 667 MET cc_start: 0.7771 (ppp) cc_final: 0.7534 (ppp) REVERT: B 1143 TRP cc_start: 0.6304 (OUTLIER) cc_final: 0.5670 (p-90) REVERT: B 1636 MET cc_start: 0.8813 (ppp) cc_final: 0.8530 (ppp) REVERT: B 1730 MET cc_start: 0.8281 (mmm) cc_final: 0.7658 (mmp) REVERT: B 1852 MET cc_start: 0.8746 (mmm) cc_final: 0.8281 (mmm) REVERT: B 1941 CYS cc_start: 0.8586 (m) cc_final: 0.8298 (m) REVERT: B 2527 PHE cc_start: 0.8337 (m-10) cc_final: 0.8023 (m-80) REVERT: B 3436 PHE cc_start: 0.8123 (t80) cc_final: 0.7845 (t80) REVERT: B 3648 MET cc_start: 0.8565 (pmm) cc_final: 0.8267 (pmm) REVERT: B 3775 LEU cc_start: 0.9457 (mp) cc_final: 0.8831 (mp) REVERT: B 3811 MET cc_start: 0.8113 (mmm) cc_final: 0.7796 (mmm) REVERT: B 4040 VAL cc_start: 0.9619 (m) cc_final: 0.9337 (p) REVERT: B 4186 GLU cc_start: 0.7599 (tp30) cc_final: 0.7241 (tp30) REVERT: B 4572 ASN cc_start: 0.8452 (m110) cc_final: 0.8127 (m110) REVERT: B 4656 ILE cc_start: 0.9210 (mt) cc_final: 0.8959 (mt) REVERT: B 4700 ASP cc_start: 0.8669 (m-30) cc_final: 0.8343 (p0) REVERT: B 4788 LEU cc_start: 0.9168 (mm) cc_final: 0.8878 (tp) REVERT: B 4794 MET cc_start: 0.8650 (tpt) cc_final: 0.8301 (tpt) REVERT: B 4847 TYR cc_start: 0.8937 (t80) cc_final: 0.8706 (t80) REVERT: B 4878 MET cc_start: 0.7949 (tpp) cc_final: 0.7647 (tpp) REVERT: B 4889 VAL cc_start: 0.9497 (OUTLIER) cc_final: 0.9295 (p) REVERT: B 4946 GLU cc_start: 0.8781 (tp30) cc_final: 0.7337 (tp30) REVERT: B 4950 GLU cc_start: 0.8708 (mm-30) cc_final: 0.8018 (mm-30) REVERT: D 202 MET cc_start: 0.7970 (ptp) cc_final: 0.7140 (mtm) REVERT: D 667 MET cc_start: 0.7778 (ppp) cc_final: 0.7547 (ppp) REVERT: D 791 PHE cc_start: 0.8428 (OUTLIER) cc_final: 0.7796 (m-80) REVERT: D 1100 MET cc_start: 0.8620 (mmm) cc_final: 0.8151 (mmt) REVERT: D 1143 TRP cc_start: 0.6244 (OUTLIER) cc_final: 0.5569 (p-90) REVERT: D 1636 MET cc_start: 0.8717 (ppp) cc_final: 0.8386 (ppp) REVERT: D 1730 MET cc_start: 0.8257 (mmm) cc_final: 0.7568 (mmp) REVERT: D 1852 MET cc_start: 0.8762 (mmm) cc_final: 0.8303 (mmm) REVERT: D 2527 PHE cc_start: 0.8343 (m-10) cc_final: 0.8040 (m-80) REVERT: D 3436 PHE cc_start: 0.8125 (t80) cc_final: 0.7849 (t80) REVERT: D 3648 MET cc_start: 0.8528 (pmm) cc_final: 0.8212 (pmm) REVERT: D 3775 LEU cc_start: 0.9390 (mp) cc_final: 0.9169 (mt) REVERT: D 3994 MET cc_start: 0.8890 (tpp) cc_final: 0.8392 (tmm) REVERT: D 4040 VAL cc_start: 0.9621 (m) cc_final: 0.9354 (p) REVERT: D 4186 GLU cc_start: 0.7602 (tp30) cc_final: 0.7248 (tp30) REVERT: D 4572 ASN cc_start: 0.8394 (m110) cc_final: 0.8108 (m110) REVERT: D 4656 ILE cc_start: 0.9200 (mt) cc_final: 0.8789 (mt) REVERT: D 4700 ASP cc_start: 0.8678 (m-30) cc_final: 0.8343 (p0) REVERT: D 4788 LEU cc_start: 0.9184 (mm) cc_final: 0.8908 (tp) REVERT: D 4847 TYR cc_start: 0.8975 (t80) cc_final: 0.8693 (t80) REVERT: D 4885 MET cc_start: 0.8665 (mmm) cc_final: 0.8378 (tpp) REVERT: E 47 LYS cc_start: 0.8637 (mppt) cc_final: 0.8322 (mptt) REVERT: E 102 GLU cc_start: 0.8104 (pp20) cc_final: 0.7774 (pp20) REVERT: F 197 GLN cc_start: 0.8285 (pp30) cc_final: 0.7848 (pp30) REVERT: F 202 MET cc_start: 0.8008 (ptp) cc_final: 0.7207 (mtm) REVERT: F 667 MET cc_start: 0.7756 (ppp) cc_final: 0.7469 (ppp) REVERT: F 791 PHE cc_start: 0.8430 (OUTLIER) cc_final: 0.7777 (m-80) REVERT: F 1100 MET cc_start: 0.8619 (mmm) cc_final: 0.8156 (mmt) REVERT: F 1132 TRP cc_start: 0.7541 (t-100) cc_final: 0.7147 (t-100) REVERT: F 1143 TRP cc_start: 0.6411 (OUTLIER) cc_final: 0.5785 (p-90) REVERT: F 1152 MET cc_start: 0.8025 (mmm) cc_final: 0.7415 (mmm) REVERT: F 1730 MET cc_start: 0.8265 (mmm) cc_final: 0.7867 (mmp) REVERT: F 1852 MET cc_start: 0.8758 (mmm) cc_final: 0.8296 (mmm) REVERT: F 2527 PHE cc_start: 0.8352 (m-10) cc_final: 0.8043 (m-80) REVERT: F 3436 PHE cc_start: 0.8133 (t80) cc_final: 0.7849 (t80) REVERT: F 3994 MET cc_start: 0.8765 (tpp) cc_final: 0.8262 (tmm) REVERT: F 4040 VAL cc_start: 0.9624 (m) cc_final: 0.9369 (p) REVERT: F 4186 GLU cc_start: 0.7572 (tp30) cc_final: 0.7225 (tp30) REVERT: F 4572 ASN cc_start: 0.8457 (m110) cc_final: 0.8094 (m110) REVERT: F 4656 ILE cc_start: 0.9205 (mt) cc_final: 0.8970 (mt) REVERT: F 4700 ASP cc_start: 0.8665 (m-30) cc_final: 0.8363 (p0) REVERT: F 4788 LEU cc_start: 0.9229 (mm) cc_final: 0.8959 (tp) REVERT: F 4847 TYR cc_start: 0.8911 (t80) cc_final: 0.8671 (t80) REVERT: F 4946 GLU cc_start: 0.8603 (tp30) cc_final: 0.8257 (tp30) REVERT: H 197 GLN cc_start: 0.8004 (pp30) cc_final: 0.7693 (pp30) REVERT: H 202 MET cc_start: 0.8010 (ptp) cc_final: 0.7292 (mtm) REVERT: H 578 ILE cc_start: 0.8764 (mm) cc_final: 0.8482 (mm) REVERT: H 667 MET cc_start: 0.7758 (ppp) cc_final: 0.7452 (ppp) REVERT: H 1143 TRP cc_start: 0.6307 (OUTLIER) cc_final: 0.5681 (p-90) REVERT: H 1730 MET cc_start: 0.8291 (mmm) cc_final: 0.7591 (mmp) REVERT: H 1852 MET cc_start: 0.8760 (mmm) cc_final: 0.8307 (mmm) REVERT: H 2527 PHE cc_start: 0.8342 (m-10) cc_final: 0.8021 (m-80) REVERT: H 3436 PHE cc_start: 0.8130 (t80) cc_final: 0.7850 (t80) REVERT: H 4186 GLU cc_start: 0.7581 (tp30) cc_final: 0.7233 (tp30) REVERT: H 4572 ASN cc_start: 0.8420 (m110) cc_final: 0.8059 (m110) REVERT: H 4656 ILE cc_start: 0.9154 (mt) cc_final: 0.8751 (mt) REVERT: H 4700 ASP cc_start: 0.8673 (m-30) cc_final: 0.8379 (p0) REVERT: H 4788 LEU cc_start: 0.9195 (mm) cc_final: 0.8909 (tp) REVERT: H 4794 MET cc_start: 0.8719 (tpt) cc_final: 0.8482 (tpt) REVERT: H 4847 TYR cc_start: 0.8956 (t80) cc_final: 0.8720 (t80) REVERT: H 4933 LEU cc_start: 0.9380 (OUTLIER) cc_final: 0.9035 (mt) REVERT: H 4946 GLU cc_start: 0.8785 (tp30) cc_final: 0.7936 (tp30) outliers start: 262 outliers final: 204 residues processed: 1412 average time/residue: 0.7742 time to fit residues: 2018.3268 Evaluate side-chains 1402 residues out of total 12212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 1190 time to evaluate : 8.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 25 HIS Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 113 HIS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 607 CYS Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 938 HIS Chi-restraints excluded: chain B residue 1143 TRP Chi-restraints excluded: chain B residue 1450 VAL Chi-restraints excluded: chain B residue 1608 MET Chi-restraints excluded: chain B residue 1637 MET Chi-restraints excluded: chain B residue 1659 LEU Chi-restraints excluded: chain B residue 1685 LEU Chi-restraints excluded: chain B residue 1769 THR Chi-restraints excluded: chain B residue 1851 VAL Chi-restraints excluded: chain B residue 1959 LEU Chi-restraints excluded: chain B residue 2124 LEU Chi-restraints excluded: chain B residue 2127 ARG Chi-restraints excluded: chain B residue 2136 LEU Chi-restraints excluded: chain B residue 2186 ILE Chi-restraints excluded: chain B residue 2281 VAL Chi-restraints excluded: chain B residue 2303 LEU Chi-restraints excluded: chain B residue 2496 VAL Chi-restraints excluded: chain B residue 3946 PHE Chi-restraints excluded: chain B residue 3964 ILE Chi-restraints excluded: chain B residue 4026 LEU Chi-restraints excluded: chain B residue 4065 ASP Chi-restraints excluded: chain B residue 4134 ILE Chi-restraints excluded: chain B residue 4200 TRP Chi-restraints excluded: chain B residue 4790 LEU Chi-restraints excluded: chain B residue 4842 LEU Chi-restraints excluded: chain B residue 4877 MET Chi-restraints excluded: chain B residue 4889 VAL Chi-restraints excluded: chain B residue 4926 LEU Chi-restraints excluded: chain B residue 4948 VAL Chi-restraints excluded: chain B residue 4991 MET Chi-restraints excluded: chain C residue 25 HIS Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain D residue 65 CYS Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 113 HIS Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 158 SER Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 346 CYS Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 607 CYS Chi-restraints excluded: chain D residue 668 VAL Chi-restraints excluded: chain D residue 672 VAL Chi-restraints excluded: chain D residue 791 PHE Chi-restraints excluded: chain D residue 938 HIS Chi-restraints excluded: chain D residue 1143 TRP Chi-restraints excluded: chain D residue 1450 VAL Chi-restraints excluded: chain D residue 1608 MET Chi-restraints excluded: chain D residue 1659 LEU Chi-restraints excluded: chain D residue 1685 LEU Chi-restraints excluded: chain D residue 1707 LEU Chi-restraints excluded: chain D residue 1769 THR Chi-restraints excluded: chain D residue 1851 VAL Chi-restraints excluded: chain D residue 1959 LEU Chi-restraints excluded: chain D residue 2124 LEU Chi-restraints excluded: chain D residue 2136 LEU Chi-restraints excluded: chain D residue 2186 ILE Chi-restraints excluded: chain D residue 2281 VAL Chi-restraints excluded: chain D residue 2303 LEU Chi-restraints excluded: chain D residue 2496 VAL Chi-restraints excluded: chain D residue 3946 PHE Chi-restraints excluded: chain D residue 3964 ILE Chi-restraints excluded: chain D residue 3996 MET Chi-restraints excluded: chain D residue 4026 LEU Chi-restraints excluded: chain D residue 4065 ASP Chi-restraints excluded: chain D residue 4134 ILE Chi-restraints excluded: chain D residue 4200 TRP Chi-restraints excluded: chain D residue 4790 LEU Chi-restraints excluded: chain D residue 4842 LEU Chi-restraints excluded: chain D residue 4877 MET Chi-restraints excluded: chain D residue 4926 LEU Chi-restraints excluded: chain D residue 4948 VAL Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 25 HIS Chi-restraints excluded: chain E residue 35 LYS Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain F residue 17 ASP Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 113 HIS Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 191 VAL Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 346 CYS Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain F residue 448 LEU Chi-restraints excluded: chain F residue 564 LEU Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain F residue 607 CYS Chi-restraints excluded: chain F residue 668 VAL Chi-restraints excluded: chain F residue 672 VAL Chi-restraints excluded: chain F residue 723 THR Chi-restraints excluded: chain F residue 791 PHE Chi-restraints excluded: chain F residue 1143 TRP Chi-restraints excluded: chain F residue 1159 THR Chi-restraints excluded: chain F residue 1450 VAL Chi-restraints excluded: chain F residue 1659 LEU Chi-restraints excluded: chain F residue 1685 LEU Chi-restraints excluded: chain F residue 1707 LEU Chi-restraints excluded: chain F residue 1769 THR Chi-restraints excluded: chain F residue 1851 VAL Chi-restraints excluded: chain F residue 2124 LEU Chi-restraints excluded: chain F residue 2127 ARG Chi-restraints excluded: chain F residue 2136 LEU Chi-restraints excluded: chain F residue 2186 ILE Chi-restraints excluded: chain F residue 2281 VAL Chi-restraints excluded: chain F residue 2496 VAL Chi-restraints excluded: chain F residue 3946 PHE Chi-restraints excluded: chain F residue 3964 ILE Chi-restraints excluded: chain F residue 3996 MET Chi-restraints excluded: chain F residue 4026 LEU Chi-restraints excluded: chain F residue 4065 ASP Chi-restraints excluded: chain F residue 4134 ILE Chi-restraints excluded: chain F residue 4200 TRP Chi-restraints excluded: chain F residue 4790 LEU Chi-restraints excluded: chain F residue 4842 LEU Chi-restraints excluded: chain F residue 4877 MET Chi-restraints excluded: chain F residue 4926 LEU Chi-restraints excluded: chain F residue 4948 VAL Chi-restraints excluded: chain F residue 4991 MET Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 25 HIS Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain H residue 17 ASP Chi-restraints excluded: chain H residue 25 ASN Chi-restraints excluded: chain H residue 65 CYS Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 113 HIS Chi-restraints excluded: chain H residue 135 VAL Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 232 THR Chi-restraints excluded: chain H residue 285 VAL Chi-restraints excluded: chain H residue 346 CYS Chi-restraints excluded: chain H residue 357 LEU Chi-restraints excluded: chain H residue 448 LEU Chi-restraints excluded: chain H residue 564 LEU Chi-restraints excluded: chain H residue 569 ILE Chi-restraints excluded: chain H residue 607 CYS Chi-restraints excluded: chain H residue 668 VAL Chi-restraints excluded: chain H residue 672 VAL Chi-restraints excluded: chain H residue 723 THR Chi-restraints excluded: chain H residue 1143 TRP Chi-restraints excluded: chain H residue 1450 VAL Chi-restraints excluded: chain H residue 1608 MET Chi-restraints excluded: chain H residue 1659 LEU Chi-restraints excluded: chain H residue 1685 LEU Chi-restraints excluded: chain H residue 1769 THR Chi-restraints excluded: chain H residue 1840 VAL Chi-restraints excluded: chain H residue 1851 VAL Chi-restraints excluded: chain H residue 1959 LEU Chi-restraints excluded: chain H residue 2124 LEU Chi-restraints excluded: chain H residue 2127 ARG Chi-restraints excluded: chain H residue 2136 LEU Chi-restraints excluded: chain H residue 2167 LEU Chi-restraints excluded: chain H residue 2186 ILE Chi-restraints excluded: chain H residue 2281 VAL Chi-restraints excluded: chain H residue 2303 LEU Chi-restraints excluded: chain H residue 2496 VAL Chi-restraints excluded: chain H residue 3793 LEU Chi-restraints excluded: chain H residue 3964 ILE Chi-restraints excluded: chain H residue 3996 MET Chi-restraints excluded: chain H residue 4026 LEU Chi-restraints excluded: chain H residue 4065 ASP Chi-restraints excluded: chain H residue 4134 ILE Chi-restraints excluded: chain H residue 4200 TRP Chi-restraints excluded: chain H residue 4790 LEU Chi-restraints excluded: chain H residue 4825 LEU Chi-restraints excluded: chain H residue 4842 LEU Chi-restraints excluded: chain H residue 4877 MET Chi-restraints excluded: chain H residue 4926 LEU Chi-restraints excluded: chain H residue 4933 LEU Chi-restraints excluded: chain H residue 4938 PHE Chi-restraints excluded: chain H residue 4948 VAL Chi-restraints excluded: chain H residue 4991 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1524 random chunks: chunk 908 optimal weight: 0.6980 chunk 586 optimal weight: 9.9990 chunk 877 optimal weight: 9.9990 chunk 442 optimal weight: 8.9990 chunk 288 optimal weight: 3.9990 chunk 284 optimal weight: 10.0000 chunk 933 optimal weight: 0.7980 chunk 1000 optimal weight: 20.0000 chunk 726 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 1154 optimal weight: 6.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 877 ASN ** B1443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2181 GLN ** B3762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3993 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 877 ASN ** D1443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3993 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 877 ASN ** F1443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F3993 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F4204 GLN ** F4712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 877 ASN ** H1443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H3993 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H4712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.4927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 107328 Z= 0.213 Angle : 0.678 16.120 146972 Z= 0.318 Chirality : 0.039 0.342 17784 Planarity : 0.004 0.056 19000 Dihedral : 3.884 22.687 15868 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.73 % Allowed : 22.41 % Favored : 74.86 % 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: 0.70 (0.07), residues: 13692 helix: 1.43 (0.06), residues: 6732 sheet: -0.38 (0.13), residues: 1644 loop : -0.42 (0.09), residues: 5316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP H1132 HIS 0.012 0.001 HIS H1640 PHE 0.022 0.001 PHE D 478 TYR 0.031 0.001 TYR D3718 ARG 0.007 0.000 ARG D1087 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27384 Ramachandran restraints generated. 13692 Oldfield, 0 Emsley, 13692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27384 Ramachandran restraints generated. 13692 Oldfield, 0 Emsley, 13692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1470 residues out of total 12212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 238 poor density : 1232 time to evaluate : 7.868 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: B 101 LEU cc_start: 0.8314 (tt) cc_final: 0.8017 (tp) REVERT: B 202 MET cc_start: 0.7986 (ptp) cc_final: 0.7160 (mtm) REVERT: B 667 MET cc_start: 0.7954 (ppp) cc_final: 0.7721 (ppp) REVERT: B 1143 TRP cc_start: 0.6350 (OUTLIER) cc_final: 0.5577 (p-90) REVERT: B 1152 MET cc_start: 0.8199 (tpp) cc_final: 0.7981 (mmm) REVERT: B 1730 MET cc_start: 0.8244 (mmm) cc_final: 0.7758 (mmp) REVERT: B 1852 MET cc_start: 0.8709 (mmm) cc_final: 0.8247 (mmm) REVERT: B 1941 CYS cc_start: 0.8586 (m) cc_final: 0.8340 (m) REVERT: B 2111 PHE cc_start: 0.8324 (OUTLIER) cc_final: 0.7731 (t80) REVERT: B 2527 PHE cc_start: 0.8352 (m-10) cc_final: 0.8095 (m-80) REVERT: B 3436 PHE cc_start: 0.8174 (t80) cc_final: 0.7900 (t80) REVERT: B 3648 MET cc_start: 0.8572 (pmm) cc_final: 0.8239 (pmm) REVERT: B 3775 LEU cc_start: 0.9486 (mp) cc_final: 0.9028 (mp) REVERT: B 3994 MET cc_start: 0.8461 (tpp) cc_final: 0.8052 (tmm) REVERT: B 4040 VAL cc_start: 0.9610 (m) cc_final: 0.9365 (p) REVERT: B 4572 ASN cc_start: 0.8300 (m110) cc_final: 0.8036 (m110) REVERT: B 4656 ILE cc_start: 0.9212 (mt) cc_final: 0.8964 (mt) REVERT: B 4700 ASP cc_start: 0.8672 (m-30) cc_final: 0.8296 (p0) REVERT: B 4788 LEU cc_start: 0.9170 (mm) cc_final: 0.8868 (tp) REVERT: B 4794 MET cc_start: 0.8762 (tpt) cc_final: 0.8359 (tpt) REVERT: B 4847 TYR cc_start: 0.8901 (t80) cc_final: 0.8693 (t80) REVERT: B 4878 MET cc_start: 0.8284 (tpp) cc_final: 0.8017 (tpp) REVERT: B 4889 VAL cc_start: 0.9493 (OUTLIER) cc_final: 0.9202 (p) REVERT: B 4946 GLU cc_start: 0.8771 (tp30) cc_final: 0.7355 (tp30) REVERT: B 4950 GLU cc_start: 0.8693 (mm-30) cc_final: 0.8013 (mm-30) REVERT: D 101 LEU cc_start: 0.8344 (tt) cc_final: 0.8065 (tp) REVERT: D 202 MET cc_start: 0.7818 (ptp) cc_final: 0.7079 (mtm) REVERT: D 667 MET cc_start: 0.7785 (ppp) cc_final: 0.7569 (ppp) REVERT: D 791 PHE cc_start: 0.8421 (OUTLIER) cc_final: 0.7770 (m-80) REVERT: D 1100 MET cc_start: 0.8608 (mmm) cc_final: 0.8123 (mmt) REVERT: D 1143 TRP cc_start: 0.6403 (OUTLIER) cc_final: 0.5648 (p-90) REVERT: D 1152 MET cc_start: 0.8197 (tpp) cc_final: 0.7973 (mmm) REVERT: D 1730 MET cc_start: 0.8219 (mmm) cc_final: 0.7582 (mmp) REVERT: D 1852 MET cc_start: 0.8715 (mmm) cc_final: 0.8250 (mmm) REVERT: D 2111 PHE cc_start: 0.8301 (OUTLIER) cc_final: 0.7712 (t80) REVERT: D 2527 PHE cc_start: 0.8337 (m-10) cc_final: 0.8089 (m-80) REVERT: D 3436 PHE cc_start: 0.8184 (t80) cc_final: 0.7908 (t80) REVERT: D 3648 MET cc_start: 0.8531 (pmm) cc_final: 0.8150 (pmm) REVERT: D 3994 MET cc_start: 0.8834 (tpp) cc_final: 0.8263 (tmm) REVERT: D 4040 VAL cc_start: 0.9608 (m) cc_final: 0.9355 (p) REVERT: D 4572 ASN cc_start: 0.8369 (m110) cc_final: 0.8028 (m110) REVERT: D 4656 ILE cc_start: 0.9167 (mt) cc_final: 0.8948 (mt) REVERT: D 4700 ASP cc_start: 0.8690 (m-30) cc_final: 0.8318 (p0) REVERT: D 4788 LEU cc_start: 0.9188 (mm) cc_final: 0.8904 (tp) REVERT: D 4847 TYR cc_start: 0.8934 (t80) cc_final: 0.8610 (t80) REVERT: D 4885 MET cc_start: 0.8669 (mmm) cc_final: 0.8332 (tpp) REVERT: D 4946 GLU cc_start: 0.8563 (tp30) cc_final: 0.8225 (tp30) REVERT: E 47 LYS cc_start: 0.8635 (mppt) cc_final: 0.8295 (mptt) REVERT: E 102 GLU cc_start: 0.8060 (pp20) cc_final: 0.7703 (pp20) REVERT: F 101 LEU cc_start: 0.8327 (tt) cc_final: 0.8024 (tp) REVERT: F 197 GLN cc_start: 0.8261 (pp30) cc_final: 0.7817 (pp30) REVERT: F 202 MET cc_start: 0.7854 (ptp) cc_final: 0.7149 (mtm) REVERT: F 667 MET cc_start: 0.7770 (ppp) cc_final: 0.7553 (ppp) REVERT: F 791 PHE cc_start: 0.8419 (OUTLIER) cc_final: 0.7789 (m-80) REVERT: F 1143 TRP cc_start: 0.6406 (OUTLIER) cc_final: 0.5669 (p-90) REVERT: F 1730 MET cc_start: 0.8235 (mmm) cc_final: 0.7833 (mmp) REVERT: F 1852 MET cc_start: 0.8701 (mmm) cc_final: 0.8246 (mmm) REVERT: F 2527 PHE cc_start: 0.8347 (m-10) cc_final: 0.8085 (m-80) REVERT: F 3436 PHE cc_start: 0.8187 (t80) cc_final: 0.7911 (t80) REVERT: F 4040 VAL cc_start: 0.9602 (m) cc_final: 0.9359 (p) REVERT: F 4186 GLU cc_start: 0.7596 (tp30) cc_final: 0.7240 (tp30) REVERT: F 4572 ASN cc_start: 0.8311 (m110) cc_final: 0.8028 (m110) REVERT: F 4656 ILE cc_start: 0.9153 (mt) cc_final: 0.8933 (mt) REVERT: F 4700 ASP cc_start: 0.8675 (m-30) cc_final: 0.8327 (p0) REVERT: F 4788 LEU cc_start: 0.9164 (mm) cc_final: 0.8864 (tp) REVERT: F 4847 TYR cc_start: 0.8890 (t80) cc_final: 0.8660 (t80) REVERT: H 101 LEU cc_start: 0.8300 (tt) cc_final: 0.7996 (tp) REVERT: H 197 GLN cc_start: 0.8055 (pp30) cc_final: 0.7737 (pp30) REVERT: H 202 MET cc_start: 0.7948 (ptp) cc_final: 0.7177 (mtm) REVERT: H 667 MET cc_start: 0.7766 (ppp) cc_final: 0.7533 (ppp) REVERT: H 1143 TRP cc_start: 0.6526 (OUTLIER) cc_final: 0.5806 (p-90) REVERT: H 1152 MET cc_start: 0.8200 (tpp) cc_final: 0.7979 (mmm) REVERT: H 1730 MET cc_start: 0.8255 (mmm) cc_final: 0.7776 (mmp) REVERT: H 1852 MET cc_start: 0.8761 (mmm) cc_final: 0.8320 (mmm) REVERT: H 2527 PHE cc_start: 0.8332 (m-10) cc_final: 0.8071 (m-80) REVERT: H 3436 PHE cc_start: 0.8183 (t80) cc_final: 0.7905 (t80) REVERT: H 3994 MET cc_start: 0.8601 (tpp) cc_final: 0.7980 (tmm) REVERT: H 4572 ASN cc_start: 0.8323 (m110) cc_final: 0.8071 (m110) REVERT: H 4656 ILE cc_start: 0.9139 (mt) cc_final: 0.8707 (mt) REVERT: H 4700 ASP cc_start: 0.8650 (m-30) cc_final: 0.8302 (p0) REVERT: H 4788 LEU cc_start: 0.9195 (mm) cc_final: 0.8904 (tp) REVERT: H 4847 TYR cc_start: 0.8897 (t80) cc_final: 0.8643 (t80) REVERT: H 4946 GLU cc_start: 0.8646 (tp30) cc_final: 0.7707 (tp30) REVERT: H 4950 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.8145 (mp0) outliers start: 238 outliers final: 207 residues processed: 1403 average time/residue: 0.7542 time to fit residues: 1954.4084 Evaluate side-chains 1404 residues out of total 12212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 217 poor density : 1187 time to evaluate : 8.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 25 HIS Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 113 HIS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 586 ILE Chi-restraints excluded: chain B residue 607 CYS Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 938 HIS Chi-restraints excluded: chain B residue 1143 TRP Chi-restraints excluded: chain B residue 1450 VAL Chi-restraints excluded: chain B residue 1637 MET Chi-restraints excluded: chain B residue 1659 LEU Chi-restraints excluded: chain B residue 1685 LEU Chi-restraints excluded: chain B residue 1769 THR Chi-restraints excluded: chain B residue 1851 VAL Chi-restraints excluded: chain B residue 1959 LEU Chi-restraints excluded: chain B residue 2111 PHE Chi-restraints excluded: chain B residue 2124 LEU Chi-restraints excluded: chain B residue 2127 ARG Chi-restraints excluded: chain B residue 2136 LEU Chi-restraints excluded: chain B residue 2186 ILE Chi-restraints excluded: chain B residue 2281 VAL Chi-restraints excluded: chain B residue 2303 LEU Chi-restraints excluded: chain B residue 2496 VAL Chi-restraints excluded: chain B residue 3869 VAL Chi-restraints excluded: chain B residue 3946 PHE Chi-restraints excluded: chain B residue 3964 ILE Chi-restraints excluded: chain B residue 3990 VAL Chi-restraints excluded: chain B residue 4026 LEU Chi-restraints excluded: chain B residue 4065 ASP Chi-restraints excluded: chain B residue 4200 TRP Chi-restraints excluded: chain B residue 4790 LEU Chi-restraints excluded: chain B residue 4842 LEU Chi-restraints excluded: chain B residue 4877 MET Chi-restraints excluded: chain B residue 4889 VAL Chi-restraints excluded: chain B residue 4926 LEU Chi-restraints excluded: chain B residue 4948 VAL Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 25 HIS Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain D residue 65 CYS Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 158 SER Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 346 CYS Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 586 ILE Chi-restraints excluded: chain D residue 607 CYS Chi-restraints excluded: chain D residue 668 VAL Chi-restraints excluded: chain D residue 672 VAL Chi-restraints excluded: chain D residue 791 PHE Chi-restraints excluded: chain D residue 1143 TRP Chi-restraints excluded: chain D residue 1450 VAL Chi-restraints excluded: chain D residue 1659 LEU Chi-restraints excluded: chain D residue 1685 LEU Chi-restraints excluded: chain D residue 1707 LEU Chi-restraints excluded: chain D residue 1769 THR Chi-restraints excluded: chain D residue 1851 VAL Chi-restraints excluded: chain D residue 1959 LEU Chi-restraints excluded: chain D residue 2111 PHE Chi-restraints excluded: chain D residue 2124 LEU Chi-restraints excluded: chain D residue 2186 ILE Chi-restraints excluded: chain D residue 2281 VAL Chi-restraints excluded: chain D residue 2303 LEU Chi-restraints excluded: chain D residue 2496 VAL Chi-restraints excluded: chain D residue 3869 VAL Chi-restraints excluded: chain D residue 3946 PHE Chi-restraints excluded: chain D residue 3964 ILE Chi-restraints excluded: chain D residue 3990 VAL Chi-restraints excluded: chain D residue 3996 MET Chi-restraints excluded: chain D residue 4026 LEU Chi-restraints excluded: chain D residue 4065 ASP Chi-restraints excluded: chain D residue 4134 ILE Chi-restraints excluded: chain D residue 4200 TRP Chi-restraints excluded: chain D residue 4790 LEU Chi-restraints excluded: chain D residue 4842 LEU Chi-restraints excluded: chain D residue 4844 VAL Chi-restraints excluded: chain D residue 4877 MET Chi-restraints excluded: chain D residue 4926 LEU Chi-restraints excluded: chain D residue 4948 VAL Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 25 HIS Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain F residue 17 ASP Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 191 VAL Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 346 CYS Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain F residue 448 LEU Chi-restraints excluded: chain F residue 564 LEU Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain F residue 586 ILE Chi-restraints excluded: chain F residue 607 CYS Chi-restraints excluded: chain F residue 668 VAL Chi-restraints excluded: chain F residue 672 VAL Chi-restraints excluded: chain F residue 723 THR Chi-restraints excluded: chain F residue 791 PHE Chi-restraints excluded: chain F residue 1143 TRP Chi-restraints excluded: chain F residue 1159 THR Chi-restraints excluded: chain F residue 1450 VAL Chi-restraints excluded: chain F residue 1637 MET Chi-restraints excluded: chain F residue 1659 LEU Chi-restraints excluded: chain F residue 1685 LEU Chi-restraints excluded: chain F residue 1707 LEU Chi-restraints excluded: chain F residue 1769 THR Chi-restraints excluded: chain F residue 1851 VAL Chi-restraints excluded: chain F residue 2124 LEU Chi-restraints excluded: chain F residue 2127 ARG Chi-restraints excluded: chain F residue 2136 LEU Chi-restraints excluded: chain F residue 2186 ILE Chi-restraints excluded: chain F residue 2281 VAL Chi-restraints excluded: chain F residue 2303 LEU Chi-restraints excluded: chain F residue 2496 VAL Chi-restraints excluded: chain F residue 3869 VAL Chi-restraints excluded: chain F residue 3946 PHE Chi-restraints excluded: chain F residue 3964 ILE Chi-restraints excluded: chain F residue 3996 MET Chi-restraints excluded: chain F residue 4026 LEU Chi-restraints excluded: chain F residue 4065 ASP Chi-restraints excluded: chain F residue 4148 HIS Chi-restraints excluded: chain F residue 4200 TRP Chi-restraints excluded: chain F residue 4790 LEU Chi-restraints excluded: chain F residue 4842 LEU Chi-restraints excluded: chain F residue 4877 MET Chi-restraints excluded: chain F residue 4926 LEU Chi-restraints excluded: chain F residue 4948 VAL Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 25 HIS Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain H residue 17 ASP Chi-restraints excluded: chain H residue 25 ASN Chi-restraints excluded: chain H residue 65 CYS Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 135 VAL Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 232 THR Chi-restraints excluded: chain H residue 262 LEU Chi-restraints excluded: chain H residue 285 VAL Chi-restraints excluded: chain H residue 346 CYS Chi-restraints excluded: chain H residue 357 LEU Chi-restraints excluded: chain H residue 448 LEU Chi-restraints excluded: chain H residue 480 GLU Chi-restraints excluded: chain H residue 564 LEU Chi-restraints excluded: chain H residue 569 ILE Chi-restraints excluded: chain H residue 586 ILE Chi-restraints excluded: chain H residue 607 CYS Chi-restraints excluded: chain H residue 668 VAL Chi-restraints excluded: chain H residue 672 VAL Chi-restraints excluded: chain H residue 723 THR Chi-restraints excluded: chain H residue 1143 TRP Chi-restraints excluded: chain H residue 1450 VAL Chi-restraints excluded: chain H residue 1637 MET Chi-restraints excluded: chain H residue 1659 LEU Chi-restraints excluded: chain H residue 1685 LEU Chi-restraints excluded: chain H residue 1769 THR Chi-restraints excluded: chain H residue 1840 VAL Chi-restraints excluded: chain H residue 1851 VAL Chi-restraints excluded: chain H residue 1959 LEU Chi-restraints excluded: chain H residue 2124 LEU Chi-restraints excluded: chain H residue 2136 LEU Chi-restraints excluded: chain H residue 2186 ILE Chi-restraints excluded: chain H residue 2281 VAL Chi-restraints excluded: chain H residue 2303 LEU Chi-restraints excluded: chain H residue 2496 VAL Chi-restraints excluded: chain H residue 3869 VAL Chi-restraints excluded: chain H residue 3960 LEU Chi-restraints excluded: chain H residue 3964 ILE Chi-restraints excluded: chain H residue 3990 VAL Chi-restraints excluded: chain H residue 3996 MET Chi-restraints excluded: chain H residue 4026 LEU Chi-restraints excluded: chain H residue 4065 ASP Chi-restraints excluded: chain H residue 4200 TRP Chi-restraints excluded: chain H residue 4790 LEU Chi-restraints excluded: chain H residue 4825 LEU Chi-restraints excluded: chain H residue 4842 LEU Chi-restraints excluded: chain H residue 4877 MET Chi-restraints excluded: chain H residue 4926 LEU Chi-restraints excluded: chain H residue 4938 PHE Chi-restraints excluded: chain H residue 4948 VAL Chi-restraints excluded: chain H residue 4950 GLU Chi-restraints excluded: chain H residue 4991 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1524 random chunks: chunk 1336 optimal weight: 3.9990 chunk 1407 optimal weight: 10.0000 chunk 1283 optimal weight: 20.0000 chunk 1368 optimal weight: 10.0000 chunk 1406 optimal weight: 20.0000 chunk 823 optimal weight: 2.9990 chunk 596 optimal weight: 0.8980 chunk 1074 optimal weight: 2.9990 chunk 420 optimal weight: 9.9990 chunk 1236 optimal weight: 5.9990 chunk 1294 optimal weight: 9.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 877 ASN B1035 ASN B3420 ASN ** B3762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3993 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 877 ASN D1035 ASN D1052 ASN ** D1443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3420 ASN ** D3973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3993 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4148 HIS ** D4712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4831 ASN E 65 GLN ** F 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 877 ASN F1035 ASN ** F1443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F3993 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F4712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 877 ASN H1035 ASN ** H3804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H3993 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H4712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.5248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 107328 Z= 0.295 Angle : 0.713 17.583 146972 Z= 0.342 Chirality : 0.041 0.315 17784 Planarity : 0.004 0.064 19000 Dihedral : 4.084 22.940 15868 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.05 % Allowed : 22.46 % Favored : 74.50 % 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: 0.55 (0.07), residues: 13692 helix: 1.34 (0.06), residues: 6732 sheet: -0.54 (0.12), residues: 1688 loop : -0.52 (0.09), residues: 5272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP F 702 HIS 0.010 0.001 HIS F3977 PHE 0.043 0.002 PHE D 478 TYR 0.025 0.002 TYR D4965 ARG 0.009 0.001 ARG D 474 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27384 Ramachandran restraints generated. 13692 Oldfield, 0 Emsley, 13692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27384 Ramachandran restraints generated. 13692 Oldfield, 0 Emsley, 13692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1450 residues out of total 12212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 266 poor density : 1184 time to evaluate : 8.273 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: B 202 MET cc_start: 0.7978 (ptp) cc_final: 0.7231 (mtm) REVERT: B 1852 MET cc_start: 0.8763 (mmm) cc_final: 0.8266 (mmm) REVERT: B 1941 CYS cc_start: 0.8584 (m) cc_final: 0.8366 (m) REVERT: B 2111 PHE cc_start: 0.8382 (OUTLIER) cc_final: 0.7717 (t80) REVERT: B 2527 PHE cc_start: 0.8355 (m-10) cc_final: 0.8119 (m-80) REVERT: B 3436 PHE cc_start: 0.8141 (t80) cc_final: 0.7859 (t80) REVERT: B 3648 MET cc_start: 0.8599 (pmm) cc_final: 0.8298 (pmm) REVERT: B 4040 VAL cc_start: 0.9625 (m) cc_final: 0.9383 (p) REVERT: B 4127 PHE cc_start: 0.7093 (OUTLIER) cc_final: 0.6828 (m-10) REVERT: B 4572 ASN cc_start: 0.8438 (m110) cc_final: 0.8137 (m110) REVERT: B 4656 ILE cc_start: 0.9218 (mt) cc_final: 0.8980 (mt) REVERT: B 4788 LEU cc_start: 0.9189 (mm) cc_final: 0.8888 (tp) REVERT: B 4794 MET cc_start: 0.8749 (tpt) cc_final: 0.8386 (tpt) REVERT: B 4796 MET cc_start: 0.8861 (mpp) cc_final: 0.8623 (mpp) REVERT: B 4847 TYR cc_start: 0.8939 (t80) cc_final: 0.8701 (t80) REVERT: B 4946 GLU cc_start: 0.8813 (tp30) cc_final: 0.8005 (tp30) REVERT: D 202 MET cc_start: 0.7862 (ptp) cc_final: 0.7121 (mtm) REVERT: D 791 PHE cc_start: 0.8454 (OUTLIER) cc_final: 0.7863 (m-80) REVERT: D 1852 MET cc_start: 0.8775 (mmm) cc_final: 0.8283 (mmm) REVERT: D 2111 PHE cc_start: 0.8348 (OUTLIER) cc_final: 0.7706 (t80) REVERT: D 2527 PHE cc_start: 0.8367 (m-10) cc_final: 0.8128 (m-80) REVERT: D 3436 PHE cc_start: 0.8238 (t80) cc_final: 0.7956 (t80) REVERT: D 3648 MET cc_start: 0.8583 (pmm) cc_final: 0.8263 (pmm) REVERT: D 4040 VAL cc_start: 0.9628 (m) cc_final: 0.9394 (p) REVERT: D 4186 GLU cc_start: 0.7654 (tp30) cc_final: 0.7312 (tp30) REVERT: D 4572 ASN cc_start: 0.8434 (m110) cc_final: 0.8164 (m110) REVERT: D 4788 LEU cc_start: 0.9203 (mm) cc_final: 0.8905 (tp) REVERT: D 4847 TYR cc_start: 0.8951 (t80) cc_final: 0.8694 (t80) REVERT: D 4885 MET cc_start: 0.8699 (mmm) cc_final: 0.8339 (tpp) REVERT: E 47 LYS cc_start: 0.8631 (mppt) cc_final: 0.8282 (mptt) REVERT: E 102 GLU cc_start: 0.8200 (pp20) cc_final: 0.7795 (pp20) REVERT: F 197 GLN cc_start: 0.8265 (pp30) cc_final: 0.7781 (pp30) REVERT: F 202 MET cc_start: 0.7902 (ptp) cc_final: 0.7189 (mtm) REVERT: F 483 MET cc_start: 0.6820 (mtp) cc_final: 0.6077 (mtp) REVERT: F 667 MET cc_start: 0.7949 (ppp) cc_final: 0.7743 (ppp) REVERT: F 791 PHE cc_start: 0.8442 (OUTLIER) cc_final: 0.7861 (m-80) REVERT: F 1152 MET cc_start: 0.7430 (tpt) cc_final: 0.7068 (mmm) REVERT: F 1852 MET cc_start: 0.8767 (mmm) cc_final: 0.8274 (mmm) REVERT: F 2111 PHE cc_start: 0.8372 (OUTLIER) cc_final: 0.7715 (t80) REVERT: F 2527 PHE cc_start: 0.8341 (m-10) cc_final: 0.8073 (m-80) REVERT: F 3436 PHE cc_start: 0.8246 (t80) cc_final: 0.7962 (t80) REVERT: F 4040 VAL cc_start: 0.9616 (m) cc_final: 0.9365 (p) REVERT: F 4572 ASN cc_start: 0.8460 (m110) cc_final: 0.8171 (m110) REVERT: F 4700 ASP cc_start: 0.8645 (m-30) cc_final: 0.8161 (p0) REVERT: F 4788 LEU cc_start: 0.9189 (mm) cc_final: 0.8886 (tp) REVERT: F 4847 TYR cc_start: 0.8935 (t80) cc_final: 0.8733 (t80) REVERT: F 4878 MET cc_start: 0.8434 (tpp) cc_final: 0.8228 (tpp) REVERT: F 4992 TYR cc_start: 0.9113 (t80) cc_final: 0.8816 (t80) REVERT: H 197 GLN cc_start: 0.8016 (pp30) cc_final: 0.7695 (pp30) REVERT: H 202 MET cc_start: 0.7996 (ptp) cc_final: 0.7207 (mtm) REVERT: H 578 ILE cc_start: 0.8719 (mm) cc_final: 0.8439 (mm) REVERT: H 1143 TRP cc_start: 0.6494 (OUTLIER) cc_final: 0.5074 (p-90) REVERT: H 1730 MET cc_start: 0.8339 (mmm) cc_final: 0.7906 (mmp) REVERT: H 1852 MET cc_start: 0.8776 (mmm) cc_final: 0.8296 (mmm) REVERT: H 2111 PHE cc_start: 0.8365 (OUTLIER) cc_final: 0.7713 (t80) REVERT: H 2527 PHE cc_start: 0.8336 (m-10) cc_final: 0.8105 (m-80) REVERT: H 3436 PHE cc_start: 0.8214 (t80) cc_final: 0.7942 (t80) REVERT: H 3994 MET cc_start: 0.8723 (tpp) cc_final: 0.8021 (tmm) REVERT: H 4572 ASN cc_start: 0.8490 (m110) cc_final: 0.8201 (m110) REVERT: H 4656 ILE cc_start: 0.9148 (mt) cc_final: 0.8937 (mt) REVERT: H 4700 ASP cc_start: 0.8637 (m-30) cc_final: 0.8275 (p0) REVERT: H 4788 LEU cc_start: 0.9222 (mm) cc_final: 0.8924 (tp) REVERT: H 4847 TYR cc_start: 0.8887 (t80) cc_final: 0.8652 (t80) REVERT: H 4946 GLU cc_start: 0.8377 (tp30) cc_final: 0.7776 (tp30) REVERT: H 4950 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.8057 (mp0) REVERT: H 4992 TYR cc_start: 0.9120 (t80) cc_final: 0.8874 (t80) outliers start: 266 outliers final: 229 residues processed: 1372 average time/residue: 0.7732 time to fit residues: 1963.7607 Evaluate side-chains 1393 residues out of total 12212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 238 poor density : 1155 time to evaluate : 8.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 25 HIS Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 113 HIS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 586 ILE Chi-restraints excluded: chain B residue 607 CYS Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 938 HIS Chi-restraints excluded: chain B residue 1143 TRP Chi-restraints excluded: chain B residue 1450 VAL Chi-restraints excluded: chain B residue 1637 MET Chi-restraints excluded: chain B residue 1659 LEU Chi-restraints excluded: chain B residue 1685 LEU Chi-restraints excluded: chain B residue 1769 THR Chi-restraints excluded: chain B residue 1851 VAL Chi-restraints excluded: chain B residue 1959 LEU Chi-restraints excluded: chain B residue 2111 PHE Chi-restraints excluded: chain B residue 2124 LEU Chi-restraints excluded: chain B residue 2127 ARG Chi-restraints excluded: chain B residue 2136 LEU Chi-restraints excluded: chain B residue 2178 LEU Chi-restraints excluded: chain B residue 2186 ILE Chi-restraints excluded: chain B residue 2204 MET Chi-restraints excluded: chain B residue 2281 VAL Chi-restraints excluded: chain B residue 2303 LEU Chi-restraints excluded: chain B residue 2496 VAL Chi-restraints excluded: chain B residue 3869 VAL Chi-restraints excluded: chain B residue 3946 PHE Chi-restraints excluded: chain B residue 3964 ILE Chi-restraints excluded: chain B residue 3990 VAL Chi-restraints excluded: chain B residue 4026 LEU Chi-restraints excluded: chain B residue 4065 ASP Chi-restraints excluded: chain B residue 4127 PHE Chi-restraints excluded: chain B residue 4134 ILE Chi-restraints excluded: chain B residue 4200 TRP Chi-restraints excluded: chain B residue 4650 LEU Chi-restraints excluded: chain B residue 4790 LEU Chi-restraints excluded: chain B residue 4842 LEU Chi-restraints excluded: chain B residue 4877 MET Chi-restraints excluded: chain B residue 4889 VAL Chi-restraints excluded: chain B residue 4926 LEU Chi-restraints excluded: chain B residue 4948 VAL Chi-restraints excluded: chain B residue 4991 MET Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 25 HIS Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain D residue 65 CYS Chi-restraints excluded: chain D residue 113 HIS Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 158 SER Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 346 CYS Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 480 GLU Chi-restraints excluded: chain D residue 522 LEU Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 586 ILE Chi-restraints excluded: chain D residue 607 CYS Chi-restraints excluded: chain D residue 668 VAL Chi-restraints excluded: chain D residue 672 VAL Chi-restraints excluded: chain D residue 723 THR Chi-restraints excluded: chain D residue 791 PHE Chi-restraints excluded: chain D residue 938 HIS Chi-restraints excluded: chain D residue 1143 TRP Chi-restraints excluded: chain D residue 1450 VAL Chi-restraints excluded: chain D residue 1542 VAL Chi-restraints excluded: chain D residue 1659 LEU Chi-restraints excluded: chain D residue 1685 LEU Chi-restraints excluded: chain D residue 1707 LEU Chi-restraints excluded: chain D residue 1769 THR Chi-restraints excluded: chain D residue 1851 VAL Chi-restraints excluded: chain D residue 1959 LEU Chi-restraints excluded: chain D residue 2111 PHE Chi-restraints excluded: chain D residue 2124 LEU Chi-restraints excluded: chain D residue 2136 LEU Chi-restraints excluded: chain D residue 2186 ILE Chi-restraints excluded: chain D residue 2281 VAL Chi-restraints excluded: chain D residue 2303 LEU Chi-restraints excluded: chain D residue 2496 VAL Chi-restraints excluded: chain D residue 3869 VAL Chi-restraints excluded: chain D residue 3946 PHE Chi-restraints excluded: chain D residue 3964 ILE Chi-restraints excluded: chain D residue 3990 VAL Chi-restraints excluded: chain D residue 3996 MET Chi-restraints excluded: chain D residue 4026 LEU Chi-restraints excluded: chain D residue 4065 ASP Chi-restraints excluded: chain D residue 4134 ILE Chi-restraints excluded: chain D residue 4148 HIS Chi-restraints excluded: chain D residue 4200 TRP Chi-restraints excluded: chain D residue 4790 LEU Chi-restraints excluded: chain D residue 4842 LEU Chi-restraints excluded: chain D residue 4844 VAL Chi-restraints excluded: chain D residue 4877 MET Chi-restraints excluded: chain D residue 4926 LEU Chi-restraints excluded: chain D residue 4948 VAL Chi-restraints excluded: chain D residue 4991 MET Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain F residue 17 ASP Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain F residue 113 HIS Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 191 VAL Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 346 CYS Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain F residue 404 ILE Chi-restraints excluded: chain F residue 448 LEU Chi-restraints excluded: chain F residue 522 LEU Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain F residue 586 ILE Chi-restraints excluded: chain F residue 607 CYS Chi-restraints excluded: chain F residue 668 VAL Chi-restraints excluded: chain F residue 672 VAL Chi-restraints excluded: chain F residue 723 THR Chi-restraints excluded: chain F residue 791 PHE Chi-restraints excluded: chain F residue 1143 TRP Chi-restraints excluded: chain F residue 1159 THR Chi-restraints excluded: chain F residue 1450 VAL Chi-restraints excluded: chain F residue 1542 VAL Chi-restraints excluded: chain F residue 1637 MET Chi-restraints excluded: chain F residue 1659 LEU Chi-restraints excluded: chain F residue 1685 LEU Chi-restraints excluded: chain F residue 1769 THR Chi-restraints excluded: chain F residue 1851 VAL Chi-restraints excluded: chain F residue 2111 PHE Chi-restraints excluded: chain F residue 2124 LEU Chi-restraints excluded: chain F residue 2127 ARG Chi-restraints excluded: chain F residue 2136 LEU Chi-restraints excluded: chain F residue 2186 ILE Chi-restraints excluded: chain F residue 2281 VAL Chi-restraints excluded: chain F residue 2303 LEU Chi-restraints excluded: chain F residue 2496 VAL Chi-restraints excluded: chain F residue 3869 VAL Chi-restraints excluded: chain F residue 3946 PHE Chi-restraints excluded: chain F residue 3964 ILE Chi-restraints excluded: chain F residue 3996 MET Chi-restraints excluded: chain F residue 4026 LEU Chi-restraints excluded: chain F residue 4065 ASP Chi-restraints excluded: chain F residue 4134 ILE Chi-restraints excluded: chain F residue 4148 HIS Chi-restraints excluded: chain F residue 4200 TRP Chi-restraints excluded: chain F residue 4790 LEU Chi-restraints excluded: chain F residue 4842 LEU Chi-restraints excluded: chain F residue 4844 VAL Chi-restraints excluded: chain F residue 4877 MET Chi-restraints excluded: chain F residue 4926 LEU Chi-restraints excluded: chain F residue 4948 VAL Chi-restraints excluded: chain F residue 4991 MET Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 25 HIS Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain H residue 17 ASP Chi-restraints excluded: chain H residue 25 ASN Chi-restraints excluded: chain H residue 65 CYS Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 113 HIS Chi-restraints excluded: chain H residue 135 VAL Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 232 THR Chi-restraints excluded: chain H residue 262 LEU Chi-restraints excluded: chain H residue 285 VAL Chi-restraints excluded: chain H residue 346 CYS Chi-restraints excluded: chain H residue 357 LEU Chi-restraints excluded: chain H residue 448 LEU Chi-restraints excluded: chain H residue 480 GLU Chi-restraints excluded: chain H residue 522 LEU Chi-restraints excluded: chain H residue 569 ILE Chi-restraints excluded: chain H residue 586 ILE Chi-restraints excluded: chain H residue 607 CYS Chi-restraints excluded: chain H residue 668 VAL Chi-restraints excluded: chain H residue 672 VAL Chi-restraints excluded: chain H residue 723 THR Chi-restraints excluded: chain H residue 1143 TRP Chi-restraints excluded: chain H residue 1450 VAL Chi-restraints excluded: chain H residue 1542 VAL Chi-restraints excluded: chain H residue 1659 LEU Chi-restraints excluded: chain H residue 1685 LEU Chi-restraints excluded: chain H residue 1769 THR Chi-restraints excluded: chain H residue 1840 VAL Chi-restraints excluded: chain H residue 1851 VAL Chi-restraints excluded: chain H residue 1959 LEU Chi-restraints excluded: chain H residue 2111 PHE Chi-restraints excluded: chain H residue 2124 LEU Chi-restraints excluded: chain H residue 2127 ARG Chi-restraints excluded: chain H residue 2136 LEU Chi-restraints excluded: chain H residue 2186 ILE Chi-restraints excluded: chain H residue 2281 VAL Chi-restraints excluded: chain H residue 2303 LEU Chi-restraints excluded: chain H residue 2496 VAL Chi-restraints excluded: chain H residue 3869 VAL Chi-restraints excluded: chain H residue 3964 ILE Chi-restraints excluded: chain H residue 3990 VAL Chi-restraints excluded: chain H residue 3996 MET Chi-restraints excluded: chain H residue 4026 LEU Chi-restraints excluded: chain H residue 4065 ASP Chi-restraints excluded: chain H residue 4200 TRP Chi-restraints excluded: chain H residue 4790 LEU Chi-restraints excluded: chain H residue 4825 LEU Chi-restraints excluded: chain H residue 4842 LEU Chi-restraints excluded: chain H residue 4877 MET Chi-restraints excluded: chain H residue 4926 LEU Chi-restraints excluded: chain H residue 4938 PHE Chi-restraints excluded: chain H residue 4948 VAL Chi-restraints excluded: chain H residue 4950 GLU Chi-restraints excluded: chain H residue 4991 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1524 random chunks: chunk 1364 optimal weight: 5.9990 chunk 898 optimal weight: 10.0000 chunk 1447 optimal weight: 0.9980 chunk 883 optimal weight: 4.9990 chunk 686 optimal weight: 0.0010 chunk 1006 optimal weight: 0.0270 chunk 1518 optimal weight: 5.9990 chunk 1397 optimal weight: 30.0000 chunk 1209 optimal weight: 0.2980 chunk 125 optimal weight: 5.9990 chunk 933 optimal weight: 5.9990 overall best weight: 1.2646 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 877 ASN ** B1443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3993 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4148 HIS ** B4712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 877 ASN ** D1443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3993 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 877 ASN ** F1443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F4712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 877 ASN ** H1443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H2261 ASN H3776 GLN H3804 ASN ** H3993 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H4712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.5270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 107328 Z= 0.177 Angle : 0.701 16.365 146972 Z= 0.323 Chirality : 0.040 0.391 17784 Planarity : 0.004 0.066 19000 Dihedral : 3.933 22.430 15868 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.28 % Allowed : 23.64 % Favored : 74.08 % 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: 0.76 (0.07), residues: 13692 helix: 1.49 (0.07), residues: 6712 sheet: -0.41 (0.13), residues: 1628 loop : -0.38 (0.09), residues: 5352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP F 882 HIS 0.028 0.001 HIS B1640 PHE 0.043 0.001 PHE D 478 TYR 0.033 0.001 TYR D 565 ARG 0.011 0.000 ARG D1087 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27384 Ramachandran restraints generated. 13692 Oldfield, 0 Emsley, 13692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27384 Ramachandran restraints generated. 13692 Oldfield, 0 Emsley, 13692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1446 residues out of total 12212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 1247 time to evaluate : 7.485 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: B 40 GLU cc_start: 0.7823 (tm-30) cc_final: 0.7041 (tp30) REVERT: B 101 LEU cc_start: 0.8290 (tt) cc_final: 0.7980 (tp) REVERT: B 202 MET cc_start: 0.7790 (ptp) cc_final: 0.7171 (mtm) REVERT: B 1143 TRP cc_start: 0.6458 (OUTLIER) cc_final: 0.5221 (p-90) REVERT: B 1730 MET cc_start: 0.8172 (mmm) cc_final: 0.7785 (mmp) REVERT: B 1852 MET cc_start: 0.8631 (mmm) cc_final: 0.8175 (mmm) REVERT: B 2111 PHE cc_start: 0.8259 (OUTLIER) cc_final: 0.7665 (t80) REVERT: B 2527 PHE cc_start: 0.8312 (m-10) cc_final: 0.8084 (m-80) REVERT: B 3436 PHE cc_start: 0.8162 (t80) cc_final: 0.7895 (t80) REVERT: B 3648 MET cc_start: 0.8537 (pmm) cc_final: 0.8204 (pmm) REVERT: B 3950 MET cc_start: 0.8100 (mmp) cc_final: 0.7772 (mtm) REVERT: B 4018 MET cc_start: 0.8628 (tpt) cc_final: 0.8281 (tpt) REVERT: B 4040 VAL cc_start: 0.9596 (m) cc_final: 0.9346 (p) REVERT: B 4656 ILE cc_start: 0.9177 (mt) cc_final: 0.8903 (mt) REVERT: B 4700 ASP cc_start: 0.8520 (m-30) cc_final: 0.8128 (p0) REVERT: B 4788 LEU cc_start: 0.9162 (mm) cc_final: 0.8910 (tp) REVERT: B 4794 MET cc_start: 0.8710 (tpt) cc_final: 0.8369 (tpt) REVERT: B 4796 MET cc_start: 0.8769 (mpp) cc_final: 0.8490 (mpp) REVERT: B 4847 TYR cc_start: 0.8897 (t80) cc_final: 0.8663 (t80) REVERT: B 4885 MET cc_start: 0.8592 (mmm) cc_final: 0.8093 (ptm) REVERT: B 4946 GLU cc_start: 0.8586 (tp30) cc_final: 0.7905 (tp30) REVERT: D 179 TYR cc_start: 0.8476 (m-80) cc_final: 0.8166 (m-80) REVERT: D 791 PHE cc_start: 0.8450 (OUTLIER) cc_final: 0.7859 (m-80) REVERT: D 1143 TRP cc_start: 0.6339 (OUTLIER) cc_final: 0.5257 (p-90) REVERT: D 1494 MET cc_start: 0.8131 (ttm) cc_final: 0.7914 (ttm) REVERT: D 1730 MET cc_start: 0.8199 (mmm) cc_final: 0.7433 (mmp) REVERT: D 1852 MET cc_start: 0.8660 (mmm) cc_final: 0.8184 (mmm) REVERT: D 2111 PHE cc_start: 0.8307 (OUTLIER) cc_final: 0.7664 (t80) REVERT: D 2251 MET cc_start: 0.8187 (mmm) cc_final: 0.7922 (mmm) REVERT: D 2527 PHE cc_start: 0.8320 (m-10) cc_final: 0.8098 (m-80) REVERT: D 3436 PHE cc_start: 0.8193 (t80) cc_final: 0.7917 (t80) REVERT: D 3648 MET cc_start: 0.8552 (pmm) cc_final: 0.8276 (pmm) REVERT: D 3950 MET cc_start: 0.8123 (mmp) cc_final: 0.7784 (mtm) REVERT: D 4040 VAL cc_start: 0.9597 (m) cc_final: 0.9352 (p) REVERT: D 4572 ASN cc_start: 0.8342 (m110) cc_final: 0.8018 (m110) REVERT: D 4700 ASP cc_start: 0.8554 (m-30) cc_final: 0.8127 (p0) REVERT: D 4788 LEU cc_start: 0.9149 (mm) cc_final: 0.8879 (tp) REVERT: D 4847 TYR cc_start: 0.8913 (t80) cc_final: 0.8672 (t80) REVERT: D 4885 MET cc_start: 0.8675 (mmm) cc_final: 0.8248 (tpp) REVERT: D 4946 GLU cc_start: 0.8464 (tp30) cc_final: 0.8140 (tp30) REVERT: F 101 LEU cc_start: 0.8313 (tt) cc_final: 0.7998 (tp) REVERT: F 197 GLN cc_start: 0.8207 (pp30) cc_final: 0.7770 (pp30) REVERT: F 202 MET cc_start: 0.7783 (ptp) cc_final: 0.7048 (mtm) REVERT: F 1143 TRP cc_start: 0.6350 (OUTLIER) cc_final: 0.5161 (p-90) REVERT: F 1494 MET cc_start: 0.8179 (ttm) cc_final: 0.7970 (ttm) REVERT: F 1730 MET cc_start: 0.8247 (mmm) cc_final: 0.7664 (mmp) REVERT: F 1852 MET cc_start: 0.8649 (mmm) cc_final: 0.8182 (mmm) REVERT: F 2111 PHE cc_start: 0.8255 (OUTLIER) cc_final: 0.7649 (t80) REVERT: F 2527 PHE cc_start: 0.8345 (m-10) cc_final: 0.8108 (m-80) REVERT: F 3436 PHE cc_start: 0.8171 (t80) cc_final: 0.7904 (t80) REVERT: F 3950 MET cc_start: 0.8110 (mmp) cc_final: 0.7766 (mtm) REVERT: F 4018 MET cc_start: 0.8636 (tpt) cc_final: 0.8279 (tpt) REVERT: F 4040 VAL cc_start: 0.9594 (m) cc_final: 0.9339 (p) REVERT: F 4572 ASN cc_start: 0.8350 (m110) cc_final: 0.8038 (m110) REVERT: F 4700 ASP cc_start: 0.8687 (m-30) cc_final: 0.8176 (p0) REVERT: F 4788 LEU cc_start: 0.9096 (mm) cc_final: 0.8864 (tp) REVERT: F 4847 TYR cc_start: 0.8917 (t80) cc_final: 0.8705 (t80) REVERT: F 4946 GLU cc_start: 0.8476 (tp30) cc_final: 0.8150 (tp30) REVERT: F 4992 TYR cc_start: 0.9055 (t80) cc_final: 0.8809 (t80) REVERT: H 101 LEU cc_start: 0.8278 (tt) cc_final: 0.7963 (tp) REVERT: H 197 GLN cc_start: 0.8041 (pp30) cc_final: 0.7718 (pp30) REVERT: H 202 MET cc_start: 0.7794 (ptp) cc_final: 0.7130 (mtm) REVERT: H 578 ILE cc_start: 0.8713 (mm) cc_final: 0.8428 (mm) REVERT: H 1143 TRP cc_start: 0.6519 (OUTLIER) cc_final: 0.5266 (p-90) REVERT: H 1730 MET cc_start: 0.8225 (mmm) cc_final: 0.7692 (mmp) REVERT: H 1852 MET cc_start: 0.8659 (mmm) cc_final: 0.8191 (mmm) REVERT: H 2111 PHE cc_start: 0.8254 (OUTLIER) cc_final: 0.7646 (t80) REVERT: H 2527 PHE cc_start: 0.8340 (m-10) cc_final: 0.8095 (m-80) REVERT: H 3436 PHE cc_start: 0.8164 (t80) cc_final: 0.7899 (t80) REVERT: H 3950 MET cc_start: 0.8123 (mmp) cc_final: 0.7769 (mtm) REVERT: H 3994 MET cc_start: 0.8626 (tpp) cc_final: 0.8050 (tmm) REVERT: H 4018 MET cc_start: 0.8612 (tpt) cc_final: 0.8292 (tpt) REVERT: H 4572 ASN cc_start: 0.8344 (m110) cc_final: 0.8039 (m110) REVERT: H 4700 ASP cc_start: 0.8683 (m-30) cc_final: 0.8253 (p0) REVERT: H 4788 LEU cc_start: 0.9163 (mm) cc_final: 0.8851 (tp) REVERT: H 4946 GLU cc_start: 0.8371 (tp30) cc_final: 0.7722 (tp30) REVERT: H 4950 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.8079 (mp0) REVERT: H 4992 TYR cc_start: 0.9083 (t80) cc_final: 0.8857 (t80) outliers start: 199 outliers final: 175 residues processed: 1390 average time/residue: 0.7712 time to fit residues: 1984.0995 Evaluate side-chains 1365 residues out of total 12212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 1180 time to evaluate : 7.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 522 LEU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 586 ILE Chi-restraints excluded: chain B residue 607 CYS Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 938 HIS Chi-restraints excluded: chain B residue 1143 TRP Chi-restraints excluded: chain B residue 1450 VAL Chi-restraints excluded: chain B residue 1637 MET Chi-restraints excluded: chain B residue 1659 LEU Chi-restraints excluded: chain B residue 1685 LEU Chi-restraints excluded: chain B residue 1769 THR Chi-restraints excluded: chain B residue 1851 VAL Chi-restraints excluded: chain B residue 1959 LEU Chi-restraints excluded: chain B residue 2111 PHE Chi-restraints excluded: chain B residue 2186 ILE Chi-restraints excluded: chain B residue 2281 VAL Chi-restraints excluded: chain B residue 2303 LEU Chi-restraints excluded: chain B residue 2496 VAL Chi-restraints excluded: chain B residue 3777 MET Chi-restraints excluded: chain B residue 3869 VAL Chi-restraints excluded: chain B residue 3946 PHE Chi-restraints excluded: chain B residue 3964 ILE Chi-restraints excluded: chain B residue 3990 VAL Chi-restraints excluded: chain B residue 4026 LEU Chi-restraints excluded: chain B residue 4065 ASP Chi-restraints excluded: chain B residue 4148 HIS Chi-restraints excluded: chain B residue 4200 TRP Chi-restraints excluded: chain B residue 4650 LEU Chi-restraints excluded: chain B residue 4790 LEU Chi-restraints excluded: chain B residue 4842 LEU Chi-restraints excluded: chain B residue 4877 MET Chi-restraints excluded: chain B residue 4948 VAL Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 25 HIS Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain D residue 65 CYS Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 158 SER Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 607 CYS Chi-restraints excluded: chain D residue 668 VAL Chi-restraints excluded: chain D residue 723 THR Chi-restraints excluded: chain D residue 791 PHE Chi-restraints excluded: chain D residue 938 HIS Chi-restraints excluded: chain D residue 1143 TRP Chi-restraints excluded: chain D residue 1450 VAL Chi-restraints excluded: chain D residue 1659 LEU Chi-restraints excluded: chain D residue 1685 LEU Chi-restraints excluded: chain D residue 1707 LEU Chi-restraints excluded: chain D residue 1769 THR Chi-restraints excluded: chain D residue 1851 VAL Chi-restraints excluded: chain D residue 1959 LEU Chi-restraints excluded: chain D residue 2111 PHE Chi-restraints excluded: chain D residue 2124 LEU Chi-restraints excluded: chain D residue 2281 VAL Chi-restraints excluded: chain D residue 2303 LEU Chi-restraints excluded: chain D residue 2496 VAL Chi-restraints excluded: chain D residue 3869 VAL Chi-restraints excluded: chain D residue 3946 PHE Chi-restraints excluded: chain D residue 3964 ILE Chi-restraints excluded: chain D residue 3990 VAL Chi-restraints excluded: chain D residue 3996 MET Chi-restraints excluded: chain D residue 4026 LEU Chi-restraints excluded: chain D residue 4065 ASP Chi-restraints excluded: chain D residue 4200 TRP Chi-restraints excluded: chain D residue 4790 LEU Chi-restraints excluded: chain D residue 4842 LEU Chi-restraints excluded: chain D residue 4877 MET Chi-restraints excluded: chain D residue 4926 LEU Chi-restraints excluded: chain D residue 4948 VAL Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 25 HIS Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 191 VAL Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 346 CYS Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain F residue 607 CYS Chi-restraints excluded: chain F residue 668 VAL Chi-restraints excluded: chain F residue 672 VAL Chi-restraints excluded: chain F residue 723 THR Chi-restraints excluded: chain F residue 1143 TRP Chi-restraints excluded: chain F residue 1159 THR Chi-restraints excluded: chain F residue 1450 VAL Chi-restraints excluded: chain F residue 1637 MET Chi-restraints excluded: chain F residue 1659 LEU Chi-restraints excluded: chain F residue 1685 LEU Chi-restraints excluded: chain F residue 1769 THR Chi-restraints excluded: chain F residue 1851 VAL Chi-restraints excluded: chain F residue 2111 PHE Chi-restraints excluded: chain F residue 2124 LEU Chi-restraints excluded: chain F residue 2186 ILE Chi-restraints excluded: chain F residue 2281 VAL Chi-restraints excluded: chain F residue 2303 LEU Chi-restraints excluded: chain F residue 2496 VAL Chi-restraints excluded: chain F residue 3793 LEU Chi-restraints excluded: chain F residue 3869 VAL Chi-restraints excluded: chain F residue 3946 PHE Chi-restraints excluded: chain F residue 3964 ILE Chi-restraints excluded: chain F residue 3996 MET Chi-restraints excluded: chain F residue 4026 LEU Chi-restraints excluded: chain F residue 4065 ASP Chi-restraints excluded: chain F residue 4148 HIS Chi-restraints excluded: chain F residue 4200 TRP Chi-restraints excluded: chain F residue 4790 LEU Chi-restraints excluded: chain F residue 4842 LEU Chi-restraints excluded: chain F residue 4877 MET Chi-restraints excluded: chain F residue 4926 LEU Chi-restraints excluded: chain F residue 4948 VAL Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 25 HIS Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain H residue 25 ASN Chi-restraints excluded: chain H residue 65 CYS Chi-restraints excluded: chain H residue 135 VAL Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 232 THR Chi-restraints excluded: chain H residue 262 LEU Chi-restraints excluded: chain H residue 285 VAL Chi-restraints excluded: chain H residue 346 CYS Chi-restraints excluded: chain H residue 357 LEU Chi-restraints excluded: chain H residue 448 LEU Chi-restraints excluded: chain H residue 522 LEU Chi-restraints excluded: chain H residue 607 CYS Chi-restraints excluded: chain H residue 668 VAL Chi-restraints excluded: chain H residue 672 VAL Chi-restraints excluded: chain H residue 723 THR Chi-restraints excluded: chain H residue 1143 TRP Chi-restraints excluded: chain H residue 1450 VAL Chi-restraints excluded: chain H residue 1659 LEU Chi-restraints excluded: chain H residue 1685 LEU Chi-restraints excluded: chain H residue 1769 THR Chi-restraints excluded: chain H residue 1851 VAL Chi-restraints excluded: chain H residue 1959 LEU Chi-restraints excluded: chain H residue 2111 PHE Chi-restraints excluded: chain H residue 2167 LEU Chi-restraints excluded: chain H residue 2186 ILE Chi-restraints excluded: chain H residue 2281 VAL Chi-restraints excluded: chain H residue 2303 LEU Chi-restraints excluded: chain H residue 2496 VAL Chi-restraints excluded: chain H residue 3869 VAL Chi-restraints excluded: chain H residue 3964 ILE Chi-restraints excluded: chain H residue 3990 VAL Chi-restraints excluded: chain H residue 3996 MET Chi-restraints excluded: chain H residue 4026 LEU Chi-restraints excluded: chain H residue 4065 ASP Chi-restraints excluded: chain H residue 4200 TRP Chi-restraints excluded: chain H residue 4790 LEU Chi-restraints excluded: chain H residue 4825 LEU Chi-restraints excluded: chain H residue 4842 LEU Chi-restraints excluded: chain H residue 4877 MET Chi-restraints excluded: chain H residue 4926 LEU Chi-restraints excluded: chain H residue 4938 PHE Chi-restraints excluded: chain H residue 4948 VAL Chi-restraints excluded: chain H residue 4950 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1524 random chunks: chunk 741 optimal weight: 3.9990 chunk 960 optimal weight: 0.0010 chunk 1287 optimal weight: 5.9990 chunk 370 optimal weight: 5.9990 chunk 1114 optimal weight: 2.9990 chunk 178 optimal weight: 0.8980 chunk 335 optimal weight: 2.9990 chunk 1210 optimal weight: 6.9990 chunk 506 optimal weight: 5.9990 chunk 1243 optimal weight: 30.0000 chunk 153 optimal weight: 0.5980 overall best weight: 1.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 HIS ** B1443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3776 GLN ** B3973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 GLN ** D 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4151 HIS ** D4712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F4712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F4831 ASN ** H 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H3973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H4712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H4831 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.076472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.058153 restraints weight = 558587.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.059608 restraints weight = 308171.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.060615 restraints weight = 201965.949| |-----------------------------------------------------------------------------| r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3158 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3158 r_free = 0.3158 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3158 r_free = 0.3158 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3158 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.5355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 107328 Z= 0.188 Angle : 0.701 16.035 146972 Z= 0.323 Chirality : 0.040 0.353 17784 Planarity : 0.004 0.053 19000 Dihedral : 3.866 20.766 15868 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.21 % Allowed : 24.21 % Favored : 73.58 % 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: 0.78 (0.07), residues: 13692 helix: 1.51 (0.07), residues: 6700 sheet: -0.37 (0.12), residues: 1716 loop : -0.39 (0.09), residues: 5276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 702 HIS 0.025 0.001 HIS B4148 PHE 0.039 0.001 PHE D 478 TYR 0.031 0.001 TYR B3718 ARG 0.008 0.000 ARG H1087 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 31154.60 seconds wall clock time: 538 minutes 38.42 seconds (32318.42 seconds total)