Starting phenix.real_space_refine on Tue Mar 26 10:14:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vk4_43304/03_2024/8vk4_43304_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vk4_43304/03_2024/8vk4_43304.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vk4_43304/03_2024/8vk4_43304.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vk4_43304/03_2024/8vk4_43304.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vk4_43304/03_2024/8vk4_43304_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vk4_43304/03_2024/8vk4_43304_updated.pdb" } resolution = 3.56 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= 0.005 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 20 9.91 5 Zn 4 6.06 5 P 32 5.49 5 S 984 5.16 5 C 94900 2.51 5 N 25548 2.21 5 O 27816 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E GLU 55": "OE1" <-> "OE2" Residue "E ASP 80": "OD1" <-> "OD2" Residue "E TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 25": "OD1" <-> "OD2" Residue "I TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 4": "OE1" <-> "OE2" Residue "J ASP 53": "OD1" <-> "OD2" Residue "J TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 6": "OE1" <-> "OE2" Residue "F GLU 32": "OE1" <-> "OE2" Residue "F GLU 62": "OE1" <-> "OE2" Residue "F ASP 80": "OD1" <-> "OD2" Residue "G GLU 55": "OE1" <-> "OE2" Residue "G ASP 80": "OD1" <-> "OD2" Residue "H GLU 55": "OE1" <-> "OE2" Residue "H GLU 62": "OE1" <-> "OE2" Residue "H ASP 80": "OD1" <-> "OD2" Residue "D GLU 145": "OE1" <-> "OE2" Residue "D GLU 249": "OE1" <-> "OE2" Residue "D ASP 386": "OD1" <-> "OD2" Residue "D GLU 510": "OE1" <-> "OE2" Residue "D GLU 631": "OE1" <-> "OE2" Residue "D TYR 664": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 758": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 784": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1735": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1807": "OE1" <-> "OE2" Residue "D TYR 1966": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1998": "OE1" <-> "OE2" Residue "D ASP 2538": "OD1" <-> "OD2" Residue "D ASP 2714": "OD1" <-> "OD2" Residue "D PHE 2974": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 3281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 3342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 3427": "OE1" <-> "OE2" Residue "D GLU 3441": "OE1" <-> "OE2" Residue "D PHE 3459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 3541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 3882": "OE1" <-> "OE2" Residue "D PHE 3995": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 4080": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 4160": "OD1" <-> "OD2" Residue "D PHE 4222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 4227": "OE1" <-> "OE2" Residue "D GLU 4247": "OE1" <-> "OE2" Residue "D TYR 4627": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 4737": "OE1" <-> "OE2" Residue "D PHE 4778": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 5012": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 5032": "OD1" <-> "OD2" Residue "A GLU 145": "OE1" <-> "OE2" Residue "A GLU 249": "OE1" <-> "OE2" Residue "A ASP 386": "OD1" <-> "OD2" Residue "A GLU 510": "OE1" <-> "OE2" Residue "A GLU 631": "OE1" <-> "OE2" Residue "A TYR 664": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 758": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 784": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1735": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1807": "OE1" <-> "OE2" Residue "A TYR 1966": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1998": "OE1" <-> "OE2" Residue "A ASP 2538": "OD1" <-> "OD2" Residue "A ASP 2714": "OD1" <-> "OD2" Residue "A PHE 2974": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 3281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 3342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 3427": "OE1" <-> "OE2" Residue "A GLU 3441": "OE1" <-> "OE2" Residue "A PHE 3459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 3541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 3882": "OE1" <-> "OE2" Residue "A PHE 3995": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 4080": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 4160": "OD1" <-> "OD2" Residue "A PHE 4222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 4227": "OE1" <-> "OE2" Residue "A GLU 4247": "OE1" <-> "OE2" Residue "A TYR 4627": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 4737": "OE1" <-> "OE2" Residue "A PHE 4778": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 5012": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 5032": "OD1" <-> "OD2" Residue "B GLU 145": "OE1" <-> "OE2" Residue "B GLU 249": "OE1" <-> "OE2" Residue "B ASP 386": "OD1" <-> "OD2" Residue "B GLU 510": "OE1" <-> "OE2" Residue "B GLU 631": "OE1" <-> "OE2" Residue "B TYR 664": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 758": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 784": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1735": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1807": "OE1" <-> "OE2" Residue "B TYR 1966": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1998": "OE1" <-> "OE2" Residue "B ASP 2538": "OD1" <-> "OD2" Residue "B ASP 2714": "OD1" <-> "OD2" Residue "B PHE 2974": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 3281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 3342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 3427": "OE1" <-> "OE2" Residue "B GLU 3441": "OE1" <-> "OE2" Residue "B PHE 3459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 3541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 3882": "OE1" <-> "OE2" Residue "B PHE 3995": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 4080": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 4160": "OD1" <-> "OD2" Residue "B PHE 4222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 4227": "OE1" <-> "OE2" Residue "B GLU 4247": "OE1" <-> "OE2" Residue "B TYR 4627": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 4737": "OE1" <-> "OE2" Residue "B PHE 4778": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 5012": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 5032": "OD1" <-> "OD2" Residue "C GLU 145": "OE1" <-> "OE2" Residue "C GLU 249": "OE1" <-> "OE2" Residue "C ASP 386": "OD1" <-> "OD2" Residue "C GLU 510": "OE1" <-> "OE2" Residue "C GLU 631": "OE1" <-> "OE2" Residue "C TYR 664": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 758": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 784": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1735": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1807": "OE1" <-> "OE2" Residue "C TYR 1966": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1998": "OE1" <-> "OE2" Residue "C ASP 2538": "OD1" <-> "OD2" Residue "C ASP 2714": "OD1" <-> "OD2" Residue "C PHE 2974": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 3281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 3342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 3427": "OE1" <-> "OE2" Residue "C GLU 3441": "OE1" <-> "OE2" Residue "C PHE 3459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 3541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 3882": "OE1" <-> "OE2" Residue "C PHE 3995": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 4080": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 4160": "OD1" <-> "OD2" Residue "C PHE 4222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 4227": "OE1" <-> "OE2" Residue "C GLU 4247": "OE1" <-> "OE2" Residue "C TYR 4627": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 4737": "OE1" <-> "OE2" Residue "C PHE 4778": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 5012": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 5032": "OD1" <-> "OD2" Residue "K PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 25": "OD1" <-> "OD2" Residue "K TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 4": "OE1" <-> "OE2" Residue "L ASP 53": "OD1" <-> "OD2" Residue "L TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 4": "OE1" <-> "OE2" Residue "N ASP 53": "OD1" <-> "OD2" Residue "N TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 25": "OD1" <-> "OD2" Residue "M TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 25": "OD1" <-> "OD2" Residue "O TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 4": "OE1" <-> "OE2" Residue "P ASP 53": "OD1" <-> "OD2" Residue "P TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.43s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 149304 Number of models: 1 Model: "" Number of chains: 28 Chain: "E" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 829 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "I" Number of atoms: 729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 729 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'TRANS': 92} Chain: "J" Number of atoms: 729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 729 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'TRANS': 92} Chain: "F" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 829 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "G" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 829 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "H" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 829 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "D" Number of atoms: 34849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4379, 34849 Classifications: {'peptide': 4379} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 2, 'PTRANS': 220, 'TRANS': 4156} Chain breaks: 13 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "A" Number of atoms: 34849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4379, 34849 Classifications: {'peptide': 4379} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 2, 'PTRANS': 220, 'TRANS': 4156} Chain breaks: 13 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 34849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4379, 34849 Classifications: {'peptide': 4379} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 2, 'PTRANS': 220, 'TRANS': 4156} Chain breaks: 13 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 34849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4379, 34849 Classifications: {'peptide': 4379} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 2, 'PTRANS': 220, 'TRANS': 4156} Chain breaks: 13 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "K" Number of atoms: 729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 729 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'TRANS': 92} Chain: "L" Number of atoms: 729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 729 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'TRANS': 92} Chain: "N" Number of atoms: 729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 729 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'TRANS': 92} Chain: "M" Number of atoms: 729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 729 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'TRANS': 92} Chain: "O" Number of atoms: 729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 729 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'TRANS': 92} Chain: "P" Number of atoms: 729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 729 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'TRANS': 92} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 186 Unusual residues: {' CA': 1, ' ZN': 1, 'ATP': 2, 'CFF': 1, 'PCW': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "A" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 186 Unusual residues: {' CA': 1, ' ZN': 1, 'ATP': 2, 'CFF': 1, 'PCW': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 186 Unusual residues: {' CA': 1, ' ZN': 1, 'ATP': 2, 'CFF': 1, 'PCW': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "C" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 186 Unusual residues: {' CA': 1, ' ZN': 1, 'ATP': 2, 'CFF': 1, 'PCW': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 38949 SG CYS D4956 168.878 170.785 88.276 1.00 96.91 S ATOM 38974 SG CYS D4959 169.063 173.440 90.969 1.00 95.36 S ATOM 73798 SG CYS A4956 193.997 168.891 88.290 1.00 96.91 S ATOM 73823 SG CYS A4959 191.341 169.071 90.983 1.00 95.36 S ATOM A06O7 SG CYS B4956 195.974 194.063 88.276 1.00 96.91 S ATOM A06OW SG CYS B4959 195.790 191.408 90.969 1.00 95.36 S ATOM A0XK8 SG CYS C4956 170.790 195.972 88.274 1.00 96.91 S ATOM A0XKX SG CYS C4959 173.445 195.787 90.967 1.00 95.36 S Time building chain proxies: 52.27, per 1000 atoms: 0.35 Number of scatterers: 149304 At special positions: 0 Unit cell: (365.687, 365.687, 208.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 Ca 20 19.99 S 984 16.00 P 32 15.00 O 27816 8.00 N 25548 7.00 C 94900 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS D3171 " - pdb=" SG CYS D3241 " distance=2.03 Simple disulfide: pdb=" SG CYS D4874 " - pdb=" SG CYS D4880 " distance=2.03 Simple disulfide: pdb=" SG CYS A3171 " - pdb=" SG CYS A3241 " distance=2.02 Simple disulfide: pdb=" SG CYS A4874 " - pdb=" SG CYS A4880 " distance=2.03 Simple disulfide: pdb=" SG CYS B3171 " - pdb=" SG CYS B3241 " distance=2.03 Simple disulfide: pdb=" SG CYS B4874 " - pdb=" SG CYS B4880 " distance=2.03 Simple disulfide: pdb=" SG CYS C3171 " - pdb=" SG CYS C3241 " distance=2.03 Simple disulfide: pdb=" SG CYS C4874 " - pdb=" SG CYS C4880 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 42.26 Conformation dependent library (CDL) restraints added in 18.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A8001 " pdb="ZN ZN A8001 " - pdb=" ND1 HIS A4981 " pdb="ZN ZN A8001 " - pdb=" NE2 HIS A4976 " pdb="ZN ZN A8001 " - pdb=" SG CYS A4956 " pdb="ZN ZN A8001 " - pdb=" SG CYS A4959 " pdb=" ZN B8001 " pdb="ZN ZN B8001 " - pdb=" ND1 HIS B4981 " pdb="ZN ZN B8001 " - pdb=" NE2 HIS B4976 " pdb="ZN ZN B8001 " - pdb=" SG CYS B4956 " pdb="ZN ZN B8001 " - pdb=" SG CYS B4959 " pdb=" ZN C5102 " pdb="ZN ZN C5102 " - pdb=" ND1 HIS C4981 " pdb="ZN ZN C5102 " - pdb=" NE2 HIS C4976 " pdb="ZN ZN C5102 " - pdb=" SG CYS C4956 " pdb="ZN ZN C5102 " - pdb=" SG CYS C4959 " pdb=" ZN D8001 " pdb="ZN ZN D8001 " - pdb=" ND1 HIS D4981 " pdb="ZN ZN D8001 " - pdb=" NE2 HIS D4976 " pdb="ZN ZN D8001 " - pdb=" SG CYS D4956 " pdb="ZN ZN D8001 " - pdb=" SG CYS D4959 " Number of angles added : 8 37104 Ramachandran restraints generated. 18552 Oldfield, 0 Emsley, 18552 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 34984 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 756 helices and 84 sheets defined 60.8% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 46.46 Creating SS restraints... Processing helix chain 'E' and resid 39 through 44 removed outlier: 3.746A pdb=" N ARG E 43 " --> pdb=" O SER E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 68 removed outlier: 5.078A pdb=" N SER E 68 " --> pdb=" O VAL E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 83 removed outlier: 4.140A pdb=" N TYR E 83 " --> pdb=" O SER E 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 39 through 44 removed outlier: 3.805A pdb=" N ARG F 43 " --> pdb=" O SER F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 68 removed outlier: 5.070A pdb=" N SER F 68 " --> pdb=" O VAL F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 83 removed outlier: 4.120A pdb=" N TYR F 83 " --> pdb=" O SER F 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 44 removed outlier: 3.843A pdb=" N ARG G 43 " --> pdb=" O SER G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 68 removed outlier: 5.027A pdb=" N SER G 68 " --> pdb=" O VAL G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 83 removed outlier: 4.121A pdb=" N TYR G 83 " --> pdb=" O SER G 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 39 through 44 removed outlier: 3.842A pdb=" N ARG H 43 " --> pdb=" O SER H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 68 removed outlier: 5.028A pdb=" N SER H 68 " --> pdb=" O VAL H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 83 removed outlier: 4.112A pdb=" N TYR H 83 " --> pdb=" O SER H 79 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 24 removed outlier: 4.238A pdb=" N GLU I 23 " --> pdb=" O HIS I 19 " (cutoff:3.500A) Processing helix chain 'I' and resid 30 through 42 Processing helix chain 'I' and resid 51 through 64 removed outlier: 3.712A pdb=" N VAL I 55 " --> pdb=" O ASP I 51 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU I 64 " --> pdb=" O LYS I 60 " (cutoff:3.500A) Processing helix chain 'I' and resid 71 through 94 removed outlier: 5.395A pdb=" N SER I 94 " --> pdb=" O PHE I 90 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 24 removed outlier: 4.238A pdb=" N GLU K 23 " --> pdb=" O HIS K 19 " (cutoff:3.500A) Processing helix chain 'K' and resid 30 through 42 Processing helix chain 'K' and resid 51 through 64 removed outlier: 3.712A pdb=" N VAL K 55 " --> pdb=" O ASP K 51 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU K 64 " --> pdb=" O LYS K 60 " (cutoff:3.500A) Processing helix chain 'K' and resid 71 through 94 removed outlier: 5.394A pdb=" N SER K 94 " --> pdb=" O PHE K 90 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 24 removed outlier: 4.238A pdb=" N GLU M 23 " --> pdb=" O HIS M 19 " (cutoff:3.500A) Processing helix chain 'M' and resid 30 through 42 Processing helix chain 'M' and resid 51 through 64 removed outlier: 3.712A pdb=" N VAL M 55 " --> pdb=" O ASP M 51 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU M 64 " --> pdb=" O LYS M 60 " (cutoff:3.500A) Processing helix chain 'M' and resid 71 through 94 removed outlier: 5.394A pdb=" N SER M 94 " --> pdb=" O PHE M 90 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 24 removed outlier: 4.238A pdb=" N GLU O 23 " --> pdb=" O HIS O 19 " (cutoff:3.500A) Processing helix chain 'O' and resid 30 through 42 Processing helix chain 'O' and resid 51 through 64 removed outlier: 3.712A pdb=" N VAL O 55 " --> pdb=" O ASP O 51 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU O 64 " --> pdb=" O LYS O 60 " (cutoff:3.500A) Processing helix chain 'O' and resid 71 through 94 removed outlier: 5.395A pdb=" N SER O 94 " --> pdb=" O PHE O 90 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 24 removed outlier: 4.232A pdb=" N GLU J 23 " --> pdb=" O HIS J 19 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLY J 24 " --> pdb=" O SER J 20 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 42 Processing helix chain 'J' and resid 51 through 64 Processing helix chain 'J' and resid 71 through 93 removed outlier: 4.047A pdb=" N TYR J 75 " --> pdb=" O ASP J 71 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ASN J 87 " --> pdb=" O THR J 83 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 24 removed outlier: 4.232A pdb=" N GLU L 23 " --> pdb=" O HIS L 19 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLY L 24 " --> pdb=" O SER L 20 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 42 Processing helix chain 'L' and resid 51 through 64 Processing helix chain 'L' and resid 71 through 93 removed outlier: 4.047A pdb=" N TYR L 75 " --> pdb=" O ASP L 71 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ASN L 87 " --> pdb=" O THR L 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 24 removed outlier: 4.233A pdb=" N GLU N 23 " --> pdb=" O HIS N 19 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLY N 24 " --> pdb=" O SER N 20 " (cutoff:3.500A) Processing helix chain 'N' and resid 30 through 42 Processing helix chain 'N' and resid 51 through 64 Processing helix chain 'N' and resid 71 through 93 removed outlier: 4.048A pdb=" N TYR N 75 " --> pdb=" O ASP N 71 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ASN N 87 " --> pdb=" O THR N 83 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 24 removed outlier: 4.232A pdb=" N GLU P 23 " --> pdb=" O HIS P 19 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLY P 24 " --> pdb=" O SER P 20 " (cutoff:3.500A) Processing helix chain 'P' and resid 30 through 42 Processing helix chain 'P' and resid 51 through 64 Processing helix chain 'P' and resid 71 through 93 removed outlier: 4.048A pdb=" N TYR P 75 " --> pdb=" O ASP P 71 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ASN P 87 " --> pdb=" O THR P 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 67 removed outlier: 4.301A pdb=" N CYS D 66 " --> pdb=" O ASP D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 85 Processing helix chain 'D' and resid 144 through 149 removed outlier: 4.195A pdb=" N TRP D 148 " --> pdb=" O GLY D 144 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N TRP D 149 " --> pdb=" O GLU D 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 144 through 149' Processing helix chain 'D' and resid 252 through 257 removed outlier: 5.340A pdb=" N ALA D 257 " --> pdb=" O VAL D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 314 Processing helix chain 'D' and resid 366 through 371 Processing helix chain 'D' and resid 395 through 423 removed outlier: 3.698A pdb=" N PHE D 422 " --> pdb=" O GLY D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 454 Processing helix chain 'D' and resid 461 through 483 Processing helix chain 'D' and resid 484 through 498 removed outlier: 4.463A pdb=" N TYR D 498 " --> pdb=" O ARG D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 500 through 508 removed outlier: 3.834A pdb=" N PHE D 507 " --> pdb=" O HIS D 503 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 532 removed outlier: 3.828A pdb=" N SER D 515 " --> pdb=" O GLU D 511 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LYS D 517 " --> pdb=" O ALA D 513 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N GLU D 518 " --> pdb=" O GLU D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 534 through 545 removed outlier: 3.717A pdb=" N LEU D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N PHE D 541 " --> pdb=" O ASN D 537 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N SER D 542 " --> pdb=" O CYS D 538 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N THR D 543 " --> pdb=" O ALA D 539 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ASN D 544 " --> pdb=" O LEU D 540 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 553 removed outlier: 4.432A pdb=" N ASP D 553 " --> pdb=" O VAL D 549 " (cutoff:3.500A) Processing helix chain 'D' and resid 557 through 572 Processing helix chain 'D' and resid 573 through 579 Processing helix chain 'D' and resid 580 through 594 removed outlier: 3.546A pdb=" N LEU D 591 " --> pdb=" O ILE D 587 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 610 removed outlier: 3.622A pdb=" N LEU D 601 " --> pdb=" O ASN D 597 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL D 609 " --> pdb=" O CYS D 605 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N CYS D 610 " --> pdb=" O SER D 606 " (cutoff:3.500A) Processing helix chain 'D' and resid 615 through 630 Proline residue: D 628 - end of helix Processing helix chain 'D' and resid 811 through 816 removed outlier: 4.419A pdb=" N ALA D 815 " --> pdb=" O PRO D 811 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL D 816 " --> pdb=" O CYS D 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 811 through 816' Processing helix chain 'D' and resid 848 through 854 removed outlier: 3.876A pdb=" N PHE D 852 " --> pdb=" O SER D 848 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL D 853 " --> pdb=" O HIS D 849 " (cutoff:3.500A) Proline residue: D 854 - end of helix No H-bonds generated for 'chain 'D' and resid 848 through 854' Processing helix chain 'D' and resid 865 through 891 removed outlier: 4.034A pdb=" N ILE D 871 " --> pdb=" O HIS D 867 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS D 874 " --> pdb=" O ARG D 870 " (cutoff:3.500A) Processing helix chain 'D' and resid 915 through 936 removed outlier: 3.748A pdb=" N LEU D 930 " --> pdb=" O SER D 926 " (cutoff:3.500A) Processing helix chain 'D' and resid 944 through 951 removed outlier: 4.542A pdb=" N GLU D 948 " --> pdb=" O ASP D 944 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASP D 949 " --> pdb=" O GLU D 945 " (cutoff:3.500A) Processing helix chain 'D' and resid 957 through 962 removed outlier: 4.947A pdb=" N MET D 962 " --> pdb=" O LYS D 958 " (cutoff:3.500A) Processing helix chain 'D' and resid 979 through 1005 Processing helix chain 'D' and resid 1029 through 1051 Processing helix chain 'D' and resid 1218 through 1223 removed outlier: 6.786A pdb=" N GLU D1222 " --> pdb=" O CYS D1218 " (cutoff:3.500A) Processing helix chain 'D' and resid 1424 through 1431 Processing helix chain 'D' and resid 1445 through 1450 removed outlier: 4.136A pdb=" N VAL D1449 " --> pdb=" O GLU D1445 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N TRP D1450 " --> pdb=" O PRO D1446 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1445 through 1450' Processing helix chain 'D' and resid 1466 through 1471 removed outlier: 3.594A pdb=" N VAL D1470 " --> pdb=" O ASP D1466 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ARG D1471 " --> pdb=" O LEU D1467 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1466 through 1471' Processing helix chain 'D' and resid 1497 through 1503 removed outlier: 3.864A pdb=" N PHE D1501 " --> pdb=" O TRP D1497 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N SER D1503 " --> pdb=" O GLY D1499 " (cutoff:3.500A) Processing helix chain 'D' and resid 1575 through 1581 removed outlier: 4.008A pdb=" N ALA D1579 " --> pdb=" O PRO D1575 " (cutoff:3.500A) Processing helix chain 'D' and resid 1650 through 1658 removed outlier: 4.470A pdb=" N LEU D1654 " --> pdb=" O ASP D1650 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N SER D1655 " --> pdb=" O ILE D1651 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N GLU D1656 " --> pdb=" O LEU D1652 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LEU D1658 " --> pdb=" O LEU D1654 " (cutoff:3.500A) Processing helix chain 'D' and resid 1659 through 1676 removed outlier: 3.591A pdb=" N SER D1669 " --> pdb=" O SER D1665 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N CYS D1675 " --> pdb=" O TYR D1671 " (cutoff:3.500A) Processing helix chain 'D' and resid 1679 through 1690 removed outlier: 3.805A pdb=" N SER D1688 " --> pdb=" O HIS D1684 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N HIS D1689 " --> pdb=" O ALA D1685 " (cutoff:3.500A) Processing helix chain 'D' and resid 1691 through 1701 Processing helix chain 'D' and resid 1705 through 1720 Processing helix chain 'D' and resid 1721 through 1733 removed outlier: 4.262A pdb=" N SER D1733 " --> pdb=" O ARG D1729 " (cutoff:3.500A) Processing helix chain 'D' and resid 1740 through 1747 removed outlier: 5.538A pdb=" N THR D1747 " --> pdb=" O THR D1743 " (cutoff:3.500A) Processing helix chain 'D' and resid 1805 through 1827 Processing helix chain 'D' and resid 1835 through 1854 Proline residue: D1842 - end of helix Processing helix chain 'D' and resid 1857 through 1869 Processing helix chain 'D' and resid 1926 through 1931 removed outlier: 4.398A pdb=" N LYS D1931 " --> pdb=" O LEU D1927 " (cutoff:3.500A) Processing helix chain 'D' and resid 1933 through 1985 removed outlier: 3.527A pdb=" N ASP D1968 " --> pdb=" O GLU D1964 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N PHE D1985 " --> pdb=" O LEU D1981 " (cutoff:3.500A) Processing helix chain 'D' and resid 1988 through 2000 removed outlier: 4.230A pdb=" N GLU D1998 " --> pdb=" O ARG D1994 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N PHE D1999 " --> pdb=" O ARG D1995 " (cutoff:3.500A) Processing helix chain 'D' and resid 2002 through 2012 Processing helix chain 'D' and resid 2018 through 2023 Proline residue: D2023 - end of helix Processing helix chain 'D' and resid 2025 through 2044 removed outlier: 3.516A pdb=" N GLU D2031 " --> pdb=" O GLU D2027 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU D2032 " --> pdb=" O ILE D2028 " (cutoff:3.500A) Processing helix chain 'D' and resid 2094 through 2110 Processing helix chain 'D' and resid 2114 through 2131 removed outlier: 3.663A pdb=" N GLY D2131 " --> pdb=" O ARG D2127 " (cutoff:3.500A) Processing helix chain 'D' and resid 2132 through 2142 Proline residue: D2140 - end of helix Processing helix chain 'D' and resid 2146 through 2170 removed outlier: 3.721A pdb=" N VAL D2150 " --> pdb=" O SER D2146 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N GLU D2151 " --> pdb=" O VAL D2147 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N ASP D2152 " --> pdb=" O SER D2148 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE D2168 " --> pdb=" O ARG D2164 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL D2169 " --> pdb=" O SER D2165 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N GLN D2170 " --> pdb=" O LEU D2166 " (cutoff:3.500A) Processing helix chain 'D' and resid 2172 through 2189 Processing helix chain 'D' and resid 2190 through 2195 Processing helix chain 'D' and resid 2196 through 2203 Processing helix chain 'D' and resid 2204 through 2220 removed outlier: 5.458A pdb=" N GLY D2219 " --> pdb=" O VAL D2215 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N GLU D2220 " --> pdb=" O LEU D2216 " (cutoff:3.500A) Processing helix chain 'D' and resid 2226 through 2245 removed outlier: 4.088A pdb=" N SER D2244 " --> pdb=" O PHE D2240 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N ARG D2245 " --> pdb=" O CYS D2241 " (cutoff:3.500A) Processing helix chain 'D' and resid 2246 through 2256 removed outlier: 3.767A pdb=" N HIS D2254 " --> pdb=" O SER D2250 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N SER D2256 " --> pdb=" O PHE D2252 " (cutoff:3.500A) Processing helix chain 'D' and resid 2257 through 2263 removed outlier: 4.428A pdb=" N GLY D2263 " --> pdb=" O LEU D2259 " (cutoff:3.500A) Processing helix chain 'D' and resid 2272 through 2282 Processing helix chain 'D' and resid 2284 through 2291 Processing helix chain 'D' and resid 2292 through 2309 Processing helix chain 'D' and resid 2311 through 2318 Processing helix chain 'D' and resid 2325 through 2341 removed outlier: 3.646A pdb=" N PHE D2335 " --> pdb=" O ARG D2331 " (cutoff:3.500A) Processing helix chain 'D' and resid 2347 through 2362 Proline residue: D2362 - end of helix Processing helix chain 'D' and resid 2376 through 2391 Proline residue: D2391 - end of helix Processing helix chain 'D' and resid 2418 through 2438 Processing helix chain 'D' and resid 2440 through 2447 Processing helix chain 'D' and resid 2448 through 2463 Proline residue: D2463 - end of helix Processing helix chain 'D' and resid 2464 through 2473 Processing helix chain 'D' and resid 2496 through 2510 removed outlier: 3.677A pdb=" N LYS D2500 " --> pdb=" O VAL D2496 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N MET D2503 " --> pdb=" O HIS D2499 " (cutoff:3.500A) Processing helix chain 'D' and resid 2515 through 2539 removed outlier: 4.538A pdb=" N LEU D2528 " --> pdb=" O ASP D2524 " (cutoff:3.500A) Proline residue: D2529 - end of helix removed outlier: 4.526A pdb=" N THR D2539 " --> pdb=" O ALA D2535 " (cutoff:3.500A) Processing helix chain 'D' and resid 2545 through 2567 removed outlier: 5.312A pdb=" N LEU D2560 " --> pdb=" O CYS D2556 " (cutoff:3.500A) Proline residue: D2561 - end of helix Processing helix chain 'D' and resid 2576 through 2593 Processing helix chain 'D' and resid 2597 through 2615 removed outlier: 3.614A pdb=" N TYR D2614 " --> pdb=" O ALA D2610 " (cutoff:3.500A) Processing helix chain 'D' and resid 2616 through 2631 removed outlier: 3.909A pdb=" N LEU D2620 " --> pdb=" O ARG D2616 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLN D2621 " --> pdb=" O PRO D2617 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N HIS D2622 " --> pdb=" O SER D2618 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N LEU D2623 " --> pdb=" O MET D2619 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE D2629 " --> pdb=" O ARG D2625 " (cutoff:3.500A) Processing helix chain 'D' and resid 2635 through 2653 removed outlier: 3.590A pdb=" N LYS D2639 " --> pdb=" O ASN D2635 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N MET D2640 " --> pdb=" O GLU D2636 " (cutoff:3.500A) Proline residue: D2641 - end of helix Processing helix chain 'D' and resid 2669 through 2690 Processing helix chain 'D' and resid 2694 through 2712 Proline residue: D2702 - end of helix Proline residue: D2712 - end of helix Processing helix chain 'D' and resid 2749 through 2775 Processing helix chain 'D' and resid 2801 through 2821 Proline residue: D2809 - end of helix Processing helix chain 'D' and resid 2862 through 2867 removed outlier: 4.866A pdb=" N VAL D2866 " --> pdb=" O ASP D2862 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N THR D2867 " --> pdb=" O LEU D2863 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2862 through 2867' Processing helix chain 'D' and resid 2869 through 2899 Processing helix chain 'D' and resid 2908 through 2913 removed outlier: 5.181A pdb=" N THR D2913 " --> pdb=" O TYR D2909 " (cutoff:3.500A) Processing helix chain 'D' and resid 2916 through 2935 removed outlier: 4.139A pdb=" N ASP D2920 " --> pdb=" O GLU D2916 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N LYS D2923 " --> pdb=" O ARG D2919 " (cutoff:3.500A) Processing helix chain 'D' and resid 2942 through 2948 Processing helix chain 'D' and resid 2950 through 2984 removed outlier: 5.999A pdb=" N PHE D2956 " --> pdb=" O ILE D2952 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ALA D2957 " --> pdb=" O GLU D2953 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N PHE D2958 " --> pdb=" O LYS D2954 " (cutoff:3.500A) Processing helix chain 'D' and resid 2992 through 3015 removed outlier: 4.347A pdb=" N LEU D3004 " --> pdb=" O ALA D3000 " (cutoff:3.500A) Proline residue: D3005 - end of helix Processing helix chain 'D' and resid 3033 through 3052 Processing helix chain 'D' and resid 3054 through 3059 removed outlier: 3.540A pdb=" N PHE D3058 " --> pdb=" O ARG D3054 " (cutoff:3.500A) Processing helix chain 'D' and resid 3060 through 3076 removed outlier: 4.794A pdb=" N ALA D3064 " --> pdb=" O THR D3060 " (cutoff:3.500A) Processing helix chain 'D' and resid 3077 through 3084 removed outlier: 3.956A pdb=" N VAL D3081 " --> pdb=" O ASP D3077 " (cutoff:3.500A) Processing helix chain 'D' and resid 3086 through 3113 Processing helix chain 'D' and resid 3124 through 3152 removed outlier: 3.647A pdb=" N LEU D3137 " --> pdb=" O THR D3133 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N LEU D3138 " --> pdb=" O THR D3134 " (cutoff:3.500A) Proline residue: D3139 - end of helix Processing helix chain 'D' and resid 3160 through 3180 removed outlier: 4.792A pdb=" N ARG D3180 " --> pdb=" O LEU D3176 " (cutoff:3.500A) Processing helix chain 'D' and resid 3181 through 3202 Proline residue: D3189 - end of helix Processing helix chain 'D' and resid 3208 through 3216 removed outlier: 4.690A pdb=" N GLU D3213 " --> pdb=" O PRO D3209 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TYR D3214 " --> pdb=" O GLU D3210 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ASN D3215 " --> pdb=" O LEU D3211 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ALA D3216 " --> pdb=" O ASN D3212 " (cutoff:3.500A) Processing helix chain 'D' and resid 3218 through 3223 Processing helix chain 'D' and resid 3224 through 3232 removed outlier: 4.094A pdb=" N ARG D3228 " --> pdb=" O SER D3224 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ALA D3229 " --> pdb=" O PRO D3225 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ILE D3230 " --> pdb=" O ARG D3226 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N LEU D3231 " --> pdb=" O GLU D3227 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N GLY D3232 " --> pdb=" O ARG D3228 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 3224 through 3232' Processing helix chain 'D' and resid 3236 through 3242 removed outlier: 3.691A pdb=" N MET D3240 " --> pdb=" O SER D3236 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N CYS D3241 " --> pdb=" O VAL D3237 " (cutoff:3.500A) Proline residue: D3242 - end of helix No H-bonds generated for 'chain 'D' and resid 3236 through 3242' Processing helix chain 'D' and resid 3246 through 3261 Processing helix chain 'D' and resid 3263 through 3268 Proline residue: D3268 - end of helix Processing helix chain 'D' and resid 3269 through 3290 removed outlier: 4.091A pdb=" N LEU D3275 " --> pdb=" O ILE D3271 " (cutoff:3.500A) Proline residue: D3276 - end of helix Proline residue: D3283 - end of helix removed outlier: 4.103A pdb=" N GLU D3287 " --> pdb=" O PRO D3283 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ARG D3288 " --> pdb=" O ARG D3284 " (cutoff:3.500A) Proline residue: D3290 - end of helix Processing helix chain 'D' and resid 3309 through 3328 Processing helix chain 'D' and resid 3333 through 3348 removed outlier: 4.209A pdb=" N LYS D3337 " --> pdb=" O ALA D3333 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ARG D3338 " --> pdb=" O SER D3334 " (cutoff:3.500A) Proline residue: D3345 - end of helix removed outlier: 4.324A pdb=" N SER D3348 " --> pdb=" O GLN D3344 " (cutoff:3.500A) Processing helix chain 'D' and resid 3351 through 3384 removed outlier: 4.744A pdb=" N LEU D3355 " --> pdb=" O ARG D3351 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ARG D3356 " --> pdb=" O PRO D3352 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N ILE D3360 " --> pdb=" O ARG D3356 " (cutoff:3.500A) Proline residue: D3361 - end of helix removed outlier: 4.579A pdb=" N ALA D3384 " --> pdb=" O LEU D3380 " (cutoff:3.500A) Processing helix chain 'D' and resid 3385 through 3421 removed outlier: 4.833A pdb=" N GLY D3391 " --> pdb=" O GLU D3387 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU D3392 " --> pdb=" O ALA D3388 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU D3393 " --> pdb=" O GLU D3389 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU D3394 " --> pdb=" O GLU D3390 " (cutoff:3.500A) Proline residue: D3411 - end of helix Processing helix chain 'D' and resid 3422 through 3428 Proline residue: D3428 - end of helix Processing helix chain 'D' and resid 3429 through 3450 removed outlier: 4.802A pdb=" N HIS D3450 " --> pdb=" O TRP D3446 " (cutoff:3.500A) Processing helix chain 'D' and resid 3451 through 3464 removed outlier: 3.710A pdb=" N GLU D3464 " --> pdb=" O VAL D3460 " (cutoff:3.500A) Processing helix chain 'D' and resid 3466 through 3472 removed outlier: 3.792A pdb=" N PHE D3470 " --> pdb=" O ASN D3466 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU D3471 " --> pdb=" O ASN D3467 " (cutoff:3.500A) Processing helix chain 'D' and resid 3505 through 3510 removed outlier: 5.308A pdb=" N LEU D3510 " --> pdb=" O VAL D3506 " (cutoff:3.500A) Processing helix chain 'D' and resid 3511 through 3527 Proline residue: D3520 - end of helix removed outlier: 3.511A pdb=" N CYS D3526 " --> pdb=" O GLY D3522 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ALA D3527 " --> pdb=" O LEU D3523 " (cutoff:3.500A) Processing helix chain 'D' and resid 3530 through 3544 Processing helix chain 'D' and resid 3546 through 3558 Processing helix chain 'D' and resid 3563 through 3568 removed outlier: 3.776A pdb=" N SER D3567 " --> pdb=" O LYS D3563 " (cutoff:3.500A) Proline residue: D3568 - end of helix No H-bonds generated for 'chain 'D' and resid 3563 through 3568' Processing helix chain 'D' and resid 3569 through 3581 Proline residue: D3581 - end of helix Processing helix chain 'D' and resid 3582 through 3587 removed outlier: 4.334A pdb=" N ASP D3586 " --> pdb=" O GLY D3582 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N ALA D3587 " --> pdb=" O ARG D3583 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 3582 through 3587' Processing helix chain 'D' and resid 3589 through 3613 removed outlier: 3.552A pdb=" N HIS D3606 " --> pdb=" O ALA D3602 " (cutoff:3.500A) Proline residue: D3613 - end of helix Processing helix chain 'D' and resid 3629 through 3638 removed outlier: 3.755A pdb=" N CYS D3636 " --> pdb=" O ALA D3632 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ARG D3638 " --> pdb=" O VAL D3634 " (cutoff:3.500A) Processing helix chain 'D' and resid 3641 through 3646 removed outlier: 4.352A pdb=" N LEU D3645 " --> pdb=" O PRO D3641 " (cutoff:3.500A) Proline residue: D3646 - end of helix No H-bonds generated for 'chain 'D' and resid 3641 through 3646' Processing helix chain 'D' and resid 3647 through 3666 removed outlier: 3.959A pdb=" N ILE D3663 " --> pdb=" O LYS D3659 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N LEU D3664 " --> pdb=" O ALA D3660 " (cutoff:3.500A) Processing helix chain 'D' and resid 3670 through 3681 removed outlier: 5.732A pdb=" N ALA D3681 " --> pdb=" O ASP D3677 " (cutoff:3.500A) Processing helix chain 'D' and resid 3683 through 3688 Processing helix chain 'D' and resid 3697 through 3712 Processing helix chain 'D' and resid 3720 through 3735 removed outlier: 3.780A pdb=" N CYS D3734 " --> pdb=" O MET D3730 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N HIS D3735 " --> pdb=" O ALA D3731 " (cutoff:3.500A) Processing helix chain 'D' and resid 3755 through 3775 removed outlier: 3.684A pdb=" N LEU D3773 " --> pdb=" O GLN D3769 " (cutoff:3.500A) Processing helix chain 'D' and resid 3777 through 3790 removed outlier: 4.107A pdb=" N LYS D3790 " --> pdb=" O ILE D3786 " (cutoff:3.500A) Processing helix chain 'D' and resid 3794 through 3809 Processing helix chain 'D' and resid 3812 through 3827 removed outlier: 3.594A pdb=" N GLN D3816 " --> pdb=" O ASN D3812 " (cutoff:3.500A) Processing helix chain 'D' and resid 3829 through 3842 Processing helix chain 'D' and resid 3846 through 3860 removed outlier: 4.960A pdb=" N GLY D3860 " --> pdb=" O ALA D3856 " (cutoff:3.500A) Processing helix chain 'D' and resid 3864 through 3869 removed outlier: 4.474A pdb=" N ILE D3869 " --> pdb=" O ASP D3865 " (cutoff:3.500A) Processing helix chain 'D' and resid 3880 through 3896 removed outlier: 3.642A pdb=" N CYS D3895 " --> pdb=" O LEU D3891 " (cutoff:3.500A) Processing helix chain 'D' and resid 3899 through 3908 removed outlier: 3.500A pdb=" N ARG D3907 " --> pdb=" O GLN D3903 " (cutoff:3.500A) Processing helix chain 'D' and resid 3917 through 3942 removed outlier: 4.743A pdb=" N GLY D3942 " --> pdb=" O TRP D3938 " (cutoff:3.500A) Processing helix chain 'D' and resid 3947 through 3973 removed outlier: 3.559A pdb=" N ILE D3972 " --> pdb=" O LEU D3968 " (cutoff:3.500A) Processing helix chain 'D' and resid 3976 through 3987 removed outlier: 4.877A pdb=" N ARG D3987 " --> pdb=" O LEU D3983 " (cutoff:3.500A) Processing helix chain 'D' and resid 3988 through 4010 removed outlier: 3.927A pdb=" N ASP D4009 " --> pdb=" O LYS D4005 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N SER D4010 " --> pdb=" O LEU D4006 " (cutoff:3.500A) Processing helix chain 'D' and resid 4011 through 4036 removed outlier: 5.672A pdb=" N LEU D4015 " --> pdb=" O SER D4011 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU D4034 " --> pdb=" O LEU D4030 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU D4035 " --> pdb=" O LEU D4031 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N GLY D4036 " --> pdb=" O SER D4032 " (cutoff:3.500A) Processing helix chain 'D' and resid 4041 through 4055 Processing helix chain 'D' and resid 4056 through 4075 removed outlier: 3.532A pdb=" N PHE D4065 " --> pdb=" O ILE D4061 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE D4068 " --> pdb=" O PHE D4064 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASP D4073 " --> pdb=" O LEU D4069 " (cutoff:3.500A) Processing helix chain 'D' and resid 4077 through 4085 removed outlier: 4.912A pdb=" N THR D4085 " --> pdb=" O GLN D4081 " (cutoff:3.500A) Processing helix chain 'D' and resid 4092 through 4104 Processing helix chain 'D' and resid 4107 through 4119 removed outlier: 4.388A pdb=" N GLU D4119 " --> pdb=" O LEU D4115 " (cutoff:3.500A) Processing helix chain 'D' and resid 4127 through 4140 removed outlier: 4.755A pdb=" N PHE D4135 " --> pdb=" O PHE D4131 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLN D4136 " --> pdb=" O ALA D4132 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N GLU D4137 " --> pdb=" O ASN D4133 " (cutoff:3.500A) Proline residue: D4138 - end of helix Processing helix chain 'D' and resid 4141 through 4158 Proline residue: D4158 - end of helix Processing helix chain 'D' and resid 4160 through 4171 removed outlier: 3.780A pdb=" N ARG D4164 " --> pdb=" O ASP D4160 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ASN D4165 " --> pdb=" O PRO D4161 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE D4166 " --> pdb=" O ARG D4162 " (cutoff:3.500A) Processing helix chain 'D' and resid 4172 through 4178 Processing helix chain 'D' and resid 4201 through 4210 Processing helix chain 'D' and resid 4211 through 4227 Processing helix chain 'D' and resid 4232 through 4255 Processing helix chain 'D' and resid 4538 through 4557 Processing helix chain 'D' and resid 4558 through 4578 removed outlier: 4.207A pdb=" N PHE D4577 " --> pdb=" O PHE D4573 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N TYR D4578 " --> pdb=" O ILE D4574 " (cutoff:3.500A) Processing helix chain 'D' and resid 4638 through 4681 removed outlier: 3.634A pdb=" N ARG D4642 " --> pdb=" O GLU D4638 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N VAL D4664 " --> pdb=" O ASN D4660 " (cutoff:3.500A) Proline residue: D4665 - end of helix Processing helix chain 'D' and resid 4694 through 4705 removed outlier: 4.240A pdb=" N LEU D4702 " --> pdb=" O GLN D4698 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N VAL D4703 " --> pdb=" O TRP D4699 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU D4704 " --> pdb=" O ASP D4700 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ASN D4705 " --> pdb=" O ARG D4701 " (cutoff:3.500A) Processing helix chain 'D' and resid 4717 through 4727 Processing helix chain 'D' and resid 4731 through 4740 Processing helix chain 'D' and resid 4742 through 4752 Processing helix chain 'D' and resid 4761 through 4769 Processing helix chain 'D' and resid 4770 through 4785 removed outlier: 5.293A pdb=" N ASN D4785 " --> pdb=" O ILE D4781 " (cutoff:3.500A) Processing helix chain 'D' and resid 4786 through 4803 Processing helix chain 'D' and resid 4804 through 4818 removed outlier: 4.719A pdb=" N ALA D4808 " --> pdb=" O ASN D4804 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ALA D4809 " --> pdb=" O PHE D4805 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N HIS D4810 " --> pdb=" O PHE D4806 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU D4811 " --> pdb=" O PHE D4807 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LEU D4812 " --> pdb=" O ALA D4808 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASP D4813 " --> pdb=" O ALA D4809 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ILE D4814 " --> pdb=" O HIS D4810 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N ALA D4815 " --> pdb=" O LEU D4811 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N MET D4816 " --> pdb=" O LEU D4812 " (cutoff:3.500A) Processing helix chain 'D' and resid 4819 through 4830 removed outlier: 3.601A pdb=" N VAL D4828 " --> pdb=" O ILE D4824 " (cutoff:3.500A) Processing helix chain 'D' and resid 4831 through 4856 Processing helix chain 'D' and resid 4857 through 4862 removed outlier: 4.275A pdb=" N TYR D4861 " --> pdb=" O PHE D4857 " (cutoff:3.500A) removed outlier: 4.982A 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 4891 removed outlier: 4.492A pdb=" N VAL D4889 " --> pdb=" O MET D4885 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ARG D4890 " --> pdb=" O TYR D4886 " (cutoff:3.500A) Processing helix chain 'D' and resid 4894 through 4900 removed outlier: 4.215A pdb=" N GLU D4898 " --> pdb=" O GLY D4894 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N GLU D4900 " --> pdb=" O GLY D4896 " (cutoff:3.500A) Processing helix chain 'D' and resid 4907 through 4922 Processing helix chain 'D' and resid 4926 through 4954 Processing helix chain 'D' and resid 4962 through 4968 removed outlier: 3.895A pdb=" N PHE D4966 " --> pdb=" O GLY D4962 " (cutoff:3.500A) Processing helix chain 'D' and resid 4971 through 4979 Processing helix chain 'D' and resid 4982 through 4996 removed outlier: 3.523A pdb=" N LEU D4990 " --> pdb=" O TYR D4986 " (cutoff:3.500A) Processing helix chain 'D' and resid 5002 through 5015 Processing helix chain 'D' and resid 5025 through 5031 Processing helix chain 'D' and resid 323 through 328 removed outlier: 4.313A pdb=" N VAL D 326 " --> pdb=" O LYS D 323 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA D 327 " --> pdb=" O LEU D 324 " (cutoff:3.500A) Proline residue: D 328 - end of helix No H-bonds generated for 'chain 'D' and resid 323 through 328' Processing helix chain 'D' and resid 4683 through 4688 Processing helix chain 'A' and resid 62 through 67 removed outlier: 4.301A pdb=" N CYS A 66 " --> pdb=" O ASP A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 85 Processing helix chain 'A' and resid 144 through 149 removed outlier: 4.196A pdb=" N TRP A 148 " --> pdb=" O GLY A 144 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N TRP A 149 " --> pdb=" O GLU A 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 144 through 149' Processing helix chain 'A' and resid 252 through 257 removed outlier: 5.340A pdb=" N ALA A 257 " --> pdb=" O VAL A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 314 Processing helix chain 'A' and resid 366 through 371 Processing helix chain 'A' and resid 395 through 423 removed outlier: 3.698A pdb=" N PHE A 422 " --> pdb=" O GLY A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 454 Processing helix chain 'A' and resid 461 through 483 Processing helix chain 'A' and resid 484 through 498 removed outlier: 4.464A pdb=" N TYR A 498 " --> pdb=" O ARG A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 508 removed outlier: 3.834A pdb=" N PHE A 507 " --> pdb=" O HIS A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 532 removed outlier: 3.828A pdb=" N SER A 515 " --> pdb=" O GLU A 511 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LYS A 517 " --> pdb=" O ALA A 513 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N GLU A 518 " --> pdb=" O GLU A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 545 removed outlier: 3.717A pdb=" N LEU A 540 " --> pdb=" O THR A 536 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N PHE A 541 " --> pdb=" O ASN A 537 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N SER A 542 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N THR A 543 " --> pdb=" O ALA A 539 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ASN A 544 " --> pdb=" O LEU A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 553 removed outlier: 4.432A pdb=" N ASP A 553 " --> pdb=" O VAL A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 572 Processing helix chain 'A' and resid 573 through 579 Processing helix chain 'A' and resid 580 through 594 removed outlier: 3.546A pdb=" N LEU A 591 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 610 removed outlier: 3.622A pdb=" N LEU A 601 " --> pdb=" O ASN A 597 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL A 609 " --> pdb=" O CYS A 605 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N CYS A 610 " --> pdb=" O SER A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 630 Proline residue: A 628 - end of helix Processing helix chain 'A' and resid 811 through 816 removed outlier: 4.419A pdb=" N ALA A 815 " --> pdb=" O PRO A 811 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N VAL A 816 " --> pdb=" O CYS A 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 811 through 816' Processing helix chain 'A' and resid 848 through 854 removed outlier: 3.877A pdb=" N PHE A 852 " --> pdb=" O SER A 848 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N VAL A 853 " --> pdb=" O HIS A 849 " (cutoff:3.500A) Proline residue: A 854 - end of helix No H-bonds generated for 'chain 'A' and resid 848 through 854' Processing helix chain 'A' and resid 865 through 891 removed outlier: 4.035A pdb=" N ILE A 871 " --> pdb=" O HIS A 867 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS A 874 " --> pdb=" O ARG A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 936 removed outlier: 3.748A pdb=" N LEU A 930 " --> pdb=" O SER A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 944 through 951 removed outlier: 4.542A pdb=" N GLU A 948 " --> pdb=" O ASP A 944 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASP A 949 " --> pdb=" O GLU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 957 through 962 removed outlier: 4.947A pdb=" N MET A 962 " --> pdb=" O LYS A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 979 through 1005 Processing helix chain 'A' and resid 1029 through 1051 Processing helix chain 'A' and resid 1218 through 1223 removed outlier: 6.786A pdb=" N GLU A1222 " --> pdb=" O CYS A1218 " (cutoff:3.500A) Processing helix chain 'A' and resid 1424 through 1431 Processing helix chain 'A' and resid 1445 through 1450 removed outlier: 4.136A pdb=" N VAL A1449 " --> pdb=" O GLU A1445 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N TRP A1450 " --> pdb=" O PRO A1446 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1445 through 1450' Processing helix chain 'A' and resid 1466 through 1471 removed outlier: 3.594A pdb=" N VAL A1470 " --> pdb=" O ASP A1466 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ARG A1471 " --> pdb=" O LEU A1467 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1466 through 1471' Processing helix chain 'A' and resid 1497 through 1503 removed outlier: 3.864A pdb=" N PHE A1501 " --> pdb=" O TRP A1497 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N SER A1503 " --> pdb=" O GLY A1499 " (cutoff:3.500A) Processing helix chain 'A' and resid 1575 through 1581 removed outlier: 4.009A pdb=" N ALA A1579 " --> pdb=" O PRO A1575 " (cutoff:3.500A) Processing helix chain 'A' and resid 1650 through 1658 removed outlier: 4.470A pdb=" N LEU A1654 " --> pdb=" O ASP A1650 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N SER A1655 " --> pdb=" O ILE A1651 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N GLU A1656 " --> pdb=" O LEU A1652 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LEU A1658 " --> pdb=" O LEU A1654 " (cutoff:3.500A) Processing helix chain 'A' and resid 1659 through 1676 removed outlier: 3.591A pdb=" N SER A1669 " --> pdb=" O SER A1665 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N CYS A1675 " --> pdb=" O TYR A1671 " (cutoff:3.500A) Processing helix chain 'A' and resid 1679 through 1690 removed outlier: 3.805A pdb=" N SER A1688 " --> pdb=" O HIS A1684 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N HIS A1689 " --> pdb=" O ALA A1685 " (cutoff:3.500A) Processing helix chain 'A' and resid 1691 through 1701 Processing helix chain 'A' and resid 1705 through 1720 Processing helix chain 'A' and resid 1721 through 1733 removed outlier: 4.262A pdb=" N SER A1733 " --> pdb=" O ARG A1729 " (cutoff:3.500A) Processing helix chain 'A' and resid 1740 through 1747 removed outlier: 5.538A pdb=" N THR A1747 " --> pdb=" O THR A1743 " (cutoff:3.500A) Processing helix chain 'A' and resid 1805 through 1827 Processing helix chain 'A' and resid 1835 through 1854 Proline residue: A1842 - end of helix Processing helix chain 'A' and resid 1857 through 1869 Processing helix chain 'A' and resid 1926 through 1931 removed outlier: 4.397A pdb=" N LYS A1931 " --> pdb=" O LEU A1927 " (cutoff:3.500A) Processing helix chain 'A' and resid 1933 through 1985 removed outlier: 3.528A pdb=" N ASP A1968 " --> pdb=" O GLU A1964 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N PHE A1985 " --> pdb=" O LEU A1981 " (cutoff:3.500A) Processing helix chain 'A' and resid 1988 through 2000 removed outlier: 4.230A pdb=" N GLU A1998 " --> pdb=" O ARG A1994 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N PHE A1999 " --> pdb=" O ARG A1995 " (cutoff:3.500A) Processing helix chain 'A' and resid 2002 through 2012 Processing helix chain 'A' and resid 2018 through 2023 Proline residue: A2023 - end of helix Processing helix chain 'A' and resid 2025 through 2044 removed outlier: 3.516A pdb=" N GLU A2031 " --> pdb=" O GLU A2027 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU A2032 " --> pdb=" O ILE A2028 " (cutoff:3.500A) Processing helix chain 'A' and resid 2094 through 2110 Processing helix chain 'A' and resid 2114 through 2131 removed outlier: 3.663A pdb=" N GLY A2131 " --> pdb=" O ARG A2127 " (cutoff:3.500A) Processing helix chain 'A' and resid 2132 through 2142 Proline residue: A2140 - end of helix Processing helix chain 'A' and resid 2146 through 2170 removed outlier: 3.720A pdb=" N VAL A2150 " --> pdb=" O SER A2146 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N GLU A2151 " --> pdb=" O VAL A2147 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N ASP A2152 " --> pdb=" O SER A2148 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE A2168 " --> pdb=" O ARG A2164 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL A2169 " --> pdb=" O SER A2165 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N GLN A2170 " --> pdb=" O LEU A2166 " (cutoff:3.500A) Processing helix chain 'A' and resid 2172 through 2189 Processing helix chain 'A' and resid 2190 through 2195 Processing helix chain 'A' and resid 2196 through 2203 Processing helix chain 'A' and resid 2204 through 2220 removed outlier: 5.457A pdb=" N GLY A2219 " --> pdb=" O VAL A2215 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N GLU A2220 " --> pdb=" O LEU A2216 " (cutoff:3.500A) Processing helix chain 'A' and resid 2226 through 2245 removed outlier: 4.089A pdb=" N SER A2244 " --> pdb=" O PHE A2240 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N ARG A2245 " --> pdb=" O CYS A2241 " (cutoff:3.500A) Processing helix chain 'A' and resid 2246 through 2256 removed outlier: 3.767A pdb=" N HIS A2254 " --> pdb=" O SER A2250 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N SER A2256 " --> pdb=" O PHE A2252 " (cutoff:3.500A) Processing helix chain 'A' and resid 2257 through 2263 removed outlier: 4.428A pdb=" N GLY A2263 " --> pdb=" O LEU A2259 " (cutoff:3.500A) Processing helix chain 'A' and resid 2272 through 2282 Processing helix chain 'A' and resid 2284 through 2291 Processing helix chain 'A' and resid 2292 through 2309 Processing helix chain 'A' and resid 2311 through 2318 Processing helix chain 'A' and resid 2325 through 2341 removed outlier: 3.646A pdb=" N PHE A2335 " --> pdb=" O ARG A2331 " (cutoff:3.500A) Processing helix chain 'A' and resid 2347 through 2362 Proline residue: A2362 - end of helix Processing helix chain 'A' and resid 2376 through 2391 Proline residue: A2391 - end of helix Processing helix chain 'A' and resid 2418 through 2438 Processing helix chain 'A' and resid 2440 through 2447 Processing helix chain 'A' and resid 2448 through 2463 Proline residue: A2463 - end of helix Processing helix chain 'A' and resid 2464 through 2473 Processing helix chain 'A' and resid 2496 through 2510 removed outlier: 3.677A pdb=" N LYS A2500 " --> pdb=" O VAL A2496 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N MET A2503 " --> pdb=" O HIS A2499 " (cutoff:3.500A) Processing helix chain 'A' and resid 2515 through 2539 removed outlier: 4.539A pdb=" N LEU A2528 " --> pdb=" O ASP A2524 " (cutoff:3.500A) Proline residue: A2529 - end of helix removed outlier: 4.525A pdb=" N THR A2539 " --> pdb=" O ALA A2535 " (cutoff:3.500A) Processing helix chain 'A' and resid 2545 through 2567 removed outlier: 5.313A pdb=" N LEU A2560 " --> pdb=" O CYS A2556 " (cutoff:3.500A) Proline residue: A2561 - end of helix Processing helix chain 'A' and resid 2576 through 2593 Processing helix chain 'A' and resid 2597 through 2615 removed outlier: 3.614A pdb=" N TYR A2614 " --> pdb=" O ALA A2610 " (cutoff:3.500A) Processing helix chain 'A' and resid 2616 through 2631 removed outlier: 3.909A pdb=" N LEU A2620 " --> pdb=" O ARG A2616 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLN A2621 " --> pdb=" O PRO A2617 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N HIS A2622 " --> pdb=" O SER A2618 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N LEU A2623 " --> pdb=" O MET A2619 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE A2629 " --> pdb=" O ARG A2625 " (cutoff:3.500A) Processing helix chain 'A' and resid 2635 through 2653 removed outlier: 3.591A pdb=" N LYS A2639 " --> pdb=" O ASN A2635 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N MET A2640 " --> pdb=" O GLU A2636 " (cutoff:3.500A) Proline residue: A2641 - end of helix Processing helix chain 'A' and resid 2669 through 2690 Processing helix chain 'A' and resid 2694 through 2712 Proline residue: A2702 - end of helix Proline residue: A2712 - end of helix Processing helix chain 'A' and resid 2749 through 2775 Processing helix chain 'A' and resid 2801 through 2821 Proline residue: A2809 - end of helix Processing helix chain 'A' and resid 2862 through 2867 removed outlier: 4.866A pdb=" N VAL A2866 " --> pdb=" O ASP A2862 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N THR A2867 " --> pdb=" O LEU A2863 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2862 through 2867' Processing helix chain 'A' and resid 2869 through 2899 Processing helix chain 'A' and resid 2908 through 2913 removed outlier: 5.181A pdb=" N THR A2913 " --> pdb=" O TYR A2909 " (cutoff:3.500A) Processing helix chain 'A' and resid 2916 through 2935 removed outlier: 4.138A pdb=" N ASP A2920 " --> pdb=" O GLU A2916 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N LYS A2923 " --> pdb=" O ARG A2919 " (cutoff:3.500A) Processing helix chain 'A' and resid 2942 through 2948 Processing helix chain 'A' and resid 2950 through 2984 removed outlier: 5.999A pdb=" N PHE A2956 " --> pdb=" O ILE A2952 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ALA A2957 " --> pdb=" O GLU A2953 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N PHE A2958 " --> pdb=" O LYS A2954 " (cutoff:3.500A) Processing helix chain 'A' and resid 2992 through 3015 removed outlier: 4.347A pdb=" N LEU A3004 " --> pdb=" O ALA A3000 " (cutoff:3.500A) Proline residue: A3005 - end of helix Processing helix chain 'A' and resid 3033 through 3052 Processing helix chain 'A' and resid 3054 through 3059 removed outlier: 3.540A pdb=" N PHE A3058 " --> pdb=" O ARG A3054 " (cutoff:3.500A) Processing helix chain 'A' and resid 3060 through 3076 removed outlier: 4.793A pdb=" N ALA A3064 " --> pdb=" O THR A3060 " (cutoff:3.500A) Processing helix chain 'A' and resid 3077 through 3084 removed outlier: 3.955A pdb=" N VAL A3081 " --> pdb=" O ASP A3077 " (cutoff:3.500A) Processing helix chain 'A' and resid 3086 through 3113 Processing helix chain 'A' and resid 3124 through 3152 removed outlier: 3.646A pdb=" N LEU A3137 " --> pdb=" O THR A3133 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N LEU A3138 " --> pdb=" O THR A3134 " (cutoff:3.500A) Proline residue: A3139 - end of helix Processing helix chain 'A' and resid 3160 through 3180 removed outlier: 4.792A pdb=" N ARG A3180 " --> pdb=" O LEU A3176 " (cutoff:3.500A) Processing helix chain 'A' and resid 3181 through 3202 Proline residue: A3189 - end of helix Processing helix chain 'A' and resid 3208 through 3216 removed outlier: 4.691A pdb=" N GLU A3213 " --> pdb=" O PRO A3209 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TYR A3214 " --> pdb=" O GLU A3210 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ASN A3215 " --> pdb=" O LEU A3211 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ALA A3216 " --> pdb=" O ASN A3212 " (cutoff:3.500A) Processing helix chain 'A' and resid 3218 through 3223 Processing helix chain 'A' and resid 3224 through 3232 removed outlier: 4.094A pdb=" N ARG A3228 " --> pdb=" O SER A3224 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ALA A3229 " --> pdb=" O PRO A3225 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ILE A3230 " --> pdb=" O ARG A3226 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N LEU A3231 " --> pdb=" O GLU A3227 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N GLY A3232 " --> pdb=" O ARG A3228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3224 through 3232' Processing helix chain 'A' and resid 3236 through 3242 removed outlier: 3.692A pdb=" N MET A3240 " --> pdb=" O SER A3236 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N CYS A3241 " --> pdb=" O VAL A3237 " (cutoff:3.500A) Proline residue: A3242 - end of helix No H-bonds generated for 'chain 'A' and resid 3236 through 3242' Processing helix chain 'A' and resid 3246 through 3261 Processing helix chain 'A' and resid 3263 through 3268 Proline residue: A3268 - end of helix Processing helix chain 'A' and resid 3269 through 3290 removed outlier: 4.091A pdb=" N LEU A3275 " --> pdb=" O ILE A3271 " (cutoff:3.500A) Proline residue: A3276 - end of helix Proline residue: A3283 - end of helix removed outlier: 4.103A pdb=" N GLU A3287 " --> pdb=" O PRO A3283 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ARG A3288 " --> pdb=" O ARG A3284 " (cutoff:3.500A) Proline residue: A3290 - end of helix Processing helix chain 'A' and resid 3309 through 3328 Processing helix chain 'A' and resid 3333 through 3348 removed outlier: 4.209A pdb=" N LYS A3337 " --> pdb=" O ALA A3333 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ARG A3338 " --> pdb=" O SER A3334 " (cutoff:3.500A) Proline residue: A3345 - end of helix removed outlier: 4.323A pdb=" N SER A3348 " --> pdb=" O GLN A3344 " (cutoff:3.500A) Processing helix chain 'A' and resid 3351 through 3384 removed outlier: 4.743A pdb=" N LEU A3355 " --> pdb=" O ARG A3351 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ARG A3356 " --> pdb=" O PRO A3352 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N ILE A3360 " --> pdb=" O ARG A3356 " (cutoff:3.500A) Proline residue: A3361 - end of helix removed outlier: 4.579A pdb=" N ALA A3384 " --> pdb=" O LEU A3380 " (cutoff:3.500A) Processing helix chain 'A' and resid 3385 through 3421 removed outlier: 4.832A pdb=" N GLY A3391 " --> pdb=" O GLU A3387 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU A3392 " --> pdb=" O ALA A3388 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LEU A3393 " --> pdb=" O GLU A3389 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU A3394 " --> pdb=" O GLU A3390 " (cutoff:3.500A) Proline residue: A3411 - end of helix Processing helix chain 'A' and resid 3422 through 3428 Proline residue: A3428 - end of helix Processing helix chain 'A' and resid 3429 through 3450 removed outlier: 4.802A pdb=" N HIS A3450 " --> pdb=" O TRP A3446 " (cutoff:3.500A) Processing helix chain 'A' and resid 3451 through 3464 removed outlier: 3.710A pdb=" N GLU A3464 " --> pdb=" O VAL A3460 " (cutoff:3.500A) Processing helix chain 'A' and resid 3466 through 3472 removed outlier: 3.792A pdb=" N PHE A3470 " --> pdb=" O ASN A3466 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU A3471 " --> pdb=" O ASN A3467 " (cutoff:3.500A) Processing helix chain 'A' and resid 3505 through 3510 removed outlier: 5.308A pdb=" N LEU A3510 " --> pdb=" O VAL A3506 " (cutoff:3.500A) Processing helix chain 'A' and resid 3511 through 3527 Proline residue: A3520 - end of helix removed outlier: 3.511A pdb=" N CYS A3526 " --> pdb=" O GLY A3522 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N ALA A3527 " --> pdb=" O LEU A3523 " (cutoff:3.500A) Processing helix chain 'A' and resid 3530 through 3544 Processing helix chain 'A' and resid 3546 through 3558 Processing helix chain 'A' and resid 3563 through 3568 removed outlier: 3.776A pdb=" N SER A3567 " --> pdb=" O LYS A3563 " (cutoff:3.500A) Proline residue: A3568 - end of helix No H-bonds generated for 'chain 'A' and resid 3563 through 3568' Processing helix chain 'A' and resid 3569 through 3581 Proline residue: A3581 - end of helix Processing helix chain 'A' and resid 3582 through 3587 removed outlier: 4.333A pdb=" N ASP A3586 " --> pdb=" O GLY A3582 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N ALA A3587 " --> pdb=" O ARG A3583 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3582 through 3587' Processing helix chain 'A' and resid 3589 through 3613 removed outlier: 3.552A pdb=" N HIS A3606 " --> pdb=" O ALA A3602 " (cutoff:3.500A) Proline residue: A3613 - end of helix Processing helix chain 'A' and resid 3629 through 3638 removed outlier: 3.756A pdb=" N CYS A3636 " --> pdb=" O ALA A3632 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ARG A3638 " --> pdb=" O VAL A3634 " (cutoff:3.500A) Processing helix chain 'A' and resid 3641 through 3646 removed outlier: 4.352A pdb=" N LEU A3645 " --> pdb=" O PRO A3641 " (cutoff:3.500A) Proline residue: A3646 - end of helix No H-bonds generated for 'chain 'A' and resid 3641 through 3646' Processing helix chain 'A' and resid 3647 through 3666 removed outlier: 3.959A pdb=" N ILE A3663 " --> pdb=" O LYS A3659 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LEU A3664 " --> pdb=" O ALA A3660 " (cutoff:3.500A) Processing helix chain 'A' and resid 3670 through 3681 removed outlier: 5.731A pdb=" N ALA A3681 " --> pdb=" O ASP A3677 " (cutoff:3.500A) Processing helix chain 'A' and resid 3683 through 3688 Processing helix chain 'A' and resid 3697 through 3712 Processing helix chain 'A' and resid 3720 through 3735 removed outlier: 3.781A pdb=" N CYS A3734 " --> pdb=" O MET A3730 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N HIS A3735 " --> pdb=" O ALA A3731 " (cutoff:3.500A) Processing helix chain 'A' and resid 3755 through 3775 removed outlier: 3.684A pdb=" N LEU A3773 " --> pdb=" O GLN A3769 " (cutoff:3.500A) Processing helix chain 'A' and resid 3777 through 3790 removed outlier: 4.107A pdb=" N LYS A3790 " --> pdb=" O ILE A3786 " (cutoff:3.500A) Processing helix chain 'A' and resid 3794 through 3809 Processing helix chain 'A' and resid 3812 through 3827 removed outlier: 3.594A pdb=" N GLN A3816 " --> pdb=" O ASN A3812 " (cutoff:3.500A) Processing helix chain 'A' and resid 3829 through 3842 Processing helix chain 'A' and resid 3846 through 3860 removed outlier: 4.960A pdb=" N GLY A3860 " --> pdb=" O ALA A3856 " (cutoff:3.500A) Processing helix chain 'A' and resid 3864 through 3869 removed outlier: 4.473A pdb=" N ILE A3869 " --> pdb=" O ASP A3865 " (cutoff:3.500A) Processing helix chain 'A' and resid 3880 through 3896 removed outlier: 3.642A pdb=" N CYS A3895 " --> pdb=" O LEU A3891 " (cutoff:3.500A) Processing helix chain 'A' and resid 3899 through 3908 removed outlier: 3.501A pdb=" N ARG A3907 " --> pdb=" O GLN A3903 " (cutoff:3.500A) Processing helix chain 'A' and resid 3917 through 3942 removed outlier: 4.744A pdb=" N GLY A3942 " --> pdb=" O TRP A3938 " (cutoff:3.500A) Processing helix chain 'A' and resid 3947 through 3973 removed outlier: 3.559A pdb=" N ILE A3972 " --> pdb=" O LEU A3968 " (cutoff:3.500A) Processing helix chain 'A' and resid 3976 through 3987 removed outlier: 4.876A pdb=" N ARG A3987 " --> pdb=" O LEU A3983 " (cutoff:3.500A) Processing helix chain 'A' and resid 3988 through 4010 removed outlier: 3.926A pdb=" N ASP A4009 " --> pdb=" O LYS A4005 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N SER A4010 " --> pdb=" O LEU A4006 " (cutoff:3.500A) Processing helix chain 'A' and resid 4011 through 4036 removed outlier: 5.672A pdb=" N LEU A4015 " --> pdb=" O SER A4011 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A4034 " --> pdb=" O LEU A4030 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU A4035 " --> pdb=" O LEU A4031 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N GLY A4036 " --> pdb=" O SER A4032 " (cutoff:3.500A) Processing helix chain 'A' and resid 4041 through 4055 Processing helix chain 'A' and resid 4056 through 4075 removed outlier: 3.531A pdb=" N PHE A4065 " --> pdb=" O ILE A4061 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE A4068 " --> pdb=" O PHE A4064 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASP A4073 " --> pdb=" O LEU A4069 " (cutoff:3.500A) Processing helix chain 'A' and resid 4077 through 4085 removed outlier: 4.911A pdb=" N THR A4085 " --> pdb=" O GLN A4081 " (cutoff:3.500A) Processing helix chain 'A' and resid 4092 through 4104 Processing helix chain 'A' and resid 4107 through 4119 removed outlier: 4.388A pdb=" N GLU A4119 " --> pdb=" O LEU A4115 " (cutoff:3.500A) Processing helix chain 'A' and resid 4127 through 4140 removed outlier: 4.756A pdb=" N PHE A4135 " --> pdb=" O PHE A4131 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLN A4136 " --> pdb=" O ALA A4132 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N GLU A4137 " --> pdb=" O ASN A4133 " (cutoff:3.500A) Proline residue: A4138 - end of helix Processing helix chain 'A' and resid 4141 through 4158 Proline residue: A4158 - end of helix Processing helix chain 'A' and resid 4160 through 4171 removed outlier: 3.780A pdb=" N ARG A4164 " --> pdb=" O ASP A4160 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ASN A4165 " --> pdb=" O PRO A4161 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE A4166 " --> pdb=" O ARG A4162 " (cutoff:3.500A) Processing helix chain 'A' and resid 4172 through 4178 Processing helix chain 'A' and resid 4201 through 4210 Processing helix chain 'A' and resid 4211 through 4227 Processing helix chain 'A' and resid 4232 through 4255 Processing helix chain 'A' and resid 4538 through 4557 Processing helix chain 'A' and resid 4558 through 4578 removed outlier: 4.207A pdb=" N PHE A4577 " --> pdb=" O PHE A4573 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N TYR A4578 " --> pdb=" O ILE A4574 " (cutoff:3.500A) Processing helix chain 'A' and resid 4638 through 4681 removed outlier: 3.634A pdb=" N ARG A4642 " --> pdb=" O GLU A4638 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N VAL A4664 " --> pdb=" O ASN A4660 " (cutoff:3.500A) Proline residue: A4665 - end of helix Processing helix chain 'A' and resid 4694 through 4705 removed outlier: 4.240A pdb=" N LEU A4702 " --> pdb=" O GLN A4698 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N VAL A4703 " --> pdb=" O TRP A4699 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU A4704 " --> pdb=" O ASP A4700 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ASN A4705 " --> pdb=" O ARG A4701 " (cutoff:3.500A) Processing helix chain 'A' and resid 4717 through 4727 Processing helix chain 'A' and resid 4731 through 4740 Processing helix chain 'A' and resid 4742 through 4752 Processing helix chain 'A' and resid 4761 through 4769 Processing helix chain 'A' and resid 4770 through 4785 removed outlier: 5.293A pdb=" N ASN A4785 " --> pdb=" O ILE A4781 " (cutoff:3.500A) Processing helix chain 'A' and resid 4786 through 4803 Processing helix chain 'A' and resid 4804 through 4818 removed outlier: 4.719A pdb=" N ALA A4808 " --> pdb=" O ASN A4804 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ALA A4809 " --> pdb=" O PHE A4805 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N HIS A4810 " --> pdb=" O PHE A4806 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU A4811 " --> pdb=" O PHE A4807 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LEU A4812 " --> pdb=" O ALA A4808 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASP A4813 " --> pdb=" O ALA A4809 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ILE A4814 " --> pdb=" O HIS A4810 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N ALA A4815 " --> pdb=" O LEU A4811 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N MET A4816 " --> pdb=" O LEU A4812 " (cutoff:3.500A) Processing helix chain 'A' and resid 4819 through 4830 removed outlier: 3.601A pdb=" N VAL A4828 " --> pdb=" O ILE A4824 " (cutoff:3.500A) Processing helix chain 'A' and resid 4831 through 4856 Processing helix chain 'A' and resid 4857 through 4862 removed outlier: 4.276A pdb=" N TYR A4861 " --> pdb=" O PHE A4857 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N ASN A4862 " --> pdb=" O ARG A4858 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4857 through 4862' Processing helix chain 'A' and resid 4876 through 4891 removed outlier: 4.492A pdb=" N VAL A4889 " --> pdb=" O MET A4885 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ARG A4890 " --> pdb=" O TYR A4886 " (cutoff:3.500A) Processing helix chain 'A' and resid 4894 through 4900 removed outlier: 4.215A pdb=" N GLU A4898 " --> pdb=" O GLY A4894 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N GLU A4900 " --> pdb=" O GLY A4896 " (cutoff:3.500A) Processing helix chain 'A' and resid 4907 through 4922 Processing helix chain 'A' and resid 4926 through 4954 Processing helix chain 'A' and resid 4962 through 4968 removed outlier: 3.895A pdb=" N PHE A4966 " --> pdb=" O GLY A4962 " (cutoff:3.500A) Processing helix chain 'A' and resid 4971 through 4979 Processing helix chain 'A' and resid 4982 through 4996 removed outlier: 3.523A pdb=" N LEU A4990 " --> pdb=" O TYR A4986 " (cutoff:3.500A) Processing helix chain 'A' and resid 5002 through 5015 Processing helix chain 'A' and resid 5025 through 5031 Processing helix chain 'A' and resid 323 through 328 removed outlier: 4.313A pdb=" N VAL A 326 " --> pdb=" O LYS A 323 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA A 327 " --> pdb=" O LEU A 324 " (cutoff:3.500A) Proline residue: A 328 - end of helix No H-bonds generated for 'chain 'A' and resid 323 through 328' Processing helix chain 'A' and resid 4683 through 4688 Processing helix chain 'B' and resid 62 through 67 removed outlier: 4.301A pdb=" N CYS B 66 " --> pdb=" O ASP B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 85 Processing helix chain 'B' and resid 144 through 149 removed outlier: 4.195A pdb=" N TRP B 148 " --> pdb=" O GLY B 144 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N TRP B 149 " --> pdb=" O GLU B 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 144 through 149' Processing helix chain 'B' and resid 252 through 257 removed outlier: 5.340A pdb=" N ALA B 257 " --> pdb=" O VAL B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 314 Processing helix chain 'B' and resid 366 through 371 Processing helix chain 'B' and resid 395 through 423 removed outlier: 3.698A pdb=" N PHE B 422 " --> pdb=" O GLY B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 454 Processing helix chain 'B' and resid 461 through 483 Processing helix chain 'B' and resid 484 through 498 removed outlier: 4.463A pdb=" N TYR B 498 " --> pdb=" O ARG B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 508 removed outlier: 3.834A pdb=" N PHE B 507 " --> pdb=" O HIS B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 532 removed outlier: 3.828A pdb=" N SER B 515 " --> pdb=" O GLU B 511 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LYS B 517 " --> pdb=" O ALA B 513 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N GLU B 518 " --> pdb=" O GLU B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 545 removed outlier: 3.717A pdb=" N LEU B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N PHE B 541 " --> pdb=" O ASN B 537 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N SER B 542 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N THR B 543 " --> pdb=" O ALA B 539 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ASN B 544 " --> pdb=" O LEU B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 553 removed outlier: 4.432A pdb=" N ASP B 553 " --> pdb=" O VAL B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 572 Processing helix chain 'B' and resid 573 through 579 Processing helix chain 'B' and resid 580 through 594 removed outlier: 3.546A pdb=" N LEU B 591 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 597 through 610 removed outlier: 3.622A pdb=" N LEU B 601 " --> pdb=" O ASN B 597 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL B 609 " --> pdb=" O CYS B 605 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N CYS B 610 " --> pdb=" O SER B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 630 Proline residue: B 628 - end of helix Processing helix chain 'B' and resid 811 through 816 removed outlier: 4.419A pdb=" N ALA B 815 " --> pdb=" O PRO B 811 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL B 816 " --> pdb=" O CYS B 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 811 through 816' Processing helix chain 'B' and resid 848 through 854 removed outlier: 3.876A pdb=" N PHE B 852 " --> pdb=" O SER B 848 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL B 853 " --> pdb=" O HIS B 849 " (cutoff:3.500A) Proline residue: B 854 - end of helix No H-bonds generated for 'chain 'B' and resid 848 through 854' Processing helix chain 'B' and resid 865 through 891 removed outlier: 4.034A pdb=" N ILE B 871 " --> pdb=" O HIS B 867 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS B 874 " --> pdb=" O ARG B 870 " (cutoff:3.500A) Processing helix chain 'B' and resid 915 through 936 removed outlier: 3.748A pdb=" N LEU B 930 " --> pdb=" O SER B 926 " (cutoff:3.500A) Processing helix chain 'B' and resid 944 through 951 removed outlier: 4.542A pdb=" N GLU B 948 " --> pdb=" O ASP B 944 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASP B 949 " --> pdb=" O GLU B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 957 through 962 removed outlier: 4.947A pdb=" N MET B 962 " --> pdb=" O LYS B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 979 through 1005 Processing helix chain 'B' and resid 1029 through 1051 Processing helix chain 'B' and resid 1218 through 1223 removed outlier: 6.785A pdb=" N GLU B1222 " --> pdb=" O CYS B1218 " (cutoff:3.500A) Processing helix chain 'B' and resid 1424 through 1431 Processing helix chain 'B' and resid 1445 through 1450 removed outlier: 4.136A pdb=" N VAL B1449 " --> pdb=" O GLU B1445 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N TRP B1450 " --> pdb=" O PRO B1446 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1445 through 1450' Processing helix chain 'B' and resid 1466 through 1471 removed outlier: 3.594A pdb=" N VAL B1470 " --> pdb=" O ASP B1466 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ARG B1471 " --> pdb=" O LEU B1467 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1466 through 1471' Processing helix chain 'B' and resid 1497 through 1503 removed outlier: 3.864A pdb=" N PHE B1501 " --> pdb=" O TRP B1497 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N SER B1503 " --> pdb=" O GLY B1499 " (cutoff:3.500A) Processing helix chain 'B' and resid 1575 through 1581 removed outlier: 4.008A pdb=" N ALA B1579 " --> pdb=" O PRO B1575 " (cutoff:3.500A) Processing helix chain 'B' and resid 1650 through 1658 removed outlier: 4.470A pdb=" N LEU B1654 " --> pdb=" O ASP B1650 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N SER B1655 " --> pdb=" O ILE B1651 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N GLU B1656 " --> pdb=" O LEU B1652 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LEU B1658 " --> pdb=" O LEU B1654 " (cutoff:3.500A) Processing helix chain 'B' and resid 1659 through 1676 removed outlier: 3.591A pdb=" N SER B1669 " --> pdb=" O SER B1665 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N CYS B1675 " --> pdb=" O TYR B1671 " (cutoff:3.500A) Processing helix chain 'B' and resid 1679 through 1690 removed outlier: 3.805A pdb=" N SER B1688 " --> pdb=" O HIS B1684 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N HIS B1689 " --> pdb=" O ALA B1685 " (cutoff:3.500A) Processing helix chain 'B' and resid 1691 through 1701 Processing helix chain 'B' and resid 1705 through 1720 Processing helix chain 'B' and resid 1721 through 1733 removed outlier: 4.262A pdb=" N SER B1733 " --> pdb=" O ARG B1729 " (cutoff:3.500A) Processing helix chain 'B' and resid 1740 through 1747 removed outlier: 5.538A pdb=" N THR B1747 " --> pdb=" O THR B1743 " (cutoff:3.500A) Processing helix chain 'B' and resid 1805 through 1827 Processing helix chain 'B' and resid 1835 through 1854 Proline residue: B1842 - end of helix Processing helix chain 'B' and resid 1857 through 1869 Processing helix chain 'B' and resid 1926 through 1931 removed outlier: 4.398A pdb=" N LYS B1931 " --> pdb=" O LEU B1927 " (cutoff:3.500A) Processing helix chain 'B' and resid 1933 through 1985 removed outlier: 3.527A pdb=" N ASP B1968 " --> pdb=" O GLU B1964 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N PHE B1985 " --> pdb=" O LEU B1981 " (cutoff:3.500A) Processing helix chain 'B' and resid 1988 through 2000 removed outlier: 4.230A pdb=" N GLU B1998 " --> pdb=" O ARG B1994 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N PHE B1999 " --> pdb=" O ARG B1995 " (cutoff:3.500A) Processing helix chain 'B' and resid 2002 through 2012 Processing helix chain 'B' and resid 2018 through 2023 Proline residue: B2023 - end of helix Processing helix chain 'B' and resid 2025 through 2044 removed outlier: 3.516A pdb=" N GLU B2031 " --> pdb=" O GLU B2027 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU B2032 " --> pdb=" O ILE B2028 " (cutoff:3.500A) Processing helix chain 'B' and resid 2094 through 2110 Processing helix chain 'B' and resid 2114 through 2131 removed outlier: 3.663A pdb=" N GLY B2131 " --> pdb=" O ARG B2127 " (cutoff:3.500A) Processing helix chain 'B' and resid 2132 through 2142 Proline residue: B2140 - end of helix Processing helix chain 'B' and resid 2146 through 2170 removed outlier: 3.721A pdb=" N VAL B2150 " --> pdb=" O SER B2146 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N GLU B2151 " --> pdb=" O VAL B2147 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N ASP B2152 " --> pdb=" O SER B2148 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE B2168 " --> pdb=" O ARG B2164 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL B2169 " --> pdb=" O SER B2165 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N GLN B2170 " --> pdb=" O LEU B2166 " (cutoff:3.500A) Processing helix chain 'B' and resid 2172 through 2189 Processing helix chain 'B' and resid 2190 through 2195 Processing helix chain 'B' and resid 2196 through 2203 Processing helix chain 'B' and resid 2204 through 2220 removed outlier: 5.458A pdb=" N GLY B2219 " --> pdb=" O VAL B2215 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N GLU B2220 " --> pdb=" O LEU B2216 " (cutoff:3.500A) Processing helix chain 'B' and resid 2226 through 2245 removed outlier: 4.088A pdb=" N SER B2244 " --> pdb=" O PHE B2240 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N ARG B2245 " --> pdb=" O CYS B2241 " (cutoff:3.500A) Processing helix chain 'B' and resid 2246 through 2256 removed outlier: 3.767A pdb=" N HIS B2254 " --> pdb=" O SER B2250 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N SER B2256 " --> pdb=" O PHE B2252 " (cutoff:3.500A) Processing helix chain 'B' and resid 2257 through 2263 removed outlier: 4.428A pdb=" N GLY B2263 " --> pdb=" O LEU B2259 " (cutoff:3.500A) Processing helix chain 'B' and resid 2272 through 2282 Processing helix chain 'B' and resid 2284 through 2291 Processing helix chain 'B' and resid 2292 through 2309 Processing helix chain 'B' and resid 2311 through 2318 Processing helix chain 'B' and resid 2325 through 2341 removed outlier: 3.646A pdb=" N PHE B2335 " --> pdb=" O ARG B2331 " (cutoff:3.500A) Processing helix chain 'B' and resid 2347 through 2362 Proline residue: B2362 - end of helix Processing helix chain 'B' and resid 2376 through 2391 Proline residue: B2391 - end of helix Processing helix chain 'B' and resid 2418 through 2438 Processing helix chain 'B' and resid 2440 through 2447 Processing helix chain 'B' and resid 2448 through 2463 Proline residue: B2463 - end of helix Processing helix chain 'B' and resid 2464 through 2473 Processing helix chain 'B' and resid 2496 through 2510 removed outlier: 3.677A pdb=" N LYS B2500 " --> pdb=" O VAL B2496 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N MET B2503 " --> pdb=" O HIS B2499 " (cutoff:3.500A) Processing helix chain 'B' and resid 2515 through 2539 removed outlier: 4.538A pdb=" N LEU B2528 " --> pdb=" O ASP B2524 " (cutoff:3.500A) Proline residue: B2529 - end of helix removed outlier: 4.526A pdb=" N THR B2539 " --> pdb=" O ALA B2535 " (cutoff:3.500A) Processing helix chain 'B' and resid 2545 through 2567 removed outlier: 5.313A pdb=" N LEU B2560 " --> pdb=" O CYS B2556 " (cutoff:3.500A) Proline residue: B2561 - end of helix Processing helix chain 'B' and resid 2576 through 2593 Processing helix chain 'B' and resid 2597 through 2615 removed outlier: 3.614A pdb=" N TYR B2614 " --> pdb=" O ALA B2610 " (cutoff:3.500A) Processing helix chain 'B' and resid 2616 through 2631 removed outlier: 3.909A pdb=" N LEU B2620 " --> pdb=" O ARG B2616 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLN B2621 " --> pdb=" O PRO B2617 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N HIS B2622 " --> pdb=" O SER B2618 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N LEU B2623 " --> pdb=" O MET B2619 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE B2629 " --> pdb=" O ARG B2625 " (cutoff:3.500A) Processing helix chain 'B' and resid 2635 through 2653 removed outlier: 3.590A pdb=" N LYS B2639 " --> pdb=" O ASN B2635 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N MET B2640 " --> pdb=" O GLU B2636 " (cutoff:3.500A) Proline residue: B2641 - end of helix Processing helix chain 'B' and resid 2669 through 2690 Processing helix chain 'B' and resid 2694 through 2712 Proline residue: B2702 - end of helix Proline residue: B2712 - end of helix Processing helix chain 'B' and resid 2749 through 2775 Processing helix chain 'B' and resid 2801 through 2821 Proline residue: B2809 - end of helix Processing helix chain 'B' and resid 2862 through 2867 removed outlier: 4.866A pdb=" N VAL B2866 " --> pdb=" O ASP B2862 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N THR B2867 " --> pdb=" O LEU B2863 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2862 through 2867' Processing helix chain 'B' and resid 2869 through 2899 Processing helix chain 'B' and resid 2908 through 2913 removed outlier: 5.181A pdb=" N THR B2913 " --> pdb=" O TYR B2909 " (cutoff:3.500A) Processing helix chain 'B' and resid 2916 through 2935 removed outlier: 4.139A pdb=" N ASP B2920 " --> pdb=" O GLU B2916 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N LYS B2923 " --> pdb=" O ARG B2919 " (cutoff:3.500A) Processing helix chain 'B' and resid 2942 through 2948 Processing helix chain 'B' and resid 2950 through 2984 removed outlier: 5.999A pdb=" N PHE B2956 " --> pdb=" O ILE B2952 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ALA B2957 " --> pdb=" O GLU B2953 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N PHE B2958 " --> pdb=" O LYS B2954 " (cutoff:3.500A) Processing helix chain 'B' and resid 2992 through 3015 removed outlier: 4.346A pdb=" N LEU B3004 " --> pdb=" O ALA B3000 " (cutoff:3.500A) Proline residue: B3005 - end of helix Processing helix chain 'B' and resid 3033 through 3052 Processing helix chain 'B' and resid 3054 through 3059 removed outlier: 3.540A pdb=" N PHE B3058 " --> pdb=" O ARG B3054 " (cutoff:3.500A) Processing helix chain 'B' and resid 3060 through 3076 removed outlier: 4.794A pdb=" N ALA B3064 " --> pdb=" O THR B3060 " (cutoff:3.500A) Processing helix chain 'B' and resid 3077 through 3084 removed outlier: 3.956A pdb=" N VAL B3081 " --> pdb=" O ASP B3077 " (cutoff:3.500A) Processing helix chain 'B' and resid 3086 through 3113 Processing helix chain 'B' and resid 3124 through 3152 removed outlier: 3.647A pdb=" N LEU B3137 " --> pdb=" O THR B3133 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N LEU B3138 " --> pdb=" O THR B3134 " (cutoff:3.500A) Proline residue: B3139 - end of helix Processing helix chain 'B' and resid 3160 through 3180 removed outlier: 4.792A pdb=" N ARG B3180 " --> pdb=" O LEU B3176 " (cutoff:3.500A) Processing helix chain 'B' and resid 3181 through 3202 Proline residue: B3189 - end of helix Processing helix chain 'B' and resid 3208 through 3216 removed outlier: 4.690A pdb=" N GLU B3213 " --> pdb=" O PRO B3209 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TYR B3214 " --> pdb=" O GLU B3210 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ASN B3215 " --> pdb=" O LEU B3211 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ALA B3216 " --> pdb=" O ASN B3212 " (cutoff:3.500A) Processing helix chain 'B' and resid 3218 through 3223 Processing helix chain 'B' and resid 3224 through 3232 removed outlier: 4.094A pdb=" N ARG B3228 " --> pdb=" O SER B3224 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ALA B3229 " --> pdb=" O PRO B3225 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ILE B3230 " --> pdb=" O ARG B3226 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N LEU B3231 " --> pdb=" O GLU B3227 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N GLY B3232 " --> pdb=" O ARG B3228 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3224 through 3232' Processing helix chain 'B' and resid 3236 through 3242 removed outlier: 3.691A pdb=" N MET B3240 " --> pdb=" O SER B3236 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N CYS B3241 " --> pdb=" O VAL B3237 " (cutoff:3.500A) Proline residue: B3242 - end of helix No H-bonds generated for 'chain 'B' and resid 3236 through 3242' Processing helix chain 'B' and resid 3246 through 3261 Processing helix chain 'B' and resid 3263 through 3268 Proline residue: B3268 - end of helix Processing helix chain 'B' and resid 3269 through 3290 removed outlier: 4.091A pdb=" N LEU B3275 " --> pdb=" O ILE B3271 " (cutoff:3.500A) Proline residue: B3276 - end of helix Proline residue: B3283 - end of helix removed outlier: 4.103A pdb=" N GLU B3287 " --> pdb=" O PRO B3283 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ARG B3288 " --> pdb=" O ARG B3284 " (cutoff:3.500A) Proline residue: B3290 - end of helix Processing helix chain 'B' and resid 3309 through 3328 Processing helix chain 'B' and resid 3333 through 3348 removed outlier: 4.209A pdb=" N LYS B3337 " --> pdb=" O ALA B3333 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ARG B3338 " --> pdb=" O SER B3334 " (cutoff:3.500A) Proline residue: B3345 - end of helix removed outlier: 4.324A pdb=" N SER B3348 " --> pdb=" O GLN B3344 " (cutoff:3.500A) Processing helix chain 'B' and resid 3351 through 3384 removed outlier: 4.744A pdb=" N LEU B3355 " --> pdb=" O ARG B3351 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ARG B3356 " --> pdb=" O PRO B3352 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N ILE B3360 " --> pdb=" O ARG B3356 " (cutoff:3.500A) Proline residue: B3361 - end of helix removed outlier: 4.578A pdb=" N ALA B3384 " --> pdb=" O LEU B3380 " (cutoff:3.500A) Processing helix chain 'B' and resid 3385 through 3421 removed outlier: 4.833A pdb=" N GLY B3391 " --> pdb=" O GLU B3387 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU B3392 " --> pdb=" O ALA B3388 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU B3393 " --> pdb=" O GLU B3389 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU B3394 " --> pdb=" O GLU B3390 " (cutoff:3.500A) Proline residue: B3411 - end of helix Processing helix chain 'B' and resid 3422 through 3428 Proline residue: B3428 - end of helix Processing helix chain 'B' and resid 3429 through 3450 removed outlier: 4.802A pdb=" N HIS B3450 " --> pdb=" O TRP B3446 " (cutoff:3.500A) Processing helix chain 'B' and resid 3451 through 3464 removed outlier: 3.710A pdb=" N GLU B3464 " --> pdb=" O VAL B3460 " (cutoff:3.500A) Processing helix chain 'B' and resid 3466 through 3472 removed outlier: 3.792A pdb=" N PHE B3470 " --> pdb=" O ASN B3466 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU B3471 " --> pdb=" O ASN B3467 " (cutoff:3.500A) Processing helix chain 'B' and resid 3505 through 3510 removed outlier: 5.308A pdb=" N LEU B3510 " --> pdb=" O VAL B3506 " (cutoff:3.500A) Processing helix chain 'B' and resid 3511 through 3527 Proline residue: B3520 - end of helix removed outlier: 3.511A pdb=" N CYS B3526 " --> pdb=" O GLY B3522 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N ALA B3527 " --> pdb=" O LEU B3523 " (cutoff:3.500A) Processing helix chain 'B' and resid 3530 through 3544 Processing helix chain 'B' and resid 3546 through 3558 Processing helix chain 'B' and resid 3563 through 3568 removed outlier: 3.776A pdb=" N SER B3567 " --> pdb=" O LYS B3563 " (cutoff:3.500A) Proline residue: B3568 - end of helix No H-bonds generated for 'chain 'B' and resid 3563 through 3568' Processing helix chain 'B' and resid 3569 through 3581 Proline residue: B3581 - end of helix Processing helix chain 'B' and resid 3582 through 3587 removed outlier: 4.334A pdb=" N ASP B3586 " --> pdb=" O GLY B3582 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N ALA B3587 " --> pdb=" O ARG B3583 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3582 through 3587' Processing helix chain 'B' and resid 3589 through 3613 removed outlier: 3.552A pdb=" N HIS B3606 " --> pdb=" O ALA B3602 " (cutoff:3.500A) Proline residue: B3613 - end of helix Processing helix chain 'B' and resid 3629 through 3638 removed outlier: 3.755A pdb=" N CYS B3636 " --> pdb=" O ALA B3632 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ARG B3638 " --> pdb=" O VAL B3634 " (cutoff:3.500A) Processing helix chain 'B' and resid 3641 through 3646 removed outlier: 4.352A pdb=" N LEU B3645 " --> pdb=" O PRO B3641 " (cutoff:3.500A) Proline residue: B3646 - end of helix No H-bonds generated for 'chain 'B' and resid 3641 through 3646' Processing helix chain 'B' and resid 3647 through 3666 removed outlier: 3.959A pdb=" N ILE B3663 " --> pdb=" O LYS B3659 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LEU B3664 " --> pdb=" O ALA B3660 " (cutoff:3.500A) Processing helix chain 'B' and resid 3670 through 3681 removed outlier: 5.732A pdb=" N ALA B3681 " --> pdb=" O ASP B3677 " (cutoff:3.500A) Processing helix chain 'B' and resid 3683 through 3688 Processing helix chain 'B' and resid 3697 through 3712 Processing helix chain 'B' and resid 3720 through 3735 removed outlier: 3.780A pdb=" N CYS B3734 " --> pdb=" O MET B3730 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N HIS B3735 " --> pdb=" O ALA B3731 " (cutoff:3.500A) Processing helix chain 'B' and resid 3755 through 3775 removed outlier: 3.684A pdb=" N LEU B3773 " --> pdb=" O GLN B3769 " (cutoff:3.500A) Processing helix chain 'B' and resid 3777 through 3790 removed outlier: 4.108A pdb=" N LYS B3790 " --> pdb=" O ILE B3786 " (cutoff:3.500A) Processing helix chain 'B' and resid 3794 through 3809 Processing helix chain 'B' and resid 3812 through 3827 removed outlier: 3.594A pdb=" N GLN B3816 " --> pdb=" O ASN B3812 " (cutoff:3.500A) Processing helix chain 'B' and resid 3829 through 3842 Processing helix chain 'B' and resid 3846 through 3860 removed outlier: 4.960A pdb=" N GLY B3860 " --> pdb=" O ALA B3856 " (cutoff:3.500A) Processing helix chain 'B' and resid 3864 through 3869 removed outlier: 4.474A pdb=" N ILE B3869 " --> pdb=" O ASP B3865 " (cutoff:3.500A) Processing helix chain 'B' and resid 3880 through 3896 removed outlier: 3.642A pdb=" N CYS B3895 " --> pdb=" O LEU B3891 " (cutoff:3.500A) Processing helix chain 'B' and resid 3899 through 3908 removed outlier: 3.500A pdb=" N ARG B3907 " --> pdb=" O GLN B3903 " (cutoff:3.500A) Processing helix chain 'B' and resid 3917 through 3942 removed outlier: 4.743A pdb=" N GLY B3942 " --> pdb=" O TRP B3938 " (cutoff:3.500A) Processing helix chain 'B' and resid 3947 through 3973 removed outlier: 3.559A pdb=" N ILE B3972 " --> pdb=" O LEU B3968 " (cutoff:3.500A) Processing helix chain 'B' and resid 3976 through 3987 removed outlier: 4.877A pdb=" N ARG B3987 " --> pdb=" O LEU B3983 " (cutoff:3.500A) Processing helix chain 'B' and resid 3988 through 4010 removed outlier: 3.927A pdb=" N ASP B4009 " --> pdb=" O LYS B4005 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N SER B4010 " --> pdb=" O LEU B4006 " (cutoff:3.500A) Processing helix chain 'B' and resid 4011 through 4036 removed outlier: 5.672A pdb=" N LEU B4015 " --> pdb=" O SER B4011 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU B4034 " --> pdb=" O LEU B4030 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU B4035 " --> pdb=" O LEU B4031 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N GLY B4036 " --> pdb=" O SER B4032 " (cutoff:3.500A) Processing helix chain 'B' and resid 4041 through 4055 Processing helix chain 'B' and resid 4056 through 4075 removed outlier: 3.532A pdb=" N PHE B4065 " --> pdb=" O ILE B4061 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE B4068 " --> pdb=" O PHE B4064 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASP B4073 " --> pdb=" O LEU B4069 " (cutoff:3.500A) Processing helix chain 'B' and resid 4077 through 4085 removed outlier: 4.912A pdb=" N THR B4085 " --> pdb=" O GLN B4081 " (cutoff:3.500A) Processing helix chain 'B' and resid 4092 through 4104 Processing helix chain 'B' and resid 4107 through 4119 removed outlier: 4.388A pdb=" N GLU B4119 " --> pdb=" O LEU B4115 " (cutoff:3.500A) Processing helix chain 'B' and resid 4127 through 4140 removed outlier: 4.755A pdb=" N PHE B4135 " --> pdb=" O PHE B4131 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLN B4136 " --> pdb=" O ALA B4132 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N GLU B4137 " --> pdb=" O ASN B4133 " (cutoff:3.500A) Proline residue: B4138 - end of helix Processing helix chain 'B' and resid 4141 through 4158 Proline residue: B4158 - end of helix Processing helix chain 'B' and resid 4160 through 4171 removed outlier: 3.780A pdb=" N ARG B4164 " --> pdb=" O ASP B4160 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ASN B4165 " --> pdb=" O PRO B4161 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE B4166 " --> pdb=" O ARG B4162 " (cutoff:3.500A) Processing helix chain 'B' and resid 4172 through 4178 Processing helix chain 'B' and resid 4201 through 4210 Processing helix chain 'B' and resid 4211 through 4227 Processing helix chain 'B' and resid 4232 through 4255 Processing helix chain 'B' and resid 4538 through 4557 Processing helix chain 'B' and resid 4558 through 4578 removed outlier: 4.207A pdb=" N PHE B4577 " --> pdb=" O PHE B4573 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N TYR B4578 " --> pdb=" O ILE B4574 " (cutoff:3.500A) Processing helix chain 'B' and resid 4638 through 4681 removed outlier: 3.633A pdb=" N ARG B4642 " --> pdb=" O GLU B4638 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N VAL B4664 " --> pdb=" O ASN B4660 " (cutoff:3.500A) Proline residue: B4665 - end of helix Processing helix chain 'B' and resid 4694 through 4705 removed outlier: 4.240A pdb=" N LEU B4702 " --> pdb=" O GLN B4698 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N VAL B4703 " --> pdb=" O TRP B4699 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU B4704 " --> pdb=" O ASP B4700 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ASN B4705 " --> pdb=" O ARG B4701 " (cutoff:3.500A) Processing helix chain 'B' and resid 4717 through 4727 Processing helix chain 'B' and resid 4731 through 4740 Processing helix chain 'B' and resid 4742 through 4752 Processing helix chain 'B' and resid 4761 through 4769 Processing helix chain 'B' and resid 4770 through 4785 removed outlier: 5.293A pdb=" N ASN B4785 " --> pdb=" O ILE B4781 " (cutoff:3.500A) Processing helix chain 'B' and resid 4786 through 4803 Processing helix chain 'B' and resid 4804 through 4818 removed outlier: 4.718A pdb=" N ALA B4808 " --> pdb=" O ASN B4804 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ALA B4809 " --> pdb=" O PHE B4805 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N HIS B4810 " --> pdb=" O PHE B4806 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU B4811 " --> pdb=" O PHE B4807 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LEU B4812 " --> pdb=" O ALA B4808 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ASP B4813 " --> pdb=" O ALA B4809 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ILE B4814 " --> pdb=" O HIS B4810 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N ALA B4815 " --> pdb=" O LEU B4811 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N MET B4816 " --> pdb=" O LEU B4812 " (cutoff:3.500A) Processing helix chain 'B' and resid 4819 through 4830 removed outlier: 3.601A pdb=" N VAL B4828 " --> pdb=" O ILE B4824 " (cutoff:3.500A) Processing helix chain 'B' and resid 4831 through 4856 Processing helix chain 'B' and resid 4857 through 4862 removed outlier: 4.275A pdb=" N TYR B4861 " --> pdb=" O PHE B4857 " (cutoff:3.500A) removed outlier: 4.982A 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 4891 removed outlier: 4.492A pdb=" N VAL B4889 " --> pdb=" O MET B4885 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ARG B4890 " --> pdb=" O TYR B4886 " (cutoff:3.500A) Processing helix chain 'B' and resid 4894 through 4900 removed outlier: 4.215A pdb=" N GLU B4898 " --> pdb=" O GLY B4894 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N GLU B4900 " --> pdb=" O GLY B4896 " (cutoff:3.500A) Processing helix chain 'B' and resid 4907 through 4922 Processing helix chain 'B' and resid 4926 through 4954 Processing helix chain 'B' and resid 4962 through 4968 removed outlier: 3.894A pdb=" N PHE B4966 " --> pdb=" O GLY B4962 " (cutoff:3.500A) Processing helix chain 'B' and resid 4971 through 4979 Processing helix chain 'B' and resid 4982 through 4996 removed outlier: 3.523A pdb=" N LEU B4990 " --> pdb=" O TYR B4986 " (cutoff:3.500A) Processing helix chain 'B' and resid 5002 through 5015 Processing helix chain 'B' and resid 5025 through 5031 Processing helix chain 'B' and resid 323 through 328 removed outlier: 4.313A pdb=" N VAL B 326 " --> pdb=" O LYS B 323 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA B 327 " --> pdb=" O LEU B 324 " (cutoff:3.500A) Proline residue: B 328 - end of helix No H-bonds generated for 'chain 'B' and resid 323 through 328' Processing helix chain 'B' and resid 4683 through 4688 Processing helix chain 'C' and resid 62 through 67 removed outlier: 4.301A pdb=" N CYS C 66 " --> pdb=" O ASP C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 85 Processing helix chain 'C' and resid 144 through 149 removed outlier: 4.195A pdb=" N TRP C 148 " --> pdb=" O GLY C 144 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N TRP C 149 " --> pdb=" O GLU C 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 144 through 149' Processing helix chain 'C' and resid 252 through 257 removed outlier: 5.341A pdb=" N ALA C 257 " --> pdb=" O VAL C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 314 Processing helix chain 'C' and resid 366 through 371 Processing helix chain 'C' and resid 395 through 423 removed outlier: 3.698A pdb=" N PHE C 422 " --> pdb=" O GLY C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 454 Processing helix chain 'C' and resid 461 through 483 Processing helix chain 'C' and resid 484 through 498 removed outlier: 4.463A pdb=" N TYR C 498 " --> pdb=" O ARG C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 508 removed outlier: 3.834A pdb=" N PHE C 507 " --> pdb=" O HIS C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 532 removed outlier: 3.828A pdb=" N SER C 515 " --> pdb=" O GLU C 511 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LYS C 517 " --> pdb=" O ALA C 513 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N GLU C 518 " --> pdb=" O GLU C 514 " (cutoff:3.500A) Processing helix chain 'C' and resid 534 through 545 removed outlier: 3.717A pdb=" N LEU C 540 " --> pdb=" O THR C 536 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N PHE C 541 " --> pdb=" O ASN C 537 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N SER C 542 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N THR C 543 " --> pdb=" O ALA C 539 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ASN C 544 " --> pdb=" O LEU C 540 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 553 removed outlier: 4.432A pdb=" N ASP C 553 " --> pdb=" O VAL C 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 572 Processing helix chain 'C' and resid 573 through 579 Processing helix chain 'C' and resid 580 through 594 removed outlier: 3.546A pdb=" N LEU C 591 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing helix chain 'C' and resid 597 through 610 removed outlier: 3.622A pdb=" N LEU C 601 " --> pdb=" O ASN C 597 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL C 609 " --> pdb=" O CYS C 605 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N CYS C 610 " --> pdb=" O SER C 606 " (cutoff:3.500A) Processing helix chain 'C' and resid 615 through 630 Proline residue: C 628 - end of helix Processing helix chain 'C' and resid 811 through 816 removed outlier: 4.419A pdb=" N ALA C 815 " --> pdb=" O PRO C 811 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL C 816 " --> pdb=" O CYS C 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 811 through 816' Processing helix chain 'C' and resid 848 through 854 removed outlier: 3.876A pdb=" N PHE C 852 " --> pdb=" O SER C 848 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL C 853 " --> pdb=" O HIS C 849 " (cutoff:3.500A) Proline residue: C 854 - end of helix No H-bonds generated for 'chain 'C' and resid 848 through 854' Processing helix chain 'C' and resid 865 through 891 removed outlier: 4.034A pdb=" N ILE C 871 " --> pdb=" O HIS C 867 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS C 874 " --> pdb=" O ARG C 870 " (cutoff:3.500A) Processing helix chain 'C' and resid 915 through 936 removed outlier: 3.748A pdb=" N LEU C 930 " --> pdb=" O SER C 926 " (cutoff:3.500A) Processing helix chain 'C' and resid 944 through 951 removed outlier: 4.543A pdb=" N GLU C 948 " --> pdb=" O ASP C 944 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASP C 949 " --> pdb=" O GLU C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 957 through 962 removed outlier: 4.947A pdb=" N MET C 962 " --> pdb=" O LYS C 958 " (cutoff:3.500A) Processing helix chain 'C' and resid 979 through 1005 Processing helix chain 'C' and resid 1029 through 1051 Processing helix chain 'C' and resid 1218 through 1223 removed outlier: 6.786A pdb=" N GLU C1222 " --> pdb=" O CYS C1218 " (cutoff:3.500A) Processing helix chain 'C' and resid 1424 through 1431 Processing helix chain 'C' and resid 1445 through 1450 removed outlier: 4.136A pdb=" N VAL C1449 " --> pdb=" O GLU C1445 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N TRP C1450 " --> pdb=" O PRO C1446 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1445 through 1450' Processing helix chain 'C' and resid 1466 through 1471 removed outlier: 3.594A pdb=" N VAL C1470 " --> pdb=" O ASP C1466 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ARG C1471 " --> pdb=" O LEU C1467 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1466 through 1471' Processing helix chain 'C' and resid 1497 through 1503 removed outlier: 3.863A pdb=" N PHE C1501 " --> pdb=" O TRP C1497 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N SER C1503 " --> pdb=" O GLY C1499 " (cutoff:3.500A) Processing helix chain 'C' and resid 1575 through 1581 removed outlier: 4.008A pdb=" N ALA C1579 " --> pdb=" O PRO C1575 " (cutoff:3.500A) Processing helix chain 'C' and resid 1650 through 1658 removed outlier: 4.470A pdb=" N LEU C1654 " --> pdb=" O ASP C1650 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N SER C1655 " --> pdb=" O ILE C1651 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N GLU C1656 " --> pdb=" O LEU C1652 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LEU C1658 " --> pdb=" O LEU C1654 " (cutoff:3.500A) Processing helix chain 'C' and resid 1659 through 1676 removed outlier: 3.590A pdb=" N SER C1669 " --> pdb=" O SER C1665 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N CYS C1675 " --> pdb=" O TYR C1671 " (cutoff:3.500A) Processing helix chain 'C' and resid 1679 through 1690 removed outlier: 3.805A pdb=" N SER C1688 " --> pdb=" O HIS C1684 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N HIS C1689 " --> pdb=" O ALA C1685 " (cutoff:3.500A) Processing helix chain 'C' and resid 1691 through 1701 Processing helix chain 'C' and resid 1705 through 1720 Processing helix chain 'C' and resid 1721 through 1733 removed outlier: 4.262A pdb=" N SER C1733 " --> pdb=" O ARG C1729 " (cutoff:3.500A) Processing helix chain 'C' and resid 1740 through 1747 removed outlier: 5.538A pdb=" N THR C1747 " --> pdb=" O THR C1743 " (cutoff:3.500A) Processing helix chain 'C' and resid 1805 through 1827 Processing helix chain 'C' and resid 1835 through 1854 Proline residue: C1842 - end of helix Processing helix chain 'C' and resid 1857 through 1869 Processing helix chain 'C' and resid 1926 through 1931 removed outlier: 4.398A pdb=" N LYS C1931 " --> pdb=" O LEU C1927 " (cutoff:3.500A) Processing helix chain 'C' and resid 1933 through 1985 removed outlier: 3.527A pdb=" N ASP C1968 " --> pdb=" O GLU C1964 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N PHE C1985 " --> pdb=" O LEU C1981 " (cutoff:3.500A) Processing helix chain 'C' and resid 1988 through 2000 removed outlier: 4.230A pdb=" N GLU C1998 " --> pdb=" O ARG C1994 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N PHE C1999 " --> pdb=" O ARG C1995 " (cutoff:3.500A) Processing helix chain 'C' and resid 2002 through 2012 Processing helix chain 'C' and resid 2018 through 2023 Proline residue: C2023 - end of helix Processing helix chain 'C' and resid 2025 through 2044 removed outlier: 3.516A pdb=" N GLU C2031 " --> pdb=" O GLU C2027 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU C2032 " --> pdb=" O ILE C2028 " (cutoff:3.500A) Processing helix chain 'C' and resid 2094 through 2110 Processing helix chain 'C' and resid 2114 through 2131 removed outlier: 3.663A pdb=" N GLY C2131 " --> pdb=" O ARG C2127 " (cutoff:3.500A) Processing helix chain 'C' and resid 2132 through 2142 Proline residue: C2140 - end of helix Processing helix chain 'C' and resid 2146 through 2170 removed outlier: 3.721A pdb=" N VAL C2150 " --> pdb=" O SER C2146 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N GLU C2151 " --> pdb=" O VAL C2147 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N ASP C2152 " --> pdb=" O SER C2148 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE C2168 " --> pdb=" O ARG C2164 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL C2169 " --> pdb=" O SER C2165 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N GLN C2170 " --> pdb=" O LEU C2166 " (cutoff:3.500A) Processing helix chain 'C' and resid 2172 through 2189 Processing helix chain 'C' and resid 2190 through 2195 Processing helix chain 'C' and resid 2196 through 2203 Processing helix chain 'C' and resid 2204 through 2220 removed outlier: 5.458A pdb=" N GLY C2219 " --> pdb=" O VAL C2215 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N GLU C2220 " --> pdb=" O LEU C2216 " (cutoff:3.500A) Processing helix chain 'C' and resid 2226 through 2245 removed outlier: 4.088A pdb=" N SER C2244 " --> pdb=" O PHE C2240 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N ARG C2245 " --> pdb=" O CYS C2241 " (cutoff:3.500A) Processing helix chain 'C' and resid 2246 through 2256 removed outlier: 3.767A pdb=" N HIS C2254 " --> pdb=" O SER C2250 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N SER C2256 " --> pdb=" O PHE C2252 " (cutoff:3.500A) Processing helix chain 'C' and resid 2257 through 2263 removed outlier: 4.428A pdb=" N GLY C2263 " --> pdb=" O LEU C2259 " (cutoff:3.500A) Processing helix chain 'C' and resid 2272 through 2282 Processing helix chain 'C' and resid 2284 through 2291 Processing helix chain 'C' and resid 2292 through 2309 Processing helix chain 'C' and resid 2311 through 2318 Processing helix chain 'C' and resid 2325 through 2341 removed outlier: 3.646A pdb=" N PHE C2335 " --> pdb=" O ARG C2331 " (cutoff:3.500A) Processing helix chain 'C' and resid 2347 through 2362 Proline residue: C2362 - end of helix Processing helix chain 'C' and resid 2376 through 2391 Proline residue: C2391 - end of helix Processing helix chain 'C' and resid 2418 through 2438 Processing helix chain 'C' and resid 2440 through 2447 Processing helix chain 'C' and resid 2448 through 2463 Proline residue: C2463 - end of helix Processing helix chain 'C' and resid 2464 through 2473 Processing helix chain 'C' and resid 2496 through 2510 removed outlier: 3.677A pdb=" N LYS C2500 " --> pdb=" O VAL C2496 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N MET C2503 " --> pdb=" O HIS C2499 " (cutoff:3.500A) Processing helix chain 'C' and resid 2515 through 2539 removed outlier: 4.538A pdb=" N LEU C2528 " --> pdb=" O ASP C2524 " (cutoff:3.500A) Proline residue: C2529 - end of helix removed outlier: 4.526A pdb=" N THR C2539 " --> pdb=" O ALA C2535 " (cutoff:3.500A) Processing helix chain 'C' and resid 2545 through 2567 removed outlier: 5.312A pdb=" N LEU C2560 " --> pdb=" O CYS C2556 " (cutoff:3.500A) Proline residue: C2561 - end of helix Processing helix chain 'C' and resid 2576 through 2593 Processing helix chain 'C' and resid 2597 through 2615 removed outlier: 3.615A pdb=" N TYR C2614 " --> pdb=" O ALA C2610 " (cutoff:3.500A) Processing helix chain 'C' and resid 2616 through 2631 removed outlier: 3.909A pdb=" N LEU C2620 " --> pdb=" O ARG C2616 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLN C2621 " --> pdb=" O PRO C2617 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N HIS C2622 " --> pdb=" O SER C2618 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N LEU C2623 " --> pdb=" O MET C2619 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE C2629 " --> pdb=" O ARG C2625 " (cutoff:3.500A) Processing helix chain 'C' and resid 2635 through 2653 removed outlier: 3.590A pdb=" N LYS C2639 " --> pdb=" O ASN C2635 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N MET C2640 " --> pdb=" O GLU C2636 " (cutoff:3.500A) Proline residue: C2641 - end of helix Processing helix chain 'C' and resid 2669 through 2690 Processing helix chain 'C' and resid 2694 through 2712 Proline residue: C2702 - end of helix Proline residue: C2712 - end of helix Processing helix chain 'C' and resid 2749 through 2775 Processing helix chain 'C' and resid 2801 through 2821 Proline residue: C2809 - end of helix Processing helix chain 'C' and resid 2862 through 2867 removed outlier: 4.867A pdb=" N VAL C2866 " --> pdb=" O ASP C2862 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N THR C2867 " --> pdb=" O LEU C2863 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2862 through 2867' Processing helix chain 'C' and resid 2869 through 2899 Processing helix chain 'C' and resid 2908 through 2913 removed outlier: 5.182A pdb=" N THR C2913 " --> pdb=" O TYR C2909 " (cutoff:3.500A) Processing helix chain 'C' and resid 2916 through 2935 removed outlier: 4.139A pdb=" N ASP C2920 " --> pdb=" O GLU C2916 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N LYS C2923 " --> pdb=" O ARG C2919 " (cutoff:3.500A) Processing helix chain 'C' and resid 2942 through 2948 Processing helix chain 'C' and resid 2950 through 2984 removed outlier: 5.999A pdb=" N PHE C2956 " --> pdb=" O ILE C2952 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ALA C2957 " --> pdb=" O GLU C2953 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N PHE C2958 " --> pdb=" O LYS C2954 " (cutoff:3.500A) Processing helix chain 'C' and resid 2992 through 3015 removed outlier: 4.347A pdb=" N LEU C3004 " --> pdb=" O ALA C3000 " (cutoff:3.500A) Proline residue: C3005 - end of helix Processing helix chain 'C' and resid 3033 through 3052 Processing helix chain 'C' and resid 3054 through 3059 removed outlier: 3.540A pdb=" N PHE C3058 " --> pdb=" O ARG C3054 " (cutoff:3.500A) Processing helix chain 'C' and resid 3060 through 3076 removed outlier: 4.794A pdb=" N ALA C3064 " --> pdb=" O THR C3060 " (cutoff:3.500A) Processing helix chain 'C' and resid 3077 through 3084 removed outlier: 3.956A pdb=" N VAL C3081 " --> pdb=" O ASP C3077 " (cutoff:3.500A) Processing helix chain 'C' and resid 3086 through 3113 Processing helix chain 'C' and resid 3124 through 3152 removed outlier: 3.647A pdb=" N LEU C3137 " --> pdb=" O THR C3133 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N LEU C3138 " --> pdb=" O THR C3134 " (cutoff:3.500A) Proline residue: C3139 - end of helix Processing helix chain 'C' and resid 3160 through 3180 removed outlier: 4.792A pdb=" N ARG C3180 " --> pdb=" O LEU C3176 " (cutoff:3.500A) Processing helix chain 'C' and resid 3181 through 3202 Proline residue: C3189 - end of helix Processing helix chain 'C' and resid 3208 through 3216 removed outlier: 4.690A pdb=" N GLU C3213 " --> pdb=" O PRO C3209 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TYR C3214 " --> pdb=" O GLU C3210 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ASN C3215 " --> pdb=" O LEU C3211 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ALA C3216 " --> pdb=" O ASN C3212 " (cutoff:3.500A) Processing helix chain 'C' and resid 3218 through 3223 Processing helix chain 'C' and resid 3224 through 3232 removed outlier: 4.094A pdb=" N ARG C3228 " --> pdb=" O SER C3224 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ALA C3229 " --> pdb=" O PRO C3225 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ILE C3230 " --> pdb=" O ARG C3226 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N LEU C3231 " --> pdb=" O GLU C3227 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N GLY C3232 " --> pdb=" O ARG C3228 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 3224 through 3232' Processing helix chain 'C' and resid 3236 through 3242 removed outlier: 3.691A pdb=" N MET C3240 " --> pdb=" O SER C3236 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N CYS C3241 " --> pdb=" O VAL C3237 " (cutoff:3.500A) Proline residue: C3242 - end of helix No H-bonds generated for 'chain 'C' and resid 3236 through 3242' Processing helix chain 'C' and resid 3246 through 3261 Processing helix chain 'C' and resid 3263 through 3268 Proline residue: C3268 - end of helix Processing helix chain 'C' and resid 3269 through 3290 removed outlier: 4.091A pdb=" N LEU C3275 " --> pdb=" O ILE C3271 " (cutoff:3.500A) Proline residue: C3276 - end of helix Proline residue: C3283 - end of helix removed outlier: 4.104A pdb=" N GLU C3287 " --> pdb=" O PRO C3283 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ARG C3288 " --> pdb=" O ARG C3284 " (cutoff:3.500A) Proline residue: C3290 - end of helix Processing helix chain 'C' and resid 3309 through 3328 Processing helix chain 'C' and resid 3333 through 3348 removed outlier: 4.209A pdb=" N LYS C3337 " --> pdb=" O ALA C3333 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ARG C3338 " --> pdb=" O SER C3334 " (cutoff:3.500A) Proline residue: C3345 - end of helix removed outlier: 4.324A pdb=" N SER C3348 " --> pdb=" O GLN C3344 " (cutoff:3.500A) Processing helix chain 'C' and resid 3351 through 3384 removed outlier: 4.744A pdb=" N LEU C3355 " --> pdb=" O ARG C3351 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ARG C3356 " --> pdb=" O PRO C3352 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ILE C3360 " --> pdb=" O ARG C3356 " (cutoff:3.500A) Proline residue: C3361 - end of helix removed outlier: 4.579A pdb=" N ALA C3384 " --> pdb=" O LEU C3380 " (cutoff:3.500A) Processing helix chain 'C' and resid 3385 through 3421 removed outlier: 4.833A pdb=" N GLY C3391 " --> pdb=" O GLU C3387 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU C3392 " --> pdb=" O ALA C3388 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LEU C3393 " --> pdb=" O GLU C3389 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU C3394 " --> pdb=" O GLU C3390 " (cutoff:3.500A) Proline residue: C3411 - end of helix Processing helix chain 'C' and resid 3422 through 3428 Proline residue: C3428 - end of helix Processing helix chain 'C' and resid 3429 through 3450 removed outlier: 4.801A pdb=" N HIS C3450 " --> pdb=" O TRP C3446 " (cutoff:3.500A) Processing helix chain 'C' and resid 3451 through 3464 removed outlier: 3.710A pdb=" N GLU C3464 " --> pdb=" O VAL C3460 " (cutoff:3.500A) Processing helix chain 'C' and resid 3466 through 3472 removed outlier: 3.792A pdb=" N PHE C3470 " --> pdb=" O ASN C3466 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU C3471 " --> pdb=" O ASN C3467 " (cutoff:3.500A) Processing helix chain 'C' and resid 3505 through 3510 removed outlier: 5.308A pdb=" N LEU C3510 " --> pdb=" O VAL C3506 " (cutoff:3.500A) Processing helix chain 'C' and resid 3511 through 3527 Proline residue: C3520 - end of helix removed outlier: 3.511A pdb=" N CYS C3526 " --> pdb=" O GLY C3522 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ALA C3527 " --> pdb=" O LEU C3523 " (cutoff:3.500A) Processing helix chain 'C' and resid 3530 through 3544 Processing helix chain 'C' and resid 3546 through 3558 Processing helix chain 'C' and resid 3563 through 3568 removed outlier: 3.776A pdb=" N SER C3567 " --> pdb=" O LYS C3563 " (cutoff:3.500A) Proline residue: C3568 - end of helix No H-bonds generated for 'chain 'C' and resid 3563 through 3568' Processing helix chain 'C' and resid 3569 through 3581 Proline residue: C3581 - end of helix Processing helix chain 'C' and resid 3582 through 3587 removed outlier: 4.334A pdb=" N ASP C3586 " --> pdb=" O GLY C3582 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N ALA C3587 " --> pdb=" O ARG C3583 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 3582 through 3587' Processing helix chain 'C' and resid 3589 through 3613 removed outlier: 3.552A pdb=" N HIS C3606 " --> pdb=" O ALA C3602 " (cutoff:3.500A) Proline residue: C3613 - end of helix Processing helix chain 'C' and resid 3629 through 3638 removed outlier: 3.756A pdb=" N CYS C3636 " --> pdb=" O ALA C3632 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ARG C3638 " --> pdb=" O VAL C3634 " (cutoff:3.500A) Processing helix chain 'C' and resid 3641 through 3646 removed outlier: 4.352A pdb=" N LEU C3645 " --> pdb=" O PRO C3641 " (cutoff:3.500A) Proline residue: C3646 - end of helix No H-bonds generated for 'chain 'C' and resid 3641 through 3646' Processing helix chain 'C' and resid 3647 through 3666 removed outlier: 3.959A pdb=" N ILE C3663 " --> pdb=" O LYS C3659 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N LEU C3664 " --> pdb=" O ALA C3660 " (cutoff:3.500A) Processing helix chain 'C' and resid 3670 through 3681 removed outlier: 5.732A pdb=" N ALA C3681 " --> pdb=" O ASP C3677 " (cutoff:3.500A) Processing helix chain 'C' and resid 3683 through 3688 Processing helix chain 'C' and resid 3697 through 3712 Processing helix chain 'C' and resid 3720 through 3735 removed outlier: 3.780A pdb=" N CYS C3734 " --> pdb=" O MET C3730 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N HIS C3735 " --> pdb=" O ALA C3731 " (cutoff:3.500A) Processing helix chain 'C' and resid 3755 through 3775 removed outlier: 3.684A pdb=" N LEU C3773 " --> pdb=" O GLN C3769 " (cutoff:3.500A) Processing helix chain 'C' and resid 3777 through 3790 removed outlier: 4.107A pdb=" N LYS C3790 " --> pdb=" O ILE C3786 " (cutoff:3.500A) Processing helix chain 'C' and resid 3794 through 3809 Processing helix chain 'C' and resid 3812 through 3827 removed outlier: 3.594A pdb=" N GLN C3816 " --> pdb=" O ASN C3812 " (cutoff:3.500A) Processing helix chain 'C' and resid 3829 through 3842 Processing helix chain 'C' and resid 3846 through 3860 removed outlier: 4.960A pdb=" N GLY C3860 " --> pdb=" O ALA C3856 " (cutoff:3.500A) Processing helix chain 'C' and resid 3864 through 3869 removed outlier: 4.473A pdb=" N ILE C3869 " --> pdb=" O ASP C3865 " (cutoff:3.500A) Processing helix chain 'C' and resid 3880 through 3896 removed outlier: 3.642A pdb=" N CYS C3895 " --> pdb=" O LEU C3891 " (cutoff:3.500A) Processing helix chain 'C' and resid 3899 through 3908 removed outlier: 3.500A pdb=" N ARG C3907 " --> pdb=" O GLN C3903 " (cutoff:3.500A) Processing helix chain 'C' and resid 3917 through 3942 removed outlier: 4.743A pdb=" N GLY C3942 " --> pdb=" O TRP C3938 " (cutoff:3.500A) Processing helix chain 'C' and resid 3947 through 3973 removed outlier: 3.559A pdb=" N ILE C3972 " --> pdb=" O LEU C3968 " (cutoff:3.500A) Processing helix chain 'C' and resid 3976 through 3987 removed outlier: 4.877A pdb=" N ARG C3987 " --> pdb=" O LEU C3983 " (cutoff:3.500A) Processing helix chain 'C' and resid 3988 through 4010 removed outlier: 3.927A pdb=" N ASP C4009 " --> pdb=" O LYS C4005 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N SER C4010 " --> pdb=" O LEU C4006 " (cutoff:3.500A) Processing helix chain 'C' and resid 4011 through 4036 removed outlier: 5.672A pdb=" N LEU C4015 " --> pdb=" O SER C4011 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU C4034 " --> pdb=" O LEU C4030 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU C4035 " --> pdb=" O LEU C4031 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N GLY C4036 " --> pdb=" O SER C4032 " (cutoff:3.500A) Processing helix chain 'C' and resid 4041 through 4055 Processing helix chain 'C' and resid 4056 through 4075 removed outlier: 3.532A pdb=" N PHE C4065 " --> pdb=" O ILE C4061 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE C4068 " --> pdb=" O PHE C4064 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASP C4073 " --> pdb=" O LEU C4069 " (cutoff:3.500A) Processing helix chain 'C' and resid 4077 through 4085 removed outlier: 4.911A pdb=" N THR C4085 " --> pdb=" O GLN C4081 " (cutoff:3.500A) Processing helix chain 'C' and resid 4092 through 4104 Processing helix chain 'C' and resid 4107 through 4119 removed outlier: 4.388A pdb=" N GLU C4119 " --> pdb=" O LEU C4115 " (cutoff:3.500A) Processing helix chain 'C' and resid 4127 through 4140 removed outlier: 4.755A pdb=" N PHE C4135 " --> pdb=" O PHE C4131 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLN C4136 " --> pdb=" O ALA C4132 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N GLU C4137 " --> pdb=" O ASN C4133 " (cutoff:3.500A) Proline residue: C4138 - end of helix Processing helix chain 'C' and resid 4141 through 4158 Proline residue: C4158 - end of helix Processing helix chain 'C' and resid 4160 through 4171 removed outlier: 3.780A pdb=" N ARG C4164 " --> pdb=" O ASP C4160 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ASN C4165 " --> pdb=" O PRO C4161 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE C4166 " --> pdb=" O ARG C4162 " (cutoff:3.500A) Processing helix chain 'C' and resid 4172 through 4178 Processing helix chain 'C' and resid 4201 through 4210 Processing helix chain 'C' and resid 4211 through 4227 Processing helix chain 'C' and resid 4232 through 4255 Processing helix chain 'C' and resid 4538 through 4557 Processing helix chain 'C' and resid 4558 through 4578 removed outlier: 4.207A pdb=" N PHE C4577 " --> pdb=" O PHE C4573 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N TYR C4578 " --> pdb=" O ILE C4574 " (cutoff:3.500A) Processing helix chain 'C' and resid 4638 through 4681 removed outlier: 3.634A pdb=" N ARG C4642 " --> pdb=" O GLU C4638 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N VAL C4664 " --> pdb=" O ASN C4660 " (cutoff:3.500A) Proline residue: C4665 - end of helix Processing helix chain 'C' and resid 4694 through 4705 removed outlier: 4.240A pdb=" N LEU C4702 " --> pdb=" O GLN C4698 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N VAL C4703 " --> pdb=" O TRP C4699 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU C4704 " --> pdb=" O ASP C4700 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ASN C4705 " --> pdb=" O ARG C4701 " (cutoff:3.500A) Processing helix chain 'C' and resid 4717 through 4727 Processing helix chain 'C' and resid 4731 through 4740 Processing helix chain 'C' and resid 4742 through 4752 Processing helix chain 'C' and resid 4761 through 4769 Processing helix chain 'C' and resid 4770 through 4785 removed outlier: 5.294A pdb=" N ASN C4785 " --> pdb=" O ILE C4781 " (cutoff:3.500A) Processing helix chain 'C' and resid 4786 through 4803 Processing helix chain 'C' and resid 4804 through 4818 removed outlier: 4.719A pdb=" N ALA C4808 " --> pdb=" O ASN C4804 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ALA C4809 " --> pdb=" O PHE C4805 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N HIS C4810 " --> pdb=" O PHE C4806 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU C4811 " --> pdb=" O PHE C4807 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LEU C4812 " --> pdb=" O ALA C4808 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASP C4813 " --> pdb=" O ALA C4809 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ILE C4814 " --> pdb=" O HIS C4810 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N ALA C4815 " --> pdb=" O LEU C4811 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N MET C4816 " --> pdb=" O LEU C4812 " (cutoff:3.500A) Processing helix chain 'C' and resid 4819 through 4830 removed outlier: 3.601A pdb=" N VAL C4828 " --> pdb=" O ILE C4824 " (cutoff:3.500A) Processing helix chain 'C' and resid 4831 through 4856 Processing helix chain 'C' and resid 4857 through 4862 removed outlier: 4.276A pdb=" N TYR C4861 " --> pdb=" O PHE C4857 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N ASN C4862 " --> pdb=" O ARG C4858 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 4857 through 4862' Processing helix chain 'C' and resid 4876 through 4891 removed outlier: 4.492A pdb=" N VAL C4889 " --> pdb=" O MET C4885 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ARG C4890 " --> pdb=" O TYR C4886 " (cutoff:3.500A) Processing helix chain 'C' and resid 4894 through 4900 removed outlier: 4.215A pdb=" N GLU C4898 " --> pdb=" O GLY C4894 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N GLU C4900 " --> pdb=" O GLY C4896 " (cutoff:3.500A) Processing helix chain 'C' and resid 4907 through 4922 Processing helix chain 'C' and resid 4926 through 4954 Processing helix chain 'C' and resid 4962 through 4968 removed outlier: 3.895A pdb=" N PHE C4966 " --> pdb=" O GLY C4962 " (cutoff:3.500A) Processing helix chain 'C' and resid 4971 through 4979 Processing helix chain 'C' and resid 4982 through 4996 removed outlier: 3.523A pdb=" N LEU C4990 " --> pdb=" O TYR C4986 " (cutoff:3.500A) Processing helix chain 'C' and resid 5002 through 5015 Processing helix chain 'C' and resid 5025 through 5031 Processing helix chain 'C' and resid 323 through 328 removed outlier: 4.313A pdb=" N VAL C 326 " --> pdb=" O LYS C 323 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA C 327 " --> pdb=" O LEU C 324 " (cutoff:3.500A) Proline residue: C 328 - end of helix No H-bonds generated for 'chain 'C' and resid 323 through 328' Processing helix chain 'C' and resid 4683 through 4688 Processing sheet with id= 1, first strand: chain 'E' and resid 3 through 8 removed outlier: 6.595A pdb=" N ARG E 72 " --> pdb=" O ILE E 8 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLN E 71 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N VAL E 24 " --> pdb=" O LEU E 105 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'F' and resid 3 through 8 removed outlier: 6.628A pdb=" N ARG F 72 " --> pdb=" O ILE F 8 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN F 71 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N VAL F 24 " --> pdb=" O LEU F 105 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'G' and resid 3 through 8 removed outlier: 6.625A pdb=" N ARG G 72 " --> pdb=" O ILE G 8 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN G 71 " --> pdb=" O LEU G 104 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL G 24 " --> pdb=" O LEU G 105 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'H' and resid 3 through 8 removed outlier: 6.629A pdb=" N ARG H 72 " --> pdb=" O ILE H 8 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN H 71 " --> pdb=" O LEU H 104 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL H 24 " --> pdb=" O LEU H 105 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'D' and resid 48 through 53 removed outlier: 6.419A pdb=" N LYS D 35 " --> pdb=" O THR D 53 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N LEU D 23 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 10.461A pdb=" N ALA D 40 " --> pdb=" O VAL D 21 " (cutoff:3.500A) removed outlier: 13.479A pdb=" N VAL D 21 " --> pdb=" O ALA D 40 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLU D 20 " --> pdb=" O ILE D 206 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'D' and resid 68 through 71 removed outlier: 6.661A pdb=" N LEU D 109 " --> pdb=" O GLU D 71 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'D' and resid 150 through 153 Processing sheet with id= 8, first strand: chain 'D' and resid 221 through 225 Processing sheet with id= 9, first strand: chain 'D' and resid 230 through 234 removed outlier: 5.354A pdb=" N VAL D 246 " --> pdb=" O ALA D 377 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'D' and resid 261 through 265 removed outlier: 4.909A pdb=" N ILE D 283 " --> pdb=" O LEU D 292 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG D 290 " --> pdb=" O HIS D 285 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'D' and resid 315 through 319 Processing sheet with id= 12, first strand: chain 'D' and resid 683 through 687 removed outlier: 3.707A pdb=" N ARG D1647 " --> pdb=" O ILE D1642 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'D' and resid 754 through 759 removed outlier: 4.068A pdb=" N ASP D 743 " --> pdb=" O VAL D 669 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LYS D 789 " --> pdb=" O ASP D 670 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'D' and resid 767 through 770 Processing sheet with id= 15, first strand: chain 'D' and resid 830 through 833 removed outlier: 4.785A pdb=" N TYR D 830 " --> pdb=" O VAL D 841 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N LEU D1203 " --> pdb=" O PRO D 838 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N GLN D1199 " --> pdb=" O GLY D 842 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N VAL D1200 " --> pdb=" O VAL D1096 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N GLY D1087 " --> pdb=" O LEU D1156 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ASP D1148 " --> pdb=" O ALA D1095 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'D' and resid 897 through 900 removed outlier: 6.742A pdb=" N VAL D 897 " --> pdb=" O PRO D 906 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'D' and resid 937 through 942 removed outlier: 7.507A pdb=" N GLY D 937 " --> pdb=" O PRO D1057 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N HIS D 939 " --> pdb=" O GLU D1055 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'D' and resid 1006 through 1009 removed outlier: 3.811A pdb=" N SER D1009 " --> pdb=" O ASN D1019 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'D' and resid 1135 through 1138 removed outlier: 7.429A pdb=" N LEU D1121 " --> pdb=" O ARG D1107 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N MET D1101 " --> pdb=" O GLY D1127 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N GLU D1100 " --> pdb=" O GLY D1196 " (cutoff:3.500A) removed outlier: 10.270A pdb=" N ALA D1073 " --> pdb=" O SER D1242 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N SER D1242 " --> pdb=" O ALA D1073 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ILE D1075 " --> pdb=" O SER D1240 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N THR D1236 " --> pdb=" O GLU D1079 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N THR D1237 " --> pdb=" O MET D1609 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'D' and resid 1268 through 1274 removed outlier: 3.724A pdb=" N VAL D1563 " --> pdb=" O LEU D1273 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL D1562 " --> pdb=" O PHE D1441 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N PHE D1441 " --> pdb=" O VAL D1562 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N GLY D1568 " --> pdb=" O TYR D1435 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N TYR D1435 " --> pdb=" O GLY D1568 " (cutoff:3.500A) removed outlier: 8.540A pdb=" N THR D1432 " --> pdb=" O LEU D1523 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N GLY D1526 " --> pdb=" O VAL D1543 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'D' and resid 1295 through 1299 removed outlier: 4.464A pdb=" N THR D1547 " --> pdb=" O PHE D1298 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N PHE D1289 " --> pdb=" O LEU D1601 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'D' and resid 2822 through 2826 removed outlier: 4.583A pdb=" N THR D2823 " --> pdb=" O THR D2939 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THR D2939 " --> pdb=" O THR D2823 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'D' and resid 4180 through 4187 removed outlier: 4.880A pdb=" N TYR D4180 " --> pdb=" O ILE D4200 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'D' and resid 4579 through 4582 Processing sheet with id= 25, first strand: chain 'A' and resid 48 through 53 removed outlier: 6.419A pdb=" N LYS A 35 " --> pdb=" O THR A 53 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N LEU A 23 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 10.461A pdb=" N ALA A 40 " --> pdb=" O VAL A 21 " (cutoff:3.500A) removed outlier: 13.479A pdb=" N VAL A 21 " --> pdb=" O ALA A 40 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N GLU A 20 " --> pdb=" O ILE A 206 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'A' and resid 68 through 71 removed outlier: 6.660A pdb=" N LEU A 109 " --> pdb=" O GLU A 71 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'A' and resid 150 through 153 Processing sheet with id= 28, first strand: chain 'A' and resid 221 through 225 Processing sheet with id= 29, first strand: chain 'A' and resid 230 through 234 removed outlier: 5.354A pdb=" N VAL A 246 " --> pdb=" O ALA A 377 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'A' and resid 261 through 265 removed outlier: 4.909A pdb=" N ILE A 283 " --> pdb=" O LEU A 292 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG A 290 " --> pdb=" O HIS A 285 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'A' and resid 315 through 319 Processing sheet with id= 32, first strand: chain 'A' and resid 683 through 687 removed outlier: 3.707A pdb=" N ARG A1647 " --> pdb=" O ILE A1642 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'A' and resid 754 through 759 removed outlier: 4.068A pdb=" N ASP A 743 " --> pdb=" O VAL A 669 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LYS A 789 " --> pdb=" O ASP A 670 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'A' and resid 767 through 770 Processing sheet with id= 35, first strand: chain 'A' and resid 830 through 833 removed outlier: 4.785A pdb=" N TYR A 830 " --> pdb=" O VAL A 841 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N LEU A1203 " --> pdb=" O PRO A 838 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N GLN A1199 " --> pdb=" O GLY A 842 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N VAL A1200 " --> pdb=" O VAL A1096 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N GLY A1087 " --> pdb=" O LEU A1156 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ASP A1148 " --> pdb=" O ALA A1095 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'A' and resid 897 through 900 removed outlier: 6.742A pdb=" N VAL A 897 " --> pdb=" O PRO A 906 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'A' and resid 937 through 942 removed outlier: 7.508A pdb=" N GLY A 937 " --> pdb=" O PRO A1057 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N HIS A 939 " --> pdb=" O GLU A1055 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'A' and resid 1006 through 1009 removed outlier: 3.810A pdb=" N SER A1009 " --> pdb=" O ASN A1019 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'A' and resid 1135 through 1138 removed outlier: 7.429A pdb=" N LEU A1121 " --> pdb=" O ARG A1107 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N MET A1101 " --> pdb=" O GLY A1127 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N GLU A1100 " --> pdb=" O GLY A1196 " (cutoff:3.500A) removed outlier: 10.270A pdb=" N ALA A1073 " --> pdb=" O SER A1242 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N SER A1242 " --> pdb=" O ALA A1073 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ILE A1075 " --> pdb=" O SER A1240 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N THR A1236 " --> pdb=" O GLU A1079 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N THR A1237 " --> pdb=" O MET A1609 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'A' and resid 1268 through 1274 removed outlier: 3.724A pdb=" N VAL A1563 " --> pdb=" O LEU A1273 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL A1562 " --> pdb=" O PHE A1441 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N PHE A1441 " --> pdb=" O VAL A1562 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N GLY A1568 " --> pdb=" O TYR A1435 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N TYR A1435 " --> pdb=" O GLY A1568 " (cutoff:3.500A) removed outlier: 8.540A pdb=" N THR A1432 " --> pdb=" O LEU A1523 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N GLY A1526 " --> pdb=" O VAL A1543 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'A' and resid 1295 through 1299 removed outlier: 4.464A pdb=" N THR A1547 " --> pdb=" O PHE A1298 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N PHE A1289 " --> pdb=" O LEU A1601 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'A' and resid 2822 through 2826 removed outlier: 4.583A pdb=" N THR A2823 " --> pdb=" O THR A2939 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N THR A2939 " --> pdb=" O THR A2823 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'A' and resid 4180 through 4187 removed outlier: 4.881A pdb=" N TYR A4180 " --> pdb=" O ILE A4200 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'A' and resid 4579 through 4582 Processing sheet with id= 45, first strand: chain 'B' and resid 48 through 53 removed outlier: 6.419A pdb=" N LYS B 35 " --> pdb=" O THR B 53 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N LEU B 23 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 10.461A pdb=" N ALA B 40 " --> pdb=" O VAL B 21 " (cutoff:3.500A) removed outlier: 13.479A pdb=" N VAL B 21 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N GLU B 20 " --> pdb=" O ILE B 206 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'B' and resid 68 through 71 removed outlier: 6.661A pdb=" N LEU B 109 " --> pdb=" O GLU B 71 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'B' and resid 150 through 153 Processing sheet with id= 48, first strand: chain 'B' and resid 221 through 225 Processing sheet with id= 49, first strand: chain 'B' and resid 230 through 234 removed outlier: 5.354A pdb=" N VAL B 246 " --> pdb=" O ALA B 377 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'B' and resid 261 through 265 removed outlier: 4.909A pdb=" N ILE B 283 " --> pdb=" O LEU B 292 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG B 290 " --> pdb=" O HIS B 285 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'B' and resid 315 through 319 Processing sheet with id= 52, first strand: chain 'B' and resid 683 through 687 removed outlier: 3.707A pdb=" N ARG B1647 " --> pdb=" O ILE B1642 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'B' and resid 754 through 759 removed outlier: 4.068A pdb=" N ASP B 743 " --> pdb=" O VAL B 669 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LYS B 789 " --> pdb=" O ASP B 670 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'B' and resid 767 through 770 Processing sheet with id= 55, first strand: chain 'B' and resid 830 through 833 removed outlier: 4.785A pdb=" N TYR B 830 " --> pdb=" O VAL B 841 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N LEU B1203 " --> pdb=" O PRO B 838 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N GLN B1199 " --> pdb=" O GLY B 842 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N VAL B1200 " --> pdb=" O VAL B1096 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N GLY B1087 " --> pdb=" O LEU B1156 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ASP B1148 " --> pdb=" O ALA B1095 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'B' and resid 897 through 900 removed outlier: 6.742A pdb=" N VAL B 897 " --> pdb=" O PRO B 906 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'B' and resid 937 through 942 removed outlier: 7.507A pdb=" N GLY B 937 " --> pdb=" O PRO B1057 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N HIS B 939 " --> pdb=" O GLU B1055 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'B' and resid 1006 through 1009 removed outlier: 3.811A pdb=" N SER B1009 " --> pdb=" O ASN B1019 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'B' and resid 1135 through 1138 removed outlier: 7.429A pdb=" N LEU B1121 " --> pdb=" O ARG B1107 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N MET B1101 " --> pdb=" O GLY B1127 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N GLU B1100 " --> pdb=" O GLY B1196 " (cutoff:3.500A) removed outlier: 10.270A pdb=" N ALA B1073 " --> pdb=" O SER B1242 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N SER B1242 " --> pdb=" O ALA B1073 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ILE B1075 " --> pdb=" O SER B1240 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N THR B1236 " --> pdb=" O GLU B1079 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N THR B1237 " --> pdb=" O MET B1609 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'B' and resid 1268 through 1274 removed outlier: 3.724A pdb=" N VAL B1563 " --> pdb=" O LEU B1273 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL B1562 " --> pdb=" O PHE B1441 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N PHE B1441 " --> pdb=" O VAL B1562 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N GLY B1568 " --> pdb=" O TYR B1435 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N TYR B1435 " --> pdb=" O GLY B1568 " (cutoff:3.500A) removed outlier: 8.539A pdb=" N THR B1432 " --> pdb=" O LEU B1523 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N GLY B1526 " --> pdb=" O VAL B1543 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'B' and resid 1295 through 1299 removed outlier: 4.465A pdb=" N THR B1547 " --> pdb=" O PHE B1298 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N PHE B1289 " --> pdb=" O LEU B1601 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'B' and resid 2822 through 2826 removed outlier: 4.583A pdb=" N THR B2823 " --> pdb=" O THR B2939 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THR B2939 " --> pdb=" O THR B2823 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'B' and resid 4180 through 4187 removed outlier: 4.880A pdb=" N TYR B4180 " --> pdb=" O ILE B4200 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'B' and resid 4579 through 4582 Processing sheet with id= 65, first strand: chain 'C' and resid 48 through 53 removed outlier: 6.418A pdb=" N LYS C 35 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N LEU C 23 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 10.461A pdb=" N ALA C 40 " --> pdb=" O VAL C 21 " (cutoff:3.500A) removed outlier: 13.479A pdb=" N VAL C 21 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLU C 20 " --> pdb=" O ILE C 206 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'C' and resid 68 through 71 removed outlier: 6.661A pdb=" N LEU C 109 " --> pdb=" O GLU C 71 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'C' and resid 150 through 153 Processing sheet with id= 68, first strand: chain 'C' and resid 221 through 225 Processing sheet with id= 69, first strand: chain 'C' and resid 230 through 234 removed outlier: 5.354A pdb=" N VAL C 246 " --> pdb=" O ALA C 377 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'C' and resid 261 through 265 removed outlier: 4.909A pdb=" N ILE C 283 " --> pdb=" O LEU C 292 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG C 290 " --> pdb=" O HIS C 285 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'C' and resid 315 through 319 Processing sheet with id= 72, first strand: chain 'C' and resid 683 through 687 removed outlier: 3.707A pdb=" N ARG C1647 " --> pdb=" O ILE C1642 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'C' and resid 754 through 759 removed outlier: 4.068A pdb=" N ASP C 743 " --> pdb=" O VAL C 669 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LYS C 789 " --> pdb=" O ASP C 670 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'C' and resid 767 through 770 Processing sheet with id= 75, first strand: chain 'C' and resid 830 through 833 removed outlier: 4.785A pdb=" N TYR C 830 " --> pdb=" O VAL C 841 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N LEU C1203 " --> pdb=" O PRO C 838 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N GLN C1199 " --> pdb=" O GLY C 842 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N VAL C1200 " --> pdb=" O VAL C1096 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N GLY C1087 " --> pdb=" O LEU C1156 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ASP C1148 " --> pdb=" O ALA C1095 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'C' and resid 897 through 900 removed outlier: 6.742A pdb=" N VAL C 897 " --> pdb=" O PRO C 906 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'C' and resid 937 through 942 removed outlier: 7.507A pdb=" N GLY C 937 " --> pdb=" O PRO C1057 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N HIS C 939 " --> pdb=" O GLU C1055 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'C' and resid 1006 through 1009 removed outlier: 3.811A pdb=" N SER C1009 " --> pdb=" O ASN C1019 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'C' and resid 1135 through 1138 removed outlier: 7.429A pdb=" N LEU C1121 " --> pdb=" O ARG C1107 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N MET C1101 " --> pdb=" O GLY C1127 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N GLU C1100 " --> pdb=" O GLY C1196 " (cutoff:3.500A) removed outlier: 10.270A pdb=" N ALA C1073 " --> pdb=" O SER C1242 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N SER C1242 " --> pdb=" O ALA C1073 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N ILE C1075 " --> pdb=" O SER C1240 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N THR C1236 " --> pdb=" O GLU C1079 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N THR C1237 " --> pdb=" O MET C1609 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'C' and resid 1268 through 1274 removed outlier: 3.724A pdb=" N VAL C1563 " --> pdb=" O LEU C1273 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL C1562 " --> pdb=" O PHE C1441 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N PHE C1441 " --> pdb=" O VAL C1562 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N GLY C1568 " --> pdb=" O TYR C1435 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N TYR C1435 " --> pdb=" O GLY C1568 " (cutoff:3.500A) removed outlier: 8.540A pdb=" N THR C1432 " --> pdb=" O LEU C1523 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N GLY C1526 " --> pdb=" O VAL C1543 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain 'C' and resid 1295 through 1299 removed outlier: 4.464A pdb=" N THR C1547 " --> pdb=" O PHE C1298 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N PHE C1289 " --> pdb=" O LEU C1601 " (cutoff:3.500A) Processing sheet with id= 82, first strand: chain 'C' and resid 2822 through 2826 removed outlier: 4.583A pdb=" N THR C2823 " --> pdb=" O THR C2939 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THR C2939 " --> pdb=" O THR C2823 " (cutoff:3.500A) Processing sheet with id= 83, first strand: chain 'C' and resid 4180 through 4187 removed outlier: 4.880A pdb=" N TYR C4180 " --> pdb=" O ILE C4200 " (cutoff:3.500A) Processing sheet with id= 84, first strand: chain 'C' and resid 4579 through 4582 8120 hydrogen bonds defined for protein. 24312 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: 134.97 Time building geometry restraints manager: 46.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 25124 1.31 - 1.44: 39800 1.44 - 1.56: 86033 1.56 - 1.69: 87 1.69 - 1.82: 1556 Bond restraints: 152600 Sorted by residual: bond pdb=" C11 PCW D8006 " pdb=" O3 PCW D8006 " ideal model delta sigma weight residual 1.326 1.419 -0.093 2.00e-02 2.50e+03 2.15e+01 bond pdb=" C11 PCW C5107 " pdb=" O3 PCW C5107 " ideal model delta sigma weight residual 1.326 1.419 -0.093 2.00e-02 2.50e+03 2.15e+01 bond pdb=" C11 PCW A8006 " pdb=" O3 PCW A8006 " ideal model delta sigma weight residual 1.326 1.419 -0.093 2.00e-02 2.50e+03 2.15e+01 bond pdb=" C11 PCW B8006 " pdb=" O3 PCW B8006 " ideal model delta sigma weight residual 1.326 1.419 -0.093 2.00e-02 2.50e+03 2.15e+01 bond pdb=" C11 PCW A8007 " pdb=" O3 PCW A8007 " ideal model delta sigma weight residual 1.326 1.417 -0.091 2.00e-02 2.50e+03 2.09e+01 ... (remaining 152595 not shown) Histogram of bond angle deviations from ideal: 94.08 - 106.19: 4514 106.19 - 118.30: 113526 118.30 - 130.41: 87728 130.41 - 142.52: 828 142.52 - 154.63: 8 Bond angle restraints: 206604 Sorted by residual: angle pdb=" C5 PCW D8007 " pdb=" N PCW D8007 " pdb=" C7 PCW D8007 " ideal model delta sigma weight residual 107.31 140.54 -33.23 3.00e+00 1.11e-01 1.23e+02 angle pdb=" C5 PCW A8007 " pdb=" N PCW A8007 " pdb=" C7 PCW A8007 " ideal model delta sigma weight residual 107.31 140.51 -33.20 3.00e+00 1.11e-01 1.23e+02 angle pdb=" C5 PCW C5101 " pdb=" N PCW C5101 " pdb=" C7 PCW C5101 " ideal model delta sigma weight residual 107.31 140.51 -33.20 3.00e+00 1.11e-01 1.23e+02 angle pdb=" C5 PCW B8007 " pdb=" N PCW B8007 " pdb=" C7 PCW B8007 " ideal model delta sigma weight residual 107.31 140.47 -33.16 3.00e+00 1.11e-01 1.22e+02 angle pdb=" C5 PCW B8006 " pdb=" N PCW B8006 " pdb=" C7 PCW B8006 " ideal model delta sigma weight residual 107.31 139.00 -31.69 3.00e+00 1.11e-01 1.12e+02 ... (remaining 206599 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 83671 17.56 - 35.12: 6735 35.12 - 52.68: 1260 52.68 - 70.24: 402 70.24 - 87.80: 188 Dihedral angle restraints: 92256 sinusoidal: 38080 harmonic: 54176 Sorted by residual: dihedral pdb=" CA ASP K 25 " pdb=" C ASP K 25 " pdb=" N LYS K 26 " pdb=" CA LYS K 26 " ideal model delta harmonic sigma weight residual -180.00 -158.78 -21.22 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" CA ASP I 25 " pdb=" C ASP I 25 " pdb=" N LYS I 26 " pdb=" CA LYS I 26 " ideal model delta harmonic sigma weight residual -180.00 -158.79 -21.21 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" CA ASP O 25 " pdb=" C ASP O 25 " pdb=" N LYS O 26 " pdb=" CA LYS O 26 " ideal model delta harmonic sigma weight residual -180.00 -158.80 -21.20 0 5.00e+00 4.00e-02 1.80e+01 ... (remaining 92253 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 20229 0.059 - 0.117: 2247 0.117 - 0.176: 172 0.176 - 0.235: 8 0.235 - 0.293: 16 Chirality restraints: 22672 Sorted by residual: chirality pdb=" C2' ATP A8005 " pdb=" C1' ATP A8005 " pdb=" C3' ATP A8005 " pdb=" O2' ATP A8005 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" C2' ATP B8005 " pdb=" C1' ATP B8005 " pdb=" C3' ATP B8005 " pdb=" O2' ATP B8005 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" C2' ATP D8005 " pdb=" C1' ATP D8005 " pdb=" C3' ATP D8005 " pdb=" O2' ATP D8005 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.14e+00 ... (remaining 22669 not shown) Planarity restraints: 26800 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU D1055 " 0.022 2.00e-02 2.50e+03 4.36e-02 1.90e+01 pdb=" C GLU D1055 " -0.075 2.00e-02 2.50e+03 pdb=" O GLU D1055 " 0.028 2.00e-02 2.50e+03 pdb=" N PRO D1056 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU C1055 " -0.022 2.00e-02 2.50e+03 4.36e-02 1.90e+01 pdb=" C GLU C1055 " 0.075 2.00e-02 2.50e+03 pdb=" O GLU C1055 " -0.028 2.00e-02 2.50e+03 pdb=" N PRO C1056 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B1055 " -0.022 2.00e-02 2.50e+03 4.36e-02 1.90e+01 pdb=" C GLU B1055 " 0.075 2.00e-02 2.50e+03 pdb=" O GLU B1055 " -0.028 2.00e-02 2.50e+03 pdb=" N PRO B1056 " -0.025 2.00e-02 2.50e+03 ... (remaining 26797 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.35: 445 2.35 - 2.99: 85541 2.99 - 3.63: 234499 3.63 - 4.26: 350653 4.26 - 4.90: 585480 Nonbonded interactions: 1256618 Sorted by model distance: nonbonded pdb=" NE2 GLN D2694 " pdb=" OE2 GLU O 10 " model vdw 1.718 2.520 nonbonded pdb=" NE2 GLN C2694 " pdb=" OE2 GLU M 10 " model vdw 1.718 2.520 nonbonded pdb=" OE2 GLU I 10 " pdb=" NE2 GLN A2694 " model vdw 1.718 2.520 nonbonded pdb=" NE2 GLN B2694 " pdb=" OE2 GLU K 10 " model vdw 1.718 2.520 nonbonded pdb=" OG1 THR A3309 " pdb=" OD1 ASP A3311 " model vdw 1.995 2.440 ... (remaining 1256613 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' and (resid 11 through 5035 or resid 8007)) selection = (chain 'B' and (resid 11 through 5035 or resid 8007)) selection = (chain 'C' and (resid 11 through 5035 or resid 5107)) selection = (chain 'D' and (resid 11 through 5035 or resid 8007)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.110 Extract box with map and model: 29.910 Check model and map are aligned: 1.590 Set scattering table: 0.990 Process input model: 415.720 Find NCS groups from input model: 11.490 Set up NCS constraints: 1.250 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: 0.030 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 470.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 152600 Z= 0.290 Angle : 0.737 33.233 206604 Z= 0.385 Chirality : 0.038 0.293 22672 Planarity : 0.004 0.078 26800 Dihedral : 14.063 87.799 57248 Min Nonbonded Distance : 1.718 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.05 % Allowed : 0.34 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % 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: 1.34 (0.06), residues: 18552 helix: 1.80 (0.05), residues: 9908 sheet: -0.27 (0.12), residues: 1736 loop : -0.06 (0.08), residues: 6908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP B1144 HIS 0.009 0.001 HIS A 880 PHE 0.035 0.001 PHE B3902 TYR 0.023 0.002 TYR A2257 ARG 0.014 0.001 ARG A4911 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 37104 Ramachandran restraints generated. 18552 Oldfield, 0 Emsley, 18552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 37104 Ramachandran restraints generated. 18552 Oldfield, 0 Emsley, 18552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1491 residues out of total 16268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 1483 time to evaluate : 12.603 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: E 54 GLN cc_start: 0.8983 (mp10) cc_final: 0.8637 (mp10) REVERT: I 5 LEU cc_start: 0.9188 (mm) cc_final: 0.8730 (mm) REVERT: J 75 TYR cc_start: 0.6326 (p90) cc_final: 0.6062 (p90) REVERT: J 88 ASN cc_start: 0.8815 (m-40) cc_final: 0.8418 (m-40) REVERT: F 45 LYS cc_start: 0.8612 (ttpt) cc_final: 0.8326 (ttpp) REVERT: G 45 LYS cc_start: 0.8585 (ttpt) cc_final: 0.8303 (ttpp) REVERT: G 50 THR cc_start: 0.9422 (m) cc_final: 0.9218 (m) REVERT: H 45 LYS cc_start: 0.8608 (ttpt) cc_final: 0.8325 (ttpp) REVERT: H 50 THR cc_start: 0.9425 (m) cc_final: 0.9223 (m) REVERT: D 197 MET cc_start: 0.8121 (mpp) cc_final: 0.7597 (mpp) REVERT: D 666 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7464 (mt-10) REVERT: D 828 LYS cc_start: 0.8712 (mmmt) cc_final: 0.8477 (mmmm) REVERT: D 864 LEU cc_start: 0.9022 (mt) cc_final: 0.8787 (tp) REVERT: D 905 HIS cc_start: 0.6716 (t70) cc_final: 0.6034 (t-170) REVERT: D 925 MET cc_start: 0.8492 (mtt) cc_final: 0.7932 (mtp) REVERT: D 1574 MET cc_start: 0.8774 (mmt) cc_final: 0.8504 (mmt) REVERT: D 1997 ARG cc_start: 0.8939 (tmt-80) cc_final: 0.8304 (tpt90) REVERT: D 2424 MET cc_start: 0.8549 (mpp) cc_final: 0.8337 (mpp) REVERT: D 2467 LEU cc_start: 0.9503 (mt) cc_final: 0.9176 (mt) REVERT: D 2945 MET cc_start: 0.8535 (ptt) cc_final: 0.8232 (ptt) REVERT: D 2977 HIS cc_start: 0.8973 (t70) cc_final: 0.8524 (t-170) REVERT: D 3202 MET cc_start: 0.9352 (tpp) cc_final: 0.9067 (tpp) REVERT: D 3468 MET cc_start: 0.7909 (tpp) cc_final: 0.7459 (tpp) REVERT: D 3861 MET cc_start: 0.3060 (pmm) cc_final: 0.2585 (pmm) REVERT: D 4091 ILE cc_start: 0.8106 (tp) cc_final: 0.7861 (tp) REVERT: D 4869 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8433 (mm-30) REVERT: D 5011 MET cc_start: 0.8687 (OUTLIER) cc_final: 0.8456 (mtp) REVERT: A 197 MET cc_start: 0.8062 (mpp) cc_final: 0.7578 (mpp) REVERT: A 666 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7642 (mt-10) REVERT: A 864 LEU cc_start: 0.9067 (mt) cc_final: 0.8824 (tp) REVERT: A 905 HIS cc_start: 0.6684 (t70) cc_final: 0.5935 (t-170) REVERT: A 925 MET cc_start: 0.8638 (mtt) cc_final: 0.7960 (mtp) REVERT: A 1574 MET cc_start: 0.8812 (mmt) cc_final: 0.8564 (mmt) REVERT: A 1997 ARG cc_start: 0.8974 (tmt-80) cc_final: 0.8299 (tpt90) REVERT: A 2945 MET cc_start: 0.8483 (ptt) cc_final: 0.8246 (ptt) REVERT: A 3202 MET cc_start: 0.9243 (tpp) cc_final: 0.8930 (tpp) REVERT: A 3211 LEU cc_start: 0.9495 (mm) cc_final: 0.8969 (tp) REVERT: A 3861 MET cc_start: 0.3465 (pmm) cc_final: 0.3023 (pmm) REVERT: A 4869 GLU cc_start: 0.8656 (mm-30) cc_final: 0.8436 (mm-30) REVERT: A 4991 MET cc_start: 0.9130 (mtp) cc_final: 0.8927 (mtm) REVERT: A 5011 MET cc_start: 0.8702 (OUTLIER) cc_final: 0.8499 (mtp) REVERT: B 197 MET cc_start: 0.8120 (mpp) cc_final: 0.7600 (mpp) REVERT: B 666 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7462 (mt-10) REVERT: B 828 LYS cc_start: 0.8715 (mmmt) cc_final: 0.8492 (mmmm) REVERT: B 864 LEU cc_start: 0.9014 (mt) cc_final: 0.8784 (tp) REVERT: B 905 HIS cc_start: 0.6696 (t70) cc_final: 0.6021 (t-170) REVERT: B 925 MET cc_start: 0.8502 (mtt) cc_final: 0.7927 (mtp) REVERT: B 1574 MET cc_start: 0.8758 (mmt) cc_final: 0.8479 (mmt) REVERT: B 1997 ARG cc_start: 0.8936 (tmt-80) cc_final: 0.8308 (tpt90) REVERT: B 2424 MET cc_start: 0.8551 (mpp) cc_final: 0.8347 (mpp) REVERT: B 2467 LEU cc_start: 0.9506 (mt) cc_final: 0.9184 (mt) REVERT: B 2629 PHE cc_start: 0.8809 (t80) cc_final: 0.8496 (t80) REVERT: B 2945 MET cc_start: 0.8534 (ptt) cc_final: 0.8311 (ptt) REVERT: B 2977 HIS cc_start: 0.8970 (t70) cc_final: 0.8509 (t-170) REVERT: B 3202 MET cc_start: 0.9358 (tpp) cc_final: 0.9081 (tpp) REVERT: B 3468 MET cc_start: 0.7917 (tpp) cc_final: 0.7482 (tpp) REVERT: B 3861 MET cc_start: 0.3059 (pmm) cc_final: 0.2584 (pmm) REVERT: B 4091 ILE cc_start: 0.8120 (tp) cc_final: 0.7873 (tp) REVERT: B 4869 GLU cc_start: 0.8705 (mm-30) cc_final: 0.8384 (mm-30) REVERT: B 5011 MET cc_start: 0.8690 (OUTLIER) cc_final: 0.8458 (mtp) REVERT: C 197 MET cc_start: 0.8122 (mpp) cc_final: 0.7597 (mpp) REVERT: C 666 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7465 (mt-10) REVERT: C 828 LYS cc_start: 0.8711 (mmmt) cc_final: 0.8475 (mmmm) REVERT: C 864 LEU cc_start: 0.9024 (mt) cc_final: 0.8795 (tp) REVERT: C 905 HIS cc_start: 0.6711 (t70) cc_final: 0.6029 (t-170) REVERT: C 925 MET cc_start: 0.8498 (mtt) cc_final: 0.7934 (mtp) REVERT: C 1574 MET cc_start: 0.8773 (mmt) cc_final: 0.8503 (mmt) REVERT: C 1997 ARG cc_start: 0.8930 (tmt-80) cc_final: 0.8292 (tpt90) REVERT: C 2424 MET cc_start: 0.8540 (mpp) cc_final: 0.8333 (mpp) REVERT: C 2467 LEU cc_start: 0.9504 (mt) cc_final: 0.9179 (mt) REVERT: C 2945 MET cc_start: 0.8534 (ptt) cc_final: 0.8311 (ptt) REVERT: C 2977 HIS cc_start: 0.8984 (t70) cc_final: 0.8532 (t-170) REVERT: C 3202 MET cc_start: 0.9348 (tpp) cc_final: 0.9054 (tpp) REVERT: C 3468 MET cc_start: 0.7895 (tpp) cc_final: 0.7422 (tpp) REVERT: C 3730 MET cc_start: 0.8710 (mtm) cc_final: 0.8292 (mtm) REVERT: C 3861 MET cc_start: 0.3092 (pmm) cc_final: 0.2624 (pmm) REVERT: C 4091 ILE cc_start: 0.8113 (tp) cc_final: 0.7866 (tp) REVERT: C 4869 GLU cc_start: 0.8710 (mm-30) cc_final: 0.8428 (mm-30) REVERT: C 5011 MET cc_start: 0.8687 (OUTLIER) cc_final: 0.8455 (mtp) REVERT: K 5 LEU cc_start: 0.9188 (mm) cc_final: 0.8740 (mm) REVERT: K 34 LEU cc_start: 0.8844 (tt) cc_final: 0.8634 (tt) REVERT: L 75 TYR cc_start: 0.6337 (p90) cc_final: 0.6035 (p90) REVERT: L 88 ASN cc_start: 0.8834 (m-40) cc_final: 0.8467 (m-40) REVERT: N 75 TYR cc_start: 0.6347 (p90) cc_final: 0.6049 (p90) REVERT: M 5 LEU cc_start: 0.9187 (mm) cc_final: 0.8748 (mm) REVERT: M 34 LEU cc_start: 0.8836 (tt) cc_final: 0.8625 (tt) REVERT: O 5 LEU cc_start: 0.9183 (mm) cc_final: 0.8740 (mm) REVERT: O 34 LEU cc_start: 0.8835 (tt) cc_final: 0.8632 (tt) REVERT: P 75 TYR cc_start: 0.6334 (p90) cc_final: 0.6046 (p90) REVERT: P 88 ASN cc_start: 0.8807 (m-40) cc_final: 0.8439 (m-40) outliers start: 8 outliers final: 0 residues processed: 1487 average time/residue: 1.3722 time to fit residues: 3619.3843 Evaluate side-chains 1046 residues out of total 16268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1042 time to evaluate : 12.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 5011 MET Chi-restraints excluded: chain A residue 5011 MET Chi-restraints excluded: chain B residue 5011 MET Chi-restraints excluded: chain C residue 5011 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1860 random chunks: chunk 1570 optimal weight: 6.9990 chunk 1409 optimal weight: 0.1980 chunk 782 optimal weight: 0.3980 chunk 481 optimal weight: 10.0000 chunk 950 optimal weight: 6.9990 chunk 753 optimal weight: 0.9980 chunk 1457 optimal weight: 40.0000 chunk 564 optimal weight: 8.9990 chunk 886 optimal weight: 8.9990 chunk 1085 optimal weight: 0.9990 chunk 1689 optimal weight: 0.7980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 HIS D 726 HIS D1632 GLN D1973 ASN D2128 GLN D2269 GLN ** D2893 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3668 HIS A 106 HIS A 726 HIS A1632 GLN A1973 ASN A2128 GLN A2269 GLN ** A2893 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3668 HIS B 106 HIS B 726 HIS B1632 GLN B1973 ASN B2128 GLN B2269 GLN ** B2893 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3668 HIS C 106 HIS C 726 HIS C1632 GLN C1973 ASN C2128 GLN ** C2269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2893 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3668 HIS C4648 HIS ** L 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 152600 Z= 0.177 Angle : 0.564 10.632 206604 Z= 0.287 Chirality : 0.039 0.247 22672 Planarity : 0.004 0.044 26800 Dihedral : 7.040 86.274 20908 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.66 % Allowed : 4.75 % Favored : 94.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % 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: 1.76 (0.06), residues: 18552 helix: 2.16 (0.05), residues: 9916 sheet: -0.18 (0.12), residues: 1780 loop : 0.15 (0.08), residues: 6856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP P 91 HIS 0.009 0.001 HIS I 17 PHE 0.032 0.001 PHE B2974 TYR 0.026 0.001 TYR N 27 ARG 0.006 0.000 ARG A3381 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 37104 Ramachandran restraints generated. 18552 Oldfield, 0 Emsley, 18552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 37104 Ramachandran restraints generated. 18552 Oldfield, 0 Emsley, 18552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1341 residues out of total 16268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 1234 time to evaluate : 12.824 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: E 54 GLN cc_start: 0.9006 (mp10) cc_final: 0.8621 (mp10) REVERT: E 61 GLU cc_start: 0.8762 (mm-30) cc_final: 0.8447 (mm-30) REVERT: I 42 LEU cc_start: 0.7347 (mm) cc_final: 0.6794 (tp) REVERT: J 12 LEU cc_start: 0.8484 (tp) cc_final: 0.8023 (mt) REVERT: J 39 GLN cc_start: 0.6825 (OUTLIER) cc_final: 0.6447 (pm20) REVERT: J 42 LEU cc_start: 0.9189 (tp) cc_final: 0.8655 (tp) REVERT: F 4 GLN cc_start: 0.7741 (mp10) cc_final: 0.7504 (mp10) REVERT: F 45 LYS cc_start: 0.8621 (ttpt) cc_final: 0.8346 (ttpp) REVERT: F 51 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.9054 (mt) REVERT: F 53 LYS cc_start: 0.9082 (mptt) cc_final: 0.8853 (mmtp) REVERT: F 55 GLU cc_start: 0.8617 (mt-10) cc_final: 0.8241 (mt-10) REVERT: F 61 GLU cc_start: 0.8757 (mm-30) cc_final: 0.8465 (mm-30) REVERT: G 4 GLN cc_start: 0.7728 (mp10) cc_final: 0.7495 (mp10) REVERT: G 45 LYS cc_start: 0.8610 (ttpt) cc_final: 0.8336 (ttpp) REVERT: G 53 LYS cc_start: 0.9030 (mmtp) cc_final: 0.8815 (mmtp) REVERT: G 55 GLU cc_start: 0.8603 (mt-10) cc_final: 0.8223 (mt-10) REVERT: G 61 GLU cc_start: 0.8689 (mm-30) cc_final: 0.8453 (mm-30) REVERT: H 45 LYS cc_start: 0.8626 (ttpt) cc_final: 0.8353 (ttpp) REVERT: H 53 LYS cc_start: 0.9038 (mmtp) cc_final: 0.8829 (mmtp) REVERT: H 55 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8227 (mt-10) REVERT: H 61 GLU cc_start: 0.8678 (mm-30) cc_final: 0.8429 (mm-30) REVERT: D 117 MET cc_start: 0.9287 (mtm) cc_final: 0.8787 (mtp) REVERT: D 197 MET cc_start: 0.7989 (mpp) cc_final: 0.7469 (mpp) REVERT: D 666 GLU cc_start: 0.7798 (mt-10) cc_final: 0.7410 (mt-10) REVERT: D 828 LYS cc_start: 0.8657 (mmmt) cc_final: 0.8433 (mmmm) REVERT: D 1574 MET cc_start: 0.8931 (mmt) cc_final: 0.8665 (mmt) REVERT: D 1816 MET cc_start: 0.8916 (mmm) cc_final: 0.8177 (mtt) REVERT: D 1997 ARG cc_start: 0.8930 (tmt-80) cc_final: 0.8489 (tpt170) REVERT: D 2171 MET cc_start: 0.7994 (mmm) cc_final: 0.7541 (mmm) REVERT: D 2424 MET cc_start: 0.8642 (mpp) cc_final: 0.8379 (mpp) REVERT: D 2491 MET cc_start: 0.8956 (tpp) cc_final: 0.8616 (tpp) REVERT: D 2945 MET cc_start: 0.8462 (ptt) cc_final: 0.8166 (ptt) REVERT: D 2977 HIS cc_start: 0.8978 (t70) cc_final: 0.8537 (t-170) REVERT: D 3039 MET cc_start: 0.9789 (mtm) cc_final: 0.9572 (mtm) REVERT: D 3183 TYR cc_start: 0.8073 (p90) cc_final: 0.7803 (p90) REVERT: D 3202 MET cc_start: 0.9246 (tpp) cc_final: 0.8971 (tpp) REVERT: D 3211 LEU cc_start: 0.9387 (mm) cc_final: 0.8879 (tp) REVERT: D 3240 MET cc_start: 0.7435 (tpp) cc_final: 0.7165 (tpp) REVERT: D 3468 MET cc_start: 0.7896 (tpp) cc_final: 0.7391 (tpp) REVERT: D 3574 MET cc_start: 0.8973 (tpt) cc_final: 0.8566 (tpp) REVERT: D 3653 MET cc_start: 0.9233 (mtm) cc_final: 0.9030 (mtm) REVERT: D 3839 MET cc_start: 0.9007 (mtp) cc_final: 0.8727 (mtp) REVERT: D 4730 PHE cc_start: 0.7956 (t80) cc_final: 0.7579 (t80) REVERT: D 5011 MET cc_start: 0.8769 (OUTLIER) cc_final: 0.8493 (mtp) REVERT: A 197 MET cc_start: 0.7927 (mpp) cc_final: 0.7432 (mpp) REVERT: A 666 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7577 (mt-10) REVERT: A 905 HIS cc_start: 0.6508 (t70) cc_final: 0.6289 (t70) REVERT: A 1466 ASP cc_start: 0.8153 (m-30) cc_final: 0.7937 (m-30) REVERT: A 1574 MET cc_start: 0.8986 (mmt) cc_final: 0.8722 (mmt) REVERT: A 1816 MET cc_start: 0.8983 (mmm) cc_final: 0.8215 (mtt) REVERT: A 1997 ARG cc_start: 0.8992 (tmt-80) cc_final: 0.8513 (tpt170) REVERT: A 2171 MET cc_start: 0.8091 (mmm) cc_final: 0.7633 (mmm) REVERT: A 2528 LEU cc_start: 0.9465 (tt) cc_final: 0.8852 (tt) REVERT: A 2945 MET cc_start: 0.8384 (ptt) cc_final: 0.8081 (ptt) REVERT: A 3039 MET cc_start: 0.9747 (mtm) cc_final: 0.9540 (mtm) REVERT: A 3183 TYR cc_start: 0.7953 (p90) cc_final: 0.7646 (p90) REVERT: A 3202 MET cc_start: 0.9090 (tpp) cc_final: 0.8825 (tpp) REVERT: A 3211 LEU cc_start: 0.9402 (mm) cc_final: 0.8936 (tp) REVERT: A 3320 ILE cc_start: 0.9090 (OUTLIER) cc_final: 0.8821 (mp) REVERT: A 3436 PHE cc_start: 0.9555 (t80) cc_final: 0.9350 (t80) REVERT: A 3518 MET cc_start: 0.9149 (mmm) cc_final: 0.8831 (mmm) REVERT: A 3574 MET cc_start: 0.8874 (tpt) cc_final: 0.8397 (tpp) REVERT: A 3839 MET cc_start: 0.9030 (mtp) cc_final: 0.8699 (mtp) REVERT: A 4730 PHE cc_start: 0.8015 (t80) cc_final: 0.7659 (t80) REVERT: A 4869 GLU cc_start: 0.8686 (mm-30) cc_final: 0.8474 (mm-30) REVERT: A 5011 MET cc_start: 0.8796 (OUTLIER) cc_final: 0.8537 (mtp) REVERT: B 117 MET cc_start: 0.9285 (mtm) cc_final: 0.8789 (mtp) REVERT: B 197 MET cc_start: 0.7999 (mpp) cc_final: 0.7477 (mpp) REVERT: B 666 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7420 (mt-10) REVERT: B 828 LYS cc_start: 0.8686 (mmmt) cc_final: 0.8455 (mmmm) REVERT: B 1574 MET cc_start: 0.8915 (mmt) cc_final: 0.8629 (mmt) REVERT: B 1816 MET cc_start: 0.8924 (mmm) cc_final: 0.8195 (mtt) REVERT: B 1997 ARG cc_start: 0.8932 (tmt-80) cc_final: 0.8491 (tpt170) REVERT: B 2171 MET cc_start: 0.8001 (mmm) cc_final: 0.7553 (mmm) REVERT: B 2424 MET cc_start: 0.8631 (mpp) cc_final: 0.8365 (mpp) REVERT: B 2491 MET cc_start: 0.8942 (tpp) cc_final: 0.8608 (tpp) REVERT: B 2629 PHE cc_start: 0.8864 (t80) cc_final: 0.8502 (t80) REVERT: B 2945 MET cc_start: 0.8462 (ptt) cc_final: 0.8169 (ptt) REVERT: B 2977 HIS cc_start: 0.8953 (t70) cc_final: 0.8507 (t-170) REVERT: B 3039 MET cc_start: 0.9785 (mtm) cc_final: 0.9564 (mtm) REVERT: B 3183 TYR cc_start: 0.8079 (p90) cc_final: 0.7808 (p90) REVERT: B 3202 MET cc_start: 0.9247 (tpp) cc_final: 0.8971 (tpp) REVERT: B 3211 LEU cc_start: 0.9397 (mm) cc_final: 0.8888 (tp) REVERT: B 3240 MET cc_start: 0.7449 (tpp) cc_final: 0.7188 (tpp) REVERT: B 3468 MET cc_start: 0.7894 (tpp) cc_final: 0.7393 (tpp) REVERT: B 3574 MET cc_start: 0.8968 (tpt) cc_final: 0.8560 (tpp) REVERT: B 3839 MET cc_start: 0.9005 (mtp) cc_final: 0.8732 (mtp) REVERT: B 4730 PHE cc_start: 0.7961 (t80) cc_final: 0.7581 (t80) REVERT: B 5011 MET cc_start: 0.8760 (OUTLIER) cc_final: 0.8486 (mtp) REVERT: C 117 MET cc_start: 0.9285 (mtm) cc_final: 0.8790 (mtp) REVERT: C 197 MET cc_start: 0.7992 (mpp) cc_final: 0.7467 (mpp) REVERT: C 666 GLU cc_start: 0.7796 (mt-10) cc_final: 0.7412 (mt-10) REVERT: C 828 LYS cc_start: 0.8661 (mmmt) cc_final: 0.8439 (mmmm) REVERT: C 1574 MET cc_start: 0.8936 (mmt) cc_final: 0.8667 (mmt) REVERT: C 1816 MET cc_start: 0.8924 (mmm) cc_final: 0.8177 (mtt) REVERT: C 1997 ARG cc_start: 0.8934 (tmt-80) cc_final: 0.8490 (tpt170) REVERT: C 2171 MET cc_start: 0.8025 (mmm) cc_final: 0.7590 (mmm) REVERT: C 2424 MET cc_start: 0.8656 (mpp) cc_final: 0.8387 (mpp) REVERT: C 2491 MET cc_start: 0.8949 (tpp) cc_final: 0.8604 (tpp) REVERT: C 2528 LEU cc_start: 0.9463 (tt) cc_final: 0.8659 (tt) REVERT: C 2531 MET cc_start: 0.8948 (mtm) cc_final: 0.8695 (mtm) REVERT: C 2945 MET cc_start: 0.8453 (ptt) cc_final: 0.8157 (ptt) REVERT: C 2977 HIS cc_start: 0.8960 (t70) cc_final: 0.8528 (t-170) REVERT: C 3039 MET cc_start: 0.9788 (mtm) cc_final: 0.9566 (mtm) REVERT: C 3183 TYR cc_start: 0.8068 (p90) cc_final: 0.7797 (p90) REVERT: C 3202 MET cc_start: 0.9252 (tpp) cc_final: 0.8976 (tpp) REVERT: C 3211 LEU cc_start: 0.9387 (mm) cc_final: 0.8869 (tp) REVERT: C 3240 MET cc_start: 0.7455 (tpp) cc_final: 0.7206 (tpp) REVERT: C 3468 MET cc_start: 0.7894 (tpp) cc_final: 0.7388 (tpp) REVERT: C 3574 MET cc_start: 0.8970 (tpt) cc_final: 0.8560 (tpp) REVERT: C 3839 MET cc_start: 0.9013 (mtp) cc_final: 0.8733 (mtp) REVERT: C 4730 PHE cc_start: 0.7956 (t80) cc_final: 0.7577 (t80) REVERT: C 5011 MET cc_start: 0.8759 (OUTLIER) cc_final: 0.8484 (mtp) REVERT: K 42 LEU cc_start: 0.7269 (mm) cc_final: 0.6738 (tp) REVERT: L 12 LEU cc_start: 0.8509 (tp) cc_final: 0.8002 (mt) REVERT: L 39 GLN cc_start: 0.6958 (OUTLIER) cc_final: 0.6573 (pm20) REVERT: L 42 LEU cc_start: 0.9140 (tp) cc_final: 0.8628 (tp) REVERT: N 12 LEU cc_start: 0.8543 (tp) cc_final: 0.8051 (mt) REVERT: N 37 LEU cc_start: 0.8784 (tp) cc_final: 0.8503 (tp) REVERT: N 39 GLN cc_start: 0.6912 (OUTLIER) cc_final: 0.6469 (pm20) REVERT: N 88 ASN cc_start: 0.8154 (m-40) cc_final: 0.7792 (m-40) REVERT: M 42 LEU cc_start: 0.7272 (mm) cc_final: 0.6736 (tp) REVERT: O 42 LEU cc_start: 0.7286 (mm) cc_final: 0.6759 (tp) REVERT: P 12 LEU cc_start: 0.8560 (tp) cc_final: 0.8063 (mt) REVERT: P 39 GLN cc_start: 0.6912 (OUTLIER) cc_final: 0.6538 (pm20) REVERT: P 42 LEU cc_start: 0.9139 (tp) cc_final: 0.8632 (tp) outliers start: 107 outliers final: 50 residues processed: 1291 average time/residue: 1.2634 time to fit residues: 2912.5951 Evaluate side-chains 1138 residues out of total 16268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 1078 time to evaluate : 12.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 89 PHE Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 39 GLN Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain D residue 1171 MET Chi-restraints excluded: chain D residue 1435 TYR Chi-restraints excluded: chain D residue 2315 LEU Chi-restraints excluded: chain D residue 2707 ILE Chi-restraints excluded: chain D residue 2824 VAL Chi-restraints excluded: chain D residue 3471 LEU Chi-restraints excluded: chain D residue 3512 VAL Chi-restraints excluded: chain D residue 4751 HIS Chi-restraints excluded: chain D residue 4951 ASP Chi-restraints excluded: chain D residue 5011 MET Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 1171 MET Chi-restraints excluded: chain A residue 1435 TYR Chi-restraints excluded: chain A residue 1992 THR Chi-restraints excluded: chain A residue 2824 VAL Chi-restraints excluded: chain A residue 3320 ILE Chi-restraints excluded: chain A residue 3512 VAL Chi-restraints excluded: chain A residue 4751 HIS Chi-restraints excluded: chain A residue 4951 ASP Chi-restraints excluded: chain A residue 5011 MET Chi-restraints excluded: chain B residue 930 LEU Chi-restraints excluded: chain B residue 1171 MET Chi-restraints excluded: chain B residue 1435 TYR Chi-restraints excluded: chain B residue 2315 LEU Chi-restraints excluded: chain B residue 2707 ILE Chi-restraints excluded: chain B residue 2824 VAL Chi-restraints excluded: chain B residue 3471 LEU Chi-restraints excluded: chain B residue 3512 VAL Chi-restraints excluded: chain B residue 4751 HIS Chi-restraints excluded: chain B residue 4951 ASP Chi-restraints excluded: chain B residue 5011 MET Chi-restraints excluded: chain C residue 930 LEU Chi-restraints excluded: chain C residue 1171 MET Chi-restraints excluded: chain C residue 1435 TYR Chi-restraints excluded: chain C residue 2315 LEU Chi-restraints excluded: chain C residue 2707 ILE Chi-restraints excluded: chain C residue 3471 LEU Chi-restraints excluded: chain C residue 3512 VAL Chi-restraints excluded: chain C residue 4751 HIS Chi-restraints excluded: chain C residue 4951 ASP Chi-restraints excluded: chain C residue 5011 MET Chi-restraints excluded: chain K residue 67 ASP Chi-restraints excluded: chain K residue 89 PHE Chi-restraints excluded: chain L residue 5 LEU Chi-restraints excluded: chain L residue 39 GLN Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain M residue 89 PHE Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain O residue 89 PHE Chi-restraints excluded: chain P residue 5 LEU Chi-restraints excluded: chain P residue 39 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1860 random chunks: chunk 938 optimal weight: 3.9990 chunk 524 optimal weight: 9.9990 chunk 1405 optimal weight: 8.9990 chunk 1150 optimal weight: 6.9990 chunk 465 optimal weight: 10.0000 chunk 1692 optimal weight: 8.9990 chunk 1827 optimal weight: 0.9990 chunk 1507 optimal weight: 9.9990 chunk 1678 optimal weight: 20.0000 chunk 576 optimal weight: 3.9990 chunk 1357 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 309 HIS D 825 GLN D1564 GLN D2170 GLN D3181 ASN D3930 GLN ** D4751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D5001 HIS A 309 HIS A 825 GLN A1042 GLN A1564 GLN A2170 GLN A3110 ASN A3181 ASN A3319 ASN A3463 ASN A3930 GLN ** A4751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A5001 HIS B 309 HIS B 825 GLN B1042 GLN B1564 GLN B2170 GLN B3181 ASN B3930 GLN ** B4751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B5001 HIS C 309 HIS C 825 GLN C1564 GLN C2170 GLN ** C2269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3181 ASN C3930 GLN ** C4751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C5001 HIS K 17 HIS ** L 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 17 HIS O 17 HIS ** P 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 152600 Z= 0.385 Angle : 0.609 15.289 206604 Z= 0.310 Chirality : 0.041 0.298 22672 Planarity : 0.004 0.055 26800 Dihedral : 6.907 88.107 20908 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.45 % Allowed : 6.74 % Favored : 91.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % 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: 1.70 (0.06), residues: 18552 helix: 2.11 (0.05), residues: 9888 sheet: -0.11 (0.13), residues: 1736 loop : 0.09 (0.08), residues: 6928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP N 91 HIS 0.007 0.001 HIS D4001 PHE 0.052 0.002 PHE J 89 TYR 0.032 0.002 TYR J 75 ARG 0.012 0.001 ARG C2532 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 37104 Ramachandran restraints generated. 18552 Oldfield, 0 Emsley, 18552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 37104 Ramachandran restraints generated. 18552 Oldfield, 0 Emsley, 18552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1368 residues out of total 16268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 1132 time to evaluate : 12.592 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: E 54 GLN cc_start: 0.9059 (mp10) cc_final: 0.8626 (mp10) REVERT: I 5 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8518 (mm) REVERT: I 14 ASN cc_start: 0.9297 (m110) cc_final: 0.9028 (p0) REVERT: I 16 PHE cc_start: 0.8606 (OUTLIER) cc_final: 0.7542 (p90) REVERT: I 42 LEU cc_start: 0.7240 (mm) cc_final: 0.6764 (tp) REVERT: J 75 TYR cc_start: 0.6667 (p90) cc_final: 0.6422 (p90) REVERT: F 4 GLN cc_start: 0.7944 (mp10) cc_final: 0.7677 (mp10) REVERT: F 45 LYS cc_start: 0.8671 (ttpt) cc_final: 0.8277 (ttpp) REVERT: G 45 LYS cc_start: 0.8670 (ttpt) cc_final: 0.8283 (ttpp) REVERT: G 53 LYS cc_start: 0.9093 (mmtp) cc_final: 0.8833 (mmtp) REVERT: G 55 GLU cc_start: 0.8690 (mt-10) cc_final: 0.8482 (mt-10) REVERT: H 45 LYS cc_start: 0.8683 (ttpt) cc_final: 0.8298 (ttpp) REVERT: H 53 LYS cc_start: 0.9091 (mmtp) cc_final: 0.8837 (mmtp) REVERT: H 55 GLU cc_start: 0.8689 (mt-10) cc_final: 0.8318 (mt-10) REVERT: D 117 MET cc_start: 0.9381 (mtm) cc_final: 0.8752 (mtp) REVERT: D 197 MET cc_start: 0.8032 (mpp) cc_final: 0.7513 (mpp) REVERT: D 666 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7604 (mt-10) REVERT: D 828 LYS cc_start: 0.8751 (mmmt) cc_final: 0.8517 (mmmm) REVERT: D 864 LEU cc_start: 0.9019 (mp) cc_final: 0.8606 (tp) REVERT: D 905 HIS cc_start: 0.6999 (t70) cc_final: 0.6448 (t70) REVERT: D 1574 MET cc_start: 0.8944 (mmt) cc_final: 0.8651 (mmt) REVERT: D 1987 MET cc_start: 0.5308 (pmm) cc_final: 0.4582 (tmm) REVERT: D 1997 ARG cc_start: 0.9062 (tmt-80) cc_final: 0.8779 (tpm170) REVERT: D 2171 MET cc_start: 0.8129 (mmm) cc_final: 0.7643 (mmm) REVERT: D 2179 MET cc_start: 0.8865 (tpt) cc_final: 0.8615 (tpp) REVERT: D 2424 MET cc_start: 0.8701 (mpp) cc_final: 0.8381 (mpp) REVERT: D 2619 MET cc_start: 0.9379 (mmt) cc_final: 0.9072 (mmt) REVERT: D 2627 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8945 (mm) REVERT: D 2945 MET cc_start: 0.8464 (ptt) cc_final: 0.8162 (ptt) REVERT: D 2968 MET cc_start: 0.9381 (mmm) cc_final: 0.8986 (mmm) REVERT: D 2977 HIS cc_start: 0.9022 (t70) cc_final: 0.8611 (t-170) REVERT: D 3183 TYR cc_start: 0.8070 (p90) cc_final: 0.7694 (p90) REVERT: D 3202 MET cc_start: 0.9279 (tpp) cc_final: 0.9017 (tpp) REVERT: D 3211 LEU cc_start: 0.9412 (mm) cc_final: 0.8924 (tp) REVERT: D 3240 MET cc_start: 0.7641 (tpp) cc_final: 0.7303 (tpp) REVERT: D 3436 PHE cc_start: 0.9612 (t80) cc_final: 0.9392 (t80) REVERT: D 3468 MET cc_start: 0.7946 (tpp) cc_final: 0.7419 (tpp) REVERT: D 3574 MET cc_start: 0.9015 (tpt) cc_final: 0.8424 (tpp) REVERT: D 4125 MET cc_start: 0.8255 (tpp) cc_final: 0.8031 (tpp) REVERT: A 117 MET cc_start: 0.9348 (mtm) cc_final: 0.8813 (mtp) REVERT: A 197 MET cc_start: 0.8015 (mpp) cc_final: 0.7519 (mpp) REVERT: A 212 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7964 (tp30) REVERT: A 666 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7717 (mt-10) REVERT: A 864 LEU cc_start: 0.9122 (mp) cc_final: 0.8711 (tp) REVERT: A 905 HIS cc_start: 0.6655 (t70) cc_final: 0.6378 (t70) REVERT: A 1574 MET cc_start: 0.8965 (mmt) cc_final: 0.8672 (mmt) REVERT: A 1997 ARG cc_start: 0.9104 (tmt-80) cc_final: 0.8740 (tpm170) REVERT: A 2171 MET cc_start: 0.8129 (mmm) cc_final: 0.7671 (mmm) REVERT: A 2179 MET cc_start: 0.8883 (tpt) cc_final: 0.8603 (tpp) REVERT: A 2619 MET cc_start: 0.9356 (mmt) cc_final: 0.9102 (mmt) REVERT: A 2945 MET cc_start: 0.8423 (ptt) cc_final: 0.8120 (ptt) REVERT: A 3039 MET cc_start: 0.9744 (mtm) cc_final: 0.9534 (mtm) REVERT: A 3183 TYR cc_start: 0.7980 (p90) cc_final: 0.7557 (p90) REVERT: A 3202 MET cc_start: 0.9084 (tpp) cc_final: 0.8832 (tpp) REVERT: A 3211 LEU cc_start: 0.9419 (mm) cc_final: 0.8976 (tp) REVERT: A 3320 ILE cc_start: 0.9137 (OUTLIER) cc_final: 0.8911 (mp) REVERT: A 3394 LEU cc_start: 0.8927 (tt) cc_final: 0.8532 (tt) REVERT: A 3398 GLU cc_start: 0.9026 (OUTLIER) cc_final: 0.8646 (mp0) REVERT: A 3518 MET cc_start: 0.9277 (mmm) cc_final: 0.8844 (tpp) REVERT: A 4125 MET cc_start: 0.8173 (tpp) cc_final: 0.7924 (tpp) REVERT: A 4837 MET cc_start: 0.8805 (mmm) cc_final: 0.8420 (mmm) REVERT: A 4869 GLU cc_start: 0.8660 (mm-30) cc_final: 0.8439 (mm-30) REVERT: B 117 MET cc_start: 0.9380 (mtm) cc_final: 0.8757 (mtp) REVERT: B 197 MET cc_start: 0.8036 (mpp) cc_final: 0.7518 (mpp) REVERT: B 666 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7602 (mt-10) REVERT: B 828 LYS cc_start: 0.8749 (mmmt) cc_final: 0.8517 (mmmm) REVERT: B 864 LEU cc_start: 0.9024 (mp) cc_final: 0.8595 (tp) REVERT: B 905 HIS cc_start: 0.6986 (t70) cc_final: 0.6462 (t70) REVERT: B 1261 MET cc_start: 0.8139 (mtt) cc_final: 0.7910 (mtt) REVERT: B 1574 MET cc_start: 0.8940 (mmt) cc_final: 0.8644 (mmt) REVERT: B 1997 ARG cc_start: 0.9062 (tmt-80) cc_final: 0.8783 (tpm170) REVERT: B 2171 MET cc_start: 0.8131 (mmm) cc_final: 0.7664 (mmm) REVERT: B 2179 MET cc_start: 0.8874 (tpt) cc_final: 0.8632 (tpp) REVERT: B 2424 MET cc_start: 0.8700 (mpp) cc_final: 0.8380 (mpp) REVERT: B 2531 MET cc_start: 0.8994 (mtm) cc_final: 0.8599 (mtm) REVERT: B 2619 MET cc_start: 0.9362 (mmt) cc_final: 0.9061 (mmt) REVERT: B 2627 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8949 (mm) REVERT: B 2945 MET cc_start: 0.8461 (ptt) cc_final: 0.8154 (ptt) REVERT: B 2968 MET cc_start: 0.9392 (mmm) cc_final: 0.9001 (mmm) REVERT: B 2977 HIS cc_start: 0.9012 (t70) cc_final: 0.8603 (t-170) REVERT: B 3183 TYR cc_start: 0.8084 (p90) cc_final: 0.7713 (p90) REVERT: B 3202 MET cc_start: 0.9272 (tpp) cc_final: 0.9010 (tpp) REVERT: B 3211 LEU cc_start: 0.9414 (mm) cc_final: 0.8929 (tp) REVERT: B 3240 MET cc_start: 0.7650 (tpp) cc_final: 0.7324 (tpp) REVERT: B 3394 LEU cc_start: 0.8892 (tt) cc_final: 0.8562 (tt) REVERT: B 3398 GLU cc_start: 0.9008 (OUTLIER) cc_final: 0.8598 (mp0) REVERT: B 3436 PHE cc_start: 0.9615 (t80) cc_final: 0.9403 (t80) REVERT: B 3468 MET cc_start: 0.7953 (tpp) cc_final: 0.7420 (tpp) REVERT: B 3574 MET cc_start: 0.9009 (tpt) cc_final: 0.8417 (tpp) REVERT: B 4125 MET cc_start: 0.8264 (tpp) cc_final: 0.8043 (tpp) REVERT: B 4837 MET cc_start: 0.8812 (mmm) cc_final: 0.8426 (mmm) REVERT: C 117 MET cc_start: 0.9383 (mtm) cc_final: 0.8753 (mtp) REVERT: C 197 MET cc_start: 0.8035 (mpp) cc_final: 0.7519 (mpp) REVERT: C 666 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7600 (mt-10) REVERT: C 828 LYS cc_start: 0.8751 (mmmt) cc_final: 0.8516 (mmmm) REVERT: C 864 LEU cc_start: 0.9025 (mp) cc_final: 0.8592 (tp) REVERT: C 905 HIS cc_start: 0.6977 (t70) cc_final: 0.6458 (t70) REVERT: C 1574 MET cc_start: 0.8945 (mmt) cc_final: 0.8649 (mmt) REVERT: C 1987 MET cc_start: 0.5255 (pmm) cc_final: 0.4527 (tmm) REVERT: C 1997 ARG cc_start: 0.9066 (tmt-80) cc_final: 0.8764 (tpm170) REVERT: C 2171 MET cc_start: 0.8145 (mmm) cc_final: 0.7699 (mmm) REVERT: C 2179 MET cc_start: 0.8873 (tpt) cc_final: 0.8631 (tpp) REVERT: C 2424 MET cc_start: 0.8703 (mpp) cc_final: 0.8379 (mpp) REVERT: C 2531 MET cc_start: 0.9020 (mtm) cc_final: 0.8503 (mtm) REVERT: C 2619 MET cc_start: 0.9370 (mmt) cc_final: 0.9071 (mmt) REVERT: C 2945 MET cc_start: 0.8460 (ptt) cc_final: 0.8157 (ptt) REVERT: C 2968 MET cc_start: 0.9376 (mmm) cc_final: 0.8990 (mmm) REVERT: C 2977 HIS cc_start: 0.9016 (t70) cc_final: 0.8611 (t-170) REVERT: C 3183 TYR cc_start: 0.8072 (p90) cc_final: 0.7688 (p90) REVERT: C 3202 MET cc_start: 0.9268 (tpp) cc_final: 0.9003 (tpp) REVERT: C 3211 LEU cc_start: 0.9417 (mm) cc_final: 0.8935 (tp) REVERT: C 3240 MET cc_start: 0.7686 (tpp) cc_final: 0.7347 (tpp) REVERT: C 3394 LEU cc_start: 0.8889 (tt) cc_final: 0.8558 (tt) REVERT: C 3398 GLU cc_start: 0.9010 (OUTLIER) cc_final: 0.8593 (mp0) REVERT: C 3436 PHE cc_start: 0.9615 (t80) cc_final: 0.9399 (t80) REVERT: C 3468 MET cc_start: 0.7932 (tpp) cc_final: 0.7418 (tpp) REVERT: C 3574 MET cc_start: 0.9010 (tpt) cc_final: 0.8412 (tpp) REVERT: C 4125 MET cc_start: 0.8261 (tpp) cc_final: 0.8038 (tpp) REVERT: C 4837 MET cc_start: 0.8807 (mmm) cc_final: 0.8430 (mmm) REVERT: K 5 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8603 (mm) REVERT: K 16 PHE cc_start: 0.8825 (OUTLIER) cc_final: 0.7919 (p90) REVERT: K 42 LEU cc_start: 0.7337 (mm) cc_final: 0.6886 (tp) REVERT: L 12 LEU cc_start: 0.8358 (tp) cc_final: 0.8091 (tt) REVERT: L 75 TYR cc_start: 0.6700 (p90) cc_final: 0.6402 (p90) REVERT: N 12 LEU cc_start: 0.8395 (tp) cc_final: 0.8120 (tt) REVERT: N 75 TYR cc_start: 0.6705 (p90) cc_final: 0.6421 (p90) REVERT: M 5 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8459 (mm) REVERT: M 16 PHE cc_start: 0.8804 (OUTLIER) cc_final: 0.7871 (p90) REVERT: M 42 LEU cc_start: 0.7275 (mm) cc_final: 0.6843 (tp) REVERT: O 5 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8586 (mm) REVERT: O 16 PHE cc_start: 0.8823 (OUTLIER) cc_final: 0.7921 (p90) REVERT: O 42 LEU cc_start: 0.7292 (mm) cc_final: 0.6865 (tp) REVERT: P 12 LEU cc_start: 0.8410 (tp) cc_final: 0.8138 (tt) REVERT: P 75 TYR cc_start: 0.6675 (p90) cc_final: 0.6382 (p90) outliers start: 236 outliers final: 142 residues processed: 1267 average time/residue: 1.2547 time to fit residues: 2853.2817 Evaluate side-chains 1212 residues out of total 16268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 1055 time to evaluate : 12.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 33 ASP Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 60 TRP Chi-restraints excluded: chain E residue 78 SER Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain I residue 16 PHE Chi-restraints excluded: chain I residue 32 LYS Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 67 ASP Chi-restraints excluded: chain I residue 89 PHE Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain F residue 33 ASP Chi-restraints excluded: chain F residue 39 SER Chi-restraints excluded: chain F residue 60 TRP Chi-restraints excluded: chain F residue 78 SER Chi-restraints excluded: chain G residue 33 ASP Chi-restraints excluded: chain G residue 39 SER Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 60 TRP Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 60 TRP Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain D residue 359 THR Chi-restraints excluded: chain D residue 812 CYS Chi-restraints excluded: chain D residue 912 HIS Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain D residue 1171 MET Chi-restraints excluded: chain D residue 1429 LEU Chi-restraints excluded: chain D residue 1435 TYR Chi-restraints excluded: chain D residue 1737 VAL Chi-restraints excluded: chain D residue 2204 MET Chi-restraints excluded: chain D residue 2224 ILE Chi-restraints excluded: chain D residue 2417 VAL Chi-restraints excluded: chain D residue 2627 LEU Chi-restraints excluded: chain D residue 2743 THR Chi-restraints excluded: chain D residue 3081 VAL Chi-restraints excluded: chain D residue 3109 GLU Chi-restraints excluded: chain D residue 3170 LEU Chi-restraints excluded: chain D residue 3308 VAL Chi-restraints excluded: chain D residue 3347 VAL Chi-restraints excluded: chain D residue 3398 GLU Chi-restraints excluded: chain D residue 3471 LEU Chi-restraints excluded: chain D residue 3512 VAL Chi-restraints excluded: chain D residue 3530 ASP Chi-restraints excluded: chain D residue 3657 SER Chi-restraints excluded: chain D residue 4538 PHE Chi-restraints excluded: chain D residue 4542 LEU Chi-restraints excluded: chain D residue 4751 HIS Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 812 CYS Chi-restraints excluded: chain A residue 1171 MET Chi-restraints excluded: chain A residue 1251 LEU Chi-restraints excluded: chain A residue 1429 LEU Chi-restraints excluded: chain A residue 1435 TYR Chi-restraints excluded: chain A residue 1737 VAL Chi-restraints excluded: chain A residue 1928 LEU Chi-restraints excluded: chain A residue 1992 THR Chi-restraints excluded: chain A residue 2204 MET Chi-restraints excluded: chain A residue 2224 ILE Chi-restraints excluded: chain A residue 2417 VAL Chi-restraints excluded: chain A residue 2424 MET Chi-restraints excluded: chain A residue 2743 THR Chi-restraints excluded: chain A residue 3051 VAL Chi-restraints excluded: chain A residue 3081 VAL Chi-restraints excluded: chain A residue 3109 GLU Chi-restraints excluded: chain A residue 3170 LEU Chi-restraints excluded: chain A residue 3320 ILE Chi-restraints excluded: chain A residue 3347 VAL Chi-restraints excluded: chain A residue 3366 LEU Chi-restraints excluded: chain A residue 3398 GLU Chi-restraints excluded: chain A residue 3512 VAL Chi-restraints excluded: chain A residue 3530 ASP Chi-restraints excluded: chain A residue 3657 SER Chi-restraints excluded: chain A residue 4538 PHE Chi-restraints excluded: chain A residue 4542 LEU Chi-restraints excluded: chain A residue 4751 HIS Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 812 CYS Chi-restraints excluded: chain B residue 912 HIS Chi-restraints excluded: chain B residue 930 LEU Chi-restraints excluded: chain B residue 1171 MET Chi-restraints excluded: chain B residue 1429 LEU Chi-restraints excluded: chain B residue 1435 TYR Chi-restraints excluded: chain B residue 1737 VAL Chi-restraints excluded: chain B residue 2204 MET Chi-restraints excluded: chain B residue 2224 ILE Chi-restraints excluded: chain B residue 2417 VAL Chi-restraints excluded: chain B residue 2627 LEU Chi-restraints excluded: chain B residue 2743 THR Chi-restraints excluded: chain B residue 3081 VAL Chi-restraints excluded: chain B residue 3109 GLU Chi-restraints excluded: chain B residue 3170 LEU Chi-restraints excluded: chain B residue 3308 VAL Chi-restraints excluded: chain B residue 3347 VAL Chi-restraints excluded: chain B residue 3379 GLN Chi-restraints excluded: chain B residue 3398 GLU Chi-restraints excluded: chain B residue 3471 LEU Chi-restraints excluded: chain B residue 3512 VAL Chi-restraints excluded: chain B residue 3530 ASP Chi-restraints excluded: chain B residue 3657 SER Chi-restraints excluded: chain B residue 4538 PHE Chi-restraints excluded: chain B residue 4542 LEU Chi-restraints excluded: chain B residue 4751 HIS Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 812 CYS Chi-restraints excluded: chain C residue 912 HIS Chi-restraints excluded: chain C residue 930 LEU Chi-restraints excluded: chain C residue 1171 MET Chi-restraints excluded: chain C residue 1429 LEU Chi-restraints excluded: chain C residue 1435 TYR Chi-restraints excluded: chain C residue 1737 VAL Chi-restraints excluded: chain C residue 2204 MET Chi-restraints excluded: chain C residue 2417 VAL Chi-restraints excluded: chain C residue 3081 VAL Chi-restraints excluded: chain C residue 3109 GLU Chi-restraints excluded: chain C residue 3170 LEU Chi-restraints excluded: chain C residue 3308 VAL Chi-restraints excluded: chain C residue 3347 VAL Chi-restraints excluded: chain C residue 3379 GLN Chi-restraints excluded: chain C residue 3398 GLU Chi-restraints excluded: chain C residue 3410 TYR Chi-restraints excluded: chain C residue 3471 LEU Chi-restraints excluded: chain C residue 3512 VAL Chi-restraints excluded: chain C residue 3530 ASP Chi-restraints excluded: chain C residue 3657 SER Chi-restraints excluded: chain C residue 4538 PHE Chi-restraints excluded: chain C residue 4542 LEU Chi-restraints excluded: chain C residue 4751 HIS Chi-restraints excluded: chain K residue 5 LEU Chi-restraints excluded: chain K residue 16 PHE Chi-restraints excluded: chain K residue 32 LYS Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain K residue 55 VAL Chi-restraints excluded: chain K residue 67 ASP Chi-restraints excluded: chain K residue 89 PHE Chi-restraints excluded: chain L residue 5 LEU Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain M residue 16 PHE Chi-restraints excluded: chain M residue 32 LYS Chi-restraints excluded: chain M residue 37 LEU Chi-restraints excluded: chain M residue 55 VAL Chi-restraints excluded: chain M residue 67 ASP Chi-restraints excluded: chain M residue 89 PHE Chi-restraints excluded: chain O residue 5 LEU Chi-restraints excluded: chain O residue 16 PHE Chi-restraints excluded: chain O residue 32 LYS Chi-restraints excluded: chain O residue 37 LEU Chi-restraints excluded: chain O residue 55 VAL Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain O residue 89 PHE Chi-restraints excluded: chain P residue 5 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1860 random chunks: chunk 1671 optimal weight: 0.0370 chunk 1272 optimal weight: 3.9990 chunk 878 optimal weight: 5.9990 chunk 187 optimal weight: 0.9980 chunk 807 optimal weight: 10.0000 chunk 1136 optimal weight: 0.7980 chunk 1698 optimal weight: 8.9990 chunk 1797 optimal weight: 5.9990 chunk 887 optimal weight: 4.9990 chunk 1609 optimal weight: 0.8980 chunk 484 optimal weight: 4.9990 overall best weight: 1.3460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 825 GLN D1042 GLN D3463 ASN D4648 HIS ** D4751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4648 HIS ** A4751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3463 ASN B4057 ASN B4648 HIS ** B4751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1042 GLN C2269 GLN C3463 ASN ** C4751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 17 HIS ** K 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 19 HIS ** N 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 17 HIS ** M 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 17 HIS ** O 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 152600 Z= 0.170 Angle : 0.537 13.831 206604 Z= 0.269 Chirality : 0.038 0.223 22672 Planarity : 0.004 0.058 26800 Dihedral : 6.579 86.593 20896 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.11 % Favored : 97.87 % Rotamer: Outliers : 1.02 % Allowed : 8.39 % Favored : 90.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % 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: 1.86 (0.06), residues: 18552 helix: 2.24 (0.05), residues: 9892 sheet: -0.00 (0.12), residues: 1804 loop : 0.15 (0.08), residues: 6856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP P 91 HIS 0.005 0.001 HIS B 994 PHE 0.032 0.001 PHE A2974 TYR 0.035 0.001 TYR A2883 ARG 0.005 0.000 ARG E 14 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 37104 Ramachandran restraints generated. 18552 Oldfield, 0 Emsley, 18552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 37104 Ramachandran restraints generated. 18552 Oldfield, 0 Emsley, 18552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1291 residues out of total 16268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 1126 time to evaluate : 12.503 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: E 4 GLN cc_start: 0.8148 (mp10) cc_final: 0.7924 (mp10) REVERT: E 54 GLN cc_start: 0.9052 (mp10) cc_final: 0.8619 (mp10) REVERT: I 5 LEU cc_start: 0.8621 (mm) cc_final: 0.8359 (mm) REVERT: I 16 PHE cc_start: 0.8581 (OUTLIER) cc_final: 0.7519 (p90) REVERT: I 32 LYS cc_start: 0.9161 (OUTLIER) cc_final: 0.8748 (mmmt) REVERT: I 42 LEU cc_start: 0.7535 (mm) cc_final: 0.7115 (tp) REVERT: F 4 GLN cc_start: 0.7990 (mp10) cc_final: 0.7749 (mp10) REVERT: F 45 LYS cc_start: 0.8689 (ttpt) cc_final: 0.8303 (ttpp) REVERT: G 45 LYS cc_start: 0.8674 (ttpt) cc_final: 0.8301 (ttpp) REVERT: G 53 LYS cc_start: 0.9075 (mmtp) cc_final: 0.8801 (mmtp) REVERT: G 55 GLU cc_start: 0.8666 (mt-10) cc_final: 0.8434 (mt-10) REVERT: H 45 LYS cc_start: 0.8691 (ttpt) cc_final: 0.8321 (ttpp) REVERT: H 53 LYS cc_start: 0.9087 (mmtp) cc_final: 0.8817 (mmtp) REVERT: H 55 GLU cc_start: 0.8666 (mt-10) cc_final: 0.8437 (mt-10) REVERT: D 117 MET cc_start: 0.9342 (mtm) cc_final: 0.9061 (mtp) REVERT: D 197 MET cc_start: 0.7964 (mpp) cc_final: 0.7411 (mpp) REVERT: D 615 VAL cc_start: 0.8550 (OUTLIER) cc_final: 0.8274 (m) REVERT: D 666 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7509 (mt-10) REVERT: D 828 LYS cc_start: 0.8765 (mmmt) cc_final: 0.8537 (mmmm) REVERT: D 864 LEU cc_start: 0.9019 (mp) cc_final: 0.8596 (tp) REVERT: D 1816 MET cc_start: 0.8825 (mmm) cc_final: 0.8203 (mtt) REVERT: D 1930 MET cc_start: 0.8994 (ttm) cc_final: 0.8723 (mtp) REVERT: D 1997 ARG cc_start: 0.9066 (tmt-80) cc_final: 0.8594 (tpt170) REVERT: D 2171 MET cc_start: 0.8044 (mmm) cc_final: 0.7553 (mmm) REVERT: D 2179 MET cc_start: 0.8821 (tpt) cc_final: 0.8612 (tpp) REVERT: D 2268 MET cc_start: 0.6044 (mmp) cc_final: 0.5840 (mmp) REVERT: D 2382 GLU cc_start: 0.8780 (mt-10) cc_final: 0.8550 (mp0) REVERT: D 2424 MET cc_start: 0.8641 (OUTLIER) cc_final: 0.8289 (mpp) REVERT: D 2619 MET cc_start: 0.9313 (mmt) cc_final: 0.9012 (mmt) REVERT: D 2945 MET cc_start: 0.8503 (ptt) cc_final: 0.8287 (ptt) REVERT: D 2968 MET cc_start: 0.9391 (mmm) cc_final: 0.8998 (mmm) REVERT: D 2977 HIS cc_start: 0.9000 (t70) cc_final: 0.8605 (t-170) REVERT: D 3202 MET cc_start: 0.9245 (tpp) cc_final: 0.8998 (tpp) REVERT: D 3211 LEU cc_start: 0.9374 (mm) cc_final: 0.8882 (tp) REVERT: D 3320 ILE cc_start: 0.9014 (OUTLIER) cc_final: 0.8763 (mp) REVERT: D 3398 GLU cc_start: 0.8971 (OUTLIER) cc_final: 0.8481 (mp0) REVERT: D 3468 MET cc_start: 0.7969 (tpp) cc_final: 0.7454 (tpp) REVERT: D 3518 MET cc_start: 0.9067 (tpt) cc_final: 0.8783 (tpp) REVERT: D 3574 MET cc_start: 0.8963 (tpt) cc_final: 0.8385 (tpp) REVERT: D 4125 MET cc_start: 0.8363 (tpp) cc_final: 0.8126 (tpp) REVERT: D 4837 MET cc_start: 0.8816 (mmm) cc_final: 0.8417 (mmm) REVERT: A 117 MET cc_start: 0.9302 (mtm) cc_final: 0.8725 (mtp) REVERT: A 197 MET cc_start: 0.7955 (mpp) cc_final: 0.7482 (mpp) REVERT: A 615 VAL cc_start: 0.8576 (OUTLIER) cc_final: 0.8314 (m) REVERT: A 666 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7613 (mt-10) REVERT: A 864 LEU cc_start: 0.9129 (mp) cc_final: 0.8696 (tp) REVERT: A 905 HIS cc_start: 0.6633 (t70) cc_final: 0.6278 (t70) REVERT: A 1466 ASP cc_start: 0.8090 (m-30) cc_final: 0.7837 (m-30) REVERT: A 1574 MET cc_start: 0.8972 (mmt) cc_final: 0.8685 (mmt) REVERT: A 1816 MET cc_start: 0.8856 (mmm) cc_final: 0.8218 (mtt) REVERT: A 1997 ARG cc_start: 0.9087 (tmt-80) cc_final: 0.8415 (tpt90) REVERT: A 2171 MET cc_start: 0.8073 (mmm) cc_final: 0.7608 (mmm) REVERT: A 2268 MET cc_start: 0.5974 (mmp) cc_final: 0.5759 (mmp) REVERT: A 2382 GLU cc_start: 0.8974 (OUTLIER) cc_final: 0.8640 (mp0) REVERT: A 2643 LYS cc_start: 0.9261 (mtmm) cc_final: 0.9049 (mptt) REVERT: A 2945 MET cc_start: 0.8416 (ptt) cc_final: 0.8146 (ptt) REVERT: A 3039 MET cc_start: 0.9713 (mtm) cc_final: 0.9481 (mtm) REVERT: A 3202 MET cc_start: 0.9090 (tpp) cc_final: 0.8827 (tpp) REVERT: A 3211 LEU cc_start: 0.9367 (mm) cc_final: 0.8928 (tp) REVERT: A 3518 MET cc_start: 0.9200 (mmm) cc_final: 0.8754 (tpp) REVERT: A 3574 MET cc_start: 0.8861 (tpt) cc_final: 0.8381 (tpp) REVERT: A 4091 ILE cc_start: 0.8151 (tp) cc_final: 0.7945 (tp) REVERT: A 4837 MET cc_start: 0.8794 (mmm) cc_final: 0.8454 (mmm) REVERT: A 4872 MET cc_start: 0.9243 (mmm) cc_final: 0.8802 (mmp) REVERT: B 117 MET cc_start: 0.9340 (mtm) cc_final: 0.9063 (mtp) REVERT: B 197 MET cc_start: 0.7970 (mpp) cc_final: 0.7417 (mpp) REVERT: B 615 VAL cc_start: 0.8557 (OUTLIER) cc_final: 0.8278 (m) REVERT: B 666 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7518 (mt-10) REVERT: B 828 LYS cc_start: 0.8767 (mmmt) cc_final: 0.8539 (mmmm) REVERT: B 864 LEU cc_start: 0.9029 (mp) cc_final: 0.8606 (tp) REVERT: B 1816 MET cc_start: 0.8841 (mmm) cc_final: 0.8230 (mtt) REVERT: B 1930 MET cc_start: 0.8995 (ttm) cc_final: 0.8724 (mtp) REVERT: B 1987 MET cc_start: 0.5224 (pmm) cc_final: 0.4509 (tmm) REVERT: B 1997 ARG cc_start: 0.9059 (tmt-80) cc_final: 0.8591 (tpt170) REVERT: B 2171 MET cc_start: 0.8048 (mmm) cc_final: 0.7576 (mmm) REVERT: B 2179 MET cc_start: 0.8825 (tpt) cc_final: 0.8621 (tpp) REVERT: B 2268 MET cc_start: 0.5987 (mmp) cc_final: 0.5779 (mmp) REVERT: B 2382 GLU cc_start: 0.8776 (mt-10) cc_final: 0.8552 (mp0) REVERT: B 2424 MET cc_start: 0.8641 (OUTLIER) cc_final: 0.8286 (mpp) REVERT: B 2531 MET cc_start: 0.8945 (mtm) cc_final: 0.8409 (mtm) REVERT: B 2619 MET cc_start: 0.9302 (mmt) cc_final: 0.9027 (mmt) REVERT: B 2629 PHE cc_start: 0.8712 (t80) cc_final: 0.8499 (t80) REVERT: B 2945 MET cc_start: 0.8509 (ptt) cc_final: 0.8251 (ptt) REVERT: B 2968 MET cc_start: 0.9386 (mmm) cc_final: 0.8993 (mmm) REVERT: B 2977 HIS cc_start: 0.8995 (t70) cc_final: 0.8592 (t-170) REVERT: B 3211 LEU cc_start: 0.9375 (mm) cc_final: 0.8883 (tp) REVERT: B 3320 ILE cc_start: 0.9016 (OUTLIER) cc_final: 0.8731 (mp) REVERT: B 3468 MET cc_start: 0.7981 (tpp) cc_final: 0.7487 (tpp) REVERT: B 3518 MET cc_start: 0.9068 (tpt) cc_final: 0.8787 (tpp) REVERT: B 3574 MET cc_start: 0.8956 (tpt) cc_final: 0.8382 (tpp) REVERT: B 4125 MET cc_start: 0.8372 (tpp) cc_final: 0.8141 (tpp) REVERT: B 4837 MET cc_start: 0.8818 (mmm) cc_final: 0.8467 (mmm) REVERT: C 117 MET cc_start: 0.9345 (mtm) cc_final: 0.9066 (mtp) REVERT: C 197 MET cc_start: 0.7973 (mpp) cc_final: 0.7421 (mpp) REVERT: C 221 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.9011 (pp) REVERT: C 615 VAL cc_start: 0.8549 (OUTLIER) cc_final: 0.8269 (m) REVERT: C 666 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7514 (mt-10) REVERT: C 828 LYS cc_start: 0.8765 (mmmt) cc_final: 0.8535 (mmmm) REVERT: C 864 LEU cc_start: 0.9024 (mp) cc_final: 0.8608 (tp) REVERT: C 1816 MET cc_start: 0.8831 (mmm) cc_final: 0.8208 (mtt) REVERT: C 1930 MET cc_start: 0.8991 (ttm) cc_final: 0.8716 (mtp) REVERT: C 1997 ARG cc_start: 0.9061 (tmt-80) cc_final: 0.8591 (tpt170) REVERT: C 2171 MET cc_start: 0.8075 (mmm) cc_final: 0.7609 (mmm) REVERT: C 2179 MET cc_start: 0.8815 (tpt) cc_final: 0.8611 (tpp) REVERT: C 2382 GLU cc_start: 0.8776 (mt-10) cc_final: 0.8550 (mp0) REVERT: C 2424 MET cc_start: 0.8644 (OUTLIER) cc_final: 0.8285 (mpp) REVERT: C 2531 MET cc_start: 0.8967 (mtm) cc_final: 0.8485 (mtm) REVERT: C 2619 MET cc_start: 0.9291 (mmt) cc_final: 0.9021 (mmt) REVERT: C 2817 MET cc_start: 0.5315 (ttp) cc_final: 0.5076 (tmm) REVERT: C 2945 MET cc_start: 0.8492 (ptt) cc_final: 0.8283 (ptt) REVERT: C 2968 MET cc_start: 0.9386 (mmm) cc_final: 0.8990 (mmm) REVERT: C 3202 MET cc_start: 0.9249 (tpp) cc_final: 0.8998 (tpp) REVERT: C 3211 LEU cc_start: 0.9374 (mm) cc_final: 0.8886 (tp) REVERT: C 3320 ILE cc_start: 0.9031 (OUTLIER) cc_final: 0.8753 (mp) REVERT: C 3468 MET cc_start: 0.7958 (tpp) cc_final: 0.7426 (tpp) REVERT: C 3518 MET cc_start: 0.9068 (tpt) cc_final: 0.8773 (tpp) REVERT: C 3574 MET cc_start: 0.8951 (tpt) cc_final: 0.8371 (tpp) REVERT: C 4125 MET cc_start: 0.8371 (tpp) cc_final: 0.8134 (tpp) REVERT: C 4837 MET cc_start: 0.8797 (mmm) cc_final: 0.8466 (mmm) REVERT: K 16 PHE cc_start: 0.8691 (OUTLIER) cc_final: 0.7686 (p90) REVERT: L 12 LEU cc_start: 0.8450 (tp) cc_final: 0.8139 (tt) REVERT: N 12 LEU cc_start: 0.8444 (tp) cc_final: 0.8131 (tt) REVERT: M 5 LEU cc_start: 0.8605 (mm) cc_final: 0.8337 (mm) REVERT: M 16 PHE cc_start: 0.8675 (OUTLIER) cc_final: 0.7674 (p90) REVERT: O 16 PHE cc_start: 0.8688 (OUTLIER) cc_final: 0.7688 (p90) REVERT: P 12 LEU cc_start: 0.8459 (tp) cc_final: 0.8148 (tt) outliers start: 165 outliers final: 72 residues processed: 1210 average time/residue: 1.2412 time to fit residues: 2697.7974 Evaluate side-chains 1144 residues out of total 16268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 1054 time to evaluate : 12.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 33 ASP Chi-restraints excluded: chain I residue 16 PHE Chi-restraints excluded: chain I residue 32 LYS Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 89 PHE Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain F residue 33 ASP Chi-restraints excluded: chain F residue 60 TRP Chi-restraints excluded: chain G residue 33 ASP Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 60 TRP Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 60 TRP Chi-restraints excluded: chain D residue 615 VAL Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain D residue 1171 MET Chi-restraints excluded: chain D residue 1435 TYR Chi-restraints excluded: chain D residue 1737 VAL Chi-restraints excluded: chain D residue 2424 MET Chi-restraints excluded: chain D residue 3109 GLU Chi-restraints excluded: chain D residue 3308 VAL Chi-restraints excluded: chain D residue 3320 ILE Chi-restraints excluded: chain D residue 3394 LEU Chi-restraints excluded: chain D residue 3398 GLU Chi-restraints excluded: chain D residue 3471 LEU Chi-restraints excluded: chain D residue 3512 VAL Chi-restraints excluded: chain D residue 4542 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 1171 MET Chi-restraints excluded: chain A residue 1429 LEU Chi-restraints excluded: chain A residue 1435 TYR Chi-restraints excluded: chain A residue 1737 VAL Chi-restraints excluded: chain A residue 1992 THR Chi-restraints excluded: chain A residue 2382 GLU Chi-restraints excluded: chain A residue 2424 MET Chi-restraints excluded: chain A residue 3051 VAL Chi-restraints excluded: chain A residue 3109 GLU Chi-restraints excluded: chain A residue 3347 VAL Chi-restraints excluded: chain A residue 3398 GLU Chi-restraints excluded: chain A residue 3438 MET Chi-restraints excluded: chain A residue 3512 VAL Chi-restraints excluded: chain A residue 4542 LEU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 930 LEU Chi-restraints excluded: chain B residue 1171 MET Chi-restraints excluded: chain B residue 1435 TYR Chi-restraints excluded: chain B residue 1737 VAL Chi-restraints excluded: chain B residue 2424 MET Chi-restraints excluded: chain B residue 3109 GLU Chi-restraints excluded: chain B residue 3308 VAL Chi-restraints excluded: chain B residue 3320 ILE Chi-restraints excluded: chain B residue 3398 GLU Chi-restraints excluded: chain B residue 3471 LEU Chi-restraints excluded: chain B residue 3512 VAL Chi-restraints excluded: chain B residue 4542 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 930 LEU Chi-restraints excluded: chain C residue 1171 MET Chi-restraints excluded: chain C residue 1435 TYR Chi-restraints excluded: chain C residue 1737 VAL Chi-restraints excluded: chain C residue 2424 MET Chi-restraints excluded: chain C residue 2528 LEU Chi-restraints excluded: chain C residue 2743 THR Chi-restraints excluded: chain C residue 3109 GLU Chi-restraints excluded: chain C residue 3308 VAL Chi-restraints excluded: chain C residue 3320 ILE Chi-restraints excluded: chain C residue 3398 GLU Chi-restraints excluded: chain C residue 3471 LEU Chi-restraints excluded: chain C residue 3512 VAL Chi-restraints excluded: chain C residue 4542 LEU Chi-restraints excluded: chain K residue 16 PHE Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain K residue 55 VAL Chi-restraints excluded: chain K residue 89 PHE Chi-restraints excluded: chain L residue 5 LEU Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain M residue 16 PHE Chi-restraints excluded: chain M residue 37 LEU Chi-restraints excluded: chain M residue 55 VAL Chi-restraints excluded: chain M residue 67 ASP Chi-restraints excluded: chain M residue 89 PHE Chi-restraints excluded: chain O residue 16 PHE Chi-restraints excluded: chain O residue 37 LEU Chi-restraints excluded: chain O residue 55 VAL Chi-restraints excluded: chain O residue 89 PHE Chi-restraints excluded: chain P residue 5 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1860 random chunks: chunk 1497 optimal weight: 6.9990 chunk 1020 optimal weight: 30.0000 chunk 26 optimal weight: 20.0000 chunk 1338 optimal weight: 10.0000 chunk 741 optimal weight: 10.0000 chunk 1534 optimal weight: 0.0970 chunk 1242 optimal weight: 20.0000 chunk 2 optimal weight: 9.9990 chunk 918 optimal weight: 0.5980 chunk 1613 optimal weight: 9.9990 chunk 453 optimal weight: 8.9990 overall best weight: 5.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 26 HIS ** I 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 825 GLN ** D 880 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2128 GLN D3319 ASN D3963 GLN D4057 ASN ** D4751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4801 HIS ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 ASN A2128 GLN A3319 ASN A3963 GLN A4057 ASN ** A4751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4801 HIS ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 640 ASN ** B 880 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2128 GLN B3963 GLN ** B4751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4801 HIS ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 640 ASN ** C 880 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2128 GLN C3319 ASN C3963 GLN C4057 ASN ** C4751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C4801 HIS K 17 HIS ** K 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 17 HIS ** M 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 17 HIS ** O 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 152600 Z= 0.423 Angle : 0.630 16.150 206604 Z= 0.318 Chirality : 0.041 0.268 22672 Planarity : 0.004 0.061 26800 Dihedral : 6.714 89.364 20896 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.93 % Favored : 97.05 % Rotamer: Outliers : 1.66 % Allowed : 9.47 % Favored : 88.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % 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: 1.68 (0.06), residues: 18552 helix: 2.10 (0.05), residues: 9920 sheet: -0.11 (0.13), residues: 1696 loop : 0.06 (0.08), residues: 6936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP N 91 HIS 0.007 0.001 HIS A 682 PHE 0.030 0.002 PHE A2974 TYR 0.038 0.002 TYR A2883 ARG 0.007 0.001 ARG G 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 37104 Ramachandran restraints generated. 18552 Oldfield, 0 Emsley, 18552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 37104 Ramachandran restraints generated. 18552 Oldfield, 0 Emsley, 18552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1341 residues out of total 16268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 269 poor density : 1072 time to evaluate : 12.831 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: E 54 GLN cc_start: 0.9090 (mp10) cc_final: 0.8626 (mp10) REVERT: I 5 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8454 (mm) REVERT: I 14 ASN cc_start: 0.9294 (m110) cc_final: 0.9015 (p0) REVERT: I 16 PHE cc_start: 0.8654 (OUTLIER) cc_final: 0.7551 (p90) REVERT: I 32 LYS cc_start: 0.9236 (OUTLIER) cc_final: 0.8827 (mmmt) REVERT: J 75 TYR cc_start: 0.7073 (p90) cc_final: 0.6829 (p90) REVERT: F 4 GLN cc_start: 0.8017 (mp10) cc_final: 0.7759 (mp10) REVERT: F 45 LYS cc_start: 0.8757 (ttpt) cc_final: 0.8407 (ttpp) REVERT: G 45 LYS cc_start: 0.8719 (ttpt) cc_final: 0.8330 (ttpp) REVERT: G 53 LYS cc_start: 0.9083 (mmtp) cc_final: 0.8785 (mmtp) REVERT: G 55 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8296 (mt-10) REVERT: H 45 LYS cc_start: 0.8738 (ttpt) cc_final: 0.8353 (ttpp) REVERT: H 53 LYS cc_start: 0.9077 (mmtp) cc_final: 0.8773 (mmtp) REVERT: H 55 GLU cc_start: 0.8703 (mt-10) cc_final: 0.8313 (mt-10) REVERT: D 31 LYS cc_start: 0.8419 (pttp) cc_final: 0.8117 (pptt) REVERT: D 117 MET cc_start: 0.9403 (mtm) cc_final: 0.9103 (mtp) REVERT: D 197 MET cc_start: 0.8052 (mpp) cc_final: 0.7491 (mpp) REVERT: D 666 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7662 (mt-10) REVERT: D 905 HIS cc_start: 0.7014 (t70) cc_final: 0.6452 (t70) REVERT: D 1041 CYS cc_start: 0.9401 (OUTLIER) cc_final: 0.9116 (p) REVERT: D 1930 MET cc_start: 0.9111 (ttm) cc_final: 0.8874 (mtp) REVERT: D 1987 MET cc_start: 0.5116 (pmm) cc_final: 0.4426 (tmm) REVERT: D 1997 ARG cc_start: 0.9161 (tmt-80) cc_final: 0.8827 (tpm170) REVERT: D 2096 GLN cc_start: 0.8324 (OUTLIER) cc_final: 0.8123 (mm-40) REVERT: D 2171 MET cc_start: 0.8172 (mmm) cc_final: 0.7684 (mmm) REVERT: D 2424 MET cc_start: 0.8707 (OUTLIER) cc_final: 0.8312 (mpp) REVERT: D 2619 MET cc_start: 0.9312 (mmt) cc_final: 0.9107 (mmt) REVERT: D 2945 MET cc_start: 0.8528 (ptt) cc_final: 0.8320 (ptt) REVERT: D 2968 MET cc_start: 0.9413 (mmm) cc_final: 0.9027 (mmm) REVERT: D 3211 LEU cc_start: 0.9411 (mm) cc_final: 0.8941 (tp) REVERT: D 3240 MET cc_start: 0.7578 (tpp) cc_final: 0.7347 (tpp) REVERT: D 3436 PHE cc_start: 0.9651 (t80) cc_final: 0.9230 (t80) REVERT: D 3468 MET cc_start: 0.8012 (tpp) cc_final: 0.7486 (tpp) REVERT: D 3518 MET cc_start: 0.9163 (tpt) cc_final: 0.8648 (tpp) REVERT: D 3574 MET cc_start: 0.9009 (tpt) cc_final: 0.8437 (tpp) REVERT: D 4837 MET cc_start: 0.8851 (mmm) cc_final: 0.8503 (mmm) REVERT: A 117 MET cc_start: 0.9381 (mtm) cc_final: 0.9152 (mtp) REVERT: A 197 MET cc_start: 0.8001 (mpp) cc_final: 0.7480 (mpp) REVERT: A 212 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.8050 (tp30) REVERT: A 666 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7754 (mt-10) REVERT: A 905 HIS cc_start: 0.6800 (t70) cc_final: 0.6093 (t70) REVERT: A 1574 MET cc_start: 0.8951 (mmt) cc_final: 0.8654 (mmt) REVERT: A 1930 MET cc_start: 0.9123 (ttm) cc_final: 0.8894 (mtp) REVERT: A 1997 ARG cc_start: 0.9169 (tmt-80) cc_final: 0.8784 (tpm170) REVERT: A 2171 MET cc_start: 0.8143 (mmm) cc_final: 0.7717 (mmm) REVERT: A 2382 GLU cc_start: 0.8991 (OUTLIER) cc_final: 0.8664 (mp0) REVERT: A 2945 MET cc_start: 0.8433 (ptt) cc_final: 0.8227 (ptt) REVERT: A 3107 MET cc_start: 0.9525 (OUTLIER) cc_final: 0.8944 (ttp) REVERT: A 3211 LEU cc_start: 0.9378 (mm) cc_final: 0.8918 (tp) REVERT: A 3277 MET cc_start: 0.9511 (ttp) cc_final: 0.9280 (ttp) REVERT: A 3518 MET cc_start: 0.9292 (mmm) cc_final: 0.9037 (mmm) REVERT: A 3545 ASP cc_start: 0.8375 (OUTLIER) cc_final: 0.8019 (p0) REVERT: A 3574 MET cc_start: 0.8918 (tpt) cc_final: 0.8342 (tpp) REVERT: A 4837 MET cc_start: 0.8840 (mmm) cc_final: 0.8512 (mmm) REVERT: B 117 MET cc_start: 0.9407 (mtm) cc_final: 0.9113 (mtp) REVERT: B 197 MET cc_start: 0.8051 (mpp) cc_final: 0.7487 (mpp) REVERT: B 666 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7677 (mt-10) REVERT: B 905 HIS cc_start: 0.7015 (t70) cc_final: 0.6460 (t70) REVERT: B 1041 CYS cc_start: 0.9405 (OUTLIER) cc_final: 0.9120 (p) REVERT: B 1930 MET cc_start: 0.9117 (ttm) cc_final: 0.8885 (mtp) REVERT: B 1997 ARG cc_start: 0.9154 (tmt-80) cc_final: 0.8814 (tpm170) REVERT: B 2171 MET cc_start: 0.8171 (mmm) cc_final: 0.7703 (mmm) REVERT: B 2179 MET cc_start: 0.8849 (tpt) cc_final: 0.8647 (tpp) REVERT: B 2424 MET cc_start: 0.8701 (OUTLIER) cc_final: 0.8309 (mpp) REVERT: B 2531 MET cc_start: 0.8970 (mtm) cc_final: 0.8460 (mtm) REVERT: B 2619 MET cc_start: 0.9304 (mmt) cc_final: 0.9084 (mmt) REVERT: B 2945 MET cc_start: 0.8498 (ptt) cc_final: 0.8286 (ptt) REVERT: B 2968 MET cc_start: 0.9422 (mmm) cc_final: 0.9035 (mmm) REVERT: B 3211 LEU cc_start: 0.9415 (mm) cc_final: 0.8942 (tp) REVERT: B 3240 MET cc_start: 0.7589 (tpp) cc_final: 0.7362 (tpp) REVERT: B 3320 ILE cc_start: 0.9053 (OUTLIER) cc_final: 0.8804 (mp) REVERT: B 3436 PHE cc_start: 0.9653 (t80) cc_final: 0.9235 (t80) REVERT: B 3468 MET cc_start: 0.8025 (tpp) cc_final: 0.7517 (tpp) REVERT: B 3518 MET cc_start: 0.9172 (tpt) cc_final: 0.8672 (tpp) REVERT: B 3574 MET cc_start: 0.9003 (tpt) cc_final: 0.8430 (tpp) REVERT: B 4837 MET cc_start: 0.8850 (mmm) cc_final: 0.8514 (mmm) REVERT: C 117 MET cc_start: 0.9410 (mtm) cc_final: 0.9113 (mtp) REVERT: C 197 MET cc_start: 0.8051 (mpp) cc_final: 0.7494 (mpp) REVERT: C 666 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7667 (mt-10) REVERT: C 905 HIS cc_start: 0.7015 (t70) cc_final: 0.6457 (t70) REVERT: C 1041 CYS cc_start: 0.9400 (OUTLIER) cc_final: 0.9111 (p) REVERT: C 1930 MET cc_start: 0.9121 (ttm) cc_final: 0.8885 (mtp) REVERT: C 1987 MET cc_start: 0.5158 (pmm) cc_final: 0.4483 (tmm) REVERT: C 1997 ARG cc_start: 0.9156 (tmt-80) cc_final: 0.8813 (tpm170) REVERT: C 2096 GLN cc_start: 0.8311 (OUTLIER) cc_final: 0.8111 (mm-40) REVERT: C 2171 MET cc_start: 0.8174 (mmm) cc_final: 0.7695 (mmm) REVERT: C 2424 MET cc_start: 0.8704 (OUTLIER) cc_final: 0.8306 (mpp) REVERT: C 2531 MET cc_start: 0.8992 (mtm) cc_final: 0.8586 (mtm) REVERT: C 2619 MET cc_start: 0.9296 (mmt) cc_final: 0.9087 (mmt) REVERT: C 2817 MET cc_start: 0.5579 (ttp) cc_final: 0.5361 (tmm) REVERT: C 2945 MET cc_start: 0.8519 (ptt) cc_final: 0.8308 (ptt) REVERT: C 2968 MET cc_start: 0.9421 (mmm) cc_final: 0.9032 (mmm) REVERT: C 3211 LEU cc_start: 0.9417 (mm) cc_final: 0.8948 (tp) REVERT: C 3240 MET cc_start: 0.7627 (tpp) cc_final: 0.7396 (tpp) REVERT: C 3320 ILE cc_start: 0.9068 (OUTLIER) cc_final: 0.8824 (mp) REVERT: C 3436 PHE cc_start: 0.9647 (t80) cc_final: 0.9233 (t80) REVERT: C 3468 MET cc_start: 0.8000 (tpp) cc_final: 0.7477 (tpp) REVERT: C 3518 MET cc_start: 0.9179 (tpt) cc_final: 0.8623 (tpp) REVERT: C 3574 MET cc_start: 0.8994 (tpt) cc_final: 0.8426 (tpp) REVERT: C 4837 MET cc_start: 0.8848 (mmm) cc_final: 0.8515 (mmm) REVERT: K 16 PHE cc_start: 0.8767 (OUTLIER) cc_final: 0.7634 (p90) REVERT: K 32 LYS cc_start: 0.9159 (OUTLIER) cc_final: 0.8786 (mmmt) REVERT: L 75 TYR cc_start: 0.7007 (p90) cc_final: 0.6641 (p90) REVERT: N 75 TYR cc_start: 0.7029 (p90) cc_final: 0.6676 (p90) REVERT: M 5 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8476 (mm) REVERT: M 16 PHE cc_start: 0.8768 (OUTLIER) cc_final: 0.7629 (p90) REVERT: M 32 LYS cc_start: 0.9158 (OUTLIER) cc_final: 0.8781 (mmmt) REVERT: O 16 PHE cc_start: 0.8771 (OUTLIER) cc_final: 0.7639 (p90) REVERT: O 32 LYS cc_start: 0.9161 (OUTLIER) cc_final: 0.8787 (mmmt) REVERT: P 75 TYR cc_start: 0.7002 (p90) cc_final: 0.6637 (p90) outliers start: 269 outliers final: 164 residues processed: 1231 average time/residue: 1.2236 time to fit residues: 2705.3426 Evaluate side-chains 1216 residues out of total 16268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 1028 time to evaluate : 12.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 33 ASP Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 60 TRP Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain I residue 16 PHE Chi-restraints excluded: chain I residue 32 LYS Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 67 ASP Chi-restraints excluded: chain I residue 89 PHE Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 37 LEU Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 33 ASP Chi-restraints excluded: chain F residue 39 SER Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 60 TRP Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 33 ASP Chi-restraints excluded: chain G residue 39 SER Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 60 TRP Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 60 TRP Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 359 THR Chi-restraints excluded: chain D residue 812 CYS Chi-restraints excluded: chain D residue 912 HIS Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain D residue 939 HIS Chi-restraints excluded: chain D residue 1041 CYS Chi-restraints excluded: chain D residue 1171 MET Chi-restraints excluded: chain D residue 1183 ILE Chi-restraints excluded: chain D residue 1435 TYR Chi-restraints excluded: chain D residue 1737 VAL Chi-restraints excluded: chain D residue 1967 VAL Chi-restraints excluded: chain D residue 2096 GLN Chi-restraints excluded: chain D residue 2204 MET Chi-restraints excluded: chain D residue 2417 VAL Chi-restraints excluded: chain D residue 2424 MET Chi-restraints excluded: chain D residue 2743 THR Chi-restraints excluded: chain D residue 3109 GLU Chi-restraints excluded: chain D residue 3308 VAL Chi-restraints excluded: chain D residue 3379 GLN Chi-restraints excluded: chain D residue 3394 LEU Chi-restraints excluded: chain D residue 3398 GLU Chi-restraints excluded: chain D residue 3406 LEU Chi-restraints excluded: chain D residue 3471 LEU Chi-restraints excluded: chain D residue 3512 VAL Chi-restraints excluded: chain D residue 3545 ASP Chi-restraints excluded: chain D residue 3657 SER Chi-restraints excluded: chain D residue 4042 MET Chi-restraints excluded: chain D residue 4538 PHE Chi-restraints excluded: chain D residue 4542 LEU Chi-restraints excluded: chain D residue 4751 HIS Chi-restraints excluded: chain D residue 4951 ASP Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 812 CYS Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 939 HIS Chi-restraints excluded: chain A residue 1171 MET Chi-restraints excluded: chain A residue 1183 ILE Chi-restraints excluded: chain A residue 1251 LEU Chi-restraints excluded: chain A residue 1429 LEU Chi-restraints excluded: chain A residue 1435 TYR Chi-restraints excluded: chain A residue 1463 MET Chi-restraints excluded: chain A residue 1737 VAL Chi-restraints excluded: chain A residue 1928 LEU Chi-restraints excluded: chain A residue 1967 VAL Chi-restraints excluded: chain A residue 1992 THR Chi-restraints excluded: chain A residue 2204 MET Chi-restraints excluded: chain A residue 2382 GLU Chi-restraints excluded: chain A residue 2417 VAL Chi-restraints excluded: chain A residue 2424 MET Chi-restraints excluded: chain A residue 2743 THR Chi-restraints excluded: chain A residue 3051 VAL Chi-restraints excluded: chain A residue 3107 MET Chi-restraints excluded: chain A residue 3109 GLU Chi-restraints excluded: chain A residue 3157 VAL Chi-restraints excluded: chain A residue 3347 VAL Chi-restraints excluded: chain A residue 3366 LEU Chi-restraints excluded: chain A residue 3398 GLU Chi-restraints excluded: chain A residue 3406 LEU Chi-restraints excluded: chain A residue 3512 VAL Chi-restraints excluded: chain A residue 3545 ASP Chi-restraints excluded: chain A residue 3657 SER Chi-restraints excluded: chain A residue 4538 PHE Chi-restraints excluded: chain A residue 4542 LEU Chi-restraints excluded: chain A residue 4751 HIS Chi-restraints excluded: chain A residue 4951 ASP Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 812 CYS Chi-restraints excluded: chain B residue 912 HIS Chi-restraints excluded: chain B residue 930 LEU Chi-restraints excluded: chain B residue 939 HIS Chi-restraints excluded: chain B residue 1041 CYS Chi-restraints excluded: chain B residue 1171 MET Chi-restraints excluded: chain B residue 1435 TYR Chi-restraints excluded: chain B residue 1737 VAL Chi-restraints excluded: chain B residue 1967 VAL Chi-restraints excluded: chain B residue 2204 MET Chi-restraints excluded: chain B residue 2417 VAL Chi-restraints excluded: chain B residue 2424 MET Chi-restraints excluded: chain B residue 2743 THR Chi-restraints excluded: chain B residue 3109 GLU Chi-restraints excluded: chain B residue 3308 VAL Chi-restraints excluded: chain B residue 3320 ILE Chi-restraints excluded: chain B residue 3379 GLN Chi-restraints excluded: chain B residue 3398 GLU Chi-restraints excluded: chain B residue 3406 LEU Chi-restraints excluded: chain B residue 3471 LEU Chi-restraints excluded: chain B residue 3512 VAL Chi-restraints excluded: chain B residue 3545 ASP Chi-restraints excluded: chain B residue 3657 SER Chi-restraints excluded: chain B residue 4042 MET Chi-restraints excluded: chain B residue 4538 PHE Chi-restraints excluded: chain B residue 4542 LEU Chi-restraints excluded: chain B residue 4751 HIS Chi-restraints excluded: chain B residue 4951 ASP Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 912 HIS Chi-restraints excluded: chain C residue 930 LEU Chi-restraints excluded: chain C residue 939 HIS Chi-restraints excluded: chain C residue 1041 CYS Chi-restraints excluded: chain C residue 1171 MET Chi-restraints excluded: chain C residue 1183 ILE Chi-restraints excluded: chain C residue 1435 TYR Chi-restraints excluded: chain C residue 1737 VAL Chi-restraints excluded: chain C residue 1928 LEU Chi-restraints excluded: chain C residue 1967 VAL Chi-restraints excluded: chain C residue 2096 GLN Chi-restraints excluded: chain C residue 2204 MET Chi-restraints excluded: chain C residue 2268 MET Chi-restraints excluded: chain C residue 2417 VAL Chi-restraints excluded: chain C residue 2424 MET Chi-restraints excluded: chain C residue 2528 LEU Chi-restraints excluded: chain C residue 2627 LEU Chi-restraints excluded: chain C residue 2743 THR Chi-restraints excluded: chain C residue 3109 GLU Chi-restraints excluded: chain C residue 3170 LEU Chi-restraints excluded: chain C residue 3308 VAL Chi-restraints excluded: chain C residue 3320 ILE Chi-restraints excluded: chain C residue 3366 LEU Chi-restraints excluded: chain C residue 3379 GLN Chi-restraints excluded: chain C residue 3398 GLU Chi-restraints excluded: chain C residue 3406 LEU Chi-restraints excluded: chain C residue 3471 LEU Chi-restraints excluded: chain C residue 3512 VAL Chi-restraints excluded: chain C residue 3545 ASP Chi-restraints excluded: chain C residue 3657 SER Chi-restraints excluded: chain C residue 4042 MET Chi-restraints excluded: chain C residue 4538 PHE Chi-restraints excluded: chain C residue 4542 LEU Chi-restraints excluded: chain C residue 4751 HIS Chi-restraints excluded: chain C residue 4951 ASP Chi-restraints excluded: chain K residue 16 PHE Chi-restraints excluded: chain K residue 32 LYS Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain K residue 55 VAL Chi-restraints excluded: chain K residue 67 ASP Chi-restraints excluded: chain K residue 89 PHE Chi-restraints excluded: chain L residue 5 LEU Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain M residue 16 PHE Chi-restraints excluded: chain M residue 32 LYS Chi-restraints excluded: chain M residue 37 LEU Chi-restraints excluded: chain M residue 55 VAL Chi-restraints excluded: chain M residue 67 ASP Chi-restraints excluded: chain M residue 89 PHE Chi-restraints excluded: chain O residue 16 PHE Chi-restraints excluded: chain O residue 32 LYS Chi-restraints excluded: chain O residue 37 LEU Chi-restraints excluded: chain O residue 55 VAL Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain O residue 89 PHE Chi-restraints excluded: chain P residue 5 LEU Chi-restraints excluded: chain P residue 37 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1860 random chunks: chunk 604 optimal weight: 5.9990 chunk 1619 optimal weight: 50.0000 chunk 355 optimal weight: 20.0000 chunk 1055 optimal weight: 9.9990 chunk 443 optimal weight: 9.9990 chunk 1799 optimal weight: 3.9990 chunk 1493 optimal weight: 10.0000 chunk 833 optimal weight: 3.9990 chunk 149 optimal weight: 5.9990 chunk 595 optimal weight: 0.0170 chunk 944 optimal weight: 10.0000 overall best weight: 4.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 88 ASN ** J 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 139 GLN D 640 ASN D2195 HIS D3181 ASN ** D4751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 139 GLN A 640 ASN A2096 GLN A2195 HIS A3181 ASN A3319 ASN ** A4751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 139 GLN B 640 ASN B 880 HIS B2096 GLN B2195 HIS ** B3181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3319 ASN ** B4751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 GLN C 640 ASN C2195 HIS ** C3181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 17 HIS ** K 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 17 HIS ** M 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 17 HIS ** O 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 152600 Z= 0.321 Angle : 0.585 14.443 206604 Z= 0.294 Chirality : 0.040 0.220 22672 Planarity : 0.004 0.063 26800 Dihedral : 6.650 89.202 20896 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.70 % Favored : 97.29 % Rotamer: Outliers : 1.65 % Allowed : 10.44 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % 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: 1.66 (0.06), residues: 18552 helix: 2.10 (0.05), residues: 9948 sheet: -0.13 (0.13), residues: 1696 loop : 0.03 (0.08), residues: 6908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP L 91 HIS 0.005 0.001 HIS A 839 PHE 0.048 0.002 PHE B3637 TYR 0.039 0.001 TYR A2883 ARG 0.007 0.000 ARG E 14 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 37104 Ramachandran restraints generated. 18552 Oldfield, 0 Emsley, 18552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 37104 Ramachandran restraints generated. 18552 Oldfield, 0 Emsley, 18552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1346 residues out of total 16268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 268 poor density : 1078 time to evaluate : 12.533 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: E 54 GLN cc_start: 0.9115 (mp10) cc_final: 0.8648 (mp10) REVERT: I 5 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8477 (mm) REVERT: I 16 PHE cc_start: 0.8656 (OUTLIER) cc_final: 0.7539 (p90) REVERT: I 22 LYS cc_start: 0.8000 (pptt) cc_final: 0.7480 (pptt) REVERT: I 32 LYS cc_start: 0.9202 (OUTLIER) cc_final: 0.8832 (mmmt) REVERT: J 75 TYR cc_start: 0.7006 (p90) cc_final: 0.6563 (p90) REVERT: F 4 GLN cc_start: 0.8029 (mp10) cc_final: 0.7758 (mp10) REVERT: F 45 LYS cc_start: 0.8777 (ttpt) cc_final: 0.8430 (ttpp) REVERT: G 45 LYS cc_start: 0.8726 (ttpt) cc_final: 0.8402 (ttpp) REVERT: G 53 LYS cc_start: 0.9084 (mmtp) cc_final: 0.8834 (mmtp) REVERT: H 45 LYS cc_start: 0.8746 (ttpt) cc_final: 0.8421 (ttpp) REVERT: H 53 LYS cc_start: 0.9076 (mmtp) cc_final: 0.8825 (mmtp) REVERT: D 117 MET cc_start: 0.9422 (mtm) cc_final: 0.9143 (mtp) REVERT: D 197 MET cc_start: 0.8034 (mpp) cc_final: 0.7493 (mpp) REVERT: D 666 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7635 (mt-10) REVERT: D 1041 CYS cc_start: 0.9386 (OUTLIER) cc_final: 0.9110 (p) REVERT: D 1816 MET cc_start: 0.8990 (mmm) cc_final: 0.8104 (mtt) REVERT: D 1930 MET cc_start: 0.9084 (ttm) cc_final: 0.8827 (mtp) REVERT: D 1997 ARG cc_start: 0.9170 (tmt-80) cc_final: 0.8798 (tpm170) REVERT: D 2096 GLN cc_start: 0.8231 (OUTLIER) cc_final: 0.7964 (mm-40) REVERT: D 2171 MET cc_start: 0.8110 (mmm) cc_final: 0.7633 (mmm) REVERT: D 2424 MET cc_start: 0.8673 (OUTLIER) cc_final: 0.8325 (mpp) REVERT: D 2491 MET cc_start: 0.9189 (tpp) cc_final: 0.8970 (tpp) REVERT: D 2968 MET cc_start: 0.9420 (mmm) cc_final: 0.9010 (mmm) REVERT: D 3039 MET cc_start: 0.9519 (mtt) cc_final: 0.9264 (mtm) REVERT: D 3211 LEU cc_start: 0.9370 (mm) cc_final: 0.8893 (tp) REVERT: D 3240 MET cc_start: 0.7554 (tpp) cc_final: 0.7255 (tpp) REVERT: D 3436 PHE cc_start: 0.9635 (t80) cc_final: 0.9421 (t80) REVERT: D 3468 MET cc_start: 0.8003 (tpp) cc_final: 0.7479 (tpp) REVERT: D 3518 MET cc_start: 0.9181 (tpt) cc_final: 0.8767 (tpp) REVERT: D 3545 ASP cc_start: 0.8544 (OUTLIER) cc_final: 0.7946 (p0) REVERT: D 3574 MET cc_start: 0.8994 (tpt) cc_final: 0.8426 (tpp) REVERT: D 4837 MET cc_start: 0.8851 (mmm) cc_final: 0.8517 (mmm) REVERT: A 117 MET cc_start: 0.9377 (mtm) cc_final: 0.9140 (mtp) REVERT: A 197 MET cc_start: 0.8005 (mpp) cc_final: 0.7491 (mpp) REVERT: A 212 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.8079 (tp30) REVERT: A 666 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7736 (mt-10) REVERT: A 905 HIS cc_start: 0.6826 (t70) cc_final: 0.6156 (t70) REVERT: A 1041 CYS cc_start: 0.9384 (OUTLIER) cc_final: 0.9010 (p) REVERT: A 1574 MET cc_start: 0.8961 (mmt) cc_final: 0.8662 (mmt) REVERT: A 1816 MET cc_start: 0.9007 (mmm) cc_final: 0.8107 (mtt) REVERT: A 1930 MET cc_start: 0.9054 (ttm) cc_final: 0.8793 (mtp) REVERT: A 1997 ARG cc_start: 0.9180 (tmt-80) cc_final: 0.8783 (tpm170) REVERT: A 2171 MET cc_start: 0.8120 (mmm) cc_final: 0.7707 (mmm) REVERT: A 2382 GLU cc_start: 0.9022 (OUTLIER) cc_final: 0.8642 (mp0) REVERT: A 3039 MET cc_start: 0.9703 (mtm) cc_final: 0.9440 (mtm) REVERT: A 3107 MET cc_start: 0.9509 (OUTLIER) cc_final: 0.8934 (ttp) REVERT: A 3211 LEU cc_start: 0.9361 (mm) cc_final: 0.8903 (tp) REVERT: A 3518 MET cc_start: 0.9324 (mmm) cc_final: 0.9040 (mmm) REVERT: A 3545 ASP cc_start: 0.8214 (OUTLIER) cc_final: 0.7803 (p0) REVERT: A 3574 MET cc_start: 0.8908 (tpt) cc_final: 0.8294 (tpp) REVERT: A 3936 PHE cc_start: 0.8998 (OUTLIER) cc_final: 0.8584 (t80) REVERT: A 4872 MET cc_start: 0.9111 (mmt) cc_final: 0.8498 (mmp) REVERT: B 117 MET cc_start: 0.9411 (mtm) cc_final: 0.9115 (mtp) REVERT: B 197 MET cc_start: 0.8039 (mpp) cc_final: 0.7493 (mpp) REVERT: B 666 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7653 (mt-10) REVERT: B 1041 CYS cc_start: 0.9389 (OUTLIER) cc_final: 0.9104 (p) REVERT: B 1816 MET cc_start: 0.8985 (mmm) cc_final: 0.8110 (mtt) REVERT: B 1930 MET cc_start: 0.9087 (ttm) cc_final: 0.8851 (mtp) REVERT: B 1987 MET cc_start: 0.5172 (pmm) cc_final: 0.4572 (tmm) REVERT: B 1997 ARG cc_start: 0.9168 (tmt-80) cc_final: 0.8798 (tpm170) REVERT: B 2171 MET cc_start: 0.8122 (mmm) cc_final: 0.7669 (mmm) REVERT: B 2424 MET cc_start: 0.8672 (OUTLIER) cc_final: 0.8322 (mpp) REVERT: B 2531 MET cc_start: 0.8993 (mtm) cc_final: 0.8464 (mtm) REVERT: B 2945 MET cc_start: 0.8546 (ptt) cc_final: 0.8346 (ptt) REVERT: B 2968 MET cc_start: 0.9410 (mmm) cc_final: 0.9012 (mmm) REVERT: B 3039 MET cc_start: 0.9517 (mtt) cc_final: 0.9262 (mtm) REVERT: B 3211 LEU cc_start: 0.9377 (mm) cc_final: 0.8904 (tp) REVERT: B 3240 MET cc_start: 0.7566 (tpp) cc_final: 0.7257 (tpp) REVERT: B 3436 PHE cc_start: 0.9637 (t80) cc_final: 0.9422 (t80) REVERT: B 3468 MET cc_start: 0.8008 (tpp) cc_final: 0.7494 (tpp) REVERT: B 3518 MET cc_start: 0.9172 (tpt) cc_final: 0.8766 (tpp) REVERT: B 3545 ASP cc_start: 0.8545 (OUTLIER) cc_final: 0.7948 (p0) REVERT: B 3574 MET cc_start: 0.8993 (tpt) cc_final: 0.8426 (tpp) REVERT: C 117 MET cc_start: 0.9415 (mtm) cc_final: 0.9115 (mtp) REVERT: C 197 MET cc_start: 0.8033 (mpp) cc_final: 0.7485 (mpp) REVERT: C 666 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7653 (mt-10) REVERT: C 1041 CYS cc_start: 0.9383 (OUTLIER) cc_final: 0.9099 (p) REVERT: C 1816 MET cc_start: 0.8997 (mmm) cc_final: 0.8113 (mtt) REVERT: C 1930 MET cc_start: 0.9063 (ttm) cc_final: 0.8800 (mtp) REVERT: C 1997 ARG cc_start: 0.9168 (tmt-80) cc_final: 0.8795 (tpm170) REVERT: C 2171 MET cc_start: 0.8125 (mmm) cc_final: 0.7694 (mmm) REVERT: C 2424 MET cc_start: 0.8676 (OUTLIER) cc_final: 0.8320 (mpp) REVERT: C 2491 MET cc_start: 0.9194 (tpp) cc_final: 0.8961 (tpp) REVERT: C 2531 MET cc_start: 0.8984 (mtm) cc_final: 0.8565 (mtm) REVERT: C 2968 MET cc_start: 0.9409 (mmm) cc_final: 0.9014 (mmm) REVERT: C 3039 MET cc_start: 0.9524 (mtt) cc_final: 0.9276 (mtm) REVERT: C 3211 LEU cc_start: 0.9382 (mm) cc_final: 0.8908 (tp) REVERT: C 3240 MET cc_start: 0.7620 (tpp) cc_final: 0.7294 (tpp) REVERT: C 3436 PHE cc_start: 0.9646 (t80) cc_final: 0.9301 (t80) REVERT: C 3468 MET cc_start: 0.8000 (tpp) cc_final: 0.7462 (tpp) REVERT: C 3518 MET cc_start: 0.9170 (tpt) cc_final: 0.8769 (tpp) REVERT: C 3574 MET cc_start: 0.8973 (tpt) cc_final: 0.8408 (tpp) REVERT: K 16 PHE cc_start: 0.8634 (OUTLIER) cc_final: 0.7425 (p90) REVERT: K 32 LYS cc_start: 0.9144 (OUTLIER) cc_final: 0.8815 (mmmt) REVERT: L 59 MET cc_start: 0.7388 (ppp) cc_final: 0.6839 (ppp) REVERT: L 75 TYR cc_start: 0.7067 (p90) cc_final: 0.6593 (p90) REVERT: N 12 LEU cc_start: 0.8279 (tp) cc_final: 0.8059 (tt) REVERT: N 75 TYR cc_start: 0.6921 (p90) cc_final: 0.6439 (p90) REVERT: M 5 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8447 (mm) REVERT: M 16 PHE cc_start: 0.8651 (OUTLIER) cc_final: 0.7450 (p90) REVERT: M 32 LYS cc_start: 0.9148 (OUTLIER) cc_final: 0.8810 (mmmt) REVERT: O 16 PHE cc_start: 0.8631 (OUTLIER) cc_final: 0.7427 (p90) REVERT: O 32 LYS cc_start: 0.9143 (OUTLIER) cc_final: 0.8814 (mmmt) REVERT: P 59 MET cc_start: 0.7388 (ppp) cc_final: 0.6857 (ppp) REVERT: P 75 TYR cc_start: 0.7069 (p90) cc_final: 0.6597 (p90) outliers start: 268 outliers final: 177 residues processed: 1246 average time/residue: 1.3363 time to fit residues: 3018.4305 Evaluate side-chains 1232 residues out of total 16268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 1030 time to evaluate : 12.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 33 ASP Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 60 TRP Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain I residue 16 PHE Chi-restraints excluded: chain I residue 32 LYS Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 67 ASP Chi-restraints excluded: chain I residue 75 TYR Chi-restraints excluded: chain I residue 89 PHE Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 37 LEU Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 33 ASP Chi-restraints excluded: chain F residue 39 SER Chi-restraints excluded: chain F residue 60 TRP Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 33 ASP Chi-restraints excluded: chain G residue 39 SER Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 60 TRP Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 60 TRP Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 579 ILE Chi-restraints excluded: chain D residue 812 CYS Chi-restraints excluded: chain D residue 912 HIS Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain D residue 1041 CYS Chi-restraints excluded: chain D residue 1171 MET Chi-restraints excluded: chain D residue 1190 LEU Chi-restraints excluded: chain D residue 1435 TYR Chi-restraints excluded: chain D residue 1737 VAL Chi-restraints excluded: chain D residue 1836 VAL Chi-restraints excluded: chain D residue 2096 GLN Chi-restraints excluded: chain D residue 2169 VAL Chi-restraints excluded: chain D residue 2315 LEU Chi-restraints excluded: chain D residue 2417 VAL Chi-restraints excluded: chain D residue 2424 MET Chi-restraints excluded: chain D residue 3109 GLU Chi-restraints excluded: chain D residue 3157 VAL Chi-restraints excluded: chain D residue 3308 VAL Chi-restraints excluded: chain D residue 3366 LEU Chi-restraints excluded: chain D residue 3379 GLN Chi-restraints excluded: chain D residue 3394 LEU Chi-restraints excluded: chain D residue 3398 GLU Chi-restraints excluded: chain D residue 3406 LEU Chi-restraints excluded: chain D residue 3471 LEU Chi-restraints excluded: chain D residue 3512 VAL Chi-restraints excluded: chain D residue 3530 ASP Chi-restraints excluded: chain D residue 3545 ASP Chi-restraints excluded: chain D residue 3657 SER Chi-restraints excluded: chain D residue 3861 MET Chi-restraints excluded: chain D residue 4042 MET Chi-restraints excluded: chain D residue 4542 LEU Chi-restraints excluded: chain D residue 4887 VAL Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 812 CYS Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 1041 CYS Chi-restraints excluded: chain A residue 1171 MET Chi-restraints excluded: chain A residue 1190 LEU Chi-restraints excluded: chain A residue 1251 LEU Chi-restraints excluded: chain A residue 1429 LEU Chi-restraints excluded: chain A residue 1435 TYR Chi-restraints excluded: chain A residue 1463 MET Chi-restraints excluded: chain A residue 1737 VAL Chi-restraints excluded: chain A residue 1836 VAL Chi-restraints excluded: chain A residue 1868 ILE Chi-restraints excluded: chain A residue 1928 LEU Chi-restraints excluded: chain A residue 1967 VAL Chi-restraints excluded: chain A residue 1992 THR Chi-restraints excluded: chain A residue 2096 GLN Chi-restraints excluded: chain A residue 2169 VAL Chi-restraints excluded: chain A residue 2281 VAL Chi-restraints excluded: chain A residue 2382 GLU Chi-restraints excluded: chain A residue 2417 VAL Chi-restraints excluded: chain A residue 2424 MET Chi-restraints excluded: chain A residue 3051 VAL Chi-restraints excluded: chain A residue 3107 MET Chi-restraints excluded: chain A residue 3109 GLU Chi-restraints excluded: chain A residue 3198 LEU Chi-restraints excluded: chain A residue 3347 VAL Chi-restraints excluded: chain A residue 3366 LEU Chi-restraints excluded: chain A residue 3394 LEU Chi-restraints excluded: chain A residue 3398 GLU Chi-restraints excluded: chain A residue 3406 LEU Chi-restraints excluded: chain A residue 3438 MET Chi-restraints excluded: chain A residue 3512 VAL Chi-restraints excluded: chain A residue 3530 ASP Chi-restraints excluded: chain A residue 3545 ASP Chi-restraints excluded: chain A residue 3657 SER Chi-restraints excluded: chain A residue 3936 PHE Chi-restraints excluded: chain A residue 4042 MET Chi-restraints excluded: chain A residue 4542 LEU Chi-restraints excluded: chain A residue 4887 VAL Chi-restraints excluded: chain A residue 4951 ASP Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 668 MET Chi-restraints excluded: chain B residue 812 CYS Chi-restraints excluded: chain B residue 912 HIS Chi-restraints excluded: chain B residue 930 LEU Chi-restraints excluded: chain B residue 1041 CYS Chi-restraints excluded: chain B residue 1171 MET Chi-restraints excluded: chain B residue 1183 ILE Chi-restraints excluded: chain B residue 1190 LEU Chi-restraints excluded: chain B residue 1435 TYR Chi-restraints excluded: chain B residue 1463 MET Chi-restraints excluded: chain B residue 1737 VAL Chi-restraints excluded: chain B residue 1836 VAL Chi-restraints excluded: chain B residue 1967 VAL Chi-restraints excluded: chain B residue 2096 GLN Chi-restraints excluded: chain B residue 2169 VAL Chi-restraints excluded: chain B residue 2281 VAL Chi-restraints excluded: chain B residue 2417 VAL Chi-restraints excluded: chain B residue 2424 MET Chi-restraints excluded: chain B residue 3109 GLU Chi-restraints excluded: chain B residue 3157 VAL Chi-restraints excluded: chain B residue 3308 VAL Chi-restraints excluded: chain B residue 3394 LEU Chi-restraints excluded: chain B residue 3398 GLU Chi-restraints excluded: chain B residue 3406 LEU Chi-restraints excluded: chain B residue 3471 LEU Chi-restraints excluded: chain B residue 3512 VAL Chi-restraints excluded: chain B residue 3530 ASP Chi-restraints excluded: chain B residue 3545 ASP Chi-restraints excluded: chain B residue 3657 SER Chi-restraints excluded: chain B residue 3861 MET Chi-restraints excluded: chain B residue 4042 MET Chi-restraints excluded: chain B residue 4542 LEU Chi-restraints excluded: chain B residue 4887 VAL Chi-restraints excluded: chain B residue 4951 ASP Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 579 ILE Chi-restraints excluded: chain C residue 812 CYS Chi-restraints excluded: chain C residue 912 HIS Chi-restraints excluded: chain C residue 930 LEU Chi-restraints excluded: chain C residue 1041 CYS Chi-restraints excluded: chain C residue 1171 MET Chi-restraints excluded: chain C residue 1190 LEU Chi-restraints excluded: chain C residue 1435 TYR Chi-restraints excluded: chain C residue 1737 VAL Chi-restraints excluded: chain C residue 1836 VAL Chi-restraints excluded: chain C residue 1928 LEU Chi-restraints excluded: chain C residue 1967 VAL Chi-restraints excluded: chain C residue 2169 VAL Chi-restraints excluded: chain C residue 2417 VAL Chi-restraints excluded: chain C residue 2424 MET Chi-restraints excluded: chain C residue 2528 LEU Chi-restraints excluded: chain C residue 2743 THR Chi-restraints excluded: chain C residue 3109 GLU Chi-restraints excluded: chain C residue 3157 VAL Chi-restraints excluded: chain C residue 3308 VAL Chi-restraints excluded: chain C residue 3366 LEU Chi-restraints excluded: chain C residue 3394 LEU Chi-restraints excluded: chain C residue 3398 GLU Chi-restraints excluded: chain C residue 3406 LEU Chi-restraints excluded: chain C residue 3438 MET Chi-restraints excluded: chain C residue 3471 LEU Chi-restraints excluded: chain C residue 3512 VAL Chi-restraints excluded: chain C residue 3530 ASP Chi-restraints excluded: chain C residue 3545 ASP Chi-restraints excluded: chain C residue 3657 SER Chi-restraints excluded: chain C residue 3861 MET Chi-restraints excluded: chain C residue 4042 MET Chi-restraints excluded: chain C residue 4542 LEU Chi-restraints excluded: chain C residue 4887 VAL Chi-restraints excluded: chain C residue 4951 ASP Chi-restraints excluded: chain K residue 16 PHE Chi-restraints excluded: chain K residue 32 LYS Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain K residue 55 VAL Chi-restraints excluded: chain K residue 67 ASP Chi-restraints excluded: chain K residue 89 PHE Chi-restraints excluded: chain L residue 5 LEU Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain M residue 16 PHE Chi-restraints excluded: chain M residue 32 LYS Chi-restraints excluded: chain M residue 37 LEU Chi-restraints excluded: chain M residue 55 VAL Chi-restraints excluded: chain M residue 67 ASP Chi-restraints excluded: chain M residue 89 PHE Chi-restraints excluded: chain O residue 16 PHE Chi-restraints excluded: chain O residue 32 LYS Chi-restraints excluded: chain O residue 37 LEU Chi-restraints excluded: chain O residue 55 VAL Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain O residue 89 PHE Chi-restraints excluded: chain P residue 5 LEU Chi-restraints excluded: chain P residue 37 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1860 random chunks: chunk 1735 optimal weight: 0.6980 chunk 202 optimal weight: 5.9990 chunk 1025 optimal weight: 50.0000 chunk 1314 optimal weight: 5.9990 chunk 1018 optimal weight: 0.9990 chunk 1514 optimal weight: 7.9990 chunk 1004 optimal weight: 10.0000 chunk 1792 optimal weight: 6.9990 chunk 1121 optimal weight: 2.9990 chunk 1092 optimal weight: 0.0470 chunk 827 optimal weight: 4.9990 overall best weight: 1.9484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 640 ASN D 880 HIS D2128 GLN D2647 ASN ** D4751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 ASN A2096 GLN A2128 GLN ** A4751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 640 ASN B2096 GLN B2128 GLN B2647 ASN B3181 ASN ** B4751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 640 ASN C 880 HIS C2096 GLN C2128 GLN C2647 ASN C3181 ASN ** C4751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 17 HIS ** K 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 17 HIS ** M 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 17 HIS ** O 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 152600 Z= 0.201 Angle : 0.558 21.044 206604 Z= 0.279 Chirality : 0.039 0.339 22672 Planarity : 0.004 0.064 26800 Dihedral : 6.475 85.617 20896 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.63 % Favored : 97.35 % Rotamer: Outliers : 1.45 % Allowed : 11.19 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % 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: 1.77 (0.06), residues: 18552 helix: 2.18 (0.05), residues: 9932 sheet: -0.07 (0.13), residues: 1708 loop : 0.08 (0.08), residues: 6912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP N 91 HIS 0.008 0.001 HIS K 19 PHE 0.033 0.001 PHE A2974 TYR 0.037 0.001 TYR A2883 ARG 0.005 0.000 ARG E 14 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 37104 Ramachandran restraints generated. 18552 Oldfield, 0 Emsley, 18552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 37104 Ramachandran restraints generated. 18552 Oldfield, 0 Emsley, 18552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1331 residues out of total 16268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 235 poor density : 1096 time to evaluate : 12.640 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: E 4 GLN cc_start: 0.8165 (mp10) cc_final: 0.7907 (mp10) REVERT: E 6 GLU cc_start: 0.7789 (mp0) cc_final: 0.7566 (mp0) REVERT: E 54 GLN cc_start: 0.9088 (mp10) cc_final: 0.8620 (mp10) REVERT: E 55 GLU cc_start: 0.8740 (mt-10) cc_final: 0.8345 (mt-10) REVERT: I 5 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8486 (mm) REVERT: I 14 ASN cc_start: 0.9280 (m110) cc_final: 0.9002 (p0) REVERT: I 16 PHE cc_start: 0.8625 (OUTLIER) cc_final: 0.7507 (p90) REVERT: I 32 LYS cc_start: 0.9198 (OUTLIER) cc_final: 0.8846 (mmmt) REVERT: J 42 LEU cc_start: 0.8725 (tp) cc_final: 0.8419 (tt) REVERT: J 75 TYR cc_start: 0.6679 (p90) cc_final: 0.6342 (p90) REVERT: F 4 GLN cc_start: 0.7991 (mp10) cc_final: 0.7759 (mp10) REVERT: F 45 LYS cc_start: 0.8791 (ttpt) cc_final: 0.8444 (ttpp) REVERT: G 45 LYS cc_start: 0.8752 (ttpt) cc_final: 0.8423 (ttpp) REVERT: G 53 LYS cc_start: 0.9074 (mmtp) cc_final: 0.8834 (mmtp) REVERT: H 45 LYS cc_start: 0.8782 (ttpt) cc_final: 0.8464 (ttpp) REVERT: H 53 LYS cc_start: 0.9074 (mmtp) cc_final: 0.8832 (mmtp) REVERT: D 117 MET cc_start: 0.9406 (mtm) cc_final: 0.9120 (mtp) REVERT: D 197 MET cc_start: 0.8011 (mpp) cc_final: 0.7447 (mpp) REVERT: D 615 VAL cc_start: 0.8588 (OUTLIER) cc_final: 0.8300 (m) REVERT: D 666 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7585 (mt-10) REVERT: D 905 HIS cc_start: 0.6985 (t70) cc_final: 0.6491 (t70) REVERT: D 1041 CYS cc_start: 0.9388 (OUTLIER) cc_final: 0.9104 (p) REVERT: D 1574 MET cc_start: 0.8831 (mmt) cc_final: 0.8460 (mmt) REVERT: D 1930 MET cc_start: 0.9056 (ttm) cc_final: 0.8815 (mtp) REVERT: D 1987 MET cc_start: 0.5283 (pmm) cc_final: 0.4641 (tmm) REVERT: D 1997 ARG cc_start: 0.9153 (tmt-80) cc_final: 0.8765 (tpm170) REVERT: D 2171 MET cc_start: 0.8099 (mmm) cc_final: 0.7666 (mmm) REVERT: D 2424 MET cc_start: 0.8646 (OUTLIER) cc_final: 0.8267 (mpp) REVERT: D 2945 MET cc_start: 0.8431 (ptt) cc_final: 0.8138 (ptt) REVERT: D 2968 MET cc_start: 0.9391 (mmm) cc_final: 0.9032 (mmm) REVERT: D 3211 LEU cc_start: 0.9339 (mm) cc_final: 0.8859 (tp) REVERT: D 3240 MET cc_start: 0.7452 (tpp) cc_final: 0.7110 (tpp) REVERT: D 3468 MET cc_start: 0.8005 (tpp) cc_final: 0.7464 (tpp) REVERT: D 3518 MET cc_start: 0.9126 (tpt) cc_final: 0.8822 (tpp) REVERT: D 3545 ASP cc_start: 0.8425 (OUTLIER) cc_final: 0.7847 (p0) REVERT: D 3574 MET cc_start: 0.8963 (tpt) cc_final: 0.8385 (tpp) REVERT: A 197 MET cc_start: 0.7962 (mpp) cc_final: 0.7444 (mpp) REVERT: A 212 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.8043 (tp30) REVERT: A 615 VAL cc_start: 0.8608 (OUTLIER) cc_final: 0.8323 (m) REVERT: A 666 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7653 (mt-10) REVERT: A 905 HIS cc_start: 0.6706 (t70) cc_final: 0.6026 (t70) REVERT: A 1041 CYS cc_start: 0.9379 (OUTLIER) cc_final: 0.8991 (p) REVERT: A 1101 MET cc_start: 0.8817 (ttm) cc_final: 0.8613 (mtp) REVERT: A 1930 MET cc_start: 0.9032 (ttm) cc_final: 0.8773 (mtp) REVERT: A 1997 ARG cc_start: 0.9166 (tmt-80) cc_final: 0.8751 (tpm170) REVERT: A 2171 MET cc_start: 0.8076 (mmm) cc_final: 0.7700 (mmm) REVERT: A 2382 GLU cc_start: 0.9005 (OUTLIER) cc_final: 0.8573 (mp0) REVERT: A 2619 MET cc_start: 0.9328 (mmt) cc_final: 0.8954 (mmt) REVERT: A 2945 MET cc_start: 0.8168 (ptt) cc_final: 0.7876 (ptt) REVERT: A 3039 MET cc_start: 0.9669 (mtm) cc_final: 0.9388 (mtm) REVERT: A 3107 MET cc_start: 0.9494 (OUTLIER) cc_final: 0.9294 (ttp) REVERT: A 3211 LEU cc_start: 0.9331 (mm) cc_final: 0.8874 (tp) REVERT: A 3518 MET cc_start: 0.9290 (mmm) cc_final: 0.9071 (mmm) REVERT: A 3545 ASP cc_start: 0.8197 (OUTLIER) cc_final: 0.7738 (p0) REVERT: A 3574 MET cc_start: 0.8883 (tpt) cc_final: 0.8312 (tpp) REVERT: A 3936 PHE cc_start: 0.8994 (OUTLIER) cc_final: 0.8486 (t80) REVERT: A 4837 MET cc_start: 0.8805 (mmm) cc_final: 0.8581 (mmm) REVERT: B 117 MET cc_start: 0.9393 (mtm) cc_final: 0.9092 (mtp) REVERT: B 197 MET cc_start: 0.8013 (mpp) cc_final: 0.7446 (mpp) REVERT: B 615 VAL cc_start: 0.8597 (OUTLIER) cc_final: 0.8309 (m) REVERT: B 666 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7592 (mt-10) REVERT: B 905 HIS cc_start: 0.6987 (t70) cc_final: 0.6547 (t70) REVERT: B 1041 CYS cc_start: 0.9381 (OUTLIER) cc_final: 0.9094 (p) REVERT: B 1574 MET cc_start: 0.8839 (mmt) cc_final: 0.8468 (mmt) REVERT: B 1930 MET cc_start: 0.9045 (ttm) cc_final: 0.8792 (mtp) REVERT: B 1997 ARG cc_start: 0.9150 (tmt-80) cc_final: 0.8749 (tpm170) REVERT: B 2171 MET cc_start: 0.8085 (mmm) cc_final: 0.7638 (mmm) REVERT: B 2251 MET cc_start: 0.9487 (mmm) cc_final: 0.9263 (mmm) REVERT: B 2424 MET cc_start: 0.8642 (OUTLIER) cc_final: 0.8269 (mpp) REVERT: B 2531 MET cc_start: 0.8960 (mtm) cc_final: 0.8442 (mtm) REVERT: B 2968 MET cc_start: 0.9388 (mmm) cc_final: 0.9031 (mmm) REVERT: B 3211 LEU cc_start: 0.9345 (mm) cc_final: 0.8862 (tp) REVERT: B 3240 MET cc_start: 0.7451 (tpp) cc_final: 0.7125 (tpp) REVERT: B 3468 MET cc_start: 0.8022 (tpp) cc_final: 0.7481 (tpp) REVERT: B 3518 MET cc_start: 0.9132 (tpt) cc_final: 0.8839 (tpp) REVERT: B 3545 ASP cc_start: 0.8476 (OUTLIER) cc_final: 0.7885 (p0) REVERT: B 3574 MET cc_start: 0.8964 (tpt) cc_final: 0.8393 (tpp) REVERT: B 4837 MET cc_start: 0.8814 (mmm) cc_final: 0.8587 (mmm) REVERT: C 117 MET cc_start: 0.9397 (mtm) cc_final: 0.9092 (mtp) REVERT: C 197 MET cc_start: 0.8005 (mpp) cc_final: 0.7443 (mpp) REVERT: C 615 VAL cc_start: 0.8597 (OUTLIER) cc_final: 0.8309 (m) REVERT: C 666 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7590 (mt-10) REVERT: C 905 HIS cc_start: 0.6980 (t70) cc_final: 0.6490 (t70) REVERT: C 1041 CYS cc_start: 0.9386 (OUTLIER) cc_final: 0.9100 (p) REVERT: C 1574 MET cc_start: 0.8835 (mmt) cc_final: 0.8466 (mmt) REVERT: C 1930 MET cc_start: 0.9047 (ttm) cc_final: 0.8777 (mtp) REVERT: C 1987 MET cc_start: 0.5308 (pmm) cc_final: 0.4680 (tmm) REVERT: C 1997 ARG cc_start: 0.9148 (tmt-80) cc_final: 0.8747 (tpm170) REVERT: C 2171 MET cc_start: 0.8098 (mmm) cc_final: 0.7685 (mmm) REVERT: C 2179 MET cc_start: 0.8558 (tpp) cc_final: 0.8239 (tpp) REVERT: C 2424 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.8270 (mpp) REVERT: C 2531 MET cc_start: 0.8959 (mtm) cc_final: 0.8561 (mtm) REVERT: C 2945 MET cc_start: 0.8246 (ptt) cc_final: 0.7957 (ptt) REVERT: C 2968 MET cc_start: 0.9386 (mmm) cc_final: 0.9030 (mmm) REVERT: C 3211 LEU cc_start: 0.9345 (mm) cc_final: 0.8849 (tp) REVERT: C 3240 MET cc_start: 0.7502 (tpp) cc_final: 0.7135 (tpp) REVERT: C 3468 MET cc_start: 0.8007 (tpp) cc_final: 0.7443 (tpp) REVERT: C 3518 MET cc_start: 0.9139 (tpt) cc_final: 0.8825 (tpp) REVERT: C 3545 ASP cc_start: 0.8442 (OUTLIER) cc_final: 0.7877 (p0) REVERT: C 3574 MET cc_start: 0.8959 (tpt) cc_final: 0.8379 (tpp) REVERT: C 4837 MET cc_start: 0.8814 (mmm) cc_final: 0.8589 (mmm) REVERT: K 16 PHE cc_start: 0.8530 (OUTLIER) cc_final: 0.7351 (p90) REVERT: K 19 HIS cc_start: 0.6501 (OUTLIER) cc_final: 0.6186 (t-170) REVERT: K 32 LYS cc_start: 0.9135 (pttm) cc_final: 0.8855 (mmmt) REVERT: L 59 MET cc_start: 0.7298 (ppp) cc_final: 0.6771 (ppp) REVERT: L 75 TYR cc_start: 0.6681 (p90) cc_final: 0.6269 (p90) REVERT: N 12 LEU cc_start: 0.8230 (tp) cc_final: 0.7996 (tt) REVERT: N 75 TYR cc_start: 0.6344 (p90) cc_final: 0.5962 (p90) REVERT: M 5 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8483 (mm) REVERT: M 16 PHE cc_start: 0.8510 (OUTLIER) cc_final: 0.7303 (p90) REVERT: M 19 HIS cc_start: 0.6475 (OUTLIER) cc_final: 0.6201 (t-170) REVERT: M 32 LYS cc_start: 0.9138 (pttm) cc_final: 0.8849 (mmmt) REVERT: O 16 PHE cc_start: 0.8538 (OUTLIER) cc_final: 0.7371 (p90) REVERT: O 19 HIS cc_start: 0.6510 (OUTLIER) cc_final: 0.6198 (t-170) REVERT: O 32 LYS cc_start: 0.9134 (pttm) cc_final: 0.8855 (mmmt) REVERT: P 12 LEU cc_start: 0.8249 (tp) cc_final: 0.7785 (mt) REVERT: P 59 MET cc_start: 0.7301 (ppp) cc_final: 0.7014 (ppp) REVERT: P 75 TYR cc_start: 0.6674 (p90) cc_final: 0.6226 (p90) outliers start: 235 outliers final: 157 residues processed: 1255 average time/residue: 1.2441 time to fit residues: 2817.1658 Evaluate side-chains 1219 residues out of total 16268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 1033 time to evaluate : 12.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 60 TRP Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain I residue 16 PHE Chi-restraints excluded: chain I residue 32 LYS Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 67 ASP Chi-restraints excluded: chain I residue 89 PHE Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 37 LEU Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 33 ASP Chi-restraints excluded: chain F residue 39 SER Chi-restraints excluded: chain F residue 60 TRP Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 33 ASP Chi-restraints excluded: chain G residue 39 SER Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 60 TRP Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 60 TRP Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 579 ILE Chi-restraints excluded: chain D residue 615 VAL Chi-restraints excluded: chain D residue 812 CYS Chi-restraints excluded: chain D residue 912 HIS Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain D residue 1041 CYS Chi-restraints excluded: chain D residue 1171 MET Chi-restraints excluded: chain D residue 1190 LEU Chi-restraints excluded: chain D residue 1435 TYR Chi-restraints excluded: chain D residue 1737 VAL Chi-restraints excluded: chain D residue 1967 VAL Chi-restraints excluded: chain D residue 2204 MET Chi-restraints excluded: chain D residue 2417 VAL Chi-restraints excluded: chain D residue 2424 MET Chi-restraints excluded: chain D residue 2743 THR Chi-restraints excluded: chain D residue 3109 GLU Chi-restraints excluded: chain D residue 3308 VAL Chi-restraints excluded: chain D residue 3379 GLN Chi-restraints excluded: chain D residue 3394 LEU Chi-restraints excluded: chain D residue 3398 GLU Chi-restraints excluded: chain D residue 3471 LEU Chi-restraints excluded: chain D residue 3512 VAL Chi-restraints excluded: chain D residue 3530 ASP Chi-restraints excluded: chain D residue 3545 ASP Chi-restraints excluded: chain D residue 3657 SER Chi-restraints excluded: chain D residue 3861 MET Chi-restraints excluded: chain D residue 4542 LEU Chi-restraints excluded: chain D residue 4887 VAL Chi-restraints excluded: chain D residue 4951 ASP Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 812 CYS Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 1041 CYS Chi-restraints excluded: chain A residue 1171 MET Chi-restraints excluded: chain A residue 1190 LEU Chi-restraints excluded: chain A residue 1251 LEU Chi-restraints excluded: chain A residue 1429 LEU Chi-restraints excluded: chain A residue 1435 TYR Chi-restraints excluded: chain A residue 1737 VAL Chi-restraints excluded: chain A residue 1868 ILE Chi-restraints excluded: chain A residue 1967 VAL Chi-restraints excluded: chain A residue 1992 THR Chi-restraints excluded: chain A residue 2096 GLN Chi-restraints excluded: chain A residue 2382 GLU Chi-restraints excluded: chain A residue 2417 VAL Chi-restraints excluded: chain A residue 2424 MET Chi-restraints excluded: chain A residue 2528 LEU Chi-restraints excluded: chain A residue 2743 THR Chi-restraints excluded: chain A residue 2810 ILE Chi-restraints excluded: chain A residue 3051 VAL Chi-restraints excluded: chain A residue 3107 MET Chi-restraints excluded: chain A residue 3109 GLU Chi-restraints excluded: chain A residue 3366 LEU Chi-restraints excluded: chain A residue 3394 LEU Chi-restraints excluded: chain A residue 3398 GLU Chi-restraints excluded: chain A residue 3438 MET Chi-restraints excluded: chain A residue 3512 VAL Chi-restraints excluded: chain A residue 3530 ASP Chi-restraints excluded: chain A residue 3545 ASP Chi-restraints excluded: chain A residue 3657 SER Chi-restraints excluded: chain A residue 3936 PHE Chi-restraints excluded: chain A residue 4542 LEU Chi-restraints excluded: chain A residue 4887 VAL Chi-restraints excluded: chain A residue 4951 ASP Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 812 CYS Chi-restraints excluded: chain B residue 912 HIS Chi-restraints excluded: chain B residue 930 LEU Chi-restraints excluded: chain B residue 1041 CYS Chi-restraints excluded: chain B residue 1171 MET Chi-restraints excluded: chain B residue 1190 LEU Chi-restraints excluded: chain B residue 1435 TYR Chi-restraints excluded: chain B residue 1463 MET Chi-restraints excluded: chain B residue 1737 VAL Chi-restraints excluded: chain B residue 1836 VAL Chi-restraints excluded: chain B residue 1967 VAL Chi-restraints excluded: chain B residue 2096 GLN Chi-restraints excluded: chain B residue 2281 VAL Chi-restraints excluded: chain B residue 2417 VAL Chi-restraints excluded: chain B residue 2424 MET Chi-restraints excluded: chain B residue 2743 THR Chi-restraints excluded: chain B residue 3109 GLU Chi-restraints excluded: chain B residue 3308 VAL Chi-restraints excluded: chain B residue 3394 LEU Chi-restraints excluded: chain B residue 3398 GLU Chi-restraints excluded: chain B residue 3406 LEU Chi-restraints excluded: chain B residue 3471 LEU Chi-restraints excluded: chain B residue 3512 VAL Chi-restraints excluded: chain B residue 3530 ASP Chi-restraints excluded: chain B residue 3545 ASP Chi-restraints excluded: chain B residue 3657 SER Chi-restraints excluded: chain B residue 3861 MET Chi-restraints excluded: chain B residue 4042 MET Chi-restraints excluded: chain B residue 4091 ILE Chi-restraints excluded: chain B residue 4542 LEU Chi-restraints excluded: chain B residue 4887 VAL Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 579 ILE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 912 HIS Chi-restraints excluded: chain C residue 930 LEU Chi-restraints excluded: chain C residue 1041 CYS Chi-restraints excluded: chain C residue 1171 MET Chi-restraints excluded: chain C residue 1190 LEU Chi-restraints excluded: chain C residue 1435 TYR Chi-restraints excluded: chain C residue 1737 VAL Chi-restraints excluded: chain C residue 1928 LEU Chi-restraints excluded: chain C residue 1967 VAL Chi-restraints excluded: chain C residue 2096 GLN Chi-restraints excluded: chain C residue 2204 MET Chi-restraints excluded: chain C residue 2417 VAL Chi-restraints excluded: chain C residue 2424 MET Chi-restraints excluded: chain C residue 2528 LEU Chi-restraints excluded: chain C residue 2743 THR Chi-restraints excluded: chain C residue 3109 GLU Chi-restraints excluded: chain C residue 3308 VAL Chi-restraints excluded: chain C residue 3366 LEU Chi-restraints excluded: chain C residue 3379 GLN Chi-restraints excluded: chain C residue 3394 LEU Chi-restraints excluded: chain C residue 3398 GLU Chi-restraints excluded: chain C residue 3438 MET Chi-restraints excluded: chain C residue 3471 LEU Chi-restraints excluded: chain C residue 3512 VAL Chi-restraints excluded: chain C residue 3530 ASP Chi-restraints excluded: chain C residue 3545 ASP Chi-restraints excluded: chain C residue 3657 SER Chi-restraints excluded: chain C residue 3861 MET Chi-restraints excluded: chain C residue 4091 ILE Chi-restraints excluded: chain C residue 4542 LEU Chi-restraints excluded: chain C residue 4887 VAL Chi-restraints excluded: chain K residue 16 PHE Chi-restraints excluded: chain K residue 19 HIS Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain K residue 55 VAL Chi-restraints excluded: chain K residue 89 PHE Chi-restraints excluded: chain L residue 5 LEU Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain M residue 16 PHE Chi-restraints excluded: chain M residue 19 HIS Chi-restraints excluded: chain M residue 37 LEU Chi-restraints excluded: chain M residue 55 VAL Chi-restraints excluded: chain M residue 89 PHE Chi-restraints excluded: chain O residue 16 PHE Chi-restraints excluded: chain O residue 19 HIS Chi-restraints excluded: chain O residue 37 LEU Chi-restraints excluded: chain O residue 55 VAL Chi-restraints excluded: chain O residue 89 PHE Chi-restraints excluded: chain P residue 5 LEU Chi-restraints excluded: chain P residue 37 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1860 random chunks: chunk 1109 optimal weight: 7.9990 chunk 715 optimal weight: 0.7980 chunk 1070 optimal weight: 10.0000 chunk 540 optimal weight: 7.9990 chunk 352 optimal weight: 8.9990 chunk 347 optimal weight: 4.9990 chunk 1139 optimal weight: 1.9990 chunk 1221 optimal weight: 8.9990 chunk 886 optimal weight: 10.0000 chunk 167 optimal weight: 8.9990 chunk 1409 optimal weight: 0.0670 overall best weight: 3.1724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 640 ASN D2128 GLN ** D4751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 ASN A1012 GLN A1953 GLN A2128 GLN ** A4751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 640 ASN B2128 GLN ** B4751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 640 ASN C2128 GLN ** C4751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 17 HIS ** K 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 17 HIS ** M 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 17 HIS ** O 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 152600 Z= 0.274 Angle : 0.582 16.267 206604 Z= 0.290 Chirality : 0.039 0.320 22672 Planarity : 0.004 0.063 26800 Dihedral : 6.432 84.780 20896 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.81 % Favored : 97.18 % Rotamer: Outliers : 1.48 % Allowed : 11.68 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % 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: 1.74 (0.06), residues: 18552 helix: 2.15 (0.05), residues: 9940 sheet: -0.06 (0.13), residues: 1708 loop : 0.08 (0.08), residues: 6904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP N 91 HIS 0.005 0.001 HIS A 839 PHE 0.046 0.001 PHE D3637 TYR 0.035 0.001 TYR A2883 ARG 0.005 0.000 ARG E 14 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 37104 Ramachandran restraints generated. 18552 Oldfield, 0 Emsley, 18552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 37104 Ramachandran restraints generated. 18552 Oldfield, 0 Emsley, 18552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1295 residues out of total 16268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 241 poor density : 1054 time to evaluate : 12.716 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: E 6 GLU cc_start: 0.7780 (mp0) cc_final: 0.7532 (mp0) REVERT: E 54 GLN cc_start: 0.9094 (mp10) cc_final: 0.8608 (mp10) REVERT: I 5 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8509 (mm) REVERT: I 14 ASN cc_start: 0.9259 (m110) cc_final: 0.9023 (p0) REVERT: I 16 PHE cc_start: 0.8549 (OUTLIER) cc_final: 0.7403 (p90) REVERT: I 32 LYS cc_start: 0.9194 (OUTLIER) cc_final: 0.8836 (mmmt) REVERT: J 42 LEU cc_start: 0.8745 (tp) cc_final: 0.8434 (tt) REVERT: J 59 MET cc_start: 0.7105 (OUTLIER) cc_final: 0.6794 (ppp) REVERT: J 75 TYR cc_start: 0.6419 (p90) cc_final: 0.6018 (p90) REVERT: F 4 GLN cc_start: 0.7990 (mp10) cc_final: 0.7763 (mp10) REVERT: F 45 LYS cc_start: 0.8805 (ttpt) cc_final: 0.8459 (ttpp) REVERT: G 45 LYS cc_start: 0.8764 (ttpt) cc_final: 0.8440 (ttpp) REVERT: G 53 LYS cc_start: 0.9082 (mmtp) cc_final: 0.8832 (mmtp) REVERT: H 45 LYS cc_start: 0.8783 (ttpt) cc_final: 0.8466 (ttpp) REVERT: H 53 LYS cc_start: 0.9079 (mmtp) cc_final: 0.8832 (mmtp) REVERT: D 117 MET cc_start: 0.9421 (mtm) cc_final: 0.9133 (mtp) REVERT: D 197 MET cc_start: 0.8005 (mpp) cc_final: 0.7407 (mpp) REVERT: D 615 VAL cc_start: 0.8617 (OUTLIER) cc_final: 0.8317 (m) REVERT: D 666 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7597 (mt-10) REVERT: D 905 HIS cc_start: 0.7023 (t70) cc_final: 0.6501 (t70) REVERT: D 1041 CYS cc_start: 0.9371 (OUTLIER) cc_final: 0.9103 (p) REVERT: D 1574 MET cc_start: 0.8829 (mmt) cc_final: 0.8427 (mmt) REVERT: D 1816 MET cc_start: 0.8828 (mmm) cc_final: 0.8434 (mtt) REVERT: D 1930 MET cc_start: 0.9076 (ttm) cc_final: 0.8826 (mtp) REVERT: D 1997 ARG cc_start: 0.9170 (tmt-80) cc_final: 0.8766 (tpm170) REVERT: D 2171 MET cc_start: 0.8180 (mmm) cc_final: 0.7759 (mmm) REVERT: D 2179 MET cc_start: 0.8586 (OUTLIER) cc_final: 0.8256 (tpp) REVERT: D 2251 MET cc_start: 0.9488 (mmm) cc_final: 0.9262 (mmm) REVERT: D 2382 GLU cc_start: 0.8913 (mt-10) cc_final: 0.8711 (mt-10) REVERT: D 2424 MET cc_start: 0.8663 (OUTLIER) cc_final: 0.8302 (mpp) REVERT: D 2945 MET cc_start: 0.8394 (ptt) cc_final: 0.8170 (ptt) REVERT: D 2968 MET cc_start: 0.9384 (mmm) cc_final: 0.9020 (mmm) REVERT: D 3211 LEU cc_start: 0.9344 (mm) cc_final: 0.8864 (tp) REVERT: D 3240 MET cc_start: 0.7536 (tpp) cc_final: 0.7169 (tpp) REVERT: D 3468 MET cc_start: 0.8023 (tpp) cc_final: 0.7472 (tpp) REVERT: D 3518 MET cc_start: 0.9177 (tpt) cc_final: 0.8812 (tpp) REVERT: D 3545 ASP cc_start: 0.8471 (OUTLIER) cc_final: 0.7830 (p0) REVERT: D 3574 MET cc_start: 0.8969 (tpt) cc_final: 0.8397 (tpp) REVERT: D 4837 MET cc_start: 0.8820 (mmm) cc_final: 0.8589 (mmm) REVERT: A 197 MET cc_start: 0.7963 (mpp) cc_final: 0.7410 (mpp) REVERT: A 212 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.8050 (tp30) REVERT: A 615 VAL cc_start: 0.8642 (OUTLIER) cc_final: 0.8348 (m) REVERT: A 666 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7682 (mt-10) REVERT: A 905 HIS cc_start: 0.6752 (t70) cc_final: 0.6048 (t70) REVERT: A 1041 CYS cc_start: 0.9385 (OUTLIER) cc_final: 0.9010 (p) REVERT: A 1816 MET cc_start: 0.8835 (mmm) cc_final: 0.8445 (mtt) REVERT: A 1930 MET cc_start: 0.9069 (ttm) cc_final: 0.8813 (mtp) REVERT: A 1997 ARG cc_start: 0.9176 (tmt-80) cc_final: 0.8742 (tpm170) REVERT: A 2171 MET cc_start: 0.8103 (mmm) cc_final: 0.7724 (mmm) REVERT: A 2382 GLU cc_start: 0.9021 (OUTLIER) cc_final: 0.8578 (mp0) REVERT: A 2945 MET cc_start: 0.8186 (ptt) cc_final: 0.7860 (ptt) REVERT: A 3039 MET cc_start: 0.9678 (mtm) cc_final: 0.9390 (mtm) REVERT: A 3211 LEU cc_start: 0.9321 (mm) cc_final: 0.8865 (tp) REVERT: A 3240 MET cc_start: 0.7722 (tpp) cc_final: 0.7257 (ppp) REVERT: A 3273 ILE cc_start: 0.9475 (mp) cc_final: 0.9271 (mp) REVERT: A 3518 MET cc_start: 0.9309 (mmm) cc_final: 0.9083 (mmm) REVERT: A 3545 ASP cc_start: 0.8181 (OUTLIER) cc_final: 0.7757 (p0) REVERT: A 3574 MET cc_start: 0.8901 (tpt) cc_final: 0.8299 (tpp) REVERT: A 3936 PHE cc_start: 0.9005 (OUTLIER) cc_final: 0.8619 (t80) REVERT: A 4872 MET cc_start: 0.9132 (mmt) cc_final: 0.8537 (mmp) REVERT: B 117 MET cc_start: 0.9406 (mtm) cc_final: 0.9099 (mtp) REVERT: B 197 MET cc_start: 0.8009 (mpp) cc_final: 0.7412 (mpp) REVERT: B 615 VAL cc_start: 0.8638 (OUTLIER) cc_final: 0.8340 (m) REVERT: B 666 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7627 (mt-10) REVERT: B 905 HIS cc_start: 0.7029 (t70) cc_final: 0.6584 (t70) REVERT: B 1041 CYS cc_start: 0.9370 (OUTLIER) cc_final: 0.9100 (p) REVERT: B 1574 MET cc_start: 0.8836 (mmt) cc_final: 0.8433 (mmt) REVERT: B 1816 MET cc_start: 0.8829 (mmm) cc_final: 0.8425 (mtt) REVERT: B 1930 MET cc_start: 0.9082 (ttm) cc_final: 0.8836 (mtp) REVERT: B 1987 MET cc_start: 0.4820 (pmm) cc_final: 0.4282 (tmm) REVERT: B 1997 ARG cc_start: 0.9167 (tmt-80) cc_final: 0.8752 (tpm170) REVERT: B 2171 MET cc_start: 0.8197 (mmm) cc_final: 0.7787 (mmm) REVERT: B 2251 MET cc_start: 0.9493 (mmm) cc_final: 0.9270 (mmm) REVERT: B 2382 GLU cc_start: 0.8909 (mt-10) cc_final: 0.8708 (mt-10) REVERT: B 2424 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.8300 (mpp) REVERT: B 2531 MET cc_start: 0.8968 (mtm) cc_final: 0.8445 (mtm) REVERT: B 2945 MET cc_start: 0.8423 (ptt) cc_final: 0.8157 (ptt) REVERT: B 2968 MET cc_start: 0.9385 (mmm) cc_final: 0.9032 (mmm) REVERT: B 3211 LEU cc_start: 0.9353 (mm) cc_final: 0.8864 (tp) REVERT: B 3240 MET cc_start: 0.7534 (tpp) cc_final: 0.7178 (tpp) REVERT: B 3468 MET cc_start: 0.8032 (tpp) cc_final: 0.7483 (tpp) REVERT: B 3518 MET cc_start: 0.9178 (tpt) cc_final: 0.8820 (tpp) REVERT: B 3545 ASP cc_start: 0.8488 (OUTLIER) cc_final: 0.7826 (p0) REVERT: B 3574 MET cc_start: 0.8969 (tpt) cc_final: 0.8399 (tpp) REVERT: C 117 MET cc_start: 0.9411 (mtm) cc_final: 0.9120 (mtp) REVERT: C 197 MET cc_start: 0.8005 (mpp) cc_final: 0.7407 (mpp) REVERT: C 615 VAL cc_start: 0.8623 (OUTLIER) cc_final: 0.8323 (m) REVERT: C 666 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7620 (mt-10) REVERT: C 905 HIS cc_start: 0.7036 (t70) cc_final: 0.6524 (t70) REVERT: C 1041 CYS cc_start: 0.9368 (OUTLIER) cc_final: 0.9099 (p) REVERT: C 1574 MET cc_start: 0.8833 (mmt) cc_final: 0.8433 (mmt) REVERT: C 1816 MET cc_start: 0.8834 (mmm) cc_final: 0.8432 (mtt) REVERT: C 1930 MET cc_start: 0.9064 (ttm) cc_final: 0.8805 (mtp) REVERT: C 1997 ARG cc_start: 0.9163 (tmt-80) cc_final: 0.8750 (tpm170) REVERT: C 2171 MET cc_start: 0.8133 (mmm) cc_final: 0.7757 (mmm) REVERT: C 2179 MET cc_start: 0.8571 (tpp) cc_final: 0.8298 (tpp) REVERT: C 2251 MET cc_start: 0.9491 (mmm) cc_final: 0.9275 (mmm) REVERT: C 2424 MET cc_start: 0.8665 (OUTLIER) cc_final: 0.8308 (mpp) REVERT: C 2491 MET cc_start: 0.9167 (tpp) cc_final: 0.8963 (tpp) REVERT: C 2531 MET cc_start: 0.8958 (mtm) cc_final: 0.8581 (mtm) REVERT: C 2945 MET cc_start: 0.8251 (ptt) cc_final: 0.7926 (ptt) REVERT: C 2968 MET cc_start: 0.9381 (mmm) cc_final: 0.9031 (mmm) REVERT: C 3211 LEU cc_start: 0.9349 (mm) cc_final: 0.8877 (tp) REVERT: C 3240 MET cc_start: 0.7597 (tpp) cc_final: 0.7209 (tpp) REVERT: C 3468 MET cc_start: 0.8017 (tpp) cc_final: 0.7448 (tpp) REVERT: C 3518 MET cc_start: 0.9197 (tpt) cc_final: 0.8851 (tpp) REVERT: C 3545 ASP cc_start: 0.8473 (OUTLIER) cc_final: 0.7832 (p0) REVERT: C 3574 MET cc_start: 0.8968 (tpt) cc_final: 0.8392 (tpp) REVERT: K 16 PHE cc_start: 0.8571 (OUTLIER) cc_final: 0.7396 (p90) REVERT: K 19 HIS cc_start: 0.6527 (OUTLIER) cc_final: 0.6283 (t70) REVERT: K 32 LYS cc_start: 0.9142 (OUTLIER) cc_final: 0.8853 (mmmt) REVERT: L 12 LEU cc_start: 0.8266 (tp) cc_final: 0.7757 (mt) REVERT: L 59 MET cc_start: 0.7309 (ppp) cc_final: 0.6780 (ppp) REVERT: L 75 TYR cc_start: 0.6639 (p90) cc_final: 0.6266 (p90) REVERT: N 59 MET cc_start: 0.7210 (ppp) cc_final: 0.6881 (ppp) REVERT: N 75 TYR cc_start: 0.6569 (p90) cc_final: 0.6238 (p90) REVERT: M 5 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8493 (mm) REVERT: M 16 PHE cc_start: 0.8508 (OUTLIER) cc_final: 0.7301 (p90) REVERT: M 19 HIS cc_start: 0.6550 (OUTLIER) cc_final: 0.6176 (t-170) REVERT: M 32 LYS cc_start: 0.9146 (OUTLIER) cc_final: 0.8852 (mmmt) REVERT: O 16 PHE cc_start: 0.8568 (OUTLIER) cc_final: 0.7390 (p90) REVERT: O 19 HIS cc_start: 0.6553 (OUTLIER) cc_final: 0.6216 (t-170) REVERT: O 32 LYS cc_start: 0.9144 (OUTLIER) cc_final: 0.8852 (mmmt) REVERT: P 12 LEU cc_start: 0.8250 (tp) cc_final: 0.7761 (mt) REVERT: P 59 MET cc_start: 0.7250 (ppp) cc_final: 0.6945 (ppp) REVERT: P 75 TYR cc_start: 0.6627 (p90) cc_final: 0.6262 (p90) outliers start: 241 outliers final: 180 residues processed: 1214 average time/residue: 1.2416 time to fit residues: 2719.9502 Evaluate side-chains 1243 residues out of total 16268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 1030 time to evaluate : 11.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 33 ASP Chi-restraints excluded: chain E residue 60 TRP Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain I residue 16 PHE Chi-restraints excluded: chain I residue 19 HIS Chi-restraints excluded: chain I residue 32 LYS Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 67 ASP Chi-restraints excluded: chain I residue 75 TYR Chi-restraints excluded: chain I residue 89 PHE Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 37 LEU Chi-restraints excluded: chain J residue 59 MET Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 33 ASP Chi-restraints excluded: chain F residue 39 SER Chi-restraints excluded: chain F residue 60 TRP Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 33 ASP Chi-restraints excluded: chain G residue 39 SER Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 60 TRP Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 60 TRP Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 579 ILE Chi-restraints excluded: chain D residue 615 VAL Chi-restraints excluded: chain D residue 812 CYS Chi-restraints excluded: chain D residue 912 HIS Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain D residue 939 HIS Chi-restraints excluded: chain D residue 1041 CYS Chi-restraints excluded: chain D residue 1171 MET Chi-restraints excluded: chain D residue 1190 LEU Chi-restraints excluded: chain D residue 1435 TYR Chi-restraints excluded: chain D residue 1737 VAL Chi-restraints excluded: chain D residue 1836 VAL Chi-restraints excluded: chain D residue 1967 VAL Chi-restraints excluded: chain D residue 2179 MET Chi-restraints excluded: chain D residue 2204 MET Chi-restraints excluded: chain D residue 2315 LEU Chi-restraints excluded: chain D residue 2417 VAL Chi-restraints excluded: chain D residue 2424 MET Chi-restraints excluded: chain D residue 2743 THR Chi-restraints excluded: chain D residue 3055 VAL Chi-restraints excluded: chain D residue 3109 GLU Chi-restraints excluded: chain D residue 3308 VAL Chi-restraints excluded: chain D residue 3347 VAL Chi-restraints excluded: chain D residue 3379 GLN Chi-restraints excluded: chain D residue 3394 LEU Chi-restraints excluded: chain D residue 3398 GLU Chi-restraints excluded: chain D residue 3406 LEU Chi-restraints excluded: chain D residue 3438 MET Chi-restraints excluded: chain D residue 3471 LEU Chi-restraints excluded: chain D residue 3512 VAL Chi-restraints excluded: chain D residue 3530 ASP Chi-restraints excluded: chain D residue 3545 ASP Chi-restraints excluded: chain D residue 3657 SER Chi-restraints excluded: chain D residue 3861 MET Chi-restraints excluded: chain D residue 4042 MET Chi-restraints excluded: chain D residue 4542 LEU Chi-restraints excluded: chain D residue 4887 VAL Chi-restraints excluded: chain D residue 4951 ASP Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 812 CYS Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 939 HIS Chi-restraints excluded: chain A residue 1041 CYS Chi-restraints excluded: chain A residue 1171 MET Chi-restraints excluded: chain A residue 1190 LEU Chi-restraints excluded: chain A residue 1251 LEU Chi-restraints excluded: chain A residue 1429 LEU Chi-restraints excluded: chain A residue 1435 TYR Chi-restraints excluded: chain A residue 1737 VAL Chi-restraints excluded: chain A residue 1836 VAL Chi-restraints excluded: chain A residue 1868 ILE Chi-restraints excluded: chain A residue 1928 LEU Chi-restraints excluded: chain A residue 1967 VAL Chi-restraints excluded: chain A residue 1992 THR Chi-restraints excluded: chain A residue 2281 VAL Chi-restraints excluded: chain A residue 2382 GLU Chi-restraints excluded: chain A residue 2417 VAL Chi-restraints excluded: chain A residue 2424 MET Chi-restraints excluded: chain A residue 2743 THR Chi-restraints excluded: chain A residue 2810 ILE Chi-restraints excluded: chain A residue 3051 VAL Chi-restraints excluded: chain A residue 3055 VAL Chi-restraints excluded: chain A residue 3109 GLU Chi-restraints excluded: chain A residue 3366 LEU Chi-restraints excluded: chain A residue 3394 LEU Chi-restraints excluded: chain A residue 3398 GLU Chi-restraints excluded: chain A residue 3438 MET Chi-restraints excluded: chain A residue 3512 VAL Chi-restraints excluded: chain A residue 3530 ASP Chi-restraints excluded: chain A residue 3545 ASP Chi-restraints excluded: chain A residue 3604 LEU Chi-restraints excluded: chain A residue 3657 SER Chi-restraints excluded: chain A residue 3861 MET Chi-restraints excluded: chain A residue 3936 PHE Chi-restraints excluded: chain A residue 4042 MET Chi-restraints excluded: chain A residue 4542 LEU Chi-restraints excluded: chain A residue 4887 VAL Chi-restraints excluded: chain A residue 4951 ASP Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 812 CYS Chi-restraints excluded: chain B residue 912 HIS Chi-restraints excluded: chain B residue 930 LEU Chi-restraints excluded: chain B residue 1041 CYS Chi-restraints excluded: chain B residue 1171 MET Chi-restraints excluded: chain B residue 1183 ILE Chi-restraints excluded: chain B residue 1190 LEU Chi-restraints excluded: chain B residue 1435 TYR Chi-restraints excluded: chain B residue 1463 MET Chi-restraints excluded: chain B residue 1737 VAL Chi-restraints excluded: chain B residue 1836 VAL Chi-restraints excluded: chain B residue 1967 VAL Chi-restraints excluded: chain B residue 2281 VAL Chi-restraints excluded: chain B residue 2417 VAL Chi-restraints excluded: chain B residue 2424 MET Chi-restraints excluded: chain B residue 2743 THR Chi-restraints excluded: chain B residue 3055 VAL Chi-restraints excluded: chain B residue 3109 GLU Chi-restraints excluded: chain B residue 3308 VAL Chi-restraints excluded: chain B residue 3379 GLN Chi-restraints excluded: chain B residue 3394 LEU Chi-restraints excluded: chain B residue 3398 GLU Chi-restraints excluded: chain B residue 3406 LEU Chi-restraints excluded: chain B residue 3471 LEU Chi-restraints excluded: chain B residue 3512 VAL Chi-restraints excluded: chain B residue 3530 ASP Chi-restraints excluded: chain B residue 3545 ASP Chi-restraints excluded: chain B residue 3657 SER Chi-restraints excluded: chain B residue 3861 MET Chi-restraints excluded: chain B residue 4042 MET Chi-restraints excluded: chain B residue 4091 ILE Chi-restraints excluded: chain B residue 4542 LEU Chi-restraints excluded: chain B residue 4887 VAL Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 579 ILE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 812 CYS Chi-restraints excluded: chain C residue 912 HIS Chi-restraints excluded: chain C residue 930 LEU Chi-restraints excluded: chain C residue 939 HIS Chi-restraints excluded: chain C residue 1041 CYS Chi-restraints excluded: chain C residue 1171 MET Chi-restraints excluded: chain C residue 1190 LEU Chi-restraints excluded: chain C residue 1435 TYR Chi-restraints excluded: chain C residue 1737 VAL Chi-restraints excluded: chain C residue 1836 VAL Chi-restraints excluded: chain C residue 1928 LEU Chi-restraints excluded: chain C residue 1967 VAL Chi-restraints excluded: chain C residue 2204 MET Chi-restraints excluded: chain C residue 2417 VAL Chi-restraints excluded: chain C residue 2424 MET Chi-restraints excluded: chain C residue 2528 LEU Chi-restraints excluded: chain C residue 2743 THR Chi-restraints excluded: chain C residue 3055 VAL Chi-restraints excluded: chain C residue 3109 GLU Chi-restraints excluded: chain C residue 3308 VAL Chi-restraints excluded: chain C residue 3347 VAL Chi-restraints excluded: chain C residue 3366 LEU Chi-restraints excluded: chain C residue 3379 GLN Chi-restraints excluded: chain C residue 3394 LEU Chi-restraints excluded: chain C residue 3398 GLU Chi-restraints excluded: chain C residue 3471 LEU Chi-restraints excluded: chain C residue 3512 VAL Chi-restraints excluded: chain C residue 3530 ASP Chi-restraints excluded: chain C residue 3545 ASP Chi-restraints excluded: chain C residue 3657 SER Chi-restraints excluded: chain C residue 3861 MET Chi-restraints excluded: chain C residue 4042 MET Chi-restraints excluded: chain C residue 4091 ILE Chi-restraints excluded: chain C residue 4542 LEU Chi-restraints excluded: chain C residue 4887 VAL Chi-restraints excluded: chain K residue 16 PHE Chi-restraints excluded: chain K residue 19 HIS Chi-restraints excluded: chain K residue 32 LYS Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain K residue 89 PHE Chi-restraints excluded: chain L residue 5 LEU Chi-restraints excluded: chain L residue 19 HIS Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain M residue 16 PHE Chi-restraints excluded: chain M residue 19 HIS Chi-restraints excluded: chain M residue 32 LYS Chi-restraints excluded: chain M residue 37 LEU Chi-restraints excluded: chain M residue 89 PHE Chi-restraints excluded: chain O residue 16 PHE Chi-restraints excluded: chain O residue 19 HIS Chi-restraints excluded: chain O residue 32 LYS Chi-restraints excluded: chain O residue 37 LEU Chi-restraints excluded: chain O residue 89 PHE Chi-restraints excluded: chain P residue 5 LEU Chi-restraints excluded: chain P residue 19 HIS Chi-restraints excluded: chain P residue 37 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1860 random chunks: chunk 1630 optimal weight: 50.0000 chunk 1717 optimal weight: 7.9990 chunk 1566 optimal weight: 3.9990 chunk 1670 optimal weight: 0.4980 chunk 1716 optimal weight: 0.6980 chunk 1005 optimal weight: 9.9990 chunk 727 optimal weight: 0.2980 chunk 1311 optimal weight: 6.9990 chunk 512 optimal weight: 7.9990 chunk 1509 optimal weight: 4.9990 chunk 1580 optimal weight: 4.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 640 ASN D2128 GLN D2647 ASN D3963 GLN ** D4751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 ASN A2096 GLN A2128 GLN A3963 GLN ** A4751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 640 ASN B2096 GLN B2128 GLN B2647 ASN B3129 ASN B3963 GLN ** B4751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 640 ASN C2096 GLN C2128 GLN C2647 ASN C3963 GLN ** C4751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 17 HIS ** K 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 17 HIS ** M 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 17 HIS ** O 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 152600 Z= 0.210 Angle : 0.567 19.929 206604 Z= 0.281 Chirality : 0.039 0.309 22672 Planarity : 0.004 0.064 26800 Dihedral : 6.303 83.977 20896 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.69 % Favored : 97.30 % Rotamer: Outliers : 1.35 % Allowed : 11.88 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % 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: 1.78 (0.06), residues: 18552 helix: 2.18 (0.05), residues: 9924 sheet: -0.02 (0.13), residues: 1740 loop : 0.08 (0.08), residues: 6888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP P 91 HIS 0.004 0.001 HIS A 839 PHE 0.040 0.001 PHE P 89 TYR 0.035 0.001 TYR A2883 ARG 0.004 0.000 ARG G 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 37104 Ramachandran restraints generated. 18552 Oldfield, 0 Emsley, 18552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 37104 Ramachandran restraints generated. 18552 Oldfield, 0 Emsley, 18552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1312 residues out of total 16268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 1092 time to evaluate : 12.709 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: E 4 GLN cc_start: 0.8129 (mp10) cc_final: 0.7872 (mp10) REVERT: E 54 GLN cc_start: 0.9072 (mp10) cc_final: 0.8602 (mp10) REVERT: I 5 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8524 (mm) REVERT: I 14 ASN cc_start: 0.9264 (m110) cc_final: 0.8996 (p0) REVERT: I 16 PHE cc_start: 0.8520 (OUTLIER) cc_final: 0.7351 (p90) REVERT: I 32 LYS cc_start: 0.9188 (OUTLIER) cc_final: 0.8839 (mmmt) REVERT: I 86 CYS cc_start: 0.8562 (t) cc_final: 0.8211 (m) REVERT: J 42 LEU cc_start: 0.8637 (tp) cc_final: 0.8298 (tt) REVERT: J 59 MET cc_start: 0.6961 (ppp) cc_final: 0.6602 (ppp) REVERT: F 4 GLN cc_start: 0.7960 (mp10) cc_final: 0.7730 (mp10) REVERT: F 45 LYS cc_start: 0.8816 (ttpt) cc_final: 0.8470 (ttpp) REVERT: G 45 LYS cc_start: 0.8768 (ttpt) cc_final: 0.8442 (ttpp) REVERT: G 53 LYS cc_start: 0.9074 (mmtp) cc_final: 0.8835 (mmtp) REVERT: H 45 LYS cc_start: 0.8791 (ttpt) cc_final: 0.8467 (ttpp) REVERT: H 53 LYS cc_start: 0.9068 (mmtp) cc_final: 0.8822 (mmtp) REVERT: D 117 MET cc_start: 0.9412 (mtm) cc_final: 0.9116 (mtp) REVERT: D 197 MET cc_start: 0.7996 (mpp) cc_final: 0.7373 (mpp) REVERT: D 615 VAL cc_start: 0.8579 (OUTLIER) cc_final: 0.8282 (m) REVERT: D 666 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7560 (mt-10) REVERT: D 905 HIS cc_start: 0.7055 (t70) cc_final: 0.6470 (t70) REVERT: D 1041 CYS cc_start: 0.9362 (OUTLIER) cc_final: 0.9084 (p) REVERT: D 1574 MET cc_start: 0.8839 (mmt) cc_final: 0.8427 (mmt) REVERT: D 1816 MET cc_start: 0.8779 (mmm) cc_final: 0.8439 (mtt) REVERT: D 1930 MET cc_start: 0.9045 (ttm) cc_final: 0.8784 (mtp) REVERT: D 1987 MET cc_start: 0.4801 (pmm) cc_final: 0.4242 (tmm) REVERT: D 1997 ARG cc_start: 0.9163 (tmt-80) cc_final: 0.8745 (tpm170) REVERT: D 2171 MET cc_start: 0.8191 (mmm) cc_final: 0.7814 (mmm) REVERT: D 2251 MET cc_start: 0.9492 (mmm) cc_final: 0.9270 (mmm) REVERT: D 2382 GLU cc_start: 0.8893 (mt-10) cc_final: 0.8590 (mp0) REVERT: D 2424 MET cc_start: 0.8639 (OUTLIER) cc_final: 0.8266 (mpp) REVERT: D 2701 MET cc_start: 0.9102 (tmm) cc_final: 0.8881 (tmm) REVERT: D 2945 MET cc_start: 0.8421 (ptt) cc_final: 0.8133 (ptt) REVERT: D 2968 MET cc_start: 0.9367 (mmm) cc_final: 0.9010 (mmm) REVERT: D 3107 MET cc_start: 0.9587 (OUTLIER) cc_final: 0.8938 (ttp) REVERT: D 3211 LEU cc_start: 0.9293 (mm) cc_final: 0.8777 (tp) REVERT: D 3240 MET cc_start: 0.7422 (tpp) cc_final: 0.7043 (tpp) REVERT: D 3468 MET cc_start: 0.8040 (tpp) cc_final: 0.7488 (tpp) REVERT: D 3518 MET cc_start: 0.9156 (tpt) cc_final: 0.8838 (tpp) REVERT: D 3545 ASP cc_start: 0.8456 (OUTLIER) cc_final: 0.7838 (p0) REVERT: D 3574 MET cc_start: 0.8941 (tpt) cc_final: 0.8373 (tpp) REVERT: D 4837 MET cc_start: 0.8821 (mmm) cc_final: 0.8601 (mmm) REVERT: A 197 MET cc_start: 0.7962 (mpp) cc_final: 0.7388 (mpp) REVERT: A 212 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.8031 (tp30) REVERT: A 615 VAL cc_start: 0.8595 (OUTLIER) cc_final: 0.8301 (m) REVERT: A 666 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7648 (mt-10) REVERT: A 905 HIS cc_start: 0.6701 (t70) cc_final: 0.5990 (t70) REVERT: A 1041 CYS cc_start: 0.9380 (OUTLIER) cc_final: 0.8998 (p) REVERT: A 1816 MET cc_start: 0.8801 (mmm) cc_final: 0.8470 (mtt) REVERT: A 1930 MET cc_start: 0.9031 (ttm) cc_final: 0.8774 (mtp) REVERT: A 1997 ARG cc_start: 0.9166 (tmt-80) cc_final: 0.8725 (tpm170) REVERT: A 2171 MET cc_start: 0.8137 (mmm) cc_final: 0.7793 (mmm) REVERT: A 2382 GLU cc_start: 0.9018 (OUTLIER) cc_final: 0.8551 (mp0) REVERT: A 2701 MET cc_start: 0.9119 (tmm) cc_final: 0.8891 (tmm) REVERT: A 2945 MET cc_start: 0.8177 (ptt) cc_final: 0.7832 (ptt) REVERT: A 3039 MET cc_start: 0.9678 (mtm) cc_final: 0.9381 (mtm) REVERT: A 3211 LEU cc_start: 0.9302 (mm) cc_final: 0.8845 (tp) REVERT: A 3240 MET cc_start: 0.7561 (tpp) cc_final: 0.7157 (ppp) REVERT: A 3273 ILE cc_start: 0.9485 (mp) cc_final: 0.9277 (mp) REVERT: A 3574 MET cc_start: 0.8880 (tpt) cc_final: 0.8249 (tpp) REVERT: A 3724 MET cc_start: 0.8587 (mmm) cc_final: 0.8186 (mmm) REVERT: A 3936 PHE cc_start: 0.8977 (OUTLIER) cc_final: 0.8515 (t80) REVERT: B 117 MET cc_start: 0.9393 (mtm) cc_final: 0.9100 (mtp) REVERT: B 197 MET cc_start: 0.8002 (mpp) cc_final: 0.7388 (mpp) REVERT: B 615 VAL cc_start: 0.8589 (OUTLIER) cc_final: 0.8296 (m) REVERT: B 666 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7569 (mt-10) REVERT: B 905 HIS cc_start: 0.7040 (t70) cc_final: 0.6465 (t70) REVERT: B 1041 CYS cc_start: 0.9375 (OUTLIER) cc_final: 0.9095 (p) REVERT: B 1574 MET cc_start: 0.8848 (mmt) cc_final: 0.8433 (mmt) REVERT: B 1816 MET cc_start: 0.8796 (mmm) cc_final: 0.8443 (mtt) REVERT: B 1930 MET cc_start: 0.9040 (ttm) cc_final: 0.8789 (mtp) REVERT: B 1987 MET cc_start: 0.4953 (pmm) cc_final: 0.4357 (tmm) REVERT: B 1997 ARG cc_start: 0.9161 (tmt-80) cc_final: 0.8741 (tpm170) REVERT: B 2171 MET cc_start: 0.8137 (mmm) cc_final: 0.7740 (mmm) REVERT: B 2251 MET cc_start: 0.9495 (mmm) cc_final: 0.9277 (mmm) REVERT: B 2382 GLU cc_start: 0.8891 (mt-10) cc_final: 0.8594 (mp0) REVERT: B 2424 MET cc_start: 0.8634 (OUTLIER) cc_final: 0.8264 (mpp) REVERT: B 2491 MET cc_start: 0.8752 (tpp) cc_final: 0.8138 (tpp) REVERT: B 2531 MET cc_start: 0.8953 (mtm) cc_final: 0.8452 (mtm) REVERT: B 2945 MET cc_start: 0.8439 (ptt) cc_final: 0.8169 (ptt) REVERT: B 2968 MET cc_start: 0.9363 (mmm) cc_final: 0.9015 (mmm) REVERT: B 3107 MET cc_start: 0.9575 (OUTLIER) cc_final: 0.9003 (ttp) REVERT: B 3211 LEU cc_start: 0.9299 (mm) cc_final: 0.8781 (tp) REVERT: B 3240 MET cc_start: 0.7425 (tpp) cc_final: 0.7065 (tpp) REVERT: B 3468 MET cc_start: 0.8046 (tpp) cc_final: 0.7494 (tpp) REVERT: B 3518 MET cc_start: 0.9144 (tpt) cc_final: 0.8825 (tpp) REVERT: B 3545 ASP cc_start: 0.8456 (OUTLIER) cc_final: 0.7839 (p0) REVERT: B 3574 MET cc_start: 0.8941 (tpt) cc_final: 0.8375 (tpp) REVERT: B 3724 MET cc_start: 0.8596 (mmm) cc_final: 0.8201 (mmm) REVERT: C 117 MET cc_start: 0.9396 (mtm) cc_final: 0.9100 (mtp) REVERT: C 197 MET cc_start: 0.7998 (mpp) cc_final: 0.7382 (mpp) REVERT: C 615 VAL cc_start: 0.8578 (OUTLIER) cc_final: 0.8281 (m) REVERT: C 666 GLU cc_start: 0.7914 (mt-10) cc_final: 0.7565 (mt-10) REVERT: C 905 HIS cc_start: 0.7046 (t70) cc_final: 0.6466 (t70) REVERT: C 1041 CYS cc_start: 0.9368 (OUTLIER) cc_final: 0.9093 (p) REVERT: C 1574 MET cc_start: 0.8844 (mmt) cc_final: 0.8430 (mmt) REVERT: C 1816 MET cc_start: 0.8792 (mmm) cc_final: 0.8443 (mtt) REVERT: C 1930 MET cc_start: 0.9034 (ttm) cc_final: 0.8763 (mtp) REVERT: C 1987 MET cc_start: 0.4794 (pmm) cc_final: 0.4244 (tmm) REVERT: C 1997 ARG cc_start: 0.9161 (tmt-80) cc_final: 0.8740 (tpm170) REVERT: C 2171 MET cc_start: 0.8175 (mmm) cc_final: 0.7849 (mmm) REVERT: C 2179 MET cc_start: 0.8556 (tpp) cc_final: 0.8308 (tpp) REVERT: C 2251 MET cc_start: 0.9491 (mmm) cc_final: 0.9271 (mmm) REVERT: C 2424 MET cc_start: 0.8646 (OUTLIER) cc_final: 0.8274 (mpp) REVERT: C 2531 MET cc_start: 0.8936 (mtm) cc_final: 0.8563 (mtm) REVERT: C 2701 MET cc_start: 0.9112 (tmm) cc_final: 0.8891 (tmm) REVERT: C 2945 MET cc_start: 0.8264 (ptt) cc_final: 0.7926 (ptt) REVERT: C 2968 MET cc_start: 0.9368 (mmm) cc_final: 0.9017 (mmm) REVERT: C 3107 MET cc_start: 0.9578 (OUTLIER) cc_final: 0.8952 (ttp) REVERT: C 3211 LEU cc_start: 0.9294 (mm) cc_final: 0.8783 (tp) REVERT: C 3240 MET cc_start: 0.7470 (tpp) cc_final: 0.7088 (tpp) REVERT: C 3468 MET cc_start: 0.8035 (tpp) cc_final: 0.7466 (tpp) REVERT: C 3518 MET cc_start: 0.9170 (tpt) cc_final: 0.8811 (tpp) REVERT: C 3545 ASP cc_start: 0.8453 (OUTLIER) cc_final: 0.7837 (p0) REVERT: C 3574 MET cc_start: 0.8939 (tpt) cc_final: 0.8367 (tpp) REVERT: C 3724 MET cc_start: 0.8592 (mmm) cc_final: 0.8204 (mmm) REVERT: K 16 PHE cc_start: 0.8403 (OUTLIER) cc_final: 0.7175 (p90) REVERT: K 19 HIS cc_start: 0.6461 (OUTLIER) cc_final: 0.5727 (t-90) REVERT: K 32 LYS cc_start: 0.9137 (pttm) cc_final: 0.8879 (mmmt) REVERT: L 12 LEU cc_start: 0.8256 (tp) cc_final: 0.7778 (mt) REVERT: L 59 MET cc_start: 0.7274 (ppp) cc_final: 0.6711 (ppp) REVERT: L 75 TYR cc_start: 0.6680 (p90) cc_final: 0.6448 (p90) REVERT: N 59 MET cc_start: 0.7097 (ppp) cc_final: 0.6745 (ppp) REVERT: M 5 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8514 (mm) REVERT: M 16 PHE cc_start: 0.8407 (OUTLIER) cc_final: 0.7210 (p90) REVERT: M 19 HIS cc_start: 0.6415 (OUTLIER) cc_final: 0.5670 (t-90) REVERT: M 32 LYS cc_start: 0.9141 (pttm) cc_final: 0.8878 (mmmt) REVERT: O 16 PHE cc_start: 0.8417 (OUTLIER) cc_final: 0.7204 (p90) REVERT: O 19 HIS cc_start: 0.6467 (OUTLIER) cc_final: 0.5765 (t-90) REVERT: O 32 LYS cc_start: 0.9146 (pttm) cc_final: 0.8885 (mmmt) REVERT: P 12 LEU cc_start: 0.8250 (tp) cc_final: 0.7784 (mt) REVERT: P 59 MET cc_start: 0.7075 (ppp) cc_final: 0.6783 (ppp) REVERT: P 75 TYR cc_start: 0.6674 (p90) cc_final: 0.6457 (p90) outliers start: 220 outliers final: 174 residues processed: 1239 average time/residue: 1.2319 time to fit residues: 2752.1060 Evaluate side-chains 1265 residues out of total 16268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 1061 time to evaluate : 12.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 33 ASP Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 60 TRP Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain I residue 16 PHE Chi-restraints excluded: chain I residue 19 HIS Chi-restraints excluded: chain I residue 32 LYS Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 89 PHE Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 37 LEU Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 33 ASP Chi-restraints excluded: chain F residue 39 SER Chi-restraints excluded: chain F residue 60 TRP Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 33 ASP Chi-restraints excluded: chain G residue 39 SER Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 60 TRP Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 60 TRP Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 359 THR Chi-restraints excluded: chain D residue 579 ILE Chi-restraints excluded: chain D residue 615 VAL Chi-restraints excluded: chain D residue 812 CYS Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain D residue 1041 CYS Chi-restraints excluded: chain D residue 1171 MET Chi-restraints excluded: chain D residue 1190 LEU Chi-restraints excluded: chain D residue 1435 TYR Chi-restraints excluded: chain D residue 1737 VAL Chi-restraints excluded: chain D residue 1836 VAL Chi-restraints excluded: chain D residue 1967 VAL Chi-restraints excluded: chain D residue 2204 MET Chi-restraints excluded: chain D residue 2417 VAL Chi-restraints excluded: chain D residue 2424 MET Chi-restraints excluded: chain D residue 2743 THR Chi-restraints excluded: chain D residue 2810 ILE Chi-restraints excluded: chain D residue 3107 MET Chi-restraints excluded: chain D residue 3109 GLU Chi-restraints excluded: chain D residue 3308 VAL Chi-restraints excluded: chain D residue 3347 VAL Chi-restraints excluded: chain D residue 3379 GLN Chi-restraints excluded: chain D residue 3394 LEU Chi-restraints excluded: chain D residue 3398 GLU Chi-restraints excluded: chain D residue 3438 MET Chi-restraints excluded: chain D residue 3471 LEU Chi-restraints excluded: chain D residue 3512 VAL Chi-restraints excluded: chain D residue 3530 ASP Chi-restraints excluded: chain D residue 3545 ASP Chi-restraints excluded: chain D residue 3657 SER Chi-restraints excluded: chain D residue 3861 MET Chi-restraints excluded: chain D residue 4042 MET Chi-restraints excluded: chain D residue 4542 LEU Chi-restraints excluded: chain D residue 4887 VAL Chi-restraints excluded: chain D residue 4951 ASP Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 812 CYS Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 1041 CYS Chi-restraints excluded: chain A residue 1171 MET Chi-restraints excluded: chain A residue 1190 LEU Chi-restraints excluded: chain A residue 1429 LEU Chi-restraints excluded: chain A residue 1435 TYR Chi-restraints excluded: chain A residue 1737 VAL Chi-restraints excluded: chain A residue 1836 VAL Chi-restraints excluded: chain A residue 1868 ILE Chi-restraints excluded: chain A residue 1928 LEU Chi-restraints excluded: chain A residue 1967 VAL Chi-restraints excluded: chain A residue 1992 THR Chi-restraints excluded: chain A residue 2096 GLN Chi-restraints excluded: chain A residue 2281 VAL Chi-restraints excluded: chain A residue 2382 GLU Chi-restraints excluded: chain A residue 2417 VAL Chi-restraints excluded: chain A residue 2424 MET Chi-restraints excluded: chain A residue 2743 THR Chi-restraints excluded: chain A residue 2810 ILE Chi-restraints excluded: chain A residue 3051 VAL Chi-restraints excluded: chain A residue 3055 VAL Chi-restraints excluded: chain A residue 3109 GLU Chi-restraints excluded: chain A residue 3366 LEU Chi-restraints excluded: chain A residue 3394 LEU Chi-restraints excluded: chain A residue 3398 GLU Chi-restraints excluded: chain A residue 3438 MET Chi-restraints excluded: chain A residue 3512 VAL Chi-restraints excluded: chain A residue 3530 ASP Chi-restraints excluded: chain A residue 3657 SER Chi-restraints excluded: chain A residue 3861 MET Chi-restraints excluded: chain A residue 3936 PHE Chi-restraints excluded: chain A residue 4042 MET Chi-restraints excluded: chain A residue 4542 LEU Chi-restraints excluded: chain A residue 4887 VAL Chi-restraints excluded: chain A residue 4951 ASP Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 812 CYS Chi-restraints excluded: chain B residue 912 HIS Chi-restraints excluded: chain B residue 930 LEU Chi-restraints excluded: chain B residue 1041 CYS Chi-restraints excluded: chain B residue 1171 MET Chi-restraints excluded: chain B residue 1190 LEU Chi-restraints excluded: chain B residue 1435 TYR Chi-restraints excluded: chain B residue 1463 MET Chi-restraints excluded: chain B residue 1737 VAL Chi-restraints excluded: chain B residue 1836 VAL Chi-restraints excluded: chain B residue 1967 VAL Chi-restraints excluded: chain B residue 2096 GLN Chi-restraints excluded: chain B residue 2417 VAL Chi-restraints excluded: chain B residue 2424 MET Chi-restraints excluded: chain B residue 2743 THR Chi-restraints excluded: chain B residue 2810 ILE Chi-restraints excluded: chain B residue 3107 MET Chi-restraints excluded: chain B residue 3109 GLU Chi-restraints excluded: chain B residue 3308 VAL Chi-restraints excluded: chain B residue 3347 VAL Chi-restraints excluded: chain B residue 3379 GLN Chi-restraints excluded: chain B residue 3394 LEU Chi-restraints excluded: chain B residue 3398 GLU Chi-restraints excluded: chain B residue 3406 LEU Chi-restraints excluded: chain B residue 3471 LEU Chi-restraints excluded: chain B residue 3512 VAL Chi-restraints excluded: chain B residue 3530 ASP Chi-restraints excluded: chain B residue 3545 ASP Chi-restraints excluded: chain B residue 3657 SER Chi-restraints excluded: chain B residue 3861 MET Chi-restraints excluded: chain B residue 4042 MET Chi-restraints excluded: chain B residue 4091 ILE Chi-restraints excluded: chain B residue 4542 LEU Chi-restraints excluded: chain B residue 4887 VAL Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 579 ILE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 812 CYS Chi-restraints excluded: chain C residue 930 LEU Chi-restraints excluded: chain C residue 1041 CYS Chi-restraints excluded: chain C residue 1171 MET Chi-restraints excluded: chain C residue 1190 LEU Chi-restraints excluded: chain C residue 1435 TYR Chi-restraints excluded: chain C residue 1737 VAL Chi-restraints excluded: chain C residue 1836 VAL Chi-restraints excluded: chain C residue 1928 LEU Chi-restraints excluded: chain C residue 1967 VAL Chi-restraints excluded: chain C residue 2096 GLN Chi-restraints excluded: chain C residue 2204 MET Chi-restraints excluded: chain C residue 2417 VAL Chi-restraints excluded: chain C residue 2424 MET Chi-restraints excluded: chain C residue 2528 LEU Chi-restraints excluded: chain C residue 2743 THR Chi-restraints excluded: chain C residue 3107 MET Chi-restraints excluded: chain C residue 3109 GLU Chi-restraints excluded: chain C residue 3308 VAL Chi-restraints excluded: chain C residue 3347 VAL Chi-restraints excluded: chain C residue 3379 GLN Chi-restraints excluded: chain C residue 3394 LEU Chi-restraints excluded: chain C residue 3398 GLU Chi-restraints excluded: chain C residue 3471 LEU Chi-restraints excluded: chain C residue 3512 VAL Chi-restraints excluded: chain C residue 3530 ASP Chi-restraints excluded: chain C residue 3545 ASP Chi-restraints excluded: chain C residue 3657 SER Chi-restraints excluded: chain C residue 3861 MET Chi-restraints excluded: chain C residue 4042 MET Chi-restraints excluded: chain C residue 4542 LEU Chi-restraints excluded: chain C residue 4887 VAL Chi-restraints excluded: chain K residue 16 PHE Chi-restraints excluded: chain K residue 19 HIS Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain K residue 89 PHE Chi-restraints excluded: chain K residue 90 PHE Chi-restraints excluded: chain L residue 5 LEU Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 72 PHE Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 72 PHE Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain M residue 16 PHE Chi-restraints excluded: chain M residue 19 HIS Chi-restraints excluded: chain M residue 37 LEU Chi-restraints excluded: chain M residue 89 PHE Chi-restraints excluded: chain M residue 90 PHE Chi-restraints excluded: chain O residue 16 PHE Chi-restraints excluded: chain O residue 19 HIS Chi-restraints excluded: chain O residue 37 LEU Chi-restraints excluded: chain O residue 89 PHE Chi-restraints excluded: chain O residue 90 PHE Chi-restraints excluded: chain P residue 5 LEU Chi-restraints excluded: chain P residue 37 LEU Chi-restraints excluded: chain P residue 72 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1860 random chunks: chunk 1664 optimal weight: 10.0000 chunk 1097 optimal weight: 7.9990 chunk 1766 optimal weight: 10.0000 chunk 1078 optimal weight: 0.6980 chunk 838 optimal weight: 6.9990 chunk 1228 optimal weight: 1.9990 chunk 1853 optimal weight: 20.0000 chunk 1705 optimal weight: 6.9990 chunk 1475 optimal weight: 6.9990 chunk 153 optimal weight: 6.9990 chunk 1139 optimal weight: 0.8980 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 640 ASN D2128 GLN D3319 ASN ** D4751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 ASN A2096 GLN A2128 GLN ** A4751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 640 ASN B2096 GLN B2128 GLN ** B4751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 640 ASN C2096 GLN C2128 GLN ** C4751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 17 HIS ** K 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 17 HIS ** M 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 17 HIS ** O 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.119 152600 Z= 0.297 Angle : 0.601 24.638 206604 Z= 0.297 Chirality : 0.040 0.304 22672 Planarity : 0.004 0.062 26800 Dihedral : 6.310 84.187 20896 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.86 % Favored : 97.13 % Rotamer: Outliers : 1.40 % Allowed : 11.97 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % 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: 1.73 (0.06), residues: 18552 helix: 2.13 (0.05), residues: 9940 sheet: -0.04 (0.13), residues: 1740 loop : 0.07 (0.08), residues: 6872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP P 91 HIS 0.008 0.001 HIS C 994 PHE 0.046 0.001 PHE B3637 TYR 0.036 0.001 TYR A2883 ARG 0.004 0.000 ARG G 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 37104 Ramachandran restraints generated. 18552 Oldfield, 0 Emsley, 18552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 37104 Ramachandran restraints generated. 18552 Oldfield, 0 Emsley, 18552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1288 residues out of total 16268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 228 poor density : 1060 time to evaluate : 12.620 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: I 5 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8506 (mm) REVERT: I 16 PHE cc_start: 0.8541 (OUTLIER) cc_final: 0.7363 (p90) REVERT: I 32 LYS cc_start: 0.9197 (OUTLIER) cc_final: 0.8855 (mmmt) REVERT: I 86 CYS cc_start: 0.8609 (t) cc_final: 0.8207 (m) REVERT: J 42 LEU cc_start: 0.8631 (tp) cc_final: 0.8293 (tt) REVERT: J 59 MET cc_start: 0.6978 (ppp) cc_final: 0.6627 (ppp) REVERT: J 89 PHE cc_start: 0.8593 (OUTLIER) cc_final: 0.7947 (p90) REVERT: F 45 LYS cc_start: 0.8815 (ttpt) cc_final: 0.8468 (ttpp) REVERT: G 45 LYS cc_start: 0.8771 (ttpt) cc_final: 0.8439 (ttpp) REVERT: G 53 LYS cc_start: 0.9084 (mmtp) cc_final: 0.8838 (mmtp) REVERT: H 45 LYS cc_start: 0.8788 (ttpt) cc_final: 0.8460 (ttpp) REVERT: H 53 LYS cc_start: 0.9081 (mmtp) cc_final: 0.8842 (mmtp) REVERT: D 117 MET cc_start: 0.9424 (mtm) cc_final: 0.9129 (mtp) REVERT: D 197 MET cc_start: 0.8023 (mpp) cc_final: 0.7389 (mpp) REVERT: D 615 VAL cc_start: 0.8601 (OUTLIER) cc_final: 0.8299 (m) REVERT: D 666 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7611 (mt-10) REVERT: D 905 HIS cc_start: 0.7066 (t70) cc_final: 0.6472 (t70) REVERT: D 1041 CYS cc_start: 0.9364 (OUTLIER) cc_final: 0.9090 (p) REVERT: D 1574 MET cc_start: 0.8838 (mmt) cc_final: 0.8414 (mmt) REVERT: D 1816 MET cc_start: 0.8808 (mmm) cc_final: 0.8460 (mtt) REVERT: D 1930 MET cc_start: 0.9082 (ttm) cc_final: 0.8833 (mtp) REVERT: D 1987 MET cc_start: 0.4831 (pmm) cc_final: 0.4220 (tmm) REVERT: D 1997 ARG cc_start: 0.9181 (tmt-80) cc_final: 0.8769 (tpm170) REVERT: D 2171 MET cc_start: 0.8166 (mmm) cc_final: 0.7829 (mmm) REVERT: D 2251 MET cc_start: 0.9498 (mmm) cc_final: 0.9273 (mmm) REVERT: D 2382 GLU cc_start: 0.8904 (mt-10) cc_final: 0.8605 (mp0) REVERT: D 2424 MET cc_start: 0.8664 (OUTLIER) cc_final: 0.8312 (mpp) REVERT: D 2491 MET cc_start: 0.8834 (tpp) cc_final: 0.8291 (tpp) REVERT: D 2945 MET cc_start: 0.8418 (ptt) cc_final: 0.8174 (ptt) REVERT: D 2968 MET cc_start: 0.9379 (mmm) cc_final: 0.9021 (mmm) REVERT: D 3107 MET cc_start: 0.9594 (OUTLIER) cc_final: 0.8953 (ttp) REVERT: D 3211 LEU cc_start: 0.9299 (mm) cc_final: 0.8784 (tp) REVERT: D 3240 MET cc_start: 0.7472 (tpp) cc_final: 0.7063 (tpp) REVERT: D 3273 ILE cc_start: 0.9497 (mm) cc_final: 0.9125 (mp) REVERT: D 3438 MET cc_start: 0.8658 (OUTLIER) cc_final: 0.8414 (ttp) REVERT: D 3468 MET cc_start: 0.8046 (tpp) cc_final: 0.7495 (tpp) REVERT: D 3518 MET cc_start: 0.9170 (tpt) cc_final: 0.8831 (tpp) REVERT: D 3545 ASP cc_start: 0.8478 (OUTLIER) cc_final: 0.7855 (p0) REVERT: D 3574 MET cc_start: 0.8951 (tpt) cc_final: 0.8384 (tpp) REVERT: D 3839 MET cc_start: 0.9330 (ttm) cc_final: 0.9041 (mtp) REVERT: D 4837 MET cc_start: 0.8833 (mmm) cc_final: 0.8612 (mmm) REVERT: A 197 MET cc_start: 0.7957 (mpp) cc_final: 0.7376 (mpp) REVERT: A 212 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.8042 (tp30) REVERT: A 615 VAL cc_start: 0.8619 (OUTLIER) cc_final: 0.8321 (m) REVERT: A 666 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7690 (mt-10) REVERT: A 905 HIS cc_start: 0.6714 (t70) cc_final: 0.6001 (t70) REVERT: A 1041 CYS cc_start: 0.9381 (OUTLIER) cc_final: 0.9073 (p) REVERT: A 1816 MET cc_start: 0.8814 (mmm) cc_final: 0.8460 (mtt) REVERT: A 1930 MET cc_start: 0.9066 (ttm) cc_final: 0.8806 (mtp) REVERT: A 1997 ARG cc_start: 0.9183 (tmt-80) cc_final: 0.8744 (tpm170) REVERT: A 2171 MET cc_start: 0.8151 (mmm) cc_final: 0.7820 (mmm) REVERT: A 2382 GLU cc_start: 0.9039 (OUTLIER) cc_final: 0.8574 (mp0) REVERT: A 2701 MET cc_start: 0.9118 (tmm) cc_final: 0.8888 (tmm) REVERT: A 2945 MET cc_start: 0.8192 (ptt) cc_final: 0.7884 (ptt) REVERT: A 3039 MET cc_start: 0.9682 (mtm) cc_final: 0.9371 (mtm) REVERT: A 3211 LEU cc_start: 0.9311 (mm) cc_final: 0.8858 (tp) REVERT: A 3518 MET cc_start: 0.9195 (mmm) cc_final: 0.8881 (ttt) REVERT: A 3545 ASP cc_start: 0.8157 (OUTLIER) cc_final: 0.7722 (p0) REVERT: A 3574 MET cc_start: 0.8896 (tpt) cc_final: 0.8260 (tpp) REVERT: A 3936 PHE cc_start: 0.8986 (OUTLIER) cc_final: 0.8615 (t80) REVERT: A 4872 MET cc_start: 0.9124 (mmt) cc_final: 0.8528 (mmp) REVERT: B 117 MET cc_start: 0.9401 (mtm) cc_final: 0.9110 (mtp) REVERT: B 197 MET cc_start: 0.8012 (mpp) cc_final: 0.7383 (mpp) REVERT: B 615 VAL cc_start: 0.8611 (OUTLIER) cc_final: 0.8310 (m) REVERT: B 666 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7621 (mt-10) REVERT: B 905 HIS cc_start: 0.7034 (t70) cc_final: 0.6450 (t70) REVERT: B 1041 CYS cc_start: 0.9368 (OUTLIER) cc_final: 0.9088 (p) REVERT: B 1574 MET cc_start: 0.8845 (mmt) cc_final: 0.8420 (mmt) REVERT: B 1816 MET cc_start: 0.8819 (mmm) cc_final: 0.8461 (mtt) REVERT: B 1930 MET cc_start: 0.9076 (ttm) cc_final: 0.8831 (mtp) REVERT: B 1997 ARG cc_start: 0.9174 (tmt-80) cc_final: 0.8752 (tpm170) REVERT: B 2171 MET cc_start: 0.8132 (mmm) cc_final: 0.7759 (mmm) REVERT: B 2251 MET cc_start: 0.9499 (mmm) cc_final: 0.9273 (mmm) REVERT: B 2382 GLU cc_start: 0.8899 (mt-10) cc_final: 0.8605 (mp0) REVERT: B 2424 MET cc_start: 0.8660 (OUTLIER) cc_final: 0.8308 (mpp) REVERT: B 2491 MET cc_start: 0.8802 (tpp) cc_final: 0.8252 (tpp) REVERT: B 2531 MET cc_start: 0.8977 (mtm) cc_final: 0.8462 (mtm) REVERT: B 2945 MET cc_start: 0.8437 (ptt) cc_final: 0.8157 (ptt) REVERT: B 2968 MET cc_start: 0.9383 (mmm) cc_final: 0.9035 (mmm) REVERT: B 3107 MET cc_start: 0.9578 (OUTLIER) cc_final: 0.8997 (ttp) REVERT: B 3211 LEU cc_start: 0.9305 (mm) cc_final: 0.8789 (tp) REVERT: B 3240 MET cc_start: 0.7442 (tpp) cc_final: 0.7028 (tpp) REVERT: B 3273 ILE cc_start: 0.9515 (mm) cc_final: 0.9152 (mp) REVERT: B 3468 MET cc_start: 0.8053 (tpp) cc_final: 0.7501 (tpp) REVERT: B 3518 MET cc_start: 0.9188 (tpt) cc_final: 0.8841 (tpp) REVERT: B 3545 ASP cc_start: 0.8478 (OUTLIER) cc_final: 0.7856 (p0) REVERT: B 3574 MET cc_start: 0.8951 (tpt) cc_final: 0.8388 (tpp) REVERT: C 117 MET cc_start: 0.9401 (mtm) cc_final: 0.9110 (mtp) REVERT: C 197 MET cc_start: 0.8010 (mpp) cc_final: 0.7380 (mpp) REVERT: C 615 VAL cc_start: 0.8600 (OUTLIER) cc_final: 0.8299 (m) REVERT: C 666 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7617 (mt-10) REVERT: C 905 HIS cc_start: 0.7057 (t70) cc_final: 0.6468 (t70) REVERT: C 1041 CYS cc_start: 0.9366 (OUTLIER) cc_final: 0.9088 (p) REVERT: C 1574 MET cc_start: 0.8840 (mmt) cc_final: 0.8416 (mmt) REVERT: C 1816 MET cc_start: 0.8813 (mmm) cc_final: 0.8456 (mtt) REVERT: C 1930 MET cc_start: 0.9060 (ttm) cc_final: 0.8801 (mtp) REVERT: C 1987 MET cc_start: 0.4885 (pmm) cc_final: 0.4280 (tmm) REVERT: C 1997 ARG cc_start: 0.9169 (tmt-80) cc_final: 0.8749 (tpm170) REVERT: C 2171 MET cc_start: 0.8202 (mmm) cc_final: 0.7906 (mmm) REVERT: C 2251 MET cc_start: 0.9501 (mmm) cc_final: 0.9275 (mmm) REVERT: C 2424 MET cc_start: 0.8665 (OUTLIER) cc_final: 0.8317 (mpp) REVERT: C 2531 MET cc_start: 0.8951 (mtm) cc_final: 0.8565 (mtm) REVERT: C 2945 MET cc_start: 0.8284 (ptt) cc_final: 0.7938 (ptt) REVERT: C 2968 MET cc_start: 0.9384 (mmm) cc_final: 0.9038 (mmm) REVERT: C 3107 MET cc_start: 0.9589 (OUTLIER) cc_final: 0.8993 (ttp) REVERT: C 3211 LEU cc_start: 0.9302 (mm) cc_final: 0.8792 (tp) REVERT: C 3240 MET cc_start: 0.7531 (tpp) cc_final: 0.7142 (tpp) REVERT: C 3273 ILE cc_start: 0.9497 (mm) cc_final: 0.9122 (mp) REVERT: C 3468 MET cc_start: 0.8041 (tpp) cc_final: 0.7473 (tpp) REVERT: C 3518 MET cc_start: 0.9193 (tpt) cc_final: 0.8838 (tpp) REVERT: C 3545 ASP cc_start: 0.8476 (OUTLIER) cc_final: 0.7855 (p0) REVERT: C 3574 MET cc_start: 0.8950 (tpt) cc_final: 0.8377 (tpp) REVERT: C 3839 MET cc_start: 0.9330 (ttm) cc_final: 0.9041 (mtp) REVERT: K 16 PHE cc_start: 0.8432 (OUTLIER) cc_final: 0.7207 (p90) REVERT: K 19 HIS cc_start: 0.6506 (OUTLIER) cc_final: 0.5802 (t-90) REVERT: K 32 LYS cc_start: 0.9159 (pttm) cc_final: 0.8873 (mmmt) REVERT: L 12 LEU cc_start: 0.8273 (tp) cc_final: 0.7774 (mt) REVERT: L 59 MET cc_start: 0.7253 (ppp) cc_final: 0.6686 (ppp) REVERT: L 75 TYR cc_start: 0.6712 (p90) cc_final: 0.6457 (p90) REVERT: N 59 MET cc_start: 0.7074 (ppp) cc_final: 0.6722 (ppp) REVERT: M 5 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8518 (mm) REVERT: M 16 PHE cc_start: 0.8436 (OUTLIER) cc_final: 0.7227 (p90) REVERT: M 19 HIS cc_start: 0.6444 (OUTLIER) cc_final: 0.6165 (t70) REVERT: M 32 LYS cc_start: 0.9165 (OUTLIER) cc_final: 0.8858 (mmmt) REVERT: O 16 PHE cc_start: 0.8454 (OUTLIER) cc_final: 0.7244 (p90) REVERT: O 19 HIS cc_start: 0.6462 (OUTLIER) cc_final: 0.5726 (t-90) REVERT: O 32 LYS cc_start: 0.9166 (pttm) cc_final: 0.8886 (mmmt) REVERT: P 12 LEU cc_start: 0.8267 (tp) cc_final: 0.7778 (mt) REVERT: P 59 MET cc_start: 0.7104 (ppp) cc_final: 0.6818 (ppp) REVERT: P 75 TYR cc_start: 0.6706 (p90) cc_final: 0.6452 (p90) outliers start: 228 outliers final: 177 residues processed: 1219 average time/residue: 1.2250 time to fit residues: 2694.3006 Evaluate side-chains 1267 residues out of total 16268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 211 poor density : 1056 time to evaluate : 12.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 33 ASP Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 60 TRP Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain I residue 16 PHE Chi-restraints excluded: chain I residue 32 LYS Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 89 PHE Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 19 HIS Chi-restraints excluded: chain J residue 37 LEU Chi-restraints excluded: chain J residue 89 PHE Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 33 ASP Chi-restraints excluded: chain F residue 39 SER Chi-restraints excluded: chain F residue 60 TRP Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 33 ASP Chi-restraints excluded: chain G residue 39 SER Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 60 TRP Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 60 TRP Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 359 THR Chi-restraints excluded: chain D residue 579 ILE Chi-restraints excluded: chain D residue 615 VAL Chi-restraints excluded: chain D residue 812 CYS Chi-restraints excluded: chain D residue 1041 CYS Chi-restraints excluded: chain D residue 1171 MET Chi-restraints excluded: chain D residue 1190 LEU Chi-restraints excluded: chain D residue 1435 TYR Chi-restraints excluded: chain D residue 1737 VAL Chi-restraints excluded: chain D residue 1836 VAL Chi-restraints excluded: chain D residue 1967 VAL Chi-restraints excluded: chain D residue 2204 MET Chi-restraints excluded: chain D residue 2417 VAL Chi-restraints excluded: chain D residue 2424 MET Chi-restraints excluded: chain D residue 2743 THR Chi-restraints excluded: chain D residue 2810 ILE Chi-restraints excluded: chain D residue 3055 VAL Chi-restraints excluded: chain D residue 3107 MET Chi-restraints excluded: chain D residue 3109 GLU Chi-restraints excluded: chain D residue 3308 VAL Chi-restraints excluded: chain D residue 3347 VAL Chi-restraints excluded: chain D residue 3379 GLN Chi-restraints excluded: chain D residue 3394 LEU Chi-restraints excluded: chain D residue 3398 GLU Chi-restraints excluded: chain D residue 3438 MET Chi-restraints excluded: chain D residue 3471 LEU Chi-restraints excluded: chain D residue 3512 VAL Chi-restraints excluded: chain D residue 3545 ASP Chi-restraints excluded: chain D residue 3657 SER Chi-restraints excluded: chain D residue 3861 MET Chi-restraints excluded: chain D residue 4542 LEU Chi-restraints excluded: chain D residue 4887 VAL Chi-restraints excluded: chain D residue 4951 ASP Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 812 CYS Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 1041 CYS Chi-restraints excluded: chain A residue 1171 MET Chi-restraints excluded: chain A residue 1190 LEU Chi-restraints excluded: chain A residue 1435 TYR Chi-restraints excluded: chain A residue 1737 VAL Chi-restraints excluded: chain A residue 1836 VAL Chi-restraints excluded: chain A residue 1868 ILE Chi-restraints excluded: chain A residue 1928 LEU Chi-restraints excluded: chain A residue 1967 VAL Chi-restraints excluded: chain A residue 1992 THR Chi-restraints excluded: chain A residue 2096 GLN Chi-restraints excluded: chain A residue 2181 GLN Chi-restraints excluded: chain A residue 2281 VAL Chi-restraints excluded: chain A residue 2382 GLU Chi-restraints excluded: chain A residue 2417 VAL Chi-restraints excluded: chain A residue 2424 MET Chi-restraints excluded: chain A residue 2743 THR Chi-restraints excluded: chain A residue 2810 ILE Chi-restraints excluded: chain A residue 3055 VAL Chi-restraints excluded: chain A residue 3109 GLU Chi-restraints excluded: chain A residue 3181 ASN Chi-restraints excluded: chain A residue 3366 LEU Chi-restraints excluded: chain A residue 3394 LEU Chi-restraints excluded: chain A residue 3398 GLU Chi-restraints excluded: chain A residue 3438 MET Chi-restraints excluded: chain A residue 3512 VAL Chi-restraints excluded: chain A residue 3545 ASP Chi-restraints excluded: chain A residue 3604 LEU Chi-restraints excluded: chain A residue 3657 SER Chi-restraints excluded: chain A residue 3861 MET Chi-restraints excluded: chain A residue 3936 PHE Chi-restraints excluded: chain A residue 4042 MET Chi-restraints excluded: chain A residue 4542 LEU Chi-restraints excluded: chain A residue 4887 VAL Chi-restraints excluded: chain A residue 4951 ASP Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 812 CYS Chi-restraints excluded: chain B residue 912 HIS Chi-restraints excluded: chain B residue 1041 CYS Chi-restraints excluded: chain B residue 1171 MET Chi-restraints excluded: chain B residue 1190 LEU Chi-restraints excluded: chain B residue 1435 TYR Chi-restraints excluded: chain B residue 1463 MET Chi-restraints excluded: chain B residue 1737 VAL Chi-restraints excluded: chain B residue 1836 VAL Chi-restraints excluded: chain B residue 1967 VAL Chi-restraints excluded: chain B residue 2096 GLN Chi-restraints excluded: chain B residue 2281 VAL Chi-restraints excluded: chain B residue 2417 VAL Chi-restraints excluded: chain B residue 2424 MET Chi-restraints excluded: chain B residue 2743 THR Chi-restraints excluded: chain B residue 2810 ILE Chi-restraints excluded: chain B residue 3055 VAL Chi-restraints excluded: chain B residue 3107 MET Chi-restraints excluded: chain B residue 3109 GLU Chi-restraints excluded: chain B residue 3308 VAL Chi-restraints excluded: chain B residue 3347 VAL Chi-restraints excluded: chain B residue 3379 GLN Chi-restraints excluded: chain B residue 3394 LEU Chi-restraints excluded: chain B residue 3398 GLU Chi-restraints excluded: chain B residue 3438 MET Chi-restraints excluded: chain B residue 3471 LEU Chi-restraints excluded: chain B residue 3512 VAL Chi-restraints excluded: chain B residue 3545 ASP Chi-restraints excluded: chain B residue 3657 SER Chi-restraints excluded: chain B residue 3861 MET Chi-restraints excluded: chain B residue 4042 MET Chi-restraints excluded: chain B residue 4091 ILE Chi-restraints excluded: chain B residue 4542 LEU Chi-restraints excluded: chain B residue 4887 VAL Chi-restraints excluded: chain B residue 4951 ASP Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 579 ILE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 812 CYS Chi-restraints excluded: chain C residue 1041 CYS Chi-restraints excluded: chain C residue 1171 MET Chi-restraints excluded: chain C residue 1190 LEU Chi-restraints excluded: chain C residue 1435 TYR Chi-restraints excluded: chain C residue 1737 VAL Chi-restraints excluded: chain C residue 1836 VAL Chi-restraints excluded: chain C residue 1928 LEU Chi-restraints excluded: chain C residue 1967 VAL Chi-restraints excluded: chain C residue 2096 GLN Chi-restraints excluded: chain C residue 2204 MET Chi-restraints excluded: chain C residue 2281 VAL Chi-restraints excluded: chain C residue 2417 VAL Chi-restraints excluded: chain C residue 2424 MET Chi-restraints excluded: chain C residue 2528 LEU Chi-restraints excluded: chain C residue 2743 THR Chi-restraints excluded: chain C residue 2810 ILE Chi-restraints excluded: chain C residue 3055 VAL Chi-restraints excluded: chain C residue 3107 MET Chi-restraints excluded: chain C residue 3109 GLU Chi-restraints excluded: chain C residue 3308 VAL Chi-restraints excluded: chain C residue 3347 VAL Chi-restraints excluded: chain C residue 3379 GLN Chi-restraints excluded: chain C residue 3394 LEU Chi-restraints excluded: chain C residue 3398 GLU Chi-restraints excluded: chain C residue 3406 LEU Chi-restraints excluded: chain C residue 3471 LEU Chi-restraints excluded: chain C residue 3512 VAL Chi-restraints excluded: chain C residue 3545 ASP Chi-restraints excluded: chain C residue 3657 SER Chi-restraints excluded: chain C residue 3861 MET Chi-restraints excluded: chain C residue 4042 MET Chi-restraints excluded: chain C residue 4542 LEU Chi-restraints excluded: chain C residue 4887 VAL Chi-restraints excluded: chain K residue 16 PHE Chi-restraints excluded: chain K residue 19 HIS Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain K residue 89 PHE Chi-restraints excluded: chain K residue 90 PHE Chi-restraints excluded: chain L residue 5 LEU Chi-restraints excluded: chain L residue 19 HIS Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 72 PHE Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 72 PHE Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain M residue 16 PHE Chi-restraints excluded: chain M residue 19 HIS Chi-restraints excluded: chain M residue 32 LYS Chi-restraints excluded: chain M residue 37 LEU Chi-restraints excluded: chain M residue 89 PHE Chi-restraints excluded: chain M residue 90 PHE Chi-restraints excluded: chain O residue 16 PHE Chi-restraints excluded: chain O residue 19 HIS Chi-restraints excluded: chain O residue 37 LEU Chi-restraints excluded: chain O residue 89 PHE Chi-restraints excluded: chain O residue 90 PHE Chi-restraints excluded: chain P residue 5 LEU Chi-restraints excluded: chain P residue 37 LEU Chi-restraints excluded: chain P residue 72 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1860 random chunks: chunk 904 optimal weight: 0.0570 chunk 1172 optimal weight: 2.9990 chunk 1571 optimal weight: 8.9990 chunk 452 optimal weight: 4.9990 chunk 1360 optimal weight: 8.9990 chunk 217 optimal weight: 1.9990 chunk 410 optimal weight: 6.9990 chunk 1477 optimal weight: 0.9990 chunk 618 optimal weight: 10.0000 chunk 1517 optimal weight: 4.9990 chunk 187 optimal weight: 9.9990 overall best weight: 2.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 640 ASN D2128 GLN D3319 ASN ** D4751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 ASN A2128 GLN ** A4751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 640 ASN B2128 GLN ** B4751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1012 GLN C2096 GLN C2128 GLN ** C4751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 17 HIS ** K 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 17 HIS ** M 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 17 HIS ** O 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.068532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.046536 restraints weight = 540537.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.048109 restraints weight = 264540.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.049146 restraints weight = 174758.715| |-----------------------------------------------------------------------------| r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 152600 Z= 0.220 Angle : 0.582 23.477 206604 Z= 0.287 Chirality : 0.039 0.325 22672 Planarity : 0.004 0.063 26800 Dihedral : 6.229 83.762 20896 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.76 % Favored : 97.23 % Rotamer: Outliers : 1.35 % Allowed : 12.06 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % 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: 1.76 (0.06), residues: 18552 helix: 2.17 (0.05), residues: 9928 sheet: -0.03 (0.13), residues: 1740 loop : 0.08 (0.08), residues: 6884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP L 91 HIS 0.007 0.001 HIS C 994 PHE 0.044 0.001 PHE A3637 TYR 0.036 0.001 TYR A2883 ARG 0.008 0.000 ARG E 14 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 45962.42 seconds wall clock time: 800 minutes 46.48 seconds (48046.48 seconds total)