Starting phenix.real_space_refine on Mon Mar 18 23:35:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ua9_26416/03_2024/7ua9_26416_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ua9_26416/03_2024/7ua9_26416.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ua9_26416/03_2024/7ua9_26416.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ua9_26416/03_2024/7ua9_26416.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ua9_26416/03_2024/7ua9_26416_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ua9_26416/03_2024/7ua9_26416_updated.pdb" } resolution = 3.59 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= 0.012 sd= 0.029 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 4 9.91 5 Zn 4 6.06 5 P 24 5.49 5 S 936 5.16 5 C 88228 2.51 5 N 23612 2.21 5 O 25848 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E GLU 108": "OE1" <-> "OE2" Residue "F GLU 108": "OE1" <-> "OE2" Residue "G GLU 108": "OE1" <-> "OE2" Residue "H GLU 108": "OE1" <-> "OE2" Residue "A GLU 278": "OE1" <-> "OE2" Residue "A ASP 785": "OD1" <-> "OD2" Residue "A PHE 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 794": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1085": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1266": "OE1" <-> "OE2" Residue "A GLU 1534": "OE1" <-> "OE2" Residue "A PHE 1553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1682": "OE1" <-> "OE2" Residue "A GLU 1732": "OE1" <-> "OE2" Residue "A ASP 1785": "OD1" <-> "OD2" Residue "A ASP 2379": "OD1" <-> "OD2" Residue "A GLU 2453": "OE1" <-> "OE2" Residue "A GLU 2698": "OE1" <-> "OE2" Residue "A ARG 2772": "NH1" <-> "NH2" Residue "A ASP 2796": "OD1" <-> "OD2" Residue "A ASP 2836": "OD1" <-> "OD2" Residue "A ASP 2875": "OD1" <-> "OD2" Residue "A GLU 2942": "OE1" <-> "OE2" Residue "A GLU 3259": "OE1" <-> "OE2" Residue "A GLU 3633": "OE1" <-> "OE2" Residue "A TYR 4058": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 4161": "OE1" <-> "OE2" Residue "A ASP 4664": "OD1" <-> "OD2" Residue "A ASP 4678": "OD1" <-> "OD2" Residue "A TYR 4781": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 4846": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 4889": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 4896": "OD1" <-> "OD2" Residue "A GLU 4946": "OE1" <-> "OE2" Residue "A PHE 4951": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 278": "OE1" <-> "OE2" Residue "B ASP 785": "OD1" <-> "OD2" Residue "B PHE 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 794": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1085": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1266": "OE1" <-> "OE2" Residue "B GLU 1534": "OE1" <-> "OE2" Residue "B PHE 1553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1682": "OE1" <-> "OE2" Residue "B GLU 1732": "OE1" <-> "OE2" Residue "B ASP 1785": "OD1" <-> "OD2" Residue "B ASP 2379": "OD1" <-> "OD2" Residue "B GLU 2453": "OE1" <-> "OE2" Residue "B GLU 2698": "OE1" <-> "OE2" Residue "B ARG 2772": "NH1" <-> "NH2" Residue "B ASP 2796": "OD1" <-> "OD2" Residue "B ASP 2836": "OD1" <-> "OD2" Residue "B ASP 2875": "OD1" <-> "OD2" Residue "B GLU 2942": "OE1" <-> "OE2" Residue "B GLU 3259": "OE1" <-> "OE2" Residue "B GLU 3633": "OE1" <-> "OE2" Residue "B TYR 4058": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 4161": "OE1" <-> "OE2" Residue "B ASP 4664": "OD1" <-> "OD2" Residue "B ASP 4678": "OD1" <-> "OD2" Residue "B TYR 4781": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 4846": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 4889": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 4896": "OD1" <-> "OD2" Residue "B GLU 4946": "OE1" <-> "OE2" Residue "B PHE 4951": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 278": "OE1" <-> "OE2" Residue "C ASP 785": "OD1" <-> "OD2" Residue "C PHE 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 794": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1085": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1266": "OE1" <-> "OE2" Residue "C GLU 1534": "OE1" <-> "OE2" Residue "C PHE 1553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1682": "OE1" <-> "OE2" Residue "C GLU 1732": "OE1" <-> "OE2" Residue "C ASP 1785": "OD1" <-> "OD2" Residue "C ASP 2379": "OD1" <-> "OD2" Residue "C GLU 2453": "OE1" <-> "OE2" Residue "C GLU 2698": "OE1" <-> "OE2" Residue "C ARG 2772": "NH1" <-> "NH2" Residue "C ASP 2796": "OD1" <-> "OD2" Residue "C ASP 2836": "OD1" <-> "OD2" Residue "C ASP 2875": "OD1" <-> "OD2" Residue "C GLU 2942": "OE1" <-> "OE2" Residue "C GLU 3259": "OE1" <-> "OE2" Residue "C GLU 3633": "OE1" <-> "OE2" Residue "C TYR 4058": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 4161": "OE1" <-> "OE2" Residue "C ASP 4664": "OD1" <-> "OD2" Residue "C ASP 4678": "OD1" <-> "OD2" Residue "C TYR 4781": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 4846": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 4889": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 4896": "OD1" <-> "OD2" Residue "C GLU 4946": "OE1" <-> "OE2" Residue "C PHE 4951": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 278": "OE1" <-> "OE2" Residue "D ASP 785": "OD1" <-> "OD2" Residue "D PHE 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 794": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1085": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1266": "OE1" <-> "OE2" Residue "D GLU 1534": "OE1" <-> "OE2" Residue "D PHE 1553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1682": "OE1" <-> "OE2" Residue "D GLU 1732": "OE1" <-> "OE2" Residue "D ASP 1785": "OD1" <-> "OD2" Residue "D ASP 2379": "OD1" <-> "OD2" Residue "D GLU 2453": "OE1" <-> "OE2" Residue "D GLU 2698": "OE1" <-> "OE2" Residue "D ARG 2772": "NH1" <-> "NH2" Residue "D ASP 2796": "OD1" <-> "OD2" Residue "D ASP 2836": "OD1" <-> "OD2" Residue "D ASP 2875": "OD1" <-> "OD2" Residue "D GLU 2942": "OE1" <-> "OE2" Residue "D GLU 3259": "OE1" <-> "OE2" Residue "D GLU 3633": "OE1" <-> "OE2" Residue "D TYR 4058": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 4161": "OE1" <-> "OE2" Residue "D ASP 4664": "OD1" <-> "OD2" Residue "D ASP 4678": "OD1" <-> "OD2" Residue "D TYR 4781": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 4846": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 4889": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 4896": "OD1" <-> "OD2" Residue "D GLU 4946": "OE1" <-> "OE2" Residue "D PHE 4951": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.39s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 138656 Number of models: 1 Model: "" Number of chains: 12 Chain: "E" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "F" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "G" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "H" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "A" Number of atoms: 33771 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4224, 33763 Classifications: {'peptide': 4224} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4067} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 4224, 33763 Classifications: {'peptide': 4224} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4067} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 34485 Chain: "B" Number of atoms: 33771 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4224, 33763 Classifications: {'peptide': 4224} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4067} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 4224, 33763 Classifications: {'peptide': 4224} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4067} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 34485 Chain: "C" Number of atoms: 33771 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4224, 33763 Classifications: {'peptide': 4224} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4067} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 4224, 33763 Classifications: {'peptide': 4224} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4067} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 34485 Chain: "D" Number of atoms: 33771 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4224, 33763 Classifications: {'peptide': 4224} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4067} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 4224, 33763 Classifications: {'peptide': 4224} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4067} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 34485 Chain: "A" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 75 Unusual residues: {' CA': 1, ' ZN': 1, 'ATP': 2, 'XAN': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 75 Unusual residues: {' CA': 1, ' ZN': 1, 'ATP': 2, 'XAN': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 75 Unusual residues: {' CA': 1, ' ZN': 1, 'ATP': 2, 'XAN': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 75 Unusual residues: {' CA': 1, ' ZN': 1, 'ATP': 2, 'XAN': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 36364 SG CYS A4888 181.145 208.888 124.542 1.00168.31 S ATOM 36389 SG CYS A4891 180.719 206.409 121.665 1.00153.93 S ATOM 70135 SG CYS B4888 208.798 195.012 124.599 1.00169.95 S ATOM 70160 SG CYS B4891 206.314 195.442 121.728 1.00156.12 S ATOM A030I SG CYS C4888 195.207 167.779 124.605 1.00167.55 S ATOM A0317 SG CYS C4891 195.638 170.248 121.720 1.00153.28 S ATOM A0T2L SG CYS D4888 168.039 181.065 124.716 1.00171.50 S ATOM A0T3A SG CYS D4891 170.520 180.617 121.844 1.00158.75 S Time building chain proxies: 93.52, per 1000 atoms: 0.67 Number of scatterers: 138656 At special positions: 0 Unit cell: (376.65, 377.487, 209.25, 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 4 19.99 S 936 16.00 P 24 15.00 O 25848 8.00 N 23612 7.00 C 88228 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 36 " - pdb=" SG CYS A 65 " distance=2.03 Simple disulfide: pdb=" SG CYS A4806 " - pdb=" SG CYS A4812 " distance=2.03 Simple disulfide: pdb=" SG CYS B 36 " - pdb=" SG CYS B 65 " distance=2.03 Simple disulfide: pdb=" SG CYS B4806 " - pdb=" SG CYS B4812 " distance=2.03 Simple disulfide: pdb=" SG CYS C 36 " - pdb=" SG CYS C 65 " distance=2.03 Simple disulfide: pdb=" SG CYS C4806 " - pdb=" SG CYS C4812 " distance=2.03 Simple disulfide: pdb=" SG CYS D 36 " - pdb=" SG CYS D 65 " distance=2.03 Simple disulfide: pdb=" SG CYS D4806 " - pdb=" SG CYS D4812 " 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: 41.65 Conformation dependent library (CDL) restraints added in 33.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A5001 " pdb="ZN ZN A5001 " - pdb=" NE2 HIS A4908 " pdb="ZN ZN A5001 " - pdb=" ND1 HIS A4913 " pdb="ZN ZN A5001 " - pdb=" SG CYS A4891 " pdb="ZN ZN A5001 " - pdb=" SG CYS A4888 " pdb=" ZN B5001 " pdb="ZN ZN B5001 " - pdb=" NE2 HIS B4908 " pdb="ZN ZN B5001 " - pdb=" ND1 HIS B4913 " pdb="ZN ZN B5001 " - pdb=" SG CYS B4891 " pdb="ZN ZN B5001 " - pdb=" SG CYS B4888 " pdb=" ZN C5001 " pdb="ZN ZN C5001 " - pdb=" NE2 HIS C4908 " pdb="ZN ZN C5001 " - pdb=" ND1 HIS C4913 " pdb="ZN ZN C5001 " - pdb=" SG CYS C4891 " pdb="ZN ZN C5001 " - pdb=" SG CYS C4888 " pdb=" ZN D5001 " pdb="ZN ZN D5001 " - pdb=" NE2 HIS D4908 " pdb="ZN ZN D5001 " - pdb=" ND1 HIS D4913 " pdb="ZN ZN D5001 " - pdb=" SG CYS D4891 " pdb="ZN ZN D5001 " - pdb=" SG CYS D4888 " Number of angles added : 4 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 32464 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: 692 helices and 84 sheets defined 59.1% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 40.97 Creating SS restraints... Processing helix chain 'E' and resid 39 through 44 Processing helix chain 'E' and resid 57 through 68 removed outlier: 5.087A pdb=" N SER E 68 " --> pdb=" O ALA E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 83 removed outlier: 3.906A pdb=" N TYR E 83 " --> pdb=" O PRO E 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 39 through 44 Processing helix chain 'F' and resid 57 through 68 removed outlier: 5.088A pdb=" N SER F 68 " --> pdb=" O ALA F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 83 removed outlier: 3.906A pdb=" N TYR F 83 " --> pdb=" O PRO F 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 44 Processing helix chain 'G' and resid 57 through 68 removed outlier: 5.088A pdb=" N SER G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 83 removed outlier: 3.906A pdb=" N TYR G 83 " --> pdb=" O PRO G 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 39 through 44 Processing helix chain 'H' and resid 57 through 68 removed outlier: 5.087A pdb=" N SER H 68 " --> pdb=" O ALA H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 83 removed outlier: 3.906A pdb=" N TYR H 83 " --> pdb=" O PRO H 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 66 removed outlier: 4.031A pdb=" N CYS A 65 " --> pdb=" O ASP A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 84 Processing helix chain 'A' and resid 155 through 160 removed outlier: 4.597A pdb=" N TRP A 159 " --> pdb=" O GLY A 155 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N TRP A 160 " --> pdb=" O GLU A 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 155 through 160' Processing helix chain 'A' and resid 253 through 259 removed outlier: 4.986A pdb=" N THR A 259 " --> pdb=" O GLU A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 270 removed outlier: 4.436A pdb=" N VAL A 269 " --> pdb=" O GLY A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 328 Processing helix chain 'A' and resid 409 through 439 removed outlier: 3.680A pdb=" N LEU A 425 " --> pdb=" O SER A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 446 removed outlier: 5.262A pdb=" N ASP A 446 " --> pdb=" O ALA A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 464 Processing helix chain 'A' and resid 471 through 493 Processing helix chain 'A' and resid 494 through 508 removed outlier: 4.717A pdb=" N TYR A 508 " --> pdb=" O ARG A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 518 Processing helix chain 'A' and resid 519 through 542 removed outlier: 4.802A pdb=" N LYS A 527 " --> pdb=" O GLY A 523 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N SER A 528 " --> pdb=" O GLU A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 555 removed outlier: 3.858A pdb=" N SER A 552 " --> pdb=" O CYS A 548 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N GLY A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N SER A 554 " --> pdb=" O GLN A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 563 removed outlier: 4.125A pdb=" N ARG A 561 " --> pdb=" O TRP A 557 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LEU A 562 " --> pdb=" O LEU A 558 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N GLU A 563 " --> pdb=" O ILE A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 582 Processing helix chain 'A' and resid 583 through 590 removed outlier: 4.212A pdb=" N ASN A 587 " --> pdb=" O PRO A 583 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE A 588 " --> pdb=" O GLU A 584 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N LYS A 590 " --> pdb=" O LEU A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 604 removed outlier: 3.540A pdb=" N SER A 596 " --> pdb=" O GLY A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 620 removed outlier: 3.716A pdb=" N LEU A 611 " --> pdb=" O ASN A 607 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL A 619 " --> pdb=" O CYS A 615 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N CYS A 620 " --> pdb=" O SER A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 636 Processing helix chain 'A' and resid 821 through 826 removed outlier: 4.595A pdb=" N ALA A 825 " --> pdb=" O PRO A 821 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N VAL A 826 " --> pdb=" O CYS A 822 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 821 through 826' Processing helix chain 'A' and resid 875 through 901 removed outlier: 4.993A pdb=" N GLU A 883 " --> pdb=" O GLU A 879 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N LYS A 884 " --> pdb=" O ARG A 880 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ILE A 898 " --> pdb=" O VAL A 894 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLY A 901 " --> pdb=" O LYS A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 925 Proline residue: A 925 - end of helix Processing helix chain 'A' and resid 926 through 947 Processing helix chain 'A' and resid 954 through 961 removed outlier: 3.997A pdb=" N GLU A 958 " --> pdb=" O ASP A 954 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N VAL A 961 " --> pdb=" O ALA A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1015 Processing helix chain 'A' and resid 1039 through 1061 removed outlier: 3.703A pdb=" N GLY A1061 " --> pdb=" O LEU A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1220 through 1225 removed outlier: 3.803A pdb=" N LEU A1224 " --> pdb=" O ASP A1220 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N LYS A1225 " --> pdb=" O VAL A1221 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1220 through 1225' Processing helix chain 'A' and resid 1230 through 1235 removed outlier: 7.047A pdb=" N GLU A1234 " --> pdb=" O CYS A1230 " (cutoff:3.500A) Processing helix chain 'A' and resid 1416 through 1423 removed outlier: 4.191A pdb=" N MET A1421 " --> pdb=" O TYR A1417 " (cutoff:3.500A) Processing helix chain 'A' and resid 1437 through 1442 removed outlier: 3.982A pdb=" N VAL A1441 " --> pdb=" O GLU A1437 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N TRP A1442 " --> pdb=" O PRO A1438 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1437 through 1442' Processing helix chain 'A' and resid 1489 through 1495 removed outlier: 5.554A pdb=" N SER A1495 " --> pdb=" O GLY A1491 " (cutoff:3.500A) Processing helix chain 'A' and resid 1565 through 1571 removed outlier: 3.593A pdb=" N GLY A1569 " --> pdb=" O PRO A1565 " (cutoff:3.500A) Processing helix chain 'A' and resid 1640 through 1648 removed outlier: 4.324A pdb=" N LEU A1644 " --> pdb=" O ASP A1640 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N THR A1645 " --> pdb=" O ILE A1641 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N GLU A1646 " --> pdb=" O LEU A1642 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLN A1647 " --> pdb=" O GLU A1643 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N GLU A1648 " --> pdb=" O LEU A1644 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1640 through 1648' Processing helix chain 'A' and resid 1649 through 1666 removed outlier: 3.611A pdb=" N CYS A1665 " --> pdb=" O TYR A1661 " (cutoff:3.500A) Processing helix chain 'A' and resid 1669 through 1680 removed outlier: 3.771A pdb=" N SER A1678 " --> pdb=" O HIS A1674 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N HIS A1679 " --> pdb=" O ALA A1675 " (cutoff:3.500A) Processing helix chain 'A' and resid 1681 through 1691 removed outlier: 3.669A pdb=" N GLU A1690 " --> pdb=" O LEU A1686 " (cutoff:3.500A) Processing helix chain 'A' and resid 1695 through 1710 Processing helix chain 'A' and resid 1711 through 1723 removed outlier: 3.926A pdb=" N ASN A1722 " --> pdb=" O ARG A1718 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ASN A1723 " --> pdb=" O LEU A1719 " (cutoff:3.500A) Processing helix chain 'A' and resid 1730 through 1736 removed outlier: 3.591A pdb=" N ILE A1736 " --> pdb=" O GLU A1732 " (cutoff:3.500A) Processing helix chain 'A' and resid 1783 through 1803 removed outlier: 3.532A pdb=" N LYS A1800 " --> pdb=" O THR A1796 " (cutoff:3.500A) Processing helix chain 'A' and resid 1813 through 1832 Proline residue: A1820 - end of helix Processing helix chain 'A' and resid 1836 through 1847 Processing helix chain 'A' and resid 1892 through 1897 removed outlier: 4.394A pdb=" N LYS A1897 " --> pdb=" O LEU A1893 " (cutoff:3.500A) Processing helix chain 'A' and resid 1899 through 1944 removed outlier: 4.261A pdb=" N ASP A1931 " --> pdb=" O ALA A1927 " (cutoff:3.500A) Processing helix chain 'A' and resid 1957 through 1968 removed outlier: 4.581A pdb=" N GLU A1964 " --> pdb=" O ARG A1960 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N PHE A1965 " --> pdb=" O LYS A1961 " (cutoff:3.500A) Proline residue: A1968 - end of helix Processing helix chain 'A' and resid 1969 through 1979 removed outlier: 3.580A pdb=" N ASN A1978 " --> pdb=" O ASN A1974 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N PHE A1979 " --> pdb=" O MET A1975 " (cutoff:3.500A) Processing helix chain 'A' and resid 1989 through 2008 removed outlier: 3.581A pdb=" N GLU A2001 " --> pdb=" O LEU A1997 " (cutoff:3.500A) Processing helix chain 'A' and resid 2057 through 2073 removed outlier: 3.679A pdb=" N VAL A2067 " --> pdb=" O SER A2063 " (cutoff:3.500A) Processing helix chain 'A' and resid 2077 through 2094 removed outlier: 3.846A pdb=" N GLY A2094 " --> pdb=" O ARG A2090 " (cutoff:3.500A) Processing helix chain 'A' and resid 2095 through 2105 Proline residue: A2103 - end of helix Processing helix chain 'A' and resid 2109 through 2133 removed outlier: 3.798A pdb=" N VAL A2113 " --> pdb=" O ASN A2109 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N GLU A2114 " --> pdb=" O GLY A2110 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N ASP A2115 " --> pdb=" O VAL A2111 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU A2130 " --> pdb=" O ILE A2126 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N SER A2131 " --> pdb=" O ARG A2127 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N VAL A2132 " --> pdb=" O SER A2128 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N ARG A2133 " --> pdb=" O LEU A2129 " (cutoff:3.500A) Processing helix chain 'A' and resid 2135 through 2153 removed outlier: 5.494A pdb=" N LYS A2153 " --> pdb=" O ILE A2149 " (cutoff:3.500A) Processing helix chain 'A' and resid 2158 through 2166 removed outlier: 3.518A pdb=" N GLY A2166 " --> pdb=" O MET A2162 " (cutoff:3.500A) Processing helix chain 'A' and resid 2167 through 2183 removed outlier: 5.570A pdb=" N GLY A2182 " --> pdb=" O VAL A2178 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N GLU A2183 " --> pdb=" O LEU A2179 " (cutoff:3.500A) Processing helix chain 'A' and resid 2189 through 2208 removed outlier: 3.848A pdb=" N VAL A2193 " --> pdb=" O PHE A2189 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA A2194 " --> pdb=" O PRO A2190 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SER A2207 " --> pdb=" O PHE A2203 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ARG A2208 " --> pdb=" O CYS A2204 " (cutoff:3.500A) Processing helix chain 'A' and resid 2209 through 2219 removed outlier: 3.869A pdb=" N ASP A2216 " --> pdb=" O LYS A2212 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N HIS A2217 " --> pdb=" O ALA A2213 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU A2218 " --> pdb=" O MET A2214 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N SER A2219 " --> pdb=" O PHE A2215 " (cutoff:3.500A) Processing helix chain 'A' and resid 2220 through 2225 Processing helix chain 'A' and resid 2238 through 2248 Processing helix chain 'A' and resid 2250 through 2257 Processing helix chain 'A' and resid 2258 through 2275 removed outlier: 3.662A pdb=" N LEU A2262 " --> pdb=" O ARG A2258 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL A2265 " --> pdb=" O ASP A2261 " (cutoff:3.500A) Processing helix chain 'A' and resid 2277 through 2284 removed outlier: 3.661A pdb=" N VAL A2281 " --> pdb=" O CYS A2277 " (cutoff:3.500A) Processing helix chain 'A' and resid 2291 through 2307 removed outlier: 3.696A pdb=" N ARG A2297 " --> pdb=" O VAL A2293 " (cutoff:3.500A) Processing helix chain 'A' and resid 2313 through 2328 removed outlier: 3.524A pdb=" N VAL A2319 " --> pdb=" O GLU A2315 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL A2320 " --> pdb=" O ASN A2316 " (cutoff:3.500A) Proline residue: A2328 - end of helix Processing helix chain 'A' and resid 2342 through 2357 Proline residue: A2357 - end of helix Processing helix chain 'A' and resid 2377 through 2382 Processing helix chain 'A' and resid 2383 through 2412 Proline residue: A2404 - end of helix removed outlier: 9.212A pdb=" N HIS A2407 " --> pdb=" O ALA A2403 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LEU A2408 " --> pdb=" O PRO A2404 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE A2409 " --> pdb=" O GLU A2405 " (cutoff:3.500A) Processing helix chain 'A' and resid 2413 through 2428 Proline residue: A2428 - end of helix Processing helix chain 'A' and resid 2429 through 2439 removed outlier: 5.667A pdb=" N ALA A2439 " --> pdb=" O VAL A2435 " (cutoff:3.500A) Processing helix chain 'A' and resid 2461 through 2475 removed outlier: 3.821A pdb=" N LYS A2465 " --> pdb=" O CYS A2461 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA A2467 " --> pdb=" O ASP A2463 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N MET A2468 " --> pdb=" O HIS A2464 " (cutoff:3.500A) Processing helix chain 'A' and resid 2480 through 2504 removed outlier: 4.888A pdb=" N LEU A2493 " --> pdb=" O GLU A2489 " (cutoff:3.500A) Proline residue: A2494 - end of helix removed outlier: 3.645A pdb=" N ASP A2503 " --> pdb=" O ALA A2499 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N THR A2504 " --> pdb=" O ALA A2500 " (cutoff:3.500A) Processing helix chain 'A' and resid 2510 through 2532 removed outlier: 5.279A pdb=" N LEU A2525 " --> pdb=" O CYS A2521 " (cutoff:3.500A) Proline residue: A2526 - end of helix Processing helix chain 'A' and resid 2541 through 2559 removed outlier: 5.149A pdb=" N CYS A2559 " --> pdb=" O LEU A2555 " (cutoff:3.500A) Processing helix chain 'A' and resid 2562 through 2580 Processing helix chain 'A' and resid 2581 through 2596 removed outlier: 4.122A pdb=" N MET A2585 " --> pdb=" O ARG A2581 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N GLN A2586 " --> pdb=" O PRO A2582 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N HIS A2587 " --> pdb=" O SER A2583 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N LEU A2588 " --> pdb=" O MET A2584 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N PHE A2594 " --> pdb=" O ARG A2590 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ASP A2595 " --> pdb=" O ARG A2591 " (cutoff:3.500A) Processing helix chain 'A' and resid 2602 through 2618 Proline residue: A2606 - end of helix Processing helix chain 'A' and resid 2634 through 2655 removed outlier: 6.189A pdb=" N LEU A2638 " --> pdb=" O SER A2634 " (cutoff:3.500A) Processing helix chain 'A' and resid 2659 through 2677 Proline residue: A2667 - end of helix Proline residue: A2677 - end of helix Processing helix chain 'A' and resid 2691 through 2696 removed outlier: 4.351A pdb=" N MET A2695 " --> pdb=" O LYS A2691 " (cutoff:3.500A) Processing helix chain 'A' and resid 2716 through 2740 removed outlier: 4.508A pdb=" N PHE A2720 " --> pdb=" O LYS A2716 " (cutoff:3.500A) Processing helix chain 'A' and resid 2767 through 2784 removed outlier: 3.674A pdb=" N TYR A2771 " --> pdb=" O GLU A2767 " (cutoff:3.500A) Proline residue: A2774 - end of helix Processing helix chain 'A' and resid 2792 through 2802 removed outlier: 4.216A pdb=" N ASP A2796 " --> pdb=" O THR A2792 " (cutoff:3.500A) Processing helix chain 'A' and resid 2834 through 2864 Processing helix chain 'A' and resid 2873 through 2878 removed outlier: 5.253A pdb=" N THR A2878 " --> pdb=" O TYR A2874 " (cutoff:3.500A) Processing helix chain 'A' and resid 2881 through 2900 removed outlier: 4.359A pdb=" N ASP A2885 " --> pdb=" O GLU A2881 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE A2892 " --> pdb=" O LYS A2888 " (cutoff:3.500A) Processing helix chain 'A' and resid 2916 through 2921 removed outlier: 4.315A pdb=" N ARG A2920 " --> pdb=" O SER A2916 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N PHE A2921 " --> pdb=" O ILE A2917 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2916 through 2921' Processing helix chain 'A' and resid 2922 through 2947 Processing helix chain 'A' and resid 2956 through 2979 removed outlier: 4.298A pdb=" N LEU A2968 " --> pdb=" O ALA A2964 " (cutoff:3.500A) Proline residue: A2969 - end of helix Processing helix chain 'A' and resid 2997 through 3016 Processing helix chain 'A' and resid 3018 through 3023 removed outlier: 4.994A pdb=" N GLY A3023 " --> pdb=" O ILE A3019 " (cutoff:3.500A) Processing helix chain 'A' and resid 3025 through 3040 removed outlier: 4.303A pdb=" N LEU A3040 " --> pdb=" O LEU A3036 " (cutoff:3.500A) Processing helix chain 'A' and resid 3041 through 3048 Processing helix chain 'A' and resid 3050 through 3079 Processing helix chain 'A' and resid 3088 through 3116 removed outlier: 5.354A pdb=" N LEU A3102 " --> pdb=" O THR A3098 " (cutoff:3.500A) Proline residue: A3103 - end of helix Processing helix chain 'A' and resid 3117 through 3123 removed outlier: 4.561A pdb=" N LEU A3123 " --> pdb=" O GLU A3119 " (cutoff:3.500A) Processing helix chain 'A' and resid 3124 through 3143 removed outlier: 6.416A pdb=" N VAL A3128 " --> pdb=" O GLU A3124 " (cutoff:3.500A) Processing helix chain 'A' and resid 3145 through 3152 Processing helix chain 'A' and resid 3153 through 3166 Processing helix chain 'A' and resid 3182 through 3187 Processing helix chain 'A' and resid 3188 through 3196 removed outlier: 4.878A pdb=" N ARG A3192 " --> pdb=" O SER A3188 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N SER A3196 " --> pdb=" O ARG A3192 " (cutoff:3.500A) Processing helix chain 'A' and resid 3200 through 3206 removed outlier: 3.889A pdb=" N CYS A3205 " --> pdb=" O VAL A3201 " (cutoff:3.500A) Proline residue: A3206 - end of helix Processing helix chain 'A' and resid 3210 through 3225 Processing helix chain 'A' and resid 3231 through 3250 removed outlier: 4.552A pdb=" N MET A3235 " --> pdb=" O MET A3231 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU A3239 " --> pdb=" O MET A3235 " (cutoff:3.500A) Proline residue: A3240 - end of helix removed outlier: 3.965A pdb=" N ARG A3248 " --> pdb=" O SER A3244 " (cutoff:3.500A) Processing helix chain 'A' and resid 3253 through 3258 Proline residue: A3258 - end of helix Processing helix chain 'A' and resid 3269 through 3289 removed outlier: 3.817A pdb=" N TYR A3285 " --> pdb=" O LEU A3281 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN A3286 " --> pdb=" O LYS A3282 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLY A3289 " --> pdb=" O TYR A3285 " (cutoff:3.500A) Processing helix chain 'A' and resid 3293 through 3311 removed outlier: 4.168A pdb=" N LYS A3297 " --> pdb=" O GLY A3293 " (cutoff:3.500A) Proline residue: A3305 - end of helix removed outlier: 5.190A pdb=" N LYS A3311 " --> pdb=" O ILE A3307 " (cutoff:3.500A) Processing helix chain 'A' and resid 3312 through 3318 removed outlier: 4.928A pdb=" N THR A3317 " --> pdb=" O GLN A3313 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N HIS A3318 " --> pdb=" O LEU A3314 " (cutoff:3.500A) Processing helix chain 'A' and resid 3319 through 3331 removed outlier: 4.806A pdb=" N ALA A3331 " --> pdb=" O LYS A3327 " (cutoff:3.500A) Processing helix chain 'A' and resid 3599 through 3606 removed outlier: 5.369A pdb=" N ALA A3606 " --> pdb=" O CYS A3602 " (cutoff:3.500A) Processing helix chain 'A' and resid 3607 through 3612 removed outlier: 3.715A pdb=" N LEU A3611 " --> pdb=" O PRO A3607 " (cutoff:3.500A) Proline residue: A3612 - end of helix No H-bonds generated for 'chain 'A' and resid 3607 through 3612' Processing helix chain 'A' and resid 3613 through 3632 removed outlier: 4.609A pdb=" N GLU A3630 " --> pdb=" O LYS A3626 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N THR A3631 " --> pdb=" O SER A3627 " (cutoff:3.500A) Processing helix chain 'A' and resid 3636 through 3646 Processing helix chain 'A' and resid 3649 through 3654 removed outlier: 4.122A pdb=" N GLU A3654 " --> pdb=" O GLU A3650 " (cutoff:3.500A) Processing helix chain 'A' and resid 3662 through 3677 Processing helix chain 'A' and resid 3685 through 3701 removed outlier: 3.802A pdb=" N ASP A3693 " --> pdb=" O MET A3689 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N HIS A3700 " --> pdb=" O ALA A3696 " (cutoff:3.500A) Processing helix chain 'A' and resid 3713 through 3733 removed outlier: 3.770A pdb=" N LEU A3731 " --> pdb=" O GLN A3727 " (cutoff:3.500A) Processing helix chain 'A' and resid 3735 through 3748 removed outlier: 3.807A pdb=" N MET A3739 " --> pdb=" O GLY A3735 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LYS A3748 " --> pdb=" O ILE A3744 " (cutoff:3.500A) Processing helix chain 'A' and resid 3752 through 3767 Processing helix chain 'A' and resid 3770 through 3785 Processing helix chain 'A' and resid 3786 through 3800 removed outlier: 5.392A pdb=" N PHE A3790 " --> pdb=" O ASP A3786 " (cutoff:3.500A) Processing helix chain 'A' and resid 3804 through 3818 Processing helix chain 'A' and resid 3832 through 3848 removed outlier: 4.025A pdb=" N THR A3836 " --> pdb=" O ASP A3832 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N CYS A3847 " --> pdb=" O LEU A3843 " (cutoff:3.500A) Processing helix chain 'A' and resid 3851 through 3860 Processing helix chain 'A' and resid 3869 through 3894 removed outlier: 4.544A pdb=" N GLY A3894 " --> pdb=" O TRP A3890 " (cutoff:3.500A) Processing helix chain 'A' and resid 3899 through 3925 Processing helix chain 'A' and resid 3928 through 3939 removed outlier: 4.794A pdb=" N ARG A3939 " --> pdb=" O LEU A3935 " (cutoff:3.500A) Processing helix chain 'A' and resid 3940 through 3959 removed outlier: 3.732A pdb=" N MET A3956 " --> pdb=" O ALA A3952 " (cutoff:3.500A) Processing helix chain 'A' and resid 3964 through 3987 removed outlier: 3.629A pdb=" N GLU A3987 " --> pdb=" O LEU A3983 " (cutoff:3.500A) Processing helix chain 'A' and resid 3993 through 4007 Processing helix chain 'A' and resid 4008 through 4027 removed outlier: 4.848A pdb=" N LYS A4024 " --> pdb=" O PHE A4020 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ASP A4025 " --> pdb=" O LEU A4021 " (cutoff:3.500A) Processing helix chain 'A' and resid 4029 through 4037 Proline residue: A4037 - end of helix Processing helix chain 'A' and resid 4044 through 4056 Processing helix chain 'A' and resid 4059 through 4071 removed outlier: 5.208A pdb=" N GLU A4071 " --> pdb=" O LEU A4067 " (cutoff:3.500A) Processing helix chain 'A' and resid 4079 through 4110 removed outlier: 5.240A pdb=" N GLU A4089 " --> pdb=" O LYS A4085 " (cutoff:3.500A) Proline residue: A4090 - end of helix removed outlier: 3.770A pdb=" N PHE A4096 " --> pdb=" O LYS A4092 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ASN A4097 " --> pdb=" O ASP A4093 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL A4098 " --> pdb=" O ILE A4094 " (cutoff:3.500A) Proline residue: A4110 - end of helix Processing helix chain 'A' and resid 4112 through 4123 removed outlier: 4.038A pdb=" N GLN A4116 " --> pdb=" O ASP A4112 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR A4117 " --> pdb=" O THR A4113 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N PHE A4118 " --> pdb=" O ARG A4114 " (cutoff:3.500A) Processing helix chain 'A' and resid 4124 through 4130 Processing helix chain 'A' and resid 4153 through 4162 Processing helix chain 'A' and resid 4163 through 4179 Processing helix chain 'A' and resid 4182 through 4207 removed outlier: 4.231A pdb=" N MET A4186 " --> pdb=" O GLU A4182 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLU A4187 " --> pdb=" O LYS A4183 " (cutoff:3.500A) Processing helix chain 'A' and resid 4237 through 4261 removed outlier: 3.634A pdb=" N ILE A4252 " --> pdb=" O LEU A4248 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N THR A4254 " --> pdb=" O TYR A4250 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEU A4261 " --> pdb=" O ARG A4257 " (cutoff:3.500A) Processing helix chain 'A' and resid 4263 through 4272 removed outlier: 3.630A pdb=" N LYS A4272 " --> pdb=" O MET A4268 " (cutoff:3.500A) Processing helix chain 'A' and resid 4275 through 4310 removed outlier: 3.721A pdb=" N ALA A4282 " --> pdb=" O ASP A4278 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N PHE A4283 " --> pdb=" O MET A4279 " (cutoff:3.500A) Processing helix chain 'A' and resid 4480 through 4499 Processing helix chain 'A' and resid 4500 through 4520 removed outlier: 3.699A pdb=" N LEU A4507 " --> pdb=" O ARG A4503 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N PHE A4519 " --> pdb=" O PHE A4515 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N TYR A4520 " --> pdb=" O ILE A4516 " (cutoff:3.500A) Processing helix chain 'A' and resid 4567 through 4612 removed outlier: 3.650A pdb=" N THR A4571 " --> pdb=" O TYR A4567 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N VAL A4595 " --> pdb=" O TYR A4591 " (cutoff:3.500A) Proline residue: A4596 - end of helix Processing helix chain 'A' and resid 4625 through 4638 removed outlier: 4.146A pdb=" N LEU A4633 " --> pdb=" O GLN A4629 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N VAL A4634 " --> pdb=" O TRP A4630 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE A4635 " --> pdb=" O ASP A4631 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N ASN A4636 " --> pdb=" O ARG A4632 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N THR A4637 " --> pdb=" O LEU A4633 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N GLN A4638 " --> pdb=" O VAL A4634 " (cutoff:3.500A) Processing helix chain 'A' and resid 4648 through 4658 Processing helix chain 'A' and resid 4662 through 4671 Processing helix chain 'A' and resid 4673 through 4683 removed outlier: 4.776A pdb=" N LEU A4677 " --> pdb=" O ASP A4673 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N ASP A4678 " --> pdb=" O LYS A4674 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N PHE A4679 " --> pdb=" O ALA A4675 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ASP A4681 " --> pdb=" O LEU A4677 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ARG A4683 " --> pdb=" O PHE A4679 " (cutoff:3.500A) Processing helix chain 'A' and resid 4693 through 4702 removed outlier: 4.072A pdb=" N VAL A4697 " --> pdb=" O SER A4693 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ASP A4702 " --> pdb=" O LEU A4698 " (cutoff:3.500A) Processing helix chain 'A' and resid 4703 through 4717 removed outlier: 5.441A pdb=" N ASN A4717 " --> pdb=" O VAL A4713 " (cutoff:3.500A) Processing helix chain 'A' and resid 4718 through 4736 removed outlier: 3.740A pdb=" N TYR A4734 " --> pdb=" O VAL A4730 " (cutoff:3.500A) Processing helix chain 'A' and resid 4737 through 4751 removed outlier: 4.758A pdb=" N ALA A4741 " --> pdb=" O PHE A4737 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N HIS A4742 " --> pdb=" O PHE A4738 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU A4743 " --> pdb=" O PHE A4739 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LEU A4744 " --> pdb=" O ALA A4740 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ASP A4745 " --> pdb=" O ALA A4741 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N ILE A4746 " --> pdb=" O HIS A4742 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ALA A4747 " --> pdb=" O LEU A4743 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N LYS A4751 " --> pdb=" O ALA A4747 " (cutoff:3.500A) Processing helix chain 'A' and resid 4752 through 4762 removed outlier: 3.961A pdb=" N VAL A4760 " --> pdb=" O ILE A4756 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N THR A4761 " --> pdb=" O LEU A4757 " (cutoff:3.500A) Processing helix chain 'A' and resid 4763 through 4788 Processing helix chain 'A' and resid 4789 through 4794 removed outlier: 5.208A pdb=" N TYR A4793 " --> pdb=" O PHE A4789 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ASN A4794 " --> pdb=" O ARG A4790 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4789 through 4794' Processing helix chain 'A' and resid 4808 through 4823 removed outlier: 4.496A pdb=" N VAL A4819 " --> pdb=" O PHE A4815 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N GLY A4820 " --> pdb=" O HIS A4816 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL A4821 " --> pdb=" O MET A4817 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ARG A4822 " --> pdb=" O TYR A4818 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA A4823 " --> pdb=" O VAL A4819 " (cutoff:3.500A) Processing helix chain 'A' and resid 4826 through 4832 removed outlier: 4.581A pdb=" N GLU A4830 " --> pdb=" O GLY A4826 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N GLU A4832 " --> pdb=" O GLY A4828 " (cutoff:3.500A) Processing helix chain 'A' and resid 4839 through 4854 Processing helix chain 'A' and resid 4858 through 4887 Processing helix chain 'A' and resid 4894 through 4902 removed outlier: 4.050A pdb=" N PHE A4898 " --> pdb=" O GLY A4894 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N VAL A4901 " --> pdb=" O TYR A4897 " (cutoff:3.500A) Proline residue: A4902 - end of helix Processing helix chain 'A' and resid 4903 through 4911 Processing helix chain 'A' and resid 4914 through 4928 removed outlier: 3.854A pdb=" N TYR A4918 " --> pdb=" O ASN A4914 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU A4919 " --> pdb=" O LEU A4915 " (cutoff:3.500A) Processing helix chain 'A' and resid 4934 through 4947 Processing helix chain 'A' and resid 4957 through 4963 Processing helix chain 'A' and resid 857 through 862 removed outlier: 4.136A pdb=" N ALA A 860 " --> pdb=" O LEU A 857 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA A 861 " --> pdb=" O THR A 858 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N PHE A 862 " --> pdb=" O GLN A 859 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 857 through 862' Processing helix chain 'A' and resid 1772 through 1778 removed outlier: 4.531A pdb=" N CYS A1775 " --> pdb=" O SER A1772 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N TYR A1778 " --> pdb=" O CYS A1775 " (cutoff:3.500A) Processing helix chain 'A' and resid 4948 through 4953 removed outlier: 4.455A pdb=" N PHE A4951 " --> pdb=" O CYS A4948 " (cutoff:3.500A) Proline residue: A4953 - end of helix Processing helix chain 'A' and resid 54 through 59 Proline residue: A 59 - end of helix No H-bonds generated for 'chain 'A' and resid 54 through 59' Processing helix chain 'A' and resid 4614 through 4619 Processing helix chain 'B' and resid 61 through 66 removed outlier: 4.030A pdb=" N CYS B 65 " --> pdb=" O ASP B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 84 Processing helix chain 'B' and resid 155 through 160 removed outlier: 4.597A pdb=" N TRP B 159 " --> pdb=" O GLY B 155 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N TRP B 160 " --> pdb=" O GLU B 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 155 through 160' Processing helix chain 'B' and resid 253 through 259 removed outlier: 4.986A pdb=" N THR B 259 " --> pdb=" O GLU B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 270 removed outlier: 4.436A pdb=" N VAL B 269 " --> pdb=" O GLY B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 328 Processing helix chain 'B' and resid 409 through 439 removed outlier: 3.681A pdb=" N LEU B 425 " --> pdb=" O SER B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 446 removed outlier: 5.262A pdb=" N ASP B 446 " --> pdb=" O ALA B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 464 Processing helix chain 'B' and resid 471 through 493 Processing helix chain 'B' and resid 494 through 508 removed outlier: 4.717A pdb=" N TYR B 508 " --> pdb=" O ARG B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 518 Processing helix chain 'B' and resid 519 through 542 removed outlier: 4.802A pdb=" N LYS B 527 " --> pdb=" O GLY B 523 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N SER B 528 " --> pdb=" O GLU B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 555 removed outlier: 3.857A pdb=" N SER B 552 " --> pdb=" O CYS B 548 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N GLY B 553 " --> pdb=" O ALA B 549 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N SER B 554 " --> pdb=" O GLN B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 563 removed outlier: 4.125A pdb=" N ARG B 561 " --> pdb=" O TRP B 557 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LEU B 562 " --> pdb=" O LEU B 558 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N GLU B 563 " --> pdb=" O ILE B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 582 Processing helix chain 'B' and resid 583 through 590 removed outlier: 4.211A pdb=" N ASN B 587 " --> pdb=" O PRO B 583 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE B 588 " --> pdb=" O GLU B 584 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N LYS B 590 " --> pdb=" O LEU B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 604 removed outlier: 3.539A pdb=" N SER B 596 " --> pdb=" O GLY B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 620 removed outlier: 3.716A pdb=" N LEU B 611 " --> pdb=" O ASN B 607 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL B 619 " --> pdb=" O CYS B 615 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N CYS B 620 " --> pdb=" O SER B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 636 Processing helix chain 'B' and resid 821 through 826 removed outlier: 4.596A pdb=" N ALA B 825 " --> pdb=" O PRO B 821 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N VAL B 826 " --> pdb=" O CYS B 822 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 821 through 826' Processing helix chain 'B' and resid 875 through 901 removed outlier: 4.993A pdb=" N GLU B 883 " --> pdb=" O GLU B 879 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N LYS B 884 " --> pdb=" O ARG B 880 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ILE B 898 " --> pdb=" O VAL B 894 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLY B 901 " --> pdb=" O LYS B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 920 through 925 Proline residue: B 925 - end of helix Processing helix chain 'B' and resid 926 through 947 Processing helix chain 'B' and resid 954 through 961 removed outlier: 3.997A pdb=" N GLU B 958 " --> pdb=" O ASP B 954 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N VAL B 961 " --> pdb=" O ALA B 957 " (cutoff:3.500A) Processing helix chain 'B' and resid 989 through 1015 Processing helix chain 'B' and resid 1039 through 1061 removed outlier: 3.702A pdb=" N GLY B1061 " --> pdb=" O LEU B1057 " (cutoff:3.500A) Processing helix chain 'B' and resid 1220 through 1225 removed outlier: 3.802A pdb=" N LEU B1224 " --> pdb=" O ASP B1220 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N LYS B1225 " --> pdb=" O VAL B1221 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1220 through 1225' Processing helix chain 'B' and resid 1230 through 1235 removed outlier: 7.048A pdb=" N GLU B1234 " --> pdb=" O CYS B1230 " (cutoff:3.500A) Processing helix chain 'B' and resid 1416 through 1423 removed outlier: 4.190A pdb=" N MET B1421 " --> pdb=" O TYR B1417 " (cutoff:3.500A) Processing helix chain 'B' and resid 1437 through 1442 removed outlier: 3.981A pdb=" N VAL B1441 " --> pdb=" O GLU B1437 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N TRP B1442 " --> pdb=" O PRO B1438 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1437 through 1442' Processing helix chain 'B' and resid 1489 through 1495 removed outlier: 5.554A pdb=" N SER B1495 " --> pdb=" O GLY B1491 " (cutoff:3.500A) Processing helix chain 'B' and resid 1565 through 1571 removed outlier: 3.592A pdb=" N GLY B1569 " --> pdb=" O PRO B1565 " (cutoff:3.500A) Processing helix chain 'B' and resid 1640 through 1648 removed outlier: 4.324A pdb=" N LEU B1644 " --> pdb=" O ASP B1640 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N THR B1645 " --> pdb=" O ILE B1641 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N GLU B1646 " --> pdb=" O LEU B1642 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN B1647 " --> pdb=" O GLU B1643 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N GLU B1648 " --> pdb=" O LEU B1644 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1640 through 1648' Processing helix chain 'B' and resid 1649 through 1666 removed outlier: 3.611A pdb=" N CYS B1665 " --> pdb=" O TYR B1661 " (cutoff:3.500A) Processing helix chain 'B' and resid 1669 through 1680 removed outlier: 3.772A pdb=" N SER B1678 " --> pdb=" O HIS B1674 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N HIS B1679 " --> pdb=" O ALA B1675 " (cutoff:3.500A) Processing helix chain 'B' and resid 1681 through 1691 removed outlier: 3.669A pdb=" N GLU B1690 " --> pdb=" O LEU B1686 " (cutoff:3.500A) Processing helix chain 'B' and resid 1695 through 1710 Processing helix chain 'B' and resid 1711 through 1723 removed outlier: 3.926A pdb=" N ASN B1722 " --> pdb=" O ARG B1718 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ASN B1723 " --> pdb=" O LEU B1719 " (cutoff:3.500A) Processing helix chain 'B' and resid 1730 through 1736 removed outlier: 3.590A pdb=" N ILE B1736 " --> pdb=" O GLU B1732 " (cutoff:3.500A) Processing helix chain 'B' and resid 1783 through 1803 removed outlier: 3.532A pdb=" N LYS B1800 " --> pdb=" O THR B1796 " (cutoff:3.500A) Processing helix chain 'B' and resid 1813 through 1832 Proline residue: B1820 - end of helix Processing helix chain 'B' and resid 1836 through 1847 Processing helix chain 'B' and resid 1892 through 1897 removed outlier: 4.393A pdb=" N LYS B1897 " --> pdb=" O LEU B1893 " (cutoff:3.500A) Processing helix chain 'B' and resid 1899 through 1944 removed outlier: 4.262A pdb=" N ASP B1931 " --> pdb=" O ALA B1927 " (cutoff:3.500A) Processing helix chain 'B' and resid 1957 through 1968 removed outlier: 4.582A pdb=" N GLU B1964 " --> pdb=" O ARG B1960 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N PHE B1965 " --> pdb=" O LYS B1961 " (cutoff:3.500A) Proline residue: B1968 - end of helix Processing helix chain 'B' and resid 1969 through 1979 removed outlier: 3.581A pdb=" N ASN B1978 " --> pdb=" O ASN B1974 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N PHE B1979 " --> pdb=" O MET B1975 " (cutoff:3.500A) Processing helix chain 'B' and resid 1989 through 2008 removed outlier: 3.581A pdb=" N GLU B2001 " --> pdb=" O LEU B1997 " (cutoff:3.500A) Processing helix chain 'B' and resid 2057 through 2073 removed outlier: 3.678A pdb=" N VAL B2067 " --> pdb=" O SER B2063 " (cutoff:3.500A) Processing helix chain 'B' and resid 2077 through 2094 removed outlier: 3.846A pdb=" N GLY B2094 " --> pdb=" O ARG B2090 " (cutoff:3.500A) Processing helix chain 'B' and resid 2095 through 2105 Proline residue: B2103 - end of helix Processing helix chain 'B' and resid 2109 through 2133 removed outlier: 3.798A pdb=" N VAL B2113 " --> pdb=" O ASN B2109 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N GLU B2114 " --> pdb=" O GLY B2110 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N ASP B2115 " --> pdb=" O VAL B2111 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU B2130 " --> pdb=" O ILE B2126 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N SER B2131 " --> pdb=" O ARG B2127 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL B2132 " --> pdb=" O SER B2128 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N ARG B2133 " --> pdb=" O LEU B2129 " (cutoff:3.500A) Processing helix chain 'B' and resid 2135 through 2153 removed outlier: 5.494A pdb=" N LYS B2153 " --> pdb=" O ILE B2149 " (cutoff:3.500A) Processing helix chain 'B' and resid 2158 through 2166 removed outlier: 3.517A pdb=" N GLY B2166 " --> pdb=" O MET B2162 " (cutoff:3.500A) Processing helix chain 'B' and resid 2167 through 2183 removed outlier: 5.570A pdb=" N GLY B2182 " --> pdb=" O VAL B2178 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N GLU B2183 " --> pdb=" O LEU B2179 " (cutoff:3.500A) Processing helix chain 'B' and resid 2189 through 2208 removed outlier: 3.849A pdb=" N VAL B2193 " --> pdb=" O PHE B2189 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA B2194 " --> pdb=" O PRO B2190 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N SER B2207 " --> pdb=" O PHE B2203 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ARG B2208 " --> pdb=" O CYS B2204 " (cutoff:3.500A) Processing helix chain 'B' and resid 2209 through 2219 removed outlier: 3.869A pdb=" N ASP B2216 " --> pdb=" O LYS B2212 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N HIS B2217 " --> pdb=" O ALA B2213 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU B2218 " --> pdb=" O MET B2214 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N SER B2219 " --> pdb=" O PHE B2215 " (cutoff:3.500A) Processing helix chain 'B' and resid 2220 through 2225 Processing helix chain 'B' and resid 2238 through 2248 Processing helix chain 'B' and resid 2250 through 2257 Processing helix chain 'B' and resid 2258 through 2275 removed outlier: 3.661A pdb=" N LEU B2262 " --> pdb=" O ARG B2258 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL B2265 " --> pdb=" O ASP B2261 " (cutoff:3.500A) Processing helix chain 'B' and resid 2277 through 2284 removed outlier: 3.661A pdb=" N VAL B2281 " --> pdb=" O CYS B2277 " (cutoff:3.500A) Processing helix chain 'B' and resid 2291 through 2307 removed outlier: 3.697A pdb=" N ARG B2297 " --> pdb=" O VAL B2293 " (cutoff:3.500A) Processing helix chain 'B' and resid 2313 through 2328 removed outlier: 3.524A pdb=" N VAL B2319 " --> pdb=" O GLU B2315 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL B2320 " --> pdb=" O ASN B2316 " (cutoff:3.500A) Proline residue: B2328 - end of helix Processing helix chain 'B' and resid 2342 through 2357 Proline residue: B2357 - end of helix Processing helix chain 'B' and resid 2377 through 2382 Processing helix chain 'B' and resid 2383 through 2412 Proline residue: B2404 - end of helix removed outlier: 9.212A pdb=" N HIS B2407 " --> pdb=" O ALA B2403 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LEU B2408 " --> pdb=" O PRO B2404 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE B2409 " --> pdb=" O GLU B2405 " (cutoff:3.500A) Processing helix chain 'B' and resid 2413 through 2428 Proline residue: B2428 - end of helix Processing helix chain 'B' and resid 2429 through 2439 removed outlier: 5.666A pdb=" N ALA B2439 " --> pdb=" O VAL B2435 " (cutoff:3.500A) Processing helix chain 'B' and resid 2461 through 2475 removed outlier: 3.822A pdb=" N LYS B2465 " --> pdb=" O CYS B2461 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA B2467 " --> pdb=" O ASP B2463 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET B2468 " --> pdb=" O HIS B2464 " (cutoff:3.500A) Processing helix chain 'B' and resid 2480 through 2504 removed outlier: 4.888A pdb=" N LEU B2493 " --> pdb=" O GLU B2489 " (cutoff:3.500A) Proline residue: B2494 - end of helix removed outlier: 3.644A pdb=" N ASP B2503 " --> pdb=" O ALA B2499 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N THR B2504 " --> pdb=" O ALA B2500 " (cutoff:3.500A) Processing helix chain 'B' and resid 2510 through 2532 removed outlier: 5.280A pdb=" N LEU B2525 " --> pdb=" O CYS B2521 " (cutoff:3.500A) Proline residue: B2526 - end of helix Processing helix chain 'B' and resid 2541 through 2559 removed outlier: 5.150A pdb=" N CYS B2559 " --> pdb=" O LEU B2555 " (cutoff:3.500A) Processing helix chain 'B' and resid 2562 through 2580 Processing helix chain 'B' and resid 2581 through 2596 removed outlier: 4.122A pdb=" N MET B2585 " --> pdb=" O ARG B2581 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N GLN B2586 " --> pdb=" O PRO B2582 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N HIS B2587 " --> pdb=" O SER B2583 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N LEU B2588 " --> pdb=" O MET B2584 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N PHE B2594 " --> pdb=" O ARG B2590 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ASP B2595 " --> pdb=" O ARG B2591 " (cutoff:3.500A) Processing helix chain 'B' and resid 2602 through 2618 Proline residue: B2606 - end of helix Processing helix chain 'B' and resid 2634 through 2655 removed outlier: 6.190A pdb=" N LEU B2638 " --> pdb=" O SER B2634 " (cutoff:3.500A) Processing helix chain 'B' and resid 2659 through 2677 Proline residue: B2667 - end of helix Proline residue: B2677 - end of helix Processing helix chain 'B' and resid 2691 through 2696 removed outlier: 4.351A pdb=" N MET B2695 " --> pdb=" O LYS B2691 " (cutoff:3.500A) Processing helix chain 'B' and resid 2716 through 2740 removed outlier: 4.508A pdb=" N PHE B2720 " --> pdb=" O LYS B2716 " (cutoff:3.500A) Processing helix chain 'B' and resid 2767 through 2784 removed outlier: 3.675A pdb=" N TYR B2771 " --> pdb=" O GLU B2767 " (cutoff:3.500A) Proline residue: B2774 - end of helix Processing helix chain 'B' and resid 2792 through 2802 removed outlier: 4.216A pdb=" N ASP B2796 " --> pdb=" O THR B2792 " (cutoff:3.500A) Processing helix chain 'B' and resid 2834 through 2864 Processing helix chain 'B' and resid 2873 through 2878 removed outlier: 5.252A pdb=" N THR B2878 " --> pdb=" O TYR B2874 " (cutoff:3.500A) Processing helix chain 'B' and resid 2881 through 2900 removed outlier: 4.359A pdb=" N ASP B2885 " --> pdb=" O GLU B2881 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE B2892 " --> pdb=" O LYS B2888 " (cutoff:3.500A) Processing helix chain 'B' and resid 2916 through 2921 removed outlier: 4.314A pdb=" N ARG B2920 " --> pdb=" O SER B2916 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N PHE B2921 " --> pdb=" O ILE B2917 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2916 through 2921' Processing helix chain 'B' and resid 2922 through 2947 Processing helix chain 'B' and resid 2956 through 2979 removed outlier: 4.298A pdb=" N LEU B2968 " --> pdb=" O ALA B2964 " (cutoff:3.500A) Proline residue: B2969 - end of helix Processing helix chain 'B' and resid 2997 through 3016 Processing helix chain 'B' and resid 3018 through 3023 removed outlier: 4.994A pdb=" N GLY B3023 " --> pdb=" O ILE B3019 " (cutoff:3.500A) Processing helix chain 'B' and resid 3025 through 3040 removed outlier: 4.302A pdb=" N LEU B3040 " --> pdb=" O LEU B3036 " (cutoff:3.500A) Processing helix chain 'B' and resid 3041 through 3048 Processing helix chain 'B' and resid 3050 through 3079 Processing helix chain 'B' and resid 3088 through 3116 removed outlier: 5.354A pdb=" N LEU B3102 " --> pdb=" O THR B3098 " (cutoff:3.500A) Proline residue: B3103 - end of helix Processing helix chain 'B' and resid 3117 through 3123 removed outlier: 4.561A pdb=" N LEU B3123 " --> pdb=" O GLU B3119 " (cutoff:3.500A) Processing helix chain 'B' and resid 3124 through 3143 removed outlier: 6.418A pdb=" N VAL B3128 " --> pdb=" O GLU B3124 " (cutoff:3.500A) Processing helix chain 'B' and resid 3145 through 3152 Processing helix chain 'B' and resid 3153 through 3166 Processing helix chain 'B' and resid 3182 through 3187 Processing helix chain 'B' and resid 3188 through 3196 removed outlier: 4.879A pdb=" N ARG B3192 " --> pdb=" O SER B3188 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N SER B3196 " --> pdb=" O ARG B3192 " (cutoff:3.500A) Processing helix chain 'B' and resid 3200 through 3206 removed outlier: 3.889A pdb=" N CYS B3205 " --> pdb=" O VAL B3201 " (cutoff:3.500A) Proline residue: B3206 - end of helix Processing helix chain 'B' and resid 3210 through 3225 Processing helix chain 'B' and resid 3231 through 3250 removed outlier: 4.552A pdb=" N MET B3235 " --> pdb=" O MET B3231 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU B3239 " --> pdb=" O MET B3235 " (cutoff:3.500A) Proline residue: B3240 - end of helix removed outlier: 3.965A pdb=" N ARG B3248 " --> pdb=" O SER B3244 " (cutoff:3.500A) Processing helix chain 'B' and resid 3253 through 3258 Proline residue: B3258 - end of helix Processing helix chain 'B' and resid 3269 through 3289 removed outlier: 3.817A pdb=" N TYR B3285 " --> pdb=" O LEU B3281 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN B3286 " --> pdb=" O LYS B3282 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N GLY B3289 " --> pdb=" O TYR B3285 " (cutoff:3.500A) Processing helix chain 'B' and resid 3293 through 3311 removed outlier: 4.168A pdb=" N LYS B3297 " --> pdb=" O GLY B3293 " (cutoff:3.500A) Proline residue: B3305 - end of helix removed outlier: 5.189A pdb=" N LYS B3311 " --> pdb=" O ILE B3307 " (cutoff:3.500A) Processing helix chain 'B' and resid 3312 through 3318 removed outlier: 4.927A pdb=" N THR B3317 " --> pdb=" O GLN B3313 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N HIS B3318 " --> pdb=" O LEU B3314 " (cutoff:3.500A) Processing helix chain 'B' and resid 3319 through 3331 removed outlier: 4.806A pdb=" N ALA B3331 " --> pdb=" O LYS B3327 " (cutoff:3.500A) Processing helix chain 'B' and resid 3599 through 3606 removed outlier: 5.370A pdb=" N ALA B3606 " --> pdb=" O CYS B3602 " (cutoff:3.500A) Processing helix chain 'B' and resid 3607 through 3612 removed outlier: 3.715A pdb=" N LEU B3611 " --> pdb=" O PRO B3607 " (cutoff:3.500A) Proline residue: B3612 - end of helix No H-bonds generated for 'chain 'B' and resid 3607 through 3612' Processing helix chain 'B' and resid 3613 through 3632 removed outlier: 4.610A pdb=" N GLU B3630 " --> pdb=" O LYS B3626 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N THR B3631 " --> pdb=" O SER B3627 " (cutoff:3.500A) Processing helix chain 'B' and resid 3636 through 3646 Processing helix chain 'B' and resid 3649 through 3654 removed outlier: 4.122A pdb=" N GLU B3654 " --> pdb=" O GLU B3650 " (cutoff:3.500A) Processing helix chain 'B' and resid 3662 through 3677 Processing helix chain 'B' and resid 3685 through 3701 removed outlier: 3.801A pdb=" N ASP B3693 " --> pdb=" O MET B3689 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N HIS B3700 " --> pdb=" O ALA B3696 " (cutoff:3.500A) Processing helix chain 'B' and resid 3713 through 3733 removed outlier: 3.770A pdb=" N LEU B3731 " --> pdb=" O GLN B3727 " (cutoff:3.500A) Processing helix chain 'B' and resid 3735 through 3748 removed outlier: 3.807A pdb=" N MET B3739 " --> pdb=" O GLY B3735 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LYS B3748 " --> pdb=" O ILE B3744 " (cutoff:3.500A) Processing helix chain 'B' and resid 3752 through 3767 Processing helix chain 'B' and resid 3770 through 3785 Processing helix chain 'B' and resid 3786 through 3800 removed outlier: 5.392A pdb=" N PHE B3790 " --> pdb=" O ASP B3786 " (cutoff:3.500A) Processing helix chain 'B' and resid 3804 through 3818 Processing helix chain 'B' and resid 3832 through 3848 removed outlier: 4.025A pdb=" N THR B3836 " --> pdb=" O ASP B3832 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N CYS B3847 " --> pdb=" O LEU B3843 " (cutoff:3.500A) Processing helix chain 'B' and resid 3851 through 3860 Processing helix chain 'B' and resid 3869 through 3894 removed outlier: 4.543A pdb=" N GLY B3894 " --> pdb=" O TRP B3890 " (cutoff:3.500A) Processing helix chain 'B' and resid 3899 through 3925 Processing helix chain 'B' and resid 3928 through 3939 removed outlier: 4.794A pdb=" N ARG B3939 " --> pdb=" O LEU B3935 " (cutoff:3.500A) Processing helix chain 'B' and resid 3940 through 3959 removed outlier: 3.732A pdb=" N MET B3956 " --> pdb=" O ALA B3952 " (cutoff:3.500A) Processing helix chain 'B' and resid 3964 through 3987 removed outlier: 3.629A pdb=" N GLU B3987 " --> pdb=" O LEU B3983 " (cutoff:3.500A) Processing helix chain 'B' and resid 3993 through 4007 Processing helix chain 'B' and resid 4008 through 4027 removed outlier: 4.849A pdb=" N LYS B4024 " --> pdb=" O PHE B4020 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ASP B4025 " --> pdb=" O LEU B4021 " (cutoff:3.500A) Processing helix chain 'B' and resid 4029 through 4037 Proline residue: B4037 - end of helix Processing helix chain 'B' and resid 4044 through 4056 Processing helix chain 'B' and resid 4059 through 4071 removed outlier: 5.208A pdb=" N GLU B4071 " --> pdb=" O LEU B4067 " (cutoff:3.500A) Processing helix chain 'B' and resid 4079 through 4110 removed outlier: 5.240A pdb=" N GLU B4089 " --> pdb=" O LYS B4085 " (cutoff:3.500A) Proline residue: B4090 - end of helix removed outlier: 3.770A pdb=" N PHE B4096 " --> pdb=" O LYS B4092 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ASN B4097 " --> pdb=" O ASP B4093 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL B4098 " --> pdb=" O ILE B4094 " (cutoff:3.500A) Proline residue: B4110 - end of helix Processing helix chain 'B' and resid 4112 through 4123 removed outlier: 4.038A pdb=" N GLN B4116 " --> pdb=" O ASP B4112 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR B4117 " --> pdb=" O THR B4113 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N PHE B4118 " --> pdb=" O ARG B4114 " (cutoff:3.500A) Processing helix chain 'B' and resid 4124 through 4130 Processing helix chain 'B' and resid 4153 through 4162 Processing helix chain 'B' and resid 4163 through 4179 Processing helix chain 'B' and resid 4182 through 4207 removed outlier: 4.232A pdb=" N MET B4186 " --> pdb=" O GLU B4182 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU B4187 " --> pdb=" O LYS B4183 " (cutoff:3.500A) Processing helix chain 'B' and resid 4237 through 4261 removed outlier: 3.635A pdb=" N ILE B4252 " --> pdb=" O LEU B4248 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N THR B4254 " --> pdb=" O TYR B4250 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU B4261 " --> pdb=" O ARG B4257 " (cutoff:3.500A) Processing helix chain 'B' and resid 4263 through 4272 removed outlier: 3.630A pdb=" N LYS B4272 " --> pdb=" O MET B4268 " (cutoff:3.500A) Processing helix chain 'B' and resid 4275 through 4310 removed outlier: 3.722A pdb=" N ALA B4282 " --> pdb=" O ASP B4278 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N PHE B4283 " --> pdb=" O MET B4279 " (cutoff:3.500A) Processing helix chain 'B' and resid 4480 through 4499 Processing helix chain 'B' and resid 4500 through 4520 removed outlier: 3.698A pdb=" N LEU B4507 " --> pdb=" O ARG B4503 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N PHE B4519 " --> pdb=" O PHE B4515 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N TYR B4520 " --> pdb=" O ILE B4516 " (cutoff:3.500A) Processing helix chain 'B' and resid 4567 through 4612 removed outlier: 3.650A pdb=" N THR B4571 " --> pdb=" O TYR B4567 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N VAL B4595 " --> pdb=" O TYR B4591 " (cutoff:3.500A) Proline residue: B4596 - end of helix Processing helix chain 'B' and resid 4625 through 4638 removed outlier: 4.145A pdb=" N LEU B4633 " --> pdb=" O GLN B4629 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N VAL B4634 " --> pdb=" O TRP B4630 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE B4635 " --> pdb=" O ASP B4631 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N ASN B4636 " --> pdb=" O ARG B4632 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N THR B4637 " --> pdb=" O LEU B4633 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N GLN B4638 " --> pdb=" O VAL B4634 " (cutoff:3.500A) Processing helix chain 'B' and resid 4648 through 4658 Processing helix chain 'B' and resid 4662 through 4671 Processing helix chain 'B' and resid 4673 through 4683 removed outlier: 4.775A pdb=" N LEU B4677 " --> pdb=" O ASP B4673 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N ASP B4678 " --> pdb=" O LYS B4674 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N PHE B4679 " --> pdb=" O ALA B4675 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ASP B4681 " --> pdb=" O LEU B4677 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ARG B4683 " --> pdb=" O PHE B4679 " (cutoff:3.500A) Processing helix chain 'B' and resid 4693 through 4702 removed outlier: 4.071A pdb=" N VAL B4697 " --> pdb=" O SER B4693 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ASP B4702 " --> pdb=" O LEU B4698 " (cutoff:3.500A) Processing helix chain 'B' and resid 4703 through 4717 removed outlier: 5.441A pdb=" N ASN B4717 " --> pdb=" O VAL B4713 " (cutoff:3.500A) Processing helix chain 'B' and resid 4718 through 4736 removed outlier: 3.740A pdb=" N TYR B4734 " --> pdb=" O VAL B4730 " (cutoff:3.500A) Processing helix chain 'B' and resid 4737 through 4751 removed outlier: 4.758A pdb=" N ALA B4741 " --> pdb=" O PHE B4737 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N HIS B4742 " --> pdb=" O PHE B4738 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU B4743 " --> pdb=" O PHE B4739 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N LEU B4744 " --> pdb=" O ALA B4740 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ASP B4745 " --> pdb=" O ALA B4741 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N ILE B4746 " --> pdb=" O HIS B4742 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ALA B4747 " --> pdb=" O LEU B4743 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N LYS B4751 " --> pdb=" O ALA B4747 " (cutoff:3.500A) Processing helix chain 'B' and resid 4752 through 4762 removed outlier: 3.960A pdb=" N VAL B4760 " --> pdb=" O ILE B4756 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N THR B4761 " --> pdb=" O LEU B4757 " (cutoff:3.500A) Processing helix chain 'B' and resid 4763 through 4788 Processing helix chain 'B' and resid 4789 through 4794 removed outlier: 5.209A pdb=" N TYR B4793 " --> pdb=" O PHE B4789 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ASN B4794 " --> pdb=" O ARG B4790 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4789 through 4794' Processing helix chain 'B' and resid 4808 through 4823 removed outlier: 4.496A pdb=" N VAL B4819 " --> pdb=" O PHE B4815 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLY B4820 " --> pdb=" O HIS B4816 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL B4821 " --> pdb=" O MET B4817 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ARG B4822 " --> pdb=" O TYR B4818 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA B4823 " --> pdb=" O VAL B4819 " (cutoff:3.500A) Processing helix chain 'B' and resid 4826 through 4832 removed outlier: 4.582A pdb=" N GLU B4830 " --> pdb=" O GLY B4826 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N GLU B4832 " --> pdb=" O GLY B4828 " (cutoff:3.500A) Processing helix chain 'B' and resid 4839 through 4854 Processing helix chain 'B' and resid 4858 through 4887 Processing helix chain 'B' and resid 4894 through 4902 removed outlier: 4.050A pdb=" N PHE B4898 " --> pdb=" O GLY B4894 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N VAL B4901 " --> pdb=" O TYR B4897 " (cutoff:3.500A) Proline residue: B4902 - end of helix Processing helix chain 'B' and resid 4903 through 4911 Processing helix chain 'B' and resid 4914 through 4928 removed outlier: 3.854A pdb=" N TYR B4918 " --> pdb=" O ASN B4914 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU B4919 " --> pdb=" O LEU B4915 " (cutoff:3.500A) Processing helix chain 'B' and resid 4934 through 4947 Processing helix chain 'B' and resid 4957 through 4963 Processing helix chain 'B' and resid 857 through 862 removed outlier: 4.136A pdb=" N ALA B 860 " --> pdb=" O LEU B 857 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA B 861 " --> pdb=" O THR B 858 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N PHE B 862 " --> pdb=" O GLN B 859 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 857 through 862' Processing helix chain 'B' and resid 1772 through 1778 removed outlier: 4.530A pdb=" N CYS B1775 " --> pdb=" O SER B1772 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N TYR B1778 " --> pdb=" O CYS B1775 " (cutoff:3.500A) Processing helix chain 'B' and resid 4948 through 4953 removed outlier: 4.455A pdb=" N PHE B4951 " --> pdb=" O CYS B4948 " (cutoff:3.500A) Proline residue: B4953 - end of helix Processing helix chain 'B' and resid 54 through 59 Proline residue: B 59 - end of helix No H-bonds generated for 'chain 'B' and resid 54 through 59' Processing helix chain 'B' and resid 4614 through 4619 Processing helix chain 'C' and resid 61 through 66 removed outlier: 4.031A pdb=" N CYS C 65 " --> pdb=" O ASP C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 84 Processing helix chain 'C' and resid 155 through 160 removed outlier: 4.598A pdb=" N TRP C 159 " --> pdb=" O GLY C 155 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N TRP C 160 " --> pdb=" O GLU C 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 155 through 160' Processing helix chain 'C' and resid 253 through 259 removed outlier: 4.986A pdb=" N THR C 259 " --> pdb=" O GLU C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 270 removed outlier: 4.436A pdb=" N VAL C 269 " --> pdb=" O GLY C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 328 Processing helix chain 'C' and resid 409 through 439 removed outlier: 3.681A pdb=" N LEU C 425 " --> pdb=" O SER C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 446 removed outlier: 5.262A pdb=" N ASP C 446 " --> pdb=" O ALA C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 464 Processing helix chain 'C' and resid 471 through 493 Processing helix chain 'C' and resid 494 through 508 removed outlier: 4.717A pdb=" N TYR C 508 " --> pdb=" O ARG C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 518 Processing helix chain 'C' and resid 519 through 542 removed outlier: 4.802A pdb=" N LYS C 527 " --> pdb=" O GLY C 523 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N SER C 528 " --> pdb=" O GLU C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 555 removed outlier: 3.858A pdb=" N SER C 552 " --> pdb=" O CYS C 548 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N GLY C 553 " --> pdb=" O ALA C 549 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N SER C 554 " --> pdb=" O GLN C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 563 removed outlier: 4.126A pdb=" N ARG C 561 " --> pdb=" O TRP C 557 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LEU C 562 " --> pdb=" O LEU C 558 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N GLU C 563 " --> pdb=" O ILE C 559 " (cutoff:3.500A) Processing helix chain 'C' and resid 567 through 582 Processing helix chain 'C' and resid 583 through 590 removed outlier: 4.211A pdb=" N ASN C 587 " --> pdb=" O PRO C 583 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE C 588 " --> pdb=" O GLU C 584 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N LYS C 590 " --> pdb=" O LEU C 586 " (cutoff:3.500A) Processing helix chain 'C' and resid 591 through 604 removed outlier: 3.539A pdb=" N SER C 596 " --> pdb=" O GLY C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 620 removed outlier: 3.717A pdb=" N LEU C 611 " --> pdb=" O ASN C 607 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL C 619 " --> pdb=" O CYS C 615 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N CYS C 620 " --> pdb=" O SER C 616 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 636 Processing helix chain 'C' and resid 821 through 826 removed outlier: 4.595A pdb=" N ALA C 825 " --> pdb=" O PRO C 821 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N VAL C 826 " --> pdb=" O CYS C 822 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 821 through 826' Processing helix chain 'C' and resid 875 through 901 removed outlier: 4.993A pdb=" N GLU C 883 " --> pdb=" O GLU C 879 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N LYS C 884 " --> pdb=" O ARG C 880 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE C 898 " --> pdb=" O VAL C 894 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLY C 901 " --> pdb=" O LYS C 897 " (cutoff:3.500A) Processing helix chain 'C' and resid 920 through 925 Proline residue: C 925 - end of helix Processing helix chain 'C' and resid 926 through 947 Processing helix chain 'C' and resid 954 through 961 removed outlier: 3.997A pdb=" N GLU C 958 " --> pdb=" O ASP C 954 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N VAL C 961 " --> pdb=" O ALA C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 989 through 1015 Processing helix chain 'C' and resid 1039 through 1061 removed outlier: 3.702A pdb=" N GLY C1061 " --> pdb=" O LEU C1057 " (cutoff:3.500A) Processing helix chain 'C' and resid 1220 through 1225 removed outlier: 3.802A pdb=" N LEU C1224 " --> pdb=" O ASP C1220 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N LYS C1225 " --> pdb=" O VAL C1221 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1220 through 1225' Processing helix chain 'C' and resid 1230 through 1235 removed outlier: 7.048A pdb=" N GLU C1234 " --> pdb=" O CYS C1230 " (cutoff:3.500A) Processing helix chain 'C' and resid 1416 through 1423 removed outlier: 4.191A pdb=" N MET C1421 " --> pdb=" O TYR C1417 " (cutoff:3.500A) Processing helix chain 'C' and resid 1437 through 1442 removed outlier: 3.981A pdb=" N VAL C1441 " --> pdb=" O GLU C1437 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N TRP C1442 " --> pdb=" O PRO C1438 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1437 through 1442' Processing helix chain 'C' and resid 1489 through 1495 removed outlier: 5.554A pdb=" N SER C1495 " --> pdb=" O GLY C1491 " (cutoff:3.500A) Processing helix chain 'C' and resid 1565 through 1571 removed outlier: 3.593A pdb=" N GLY C1569 " --> pdb=" O PRO C1565 " (cutoff:3.500A) Processing helix chain 'C' and resid 1640 through 1648 removed outlier: 4.324A pdb=" N LEU C1644 " --> pdb=" O ASP C1640 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N THR C1645 " --> pdb=" O ILE C1641 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N GLU C1646 " --> pdb=" O LEU C1642 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN C1647 " --> pdb=" O GLU C1643 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N GLU C1648 " --> pdb=" O LEU C1644 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1640 through 1648' Processing helix chain 'C' and resid 1649 through 1666 removed outlier: 3.610A pdb=" N CYS C1665 " --> pdb=" O TYR C1661 " (cutoff:3.500A) Processing helix chain 'C' and resid 1669 through 1680 removed outlier: 3.772A pdb=" N SER C1678 " --> pdb=" O HIS C1674 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N HIS C1679 " --> pdb=" O ALA C1675 " (cutoff:3.500A) Processing helix chain 'C' and resid 1681 through 1691 removed outlier: 3.669A pdb=" N GLU C1690 " --> pdb=" O LEU C1686 " (cutoff:3.500A) Processing helix chain 'C' and resid 1695 through 1710 Processing helix chain 'C' and resid 1711 through 1723 removed outlier: 3.926A pdb=" N ASN C1722 " --> pdb=" O ARG C1718 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ASN C1723 " --> pdb=" O LEU C1719 " (cutoff:3.500A) Processing helix chain 'C' and resid 1730 through 1736 removed outlier: 3.591A pdb=" N ILE C1736 " --> pdb=" O GLU C1732 " (cutoff:3.500A) Processing helix chain 'C' and resid 1783 through 1803 removed outlier: 3.533A pdb=" N LYS C1800 " --> pdb=" O THR C1796 " (cutoff:3.500A) Processing helix chain 'C' and resid 1813 through 1832 Proline residue: C1820 - end of helix Processing helix chain 'C' and resid 1836 through 1847 Processing helix chain 'C' and resid 1892 through 1897 removed outlier: 4.394A pdb=" N LYS C1897 " --> pdb=" O LEU C1893 " (cutoff:3.500A) Processing helix chain 'C' and resid 1899 through 1944 removed outlier: 4.262A pdb=" N ASP C1931 " --> pdb=" O ALA C1927 " (cutoff:3.500A) Processing helix chain 'C' and resid 1957 through 1968 removed outlier: 4.582A pdb=" N GLU C1964 " --> pdb=" O ARG C1960 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N PHE C1965 " --> pdb=" O LYS C1961 " (cutoff:3.500A) Proline residue: C1968 - end of helix Processing helix chain 'C' and resid 1969 through 1979 removed outlier: 3.580A pdb=" N ASN C1978 " --> pdb=" O ASN C1974 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N PHE C1979 " --> pdb=" O MET C1975 " (cutoff:3.500A) Processing helix chain 'C' and resid 1989 through 2008 removed outlier: 3.581A pdb=" N GLU C2001 " --> pdb=" O LEU C1997 " (cutoff:3.500A) Processing helix chain 'C' and resid 2057 through 2073 removed outlier: 3.679A pdb=" N VAL C2067 " --> pdb=" O SER C2063 " (cutoff:3.500A) Processing helix chain 'C' and resid 2077 through 2094 removed outlier: 3.847A pdb=" N GLY C2094 " --> pdb=" O ARG C2090 " (cutoff:3.500A) Processing helix chain 'C' and resid 2095 through 2105 Proline residue: C2103 - end of helix Processing helix chain 'C' and resid 2109 through 2133 removed outlier: 3.798A pdb=" N VAL C2113 " --> pdb=" O ASN C2109 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N GLU C2114 " --> pdb=" O GLY C2110 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N ASP C2115 " --> pdb=" O VAL C2111 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU C2130 " --> pdb=" O ILE C2126 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N SER C2131 " --> pdb=" O ARG C2127 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N VAL C2132 " --> pdb=" O SER C2128 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N ARG C2133 " --> pdb=" O LEU C2129 " (cutoff:3.500A) Processing helix chain 'C' and resid 2135 through 2153 removed outlier: 5.494A pdb=" N LYS C2153 " --> pdb=" O ILE C2149 " (cutoff:3.500A) Processing helix chain 'C' and resid 2158 through 2166 removed outlier: 3.517A pdb=" N GLY C2166 " --> pdb=" O MET C2162 " (cutoff:3.500A) Processing helix chain 'C' and resid 2167 through 2183 removed outlier: 5.570A pdb=" N GLY C2182 " --> pdb=" O VAL C2178 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N GLU C2183 " --> pdb=" O LEU C2179 " (cutoff:3.500A) Processing helix chain 'C' and resid 2189 through 2208 removed outlier: 3.849A pdb=" N VAL C2193 " --> pdb=" O PHE C2189 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA C2194 " --> pdb=" O PRO C2190 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N SER C2207 " --> pdb=" O PHE C2203 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ARG C2208 " --> pdb=" O CYS C2204 " (cutoff:3.500A) Processing helix chain 'C' and resid 2209 through 2219 removed outlier: 3.869A pdb=" N ASP C2216 " --> pdb=" O LYS C2212 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N HIS C2217 " --> pdb=" O ALA C2213 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU C2218 " --> pdb=" O MET C2214 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N SER C2219 " --> pdb=" O PHE C2215 " (cutoff:3.500A) Processing helix chain 'C' and resid 2220 through 2225 Processing helix chain 'C' and resid 2238 through 2248 Processing helix chain 'C' and resid 2250 through 2257 Processing helix chain 'C' and resid 2258 through 2275 removed outlier: 3.662A pdb=" N LEU C2262 " --> pdb=" O ARG C2258 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL C2265 " --> pdb=" O ASP C2261 " (cutoff:3.500A) Processing helix chain 'C' and resid 2277 through 2284 removed outlier: 3.661A pdb=" N VAL C2281 " --> pdb=" O CYS C2277 " (cutoff:3.500A) Processing helix chain 'C' and resid 2291 through 2307 removed outlier: 3.696A pdb=" N ARG C2297 " --> pdb=" O VAL C2293 " (cutoff:3.500A) Processing helix chain 'C' and resid 2313 through 2328 removed outlier: 3.525A pdb=" N VAL C2319 " --> pdb=" O GLU C2315 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL C2320 " --> pdb=" O ASN C2316 " (cutoff:3.500A) Proline residue: C2328 - end of helix Processing helix chain 'C' and resid 2342 through 2357 Proline residue: C2357 - end of helix Processing helix chain 'C' and resid 2377 through 2382 Processing helix chain 'C' and resid 2383 through 2412 Proline residue: C2404 - end of helix removed outlier: 9.213A pdb=" N HIS C2407 " --> pdb=" O ALA C2403 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LEU C2408 " --> pdb=" O PRO C2404 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE C2409 " --> pdb=" O GLU C2405 " (cutoff:3.500A) Processing helix chain 'C' and resid 2413 through 2428 Proline residue: C2428 - end of helix Processing helix chain 'C' and resid 2429 through 2439 removed outlier: 5.666A pdb=" N ALA C2439 " --> pdb=" O VAL C2435 " (cutoff:3.500A) Processing helix chain 'C' and resid 2461 through 2475 removed outlier: 3.821A pdb=" N LYS C2465 " --> pdb=" O CYS C2461 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA C2467 " --> pdb=" O ASP C2463 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET C2468 " --> pdb=" O HIS C2464 " (cutoff:3.500A) Processing helix chain 'C' and resid 2480 through 2504 removed outlier: 4.888A pdb=" N LEU C2493 " --> pdb=" O GLU C2489 " (cutoff:3.500A) Proline residue: C2494 - end of helix removed outlier: 3.645A pdb=" N ASP C2503 " --> pdb=" O ALA C2499 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N THR C2504 " --> pdb=" O ALA C2500 " (cutoff:3.500A) Processing helix chain 'C' and resid 2510 through 2532 removed outlier: 5.280A pdb=" N LEU C2525 " --> pdb=" O CYS C2521 " (cutoff:3.500A) Proline residue: C2526 - end of helix Processing helix chain 'C' and resid 2541 through 2559 removed outlier: 5.150A pdb=" N CYS C2559 " --> pdb=" O LEU C2555 " (cutoff:3.500A) Processing helix chain 'C' and resid 2562 through 2580 Processing helix chain 'C' and resid 2581 through 2596 removed outlier: 4.121A pdb=" N MET C2585 " --> pdb=" O ARG C2581 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N GLN C2586 " --> pdb=" O PRO C2582 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N HIS C2587 " --> pdb=" O SER C2583 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N LEU C2588 " --> pdb=" O MET C2584 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N PHE C2594 " --> pdb=" O ARG C2590 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ASP C2595 " --> pdb=" O ARG C2591 " (cutoff:3.500A) Processing helix chain 'C' and resid 2602 through 2618 Proline residue: C2606 - end of helix Processing helix chain 'C' and resid 2634 through 2655 removed outlier: 6.190A pdb=" N LEU C2638 " --> pdb=" O SER C2634 " (cutoff:3.500A) Processing helix chain 'C' and resid 2659 through 2677 Proline residue: C2667 - end of helix Proline residue: C2677 - end of helix Processing helix chain 'C' and resid 2691 through 2696 removed outlier: 4.351A pdb=" N MET C2695 " --> pdb=" O LYS C2691 " (cutoff:3.500A) Processing helix chain 'C' and resid 2716 through 2740 removed outlier: 4.509A pdb=" N PHE C2720 " --> pdb=" O LYS C2716 " (cutoff:3.500A) Processing helix chain 'C' and resid 2767 through 2784 removed outlier: 3.674A pdb=" N TYR C2771 " --> pdb=" O GLU C2767 " (cutoff:3.500A) Proline residue: C2774 - end of helix Processing helix chain 'C' and resid 2792 through 2802 removed outlier: 4.218A pdb=" N ASP C2796 " --> pdb=" O THR C2792 " (cutoff:3.500A) Processing helix chain 'C' and resid 2834 through 2864 Processing helix chain 'C' and resid 2873 through 2878 removed outlier: 5.252A pdb=" N THR C2878 " --> pdb=" O TYR C2874 " (cutoff:3.500A) Processing helix chain 'C' and resid 2881 through 2900 removed outlier: 4.359A pdb=" N ASP C2885 " --> pdb=" O GLU C2881 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE C2892 " --> pdb=" O LYS C2888 " (cutoff:3.500A) Processing helix chain 'C' and resid 2916 through 2921 removed outlier: 4.314A pdb=" N ARG C2920 " --> pdb=" O SER C2916 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N PHE C2921 " --> pdb=" O ILE C2917 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2916 through 2921' Processing helix chain 'C' and resid 2922 through 2947 Processing helix chain 'C' and resid 2956 through 2979 removed outlier: 4.297A pdb=" N LEU C2968 " --> pdb=" O ALA C2964 " (cutoff:3.500A) Proline residue: C2969 - end of helix Processing helix chain 'C' and resid 2997 through 3016 Processing helix chain 'C' and resid 3018 through 3023 removed outlier: 4.995A pdb=" N GLY C3023 " --> pdb=" O ILE C3019 " (cutoff:3.500A) Processing helix chain 'C' and resid 3025 through 3040 removed outlier: 4.303A pdb=" N LEU C3040 " --> pdb=" O LEU C3036 " (cutoff:3.500A) Processing helix chain 'C' and resid 3041 through 3048 Processing helix chain 'C' and resid 3050 through 3079 Processing helix chain 'C' and resid 3088 through 3116 removed outlier: 5.354A pdb=" N LEU C3102 " --> pdb=" O THR C3098 " (cutoff:3.500A) Proline residue: C3103 - end of helix Processing helix chain 'C' and resid 3117 through 3123 removed outlier: 4.560A pdb=" N LEU C3123 " --> pdb=" O GLU C3119 " (cutoff:3.500A) Processing helix chain 'C' and resid 3124 through 3143 removed outlier: 6.417A pdb=" N VAL C3128 " --> pdb=" O GLU C3124 " (cutoff:3.500A) Processing helix chain 'C' and resid 3145 through 3152 Processing helix chain 'C' and resid 3153 through 3166 Processing helix chain 'C' and resid 3182 through 3187 Processing helix chain 'C' and resid 3188 through 3196 removed outlier: 4.879A pdb=" N ARG C3192 " --> pdb=" O SER C3188 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N SER C3196 " --> pdb=" O ARG C3192 " (cutoff:3.500A) Processing helix chain 'C' and resid 3200 through 3206 removed outlier: 3.890A pdb=" N CYS C3205 " --> pdb=" O VAL C3201 " (cutoff:3.500A) Proline residue: C3206 - end of helix Processing helix chain 'C' and resid 3210 through 3225 Processing helix chain 'C' and resid 3231 through 3250 removed outlier: 4.552A pdb=" N MET C3235 " --> pdb=" O MET C3231 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU C3239 " --> pdb=" O MET C3235 " (cutoff:3.500A) Proline residue: C3240 - end of helix removed outlier: 3.965A pdb=" N ARG C3248 " --> pdb=" O SER C3244 " (cutoff:3.500A) Processing helix chain 'C' and resid 3253 through 3258 Proline residue: C3258 - end of helix Processing helix chain 'C' and resid 3269 through 3289 removed outlier: 3.816A pdb=" N TYR C3285 " --> pdb=" O LEU C3281 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASN C3286 " --> pdb=" O LYS C3282 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLY C3289 " --> pdb=" O TYR C3285 " (cutoff:3.500A) Processing helix chain 'C' and resid 3293 through 3311 removed outlier: 4.168A pdb=" N LYS C3297 " --> pdb=" O GLY C3293 " (cutoff:3.500A) Proline residue: C3305 - end of helix removed outlier: 5.190A pdb=" N LYS C3311 " --> pdb=" O ILE C3307 " (cutoff:3.500A) Processing helix chain 'C' and resid 3312 through 3318 removed outlier: 4.927A pdb=" N THR C3317 " --> pdb=" O GLN C3313 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N HIS C3318 " --> pdb=" O LEU C3314 " (cutoff:3.500A) Processing helix chain 'C' and resid 3319 through 3331 removed outlier: 4.806A pdb=" N ALA C3331 " --> pdb=" O LYS C3327 " (cutoff:3.500A) Processing helix chain 'C' and resid 3599 through 3606 removed outlier: 5.369A pdb=" N ALA C3606 " --> pdb=" O CYS C3602 " (cutoff:3.500A) Processing helix chain 'C' and resid 3607 through 3612 removed outlier: 3.715A pdb=" N LEU C3611 " --> pdb=" O PRO C3607 " (cutoff:3.500A) Proline residue: C3612 - end of helix No H-bonds generated for 'chain 'C' and resid 3607 through 3612' Processing helix chain 'C' and resid 3613 through 3632 removed outlier: 4.610A pdb=" N GLU C3630 " --> pdb=" O LYS C3626 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N THR C3631 " --> pdb=" O SER C3627 " (cutoff:3.500A) Processing helix chain 'C' and resid 3636 through 3646 Processing helix chain 'C' and resid 3649 through 3654 removed outlier: 4.122A pdb=" N GLU C3654 " --> pdb=" O GLU C3650 " (cutoff:3.500A) Processing helix chain 'C' and resid 3662 through 3677 Processing helix chain 'C' and resid 3685 through 3701 removed outlier: 3.801A pdb=" N ASP C3693 " --> pdb=" O MET C3689 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N HIS C3700 " --> pdb=" O ALA C3696 " (cutoff:3.500A) Processing helix chain 'C' and resid 3713 through 3733 removed outlier: 3.770A pdb=" N LEU C3731 " --> pdb=" O GLN C3727 " (cutoff:3.500A) Processing helix chain 'C' and resid 3735 through 3748 removed outlier: 3.808A pdb=" N MET C3739 " --> pdb=" O GLY C3735 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS C3748 " --> pdb=" O ILE C3744 " (cutoff:3.500A) Processing helix chain 'C' and resid 3752 through 3767 Processing helix chain 'C' and resid 3770 through 3785 Processing helix chain 'C' and resid 3786 through 3800 removed outlier: 5.393A pdb=" N PHE C3790 " --> pdb=" O ASP C3786 " (cutoff:3.500A) Processing helix chain 'C' and resid 3804 through 3818 Processing helix chain 'C' and resid 3832 through 3848 removed outlier: 4.024A pdb=" N THR C3836 " --> pdb=" O ASP C3832 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N CYS C3847 " --> pdb=" O LEU C3843 " (cutoff:3.500A) Processing helix chain 'C' and resid 3851 through 3860 Processing helix chain 'C' and resid 3869 through 3894 removed outlier: 4.544A pdb=" N GLY C3894 " --> pdb=" O TRP C3890 " (cutoff:3.500A) Processing helix chain 'C' and resid 3899 through 3925 Processing helix chain 'C' and resid 3928 through 3939 removed outlier: 4.794A pdb=" N ARG C3939 " --> pdb=" O LEU C3935 " (cutoff:3.500A) Processing helix chain 'C' and resid 3940 through 3959 removed outlier: 3.732A pdb=" N MET C3956 " --> pdb=" O ALA C3952 " (cutoff:3.500A) Processing helix chain 'C' and resid 3964 through 3987 removed outlier: 3.629A pdb=" N GLU C3987 " --> pdb=" O LEU C3983 " (cutoff:3.500A) Processing helix chain 'C' and resid 3993 through 4007 Processing helix chain 'C' and resid 4008 through 4027 removed outlier: 4.849A pdb=" N LYS C4024 " --> pdb=" O PHE C4020 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ASP C4025 " --> pdb=" O LEU C4021 " (cutoff:3.500A) Processing helix chain 'C' and resid 4029 through 4037 Proline residue: C4037 - end of helix Processing helix chain 'C' and resid 4044 through 4056 Processing helix chain 'C' and resid 4059 through 4071 removed outlier: 5.208A pdb=" N GLU C4071 " --> pdb=" O LEU C4067 " (cutoff:3.500A) Processing helix chain 'C' and resid 4079 through 4110 removed outlier: 5.240A pdb=" N GLU C4089 " --> pdb=" O LYS C4085 " (cutoff:3.500A) Proline residue: C4090 - end of helix removed outlier: 3.770A pdb=" N PHE C4096 " --> pdb=" O LYS C4092 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ASN C4097 " --> pdb=" O ASP C4093 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL C4098 " --> pdb=" O ILE C4094 " (cutoff:3.500A) Proline residue: C4110 - end of helix Processing helix chain 'C' and resid 4112 through 4123 removed outlier: 4.037A pdb=" N GLN C4116 " --> pdb=" O ASP C4112 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR C4117 " --> pdb=" O THR C4113 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N PHE C4118 " --> pdb=" O ARG C4114 " (cutoff:3.500A) Processing helix chain 'C' and resid 4124 through 4130 Processing helix chain 'C' and resid 4153 through 4162 Processing helix chain 'C' and resid 4163 through 4179 Processing helix chain 'C' and resid 4182 through 4207 removed outlier: 4.232A pdb=" N MET C4186 " --> pdb=" O GLU C4182 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU C4187 " --> pdb=" O LYS C4183 " (cutoff:3.500A) Processing helix chain 'C' and resid 4237 through 4261 removed outlier: 3.634A pdb=" N ILE C4252 " --> pdb=" O LEU C4248 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N THR C4254 " --> pdb=" O TYR C4250 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEU C4261 " --> pdb=" O ARG C4257 " (cutoff:3.500A) Processing helix chain 'C' and resid 4263 through 4272 removed outlier: 3.630A pdb=" N LYS C4272 " --> pdb=" O MET C4268 " (cutoff:3.500A) Processing helix chain 'C' and resid 4275 through 4310 removed outlier: 3.722A pdb=" N ALA C4282 " --> pdb=" O ASP C4278 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N PHE C4283 " --> pdb=" O MET C4279 " (cutoff:3.500A) Processing helix chain 'C' and resid 4480 through 4499 Processing helix chain 'C' and resid 4500 through 4520 removed outlier: 3.698A pdb=" N LEU C4507 " --> pdb=" O ARG C4503 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N PHE C4519 " --> pdb=" O PHE C4515 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N TYR C4520 " --> pdb=" O ILE C4516 " (cutoff:3.500A) Processing helix chain 'C' and resid 4567 through 4612 removed outlier: 3.650A pdb=" N THR C4571 " --> pdb=" O TYR C4567 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N VAL C4595 " --> pdb=" O TYR C4591 " (cutoff:3.500A) Proline residue: C4596 - end of helix Processing helix chain 'C' and resid 4625 through 4638 removed outlier: 4.146A pdb=" N LEU C4633 " --> pdb=" O GLN C4629 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N VAL C4634 " --> pdb=" O TRP C4630 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE C4635 " --> pdb=" O ASP C4631 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N ASN C4636 " --> pdb=" O ARG C4632 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N THR C4637 " --> pdb=" O LEU C4633 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N GLN C4638 " --> pdb=" O VAL C4634 " (cutoff:3.500A) Processing helix chain 'C' and resid 4648 through 4658 Processing helix chain 'C' and resid 4662 through 4671 Processing helix chain 'C' and resid 4673 through 4683 removed outlier: 4.776A pdb=" N LEU C4677 " --> pdb=" O ASP C4673 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N ASP C4678 " --> pdb=" O LYS C4674 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N PHE C4679 " --> pdb=" O ALA C4675 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ASP C4681 " --> pdb=" O LEU C4677 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ARG C4683 " --> pdb=" O PHE C4679 " (cutoff:3.500A) Processing helix chain 'C' and resid 4693 through 4702 removed outlier: 4.071A pdb=" N VAL C4697 " --> pdb=" O SER C4693 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N ASP C4702 " --> pdb=" O LEU C4698 " (cutoff:3.500A) Processing helix chain 'C' and resid 4703 through 4717 removed outlier: 5.442A pdb=" N ASN C4717 " --> pdb=" O VAL C4713 " (cutoff:3.500A) Processing helix chain 'C' and resid 4718 through 4736 removed outlier: 3.741A pdb=" N TYR C4734 " --> pdb=" O VAL C4730 " (cutoff:3.500A) Processing helix chain 'C' and resid 4737 through 4751 removed outlier: 4.758A pdb=" N ALA C4741 " --> pdb=" O PHE C4737 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N HIS C4742 " --> pdb=" O PHE C4738 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU C4743 " --> pdb=" O PHE C4739 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LEU C4744 " --> pdb=" O ALA C4740 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ASP C4745 " --> pdb=" O ALA C4741 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N ILE C4746 " --> pdb=" O HIS C4742 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ALA C4747 " --> pdb=" O LEU C4743 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N LYS C4751 " --> pdb=" O ALA C4747 " (cutoff:3.500A) Processing helix chain 'C' and resid 4752 through 4762 removed outlier: 3.960A pdb=" N VAL C4760 " --> pdb=" O ILE C4756 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N THR C4761 " --> pdb=" O LEU C4757 " (cutoff:3.500A) Processing helix chain 'C' and resid 4763 through 4788 Processing helix chain 'C' and resid 4789 through 4794 removed outlier: 5.208A pdb=" N TYR C4793 " --> pdb=" O PHE C4789 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ASN C4794 " --> pdb=" O ARG C4790 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 4789 through 4794' Processing helix chain 'C' and resid 4808 through 4823 removed outlier: 4.496A pdb=" N VAL C4819 " --> pdb=" O PHE C4815 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLY C4820 " --> pdb=" O HIS C4816 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL C4821 " --> pdb=" O MET C4817 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ARG C4822 " --> pdb=" O TYR C4818 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA C4823 " --> pdb=" O VAL C4819 " (cutoff:3.500A) Processing helix chain 'C' and resid 4826 through 4832 removed outlier: 4.581A pdb=" N GLU C4830 " --> pdb=" O GLY C4826 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N GLU C4832 " --> pdb=" O GLY C4828 " (cutoff:3.500A) Processing helix chain 'C' and resid 4839 through 4854 Processing helix chain 'C' and resid 4858 through 4887 Processing helix chain 'C' and resid 4894 through 4902 removed outlier: 4.050A pdb=" N PHE C4898 " --> pdb=" O GLY C4894 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N VAL C4901 " --> pdb=" O TYR C4897 " (cutoff:3.500A) Proline residue: C4902 - end of helix Processing helix chain 'C' and resid 4903 through 4911 Processing helix chain 'C' and resid 4914 through 4928 removed outlier: 3.852A pdb=" N TYR C4918 " --> pdb=" O ASN C4914 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU C4919 " --> pdb=" O LEU C4915 " (cutoff:3.500A) Processing helix chain 'C' and resid 4934 through 4947 Processing helix chain 'C' and resid 4957 through 4963 Processing helix chain 'C' and resid 857 through 862 removed outlier: 4.136A pdb=" N ALA C 860 " --> pdb=" O LEU C 857 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA C 861 " --> pdb=" O THR C 858 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N PHE C 862 " --> pdb=" O GLN C 859 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 857 through 862' Processing helix chain 'C' and resid 1772 through 1778 removed outlier: 4.531A pdb=" N CYS C1775 " --> pdb=" O SER C1772 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N TYR C1778 " --> pdb=" O CYS C1775 " (cutoff:3.500A) Processing helix chain 'C' and resid 4948 through 4953 removed outlier: 4.455A pdb=" N PHE C4951 " --> pdb=" O CYS C4948 " (cutoff:3.500A) Proline residue: C4953 - end of helix Processing helix chain 'C' and resid 54 through 59 Proline residue: C 59 - end of helix No H-bonds generated for 'chain 'C' and resid 54 through 59' Processing helix chain 'C' and resid 4614 through 4619 Processing helix chain 'D' and resid 61 through 66 removed outlier: 4.031A pdb=" N CYS D 65 " --> pdb=" O ASP D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 84 Processing helix chain 'D' and resid 155 through 160 removed outlier: 4.597A pdb=" N TRP D 159 " --> pdb=" O GLY D 155 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N TRP D 160 " --> pdb=" O GLU D 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 155 through 160' Processing helix chain 'D' and resid 253 through 259 removed outlier: 4.987A pdb=" N THR D 259 " --> pdb=" O GLU D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 270 removed outlier: 4.436A pdb=" N VAL D 269 " --> pdb=" O GLY D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 328 Processing helix chain 'D' and resid 409 through 439 removed outlier: 3.680A pdb=" N LEU D 425 " --> pdb=" O SER D 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 441 through 446 removed outlier: 5.261A pdb=" N ASP D 446 " --> pdb=" O ALA D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 464 Processing helix chain 'D' and resid 471 through 493 Processing helix chain 'D' and resid 494 through 508 removed outlier: 4.717A pdb=" N TYR D 508 " --> pdb=" O ARG D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 518 Processing helix chain 'D' and resid 519 through 542 removed outlier: 4.802A pdb=" N LYS D 527 " --> pdb=" O GLY D 523 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N SER D 528 " --> pdb=" O GLU D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 544 through 555 removed outlier: 3.858A pdb=" N SER D 552 " --> pdb=" O CYS D 548 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N GLY D 553 " --> pdb=" O ALA D 549 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N SER D 554 " --> pdb=" O GLN D 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 556 through 563 removed outlier: 4.126A pdb=" N ARG D 561 " --> pdb=" O TRP D 557 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LEU D 562 " --> pdb=" O LEU D 558 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N GLU D 563 " --> pdb=" O ILE D 559 " (cutoff:3.500A) Processing helix chain 'D' and resid 567 through 582 Processing helix chain 'D' and resid 583 through 590 removed outlier: 4.212A pdb=" N ASN D 587 " --> pdb=" O PRO D 583 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE D 588 " --> pdb=" O GLU D 584 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N LYS D 590 " --> pdb=" O LEU D 586 " (cutoff:3.500A) Processing helix chain 'D' and resid 591 through 604 removed outlier: 3.538A pdb=" N SER D 596 " --> pdb=" O GLY D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 607 through 620 removed outlier: 3.716A pdb=" N LEU D 611 " --> pdb=" O ASN D 607 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL D 619 " --> pdb=" O CYS D 615 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N CYS D 620 " --> pdb=" O SER D 616 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 636 Processing helix chain 'D' and resid 821 through 826 removed outlier: 4.596A pdb=" N ALA D 825 " --> pdb=" O PRO D 821 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N VAL D 826 " --> pdb=" O CYS D 822 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 821 through 826' Processing helix chain 'D' and resid 875 through 901 removed outlier: 4.994A pdb=" N GLU D 883 " --> pdb=" O GLU D 879 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N LYS D 884 " --> pdb=" O ARG D 880 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE D 898 " --> pdb=" O VAL D 894 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLY D 901 " --> pdb=" O LYS D 897 " (cutoff:3.500A) Processing helix chain 'D' and resid 920 through 925 Proline residue: D 925 - end of helix Processing helix chain 'D' and resid 926 through 947 Processing helix chain 'D' and resid 954 through 961 removed outlier: 3.998A pdb=" N GLU D 958 " --> pdb=" O ASP D 954 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N VAL D 961 " --> pdb=" O ALA D 957 " (cutoff:3.500A) Processing helix chain 'D' and resid 989 through 1015 Processing helix chain 'D' and resid 1039 through 1061 removed outlier: 3.703A pdb=" N GLY D1061 " --> pdb=" O LEU D1057 " (cutoff:3.500A) Processing helix chain 'D' and resid 1220 through 1225 removed outlier: 3.803A pdb=" N LEU D1224 " --> pdb=" O ASP D1220 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N LYS D1225 " --> pdb=" O VAL D1221 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1220 through 1225' Processing helix chain 'D' and resid 1230 through 1235 removed outlier: 7.047A pdb=" N GLU D1234 " --> pdb=" O CYS D1230 " (cutoff:3.500A) Processing helix chain 'D' and resid 1416 through 1423 removed outlier: 4.191A pdb=" N MET D1421 " --> pdb=" O TYR D1417 " (cutoff:3.500A) Processing helix chain 'D' and resid 1437 through 1442 removed outlier: 3.982A pdb=" N VAL D1441 " --> pdb=" O GLU D1437 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N TRP D1442 " --> pdb=" O PRO D1438 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1437 through 1442' Processing helix chain 'D' and resid 1489 through 1495 removed outlier: 5.555A pdb=" N SER D1495 " --> pdb=" O GLY D1491 " (cutoff:3.500A) Processing helix chain 'D' and resid 1565 through 1571 removed outlier: 3.594A pdb=" N GLY D1569 " --> pdb=" O PRO D1565 " (cutoff:3.500A) Processing helix chain 'D' and resid 1640 through 1648 removed outlier: 4.324A pdb=" N LEU D1644 " --> pdb=" O ASP D1640 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N THR D1645 " --> pdb=" O ILE D1641 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N GLU D1646 " --> pdb=" O LEU D1642 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN D1647 " --> pdb=" O GLU D1643 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N GLU D1648 " --> pdb=" O LEU D1644 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1640 through 1648' Processing helix chain 'D' and resid 1649 through 1666 removed outlier: 3.610A pdb=" N CYS D1665 " --> pdb=" O TYR D1661 " (cutoff:3.500A) Processing helix chain 'D' and resid 1669 through 1680 removed outlier: 3.772A pdb=" N SER D1678 " --> pdb=" O HIS D1674 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N HIS D1679 " --> pdb=" O ALA D1675 " (cutoff:3.500A) Processing helix chain 'D' and resid 1681 through 1691 removed outlier: 3.668A pdb=" N GLU D1690 " --> pdb=" O LEU D1686 " (cutoff:3.500A) Processing helix chain 'D' and resid 1695 through 1710 Processing helix chain 'D' and resid 1711 through 1723 removed outlier: 3.927A pdb=" N ASN D1722 " --> pdb=" O ARG D1718 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N ASN D1723 " --> pdb=" O LEU D1719 " (cutoff:3.500A) Processing helix chain 'D' and resid 1730 through 1736 removed outlier: 3.590A pdb=" N ILE D1736 " --> pdb=" O GLU D1732 " (cutoff:3.500A) Processing helix chain 'D' and resid 1783 through 1803 removed outlier: 3.532A pdb=" N LYS D1800 " --> pdb=" O THR D1796 " (cutoff:3.500A) Processing helix chain 'D' and resid 1813 through 1832 Proline residue: D1820 - end of helix Processing helix chain 'D' and resid 1836 through 1847 Processing helix chain 'D' and resid 1892 through 1897 removed outlier: 4.393A pdb=" N LYS D1897 " --> pdb=" O LEU D1893 " (cutoff:3.500A) Processing helix chain 'D' and resid 1899 through 1944 removed outlier: 4.261A pdb=" N ASP D1931 " --> pdb=" O ALA D1927 " (cutoff:3.500A) Processing helix chain 'D' and resid 1957 through 1968 removed outlier: 4.581A pdb=" N GLU D1964 " --> pdb=" O ARG D1960 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N PHE D1965 " --> pdb=" O LYS D1961 " (cutoff:3.500A) Proline residue: D1968 - end of helix Processing helix chain 'D' and resid 1969 through 1979 removed outlier: 3.580A pdb=" N ASN D1978 " --> pdb=" O ASN D1974 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N PHE D1979 " --> pdb=" O MET D1975 " (cutoff:3.500A) Processing helix chain 'D' and resid 1989 through 2008 removed outlier: 3.581A pdb=" N GLU D2001 " --> pdb=" O LEU D1997 " (cutoff:3.500A) Processing helix chain 'D' and resid 2057 through 2073 removed outlier: 3.678A pdb=" N VAL D2067 " --> pdb=" O SER D2063 " (cutoff:3.500A) Processing helix chain 'D' and resid 2077 through 2094 removed outlier: 3.846A pdb=" N GLY D2094 " --> pdb=" O ARG D2090 " (cutoff:3.500A) Processing helix chain 'D' and resid 2095 through 2105 Proline residue: D2103 - end of helix Processing helix chain 'D' and resid 2109 through 2133 removed outlier: 3.797A pdb=" N VAL D2113 " --> pdb=" O ASN D2109 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N GLU D2114 " --> pdb=" O GLY D2110 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N ASP D2115 " --> pdb=" O VAL D2111 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU D2130 " --> pdb=" O ILE D2126 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N SER D2131 " --> pdb=" O ARG D2127 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL D2132 " --> pdb=" O SER D2128 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N ARG D2133 " --> pdb=" O LEU D2129 " (cutoff:3.500A) Processing helix chain 'D' and resid 2135 through 2153 removed outlier: 5.493A pdb=" N LYS D2153 " --> pdb=" O ILE D2149 " (cutoff:3.500A) Processing helix chain 'D' and resid 2158 through 2166 removed outlier: 3.517A pdb=" N GLY D2166 " --> pdb=" O MET D2162 " (cutoff:3.500A) Processing helix chain 'D' and resid 2167 through 2183 removed outlier: 5.569A pdb=" N GLY D2182 " --> pdb=" O VAL D2178 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N GLU D2183 " --> pdb=" O LEU D2179 " (cutoff:3.500A) Processing helix chain 'D' and resid 2189 through 2208 removed outlier: 3.848A pdb=" N VAL D2193 " --> pdb=" O PHE D2189 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA D2194 " --> pdb=" O PRO D2190 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N SER D2207 " --> pdb=" O PHE D2203 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ARG D2208 " --> pdb=" O CYS D2204 " (cutoff:3.500A) Processing helix chain 'D' and resid 2209 through 2219 removed outlier: 3.869A pdb=" N ASP D2216 " --> pdb=" O LYS D2212 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N HIS D2217 " --> pdb=" O ALA D2213 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU D2218 " --> pdb=" O MET D2214 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N SER D2219 " --> pdb=" O PHE D2215 " (cutoff:3.500A) Processing helix chain 'D' and resid 2220 through 2225 Processing helix chain 'D' and resid 2238 through 2248 Processing helix chain 'D' and resid 2250 through 2257 Processing helix chain 'D' and resid 2258 through 2275 removed outlier: 3.661A pdb=" N LEU D2262 " --> pdb=" O ARG D2258 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL D2265 " --> pdb=" O ASP D2261 " (cutoff:3.500A) Processing helix chain 'D' and resid 2277 through 2284 removed outlier: 3.661A pdb=" N VAL D2281 " --> pdb=" O CYS D2277 " (cutoff:3.500A) Processing helix chain 'D' and resid 2291 through 2307 removed outlier: 3.696A pdb=" N ARG D2297 " --> pdb=" O VAL D2293 " (cutoff:3.500A) Processing helix chain 'D' and resid 2313 through 2328 removed outlier: 3.524A pdb=" N VAL D2319 " --> pdb=" O GLU D2315 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL D2320 " --> pdb=" O ASN D2316 " (cutoff:3.500A) Proline residue: D2328 - end of helix Processing helix chain 'D' and resid 2342 through 2357 Proline residue: D2357 - end of helix Processing helix chain 'D' and resid 2377 through 2382 Processing helix chain 'D' and resid 2383 through 2412 Proline residue: D2404 - end of helix removed outlier: 9.212A pdb=" N HIS D2407 " --> pdb=" O ALA D2403 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LEU D2408 " --> pdb=" O PRO D2404 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE D2409 " --> pdb=" O GLU D2405 " (cutoff:3.500A) Processing helix chain 'D' and resid 2413 through 2428 Proline residue: D2428 - end of helix Processing helix chain 'D' and resid 2429 through 2439 removed outlier: 5.667A pdb=" N ALA D2439 " --> pdb=" O VAL D2435 " (cutoff:3.500A) Processing helix chain 'D' and resid 2461 through 2475 removed outlier: 3.823A pdb=" N LYS D2465 " --> pdb=" O CYS D2461 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA D2467 " --> pdb=" O ASP D2463 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET D2468 " --> pdb=" O HIS D2464 " (cutoff:3.500A) Processing helix chain 'D' and resid 2480 through 2504 removed outlier: 4.888A pdb=" N LEU D2493 " --> pdb=" O GLU D2489 " (cutoff:3.500A) Proline residue: D2494 - end of helix removed outlier: 3.644A pdb=" N ASP D2503 " --> pdb=" O ALA D2499 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N THR D2504 " --> pdb=" O ALA D2500 " (cutoff:3.500A) Processing helix chain 'D' and resid 2510 through 2532 removed outlier: 5.280A pdb=" N LEU D2525 " --> pdb=" O CYS D2521 " (cutoff:3.500A) Proline residue: D2526 - end of helix Processing helix chain 'D' and resid 2541 through 2559 removed outlier: 5.149A pdb=" N CYS D2559 " --> pdb=" O LEU D2555 " (cutoff:3.500A) Processing helix chain 'D' and resid 2562 through 2580 Processing helix chain 'D' and resid 2581 through 2596 removed outlier: 4.122A pdb=" N MET D2585 " --> pdb=" O ARG D2581 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N GLN D2586 " --> pdb=" O PRO D2582 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N HIS D2587 " --> pdb=" O SER D2583 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N LEU D2588 " --> pdb=" O MET D2584 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N PHE D2594 " --> pdb=" O ARG D2590 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ASP D2595 " --> pdb=" O ARG D2591 " (cutoff:3.500A) Processing helix chain 'D' and resid 2602 through 2618 Proline residue: D2606 - end of helix Processing helix chain 'D' and resid 2634 through 2655 removed outlier: 6.190A pdb=" N LEU D2638 " --> pdb=" O SER D2634 " (cutoff:3.500A) Processing helix chain 'D' and resid 2659 through 2677 Proline residue: D2667 - end of helix Proline residue: D2677 - end of helix Processing helix chain 'D' and resid 2691 through 2696 removed outlier: 4.352A pdb=" N MET D2695 " --> pdb=" O LYS D2691 " (cutoff:3.500A) Processing helix chain 'D' and resid 2716 through 2740 removed outlier: 4.508A pdb=" N PHE D2720 " --> pdb=" O LYS D2716 " (cutoff:3.500A) Processing helix chain 'D' and resid 2767 through 2784 removed outlier: 3.674A pdb=" N TYR D2771 " --> pdb=" O GLU D2767 " (cutoff:3.500A) Proline residue: D2774 - end of helix Processing helix chain 'D' and resid 2792 through 2802 removed outlier: 4.217A pdb=" N ASP D2796 " --> pdb=" O THR D2792 " (cutoff:3.500A) Processing helix chain 'D' and resid 2834 through 2864 Processing helix chain 'D' and resid 2873 through 2878 removed outlier: 5.253A pdb=" N THR D2878 " --> pdb=" O TYR D2874 " (cutoff:3.500A) Processing helix chain 'D' and resid 2881 through 2900 removed outlier: 4.359A pdb=" N ASP D2885 " --> pdb=" O GLU D2881 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE D2892 " --> pdb=" O LYS D2888 " (cutoff:3.500A) Processing helix chain 'D' and resid 2916 through 2921 removed outlier: 4.315A pdb=" N ARG D2920 " --> pdb=" O SER D2916 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N PHE D2921 " --> pdb=" O ILE D2917 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2916 through 2921' Processing helix chain 'D' and resid 2922 through 2947 Processing helix chain 'D' and resid 2956 through 2979 removed outlier: 4.298A pdb=" N LEU D2968 " --> pdb=" O ALA D2964 " (cutoff:3.500A) Proline residue: D2969 - end of helix Processing helix chain 'D' and resid 2997 through 3016 Processing helix chain 'D' and resid 3018 through 3023 removed outlier: 4.995A pdb=" N GLY D3023 " --> pdb=" O ILE D3019 " (cutoff:3.500A) Processing helix chain 'D' and resid 3025 through 3040 removed outlier: 4.303A pdb=" N LEU D3040 " --> pdb=" O LEU D3036 " (cutoff:3.500A) Processing helix chain 'D' and resid 3041 through 3048 Processing helix chain 'D' and resid 3050 through 3079 Processing helix chain 'D' and resid 3088 through 3116 removed outlier: 5.352A pdb=" N LEU D3102 " --> pdb=" O THR D3098 " (cutoff:3.500A) Proline residue: D3103 - end of helix Processing helix chain 'D' and resid 3117 through 3123 removed outlier: 4.561A pdb=" N LEU D3123 " --> pdb=" O GLU D3119 " (cutoff:3.500A) Processing helix chain 'D' and resid 3124 through 3143 removed outlier: 6.417A pdb=" N VAL D3128 " --> pdb=" O GLU D3124 " (cutoff:3.500A) Processing helix chain 'D' and resid 3145 through 3152 Processing helix chain 'D' and resid 3153 through 3166 Processing helix chain 'D' and resid 3182 through 3187 Processing helix chain 'D' and resid 3188 through 3196 removed outlier: 4.878A pdb=" N ARG D3192 " --> pdb=" O SER D3188 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N SER D3196 " --> pdb=" O ARG D3192 " (cutoff:3.500A) Processing helix chain 'D' and resid 3200 through 3206 removed outlier: 3.889A pdb=" N CYS D3205 " --> pdb=" O VAL D3201 " (cutoff:3.500A) Proline residue: D3206 - end of helix Processing helix chain 'D' and resid 3210 through 3225 Processing helix chain 'D' and resid 3231 through 3250 removed outlier: 4.553A pdb=" N MET D3235 " --> pdb=" O MET D3231 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU D3239 " --> pdb=" O MET D3235 " (cutoff:3.500A) Proline residue: D3240 - end of helix removed outlier: 3.964A pdb=" N ARG D3248 " --> pdb=" O SER D3244 " (cutoff:3.500A) Processing helix chain 'D' and resid 3253 through 3258 Proline residue: D3258 - end of helix Processing helix chain 'D' and resid 3269 through 3289 removed outlier: 3.816A pdb=" N TYR D3285 " --> pdb=" O LEU D3281 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN D3286 " --> pdb=" O LYS D3282 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N GLY D3289 " --> pdb=" O TYR D3285 " (cutoff:3.500A) Processing helix chain 'D' and resid 3293 through 3311 removed outlier: 4.167A pdb=" N LYS D3297 " --> pdb=" O GLY D3293 " (cutoff:3.500A) Proline residue: D3305 - end of helix removed outlier: 5.191A pdb=" N LYS D3311 " --> pdb=" O ILE D3307 " (cutoff:3.500A) Processing helix chain 'D' and resid 3312 through 3318 removed outlier: 4.927A pdb=" N THR D3317 " --> pdb=" O GLN D3313 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N HIS D3318 " --> pdb=" O LEU D3314 " (cutoff:3.500A) Processing helix chain 'D' and resid 3319 through 3331 removed outlier: 4.806A pdb=" N ALA D3331 " --> pdb=" O LYS D3327 " (cutoff:3.500A) Processing helix chain 'D' and resid 3599 through 3606 removed outlier: 5.370A pdb=" N ALA D3606 " --> pdb=" O CYS D3602 " (cutoff:3.500A) Processing helix chain 'D' and resid 3607 through 3612 removed outlier: 3.715A pdb=" N LEU D3611 " --> pdb=" O PRO D3607 " (cutoff:3.500A) Proline residue: D3612 - end of helix No H-bonds generated for 'chain 'D' and resid 3607 through 3612' Processing helix chain 'D' and resid 3613 through 3632 removed outlier: 4.609A pdb=" N GLU D3630 " --> pdb=" O LYS D3626 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N THR D3631 " --> pdb=" O SER D3627 " (cutoff:3.500A) Processing helix chain 'D' and resid 3636 through 3646 Processing helix chain 'D' and resid 3649 through 3654 removed outlier: 4.122A pdb=" N GLU D3654 " --> pdb=" O GLU D3650 " (cutoff:3.500A) Processing helix chain 'D' and resid 3662 through 3677 Processing helix chain 'D' and resid 3685 through 3701 removed outlier: 3.802A pdb=" N ASP D3693 " --> pdb=" O MET D3689 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N HIS D3700 " --> pdb=" O ALA D3696 " (cutoff:3.500A) Processing helix chain 'D' and resid 3713 through 3733 removed outlier: 3.769A pdb=" N LEU D3731 " --> pdb=" O GLN D3727 " (cutoff:3.500A) Processing helix chain 'D' and resid 3735 through 3748 removed outlier: 3.806A pdb=" N MET D3739 " --> pdb=" O GLY D3735 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS D3748 " --> pdb=" O ILE D3744 " (cutoff:3.500A) Processing helix chain 'D' and resid 3752 through 3767 Processing helix chain 'D' and resid 3770 through 3785 Processing helix chain 'D' and resid 3786 through 3800 removed outlier: 5.393A pdb=" N PHE D3790 " --> pdb=" O ASP D3786 " (cutoff:3.500A) Processing helix chain 'D' and resid 3804 through 3818 Processing helix chain 'D' and resid 3832 through 3848 removed outlier: 4.024A pdb=" N THR D3836 " --> pdb=" O ASP D3832 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N CYS D3847 " --> pdb=" O LEU D3843 " (cutoff:3.500A) Processing helix chain 'D' and resid 3851 through 3860 Processing helix chain 'D' and resid 3869 through 3894 removed outlier: 4.544A pdb=" N GLY D3894 " --> pdb=" O TRP D3890 " (cutoff:3.500A) Processing helix chain 'D' and resid 3899 through 3925 Processing helix chain 'D' and resid 3928 through 3939 removed outlier: 4.794A pdb=" N ARG D3939 " --> pdb=" O LEU D3935 " (cutoff:3.500A) Processing helix chain 'D' and resid 3940 through 3959 removed outlier: 3.733A pdb=" N MET D3956 " --> pdb=" O ALA D3952 " (cutoff:3.500A) Processing helix chain 'D' and resid 3964 through 3987 removed outlier: 3.629A pdb=" N GLU D3987 " --> pdb=" O LEU D3983 " (cutoff:3.500A) Processing helix chain 'D' and resid 3993 through 4007 Processing helix chain 'D' and resid 4008 through 4027 removed outlier: 4.848A pdb=" N LYS D4024 " --> pdb=" O PHE D4020 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ASP D4025 " --> pdb=" O LEU D4021 " (cutoff:3.500A) Processing helix chain 'D' and resid 4029 through 4037 Proline residue: D4037 - end of helix Processing helix chain 'D' and resid 4044 through 4056 Processing helix chain 'D' and resid 4059 through 4071 removed outlier: 5.208A pdb=" N GLU D4071 " --> pdb=" O LEU D4067 " (cutoff:3.500A) Processing helix chain 'D' and resid 4079 through 4110 removed outlier: 5.240A pdb=" N GLU D4089 " --> pdb=" O LYS D4085 " (cutoff:3.500A) Proline residue: D4090 - end of helix removed outlier: 3.771A pdb=" N PHE D4096 " --> pdb=" O LYS D4092 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ASN D4097 " --> pdb=" O ASP D4093 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL D4098 " --> pdb=" O ILE D4094 " (cutoff:3.500A) Proline residue: D4110 - end of helix Processing helix chain 'D' and resid 4112 through 4123 removed outlier: 4.038A pdb=" N GLN D4116 " --> pdb=" O ASP D4112 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR D4117 " --> pdb=" O THR D4113 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N PHE D4118 " --> pdb=" O ARG D4114 " (cutoff:3.500A) Processing helix chain 'D' and resid 4124 through 4130 Processing helix chain 'D' and resid 4153 through 4162 Processing helix chain 'D' and resid 4163 through 4179 Processing helix chain 'D' and resid 4182 through 4207 removed outlier: 4.231A pdb=" N MET D4186 " --> pdb=" O GLU D4182 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU D4187 " --> pdb=" O LYS D4183 " (cutoff:3.500A) Processing helix chain 'D' and resid 4237 through 4261 removed outlier: 3.635A pdb=" N ILE D4252 " --> pdb=" O LEU D4248 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N THR D4254 " --> pdb=" O TYR D4250 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEU D4261 " --> pdb=" O ARG D4257 " (cutoff:3.500A) Processing helix chain 'D' and resid 4263 through 4272 removed outlier: 3.629A pdb=" N LYS D4272 " --> pdb=" O MET D4268 " (cutoff:3.500A) Processing helix chain 'D' and resid 4275 through 4310 removed outlier: 3.721A pdb=" N ALA D4282 " --> pdb=" O ASP D4278 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N PHE D4283 " --> pdb=" O MET D4279 " (cutoff:3.500A) Processing helix chain 'D' and resid 4480 through 4499 Processing helix chain 'D' and resid 4500 through 4520 removed outlier: 3.699A pdb=" N LEU D4507 " --> pdb=" O ARG D4503 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N PHE D4519 " --> pdb=" O PHE D4515 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N TYR D4520 " --> pdb=" O ILE D4516 " (cutoff:3.500A) Processing helix chain 'D' and resid 4567 through 4612 removed outlier: 3.649A pdb=" N THR D4571 " --> pdb=" O TYR D4567 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N VAL D4595 " --> pdb=" O TYR D4591 " (cutoff:3.500A) Proline residue: D4596 - end of helix Processing helix chain 'D' and resid 4625 through 4638 removed outlier: 4.146A pdb=" N LEU D4633 " --> pdb=" O GLN D4629 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N VAL D4634 " --> pdb=" O TRP D4630 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE D4635 " --> pdb=" O ASP D4631 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N ASN D4636 " --> pdb=" O ARG D4632 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N THR D4637 " --> pdb=" O LEU D4633 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N GLN D4638 " --> pdb=" O VAL D4634 " (cutoff:3.500A) Processing helix chain 'D' and resid 4648 through 4658 Processing helix chain 'D' and resid 4662 through 4671 Processing helix chain 'D' and resid 4673 through 4683 removed outlier: 4.775A pdb=" N LEU D4677 " --> pdb=" O ASP D4673 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N ASP D4678 " --> pdb=" O LYS D4674 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N PHE D4679 " --> pdb=" O ALA D4675 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ASP D4681 " --> pdb=" O LEU D4677 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ARG D4683 " --> pdb=" O PHE D4679 " (cutoff:3.500A) Processing helix chain 'D' and resid 4693 through 4702 removed outlier: 4.072A pdb=" N VAL D4697 " --> pdb=" O SER D4693 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ASP D4702 " --> pdb=" O LEU D4698 " (cutoff:3.500A) Processing helix chain 'D' and resid 4703 through 4717 removed outlier: 5.440A pdb=" N ASN D4717 " --> pdb=" O VAL D4713 " (cutoff:3.500A) Processing helix chain 'D' and resid 4718 through 4736 removed outlier: 3.742A pdb=" N TYR D4734 " --> pdb=" O VAL D4730 " (cutoff:3.500A) Processing helix chain 'D' and resid 4737 through 4751 removed outlier: 4.759A pdb=" N ALA D4741 " --> pdb=" O PHE D4737 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N HIS D4742 " --> pdb=" O PHE D4738 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU D4743 " --> pdb=" O PHE D4739 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LEU D4744 " --> pdb=" O ALA D4740 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ASP D4745 " --> pdb=" O ALA D4741 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N ILE D4746 " --> pdb=" O HIS D4742 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ALA D4747 " --> pdb=" O LEU D4743 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N LYS D4751 " --> pdb=" O ALA D4747 " (cutoff:3.500A) Processing helix chain 'D' and resid 4752 through 4762 removed outlier: 3.960A pdb=" N VAL D4760 " --> pdb=" O ILE D4756 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N THR D4761 " --> pdb=" O LEU D4757 " (cutoff:3.500A) Processing helix chain 'D' and resid 4763 through 4788 Processing helix chain 'D' and resid 4789 through 4794 removed outlier: 5.208A pdb=" N TYR D4793 " --> pdb=" O PHE D4789 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ASN D4794 " --> pdb=" O ARG D4790 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 4789 through 4794' Processing helix chain 'D' and resid 4808 through 4823 removed outlier: 4.497A pdb=" N VAL D4819 " --> pdb=" O PHE D4815 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLY D4820 " --> pdb=" O HIS D4816 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL D4821 " --> pdb=" O MET D4817 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ARG D4822 " --> pdb=" O TYR D4818 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA D4823 " --> pdb=" O VAL D4819 " (cutoff:3.500A) Processing helix chain 'D' and resid 4826 through 4832 removed outlier: 4.581A pdb=" N GLU D4830 " --> pdb=" O GLY D4826 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N GLU D4832 " --> pdb=" O GLY D4828 " (cutoff:3.500A) Processing helix chain 'D' and resid 4839 through 4854 Processing helix chain 'D' and resid 4858 through 4887 Processing helix chain 'D' and resid 4894 through 4902 removed outlier: 4.050A pdb=" N PHE D4898 " --> pdb=" O GLY D4894 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N VAL D4901 " --> pdb=" O TYR D4897 " (cutoff:3.500A) Proline residue: D4902 - end of helix Processing helix chain 'D' and resid 4903 through 4911 Processing helix chain 'D' and resid 4914 through 4928 removed outlier: 3.853A pdb=" N TYR D4918 " --> pdb=" O ASN D4914 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU D4919 " --> pdb=" O LEU D4915 " (cutoff:3.500A) Processing helix chain 'D' and resid 4934 through 4947 Processing helix chain 'D' and resid 4957 through 4963 Processing helix chain 'D' and resid 857 through 862 removed outlier: 4.137A pdb=" N ALA D 860 " --> pdb=" O LEU D 857 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA D 861 " --> pdb=" O THR D 858 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N PHE D 862 " --> pdb=" O GLN D 859 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 857 through 862' Processing helix chain 'D' and resid 1772 through 1778 removed outlier: 4.531A pdb=" N CYS D1775 " --> pdb=" O SER D1772 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N TYR D1778 " --> pdb=" O CYS D1775 " (cutoff:3.500A) Processing helix chain 'D' and resid 4948 through 4953 removed outlier: 4.455A pdb=" N PHE D4951 " --> pdb=" O CYS D4948 " (cutoff:3.500A) Proline residue: D4953 - end of helix Processing helix chain 'D' and resid 54 through 59 Proline residue: D 59 - end of helix No H-bonds generated for 'chain 'D' and resid 54 through 59' Processing helix chain 'D' and resid 4614 through 4619 Processing sheet with id= 1, first strand: chain 'E' and resid 3 through 8 removed outlier: 6.529A pdb=" N ARG E 72 " --> pdb=" O ILE E 8 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLN E 71 " --> pdb=" O LEU E 104 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'E' and resid 46 through 50 Processing sheet with id= 3, first strand: chain 'F' and resid 3 through 8 removed outlier: 6.529A pdb=" N ARG F 72 " --> pdb=" O ILE F 8 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLN F 71 " --> pdb=" O LEU F 104 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'F' and resid 46 through 50 Processing sheet with id= 5, first strand: chain 'G' and resid 3 through 8 removed outlier: 6.529A pdb=" N ARG G 72 " --> pdb=" O ILE G 8 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLN G 71 " --> pdb=" O LEU G 104 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'G' and resid 46 through 50 Processing sheet with id= 7, first strand: chain 'H' and resid 3 through 8 removed outlier: 6.529A pdb=" N ARG H 72 " --> pdb=" O ILE H 8 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLN H 71 " --> pdb=" O LEU H 104 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'H' and resid 46 through 50 Processing sheet with id= 9, first strand: chain 'A' and resid 47 through 52 removed outlier: 3.589A pdb=" N GLU A 50 " --> pdb=" O CYS A 36 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LYS A 34 " --> pdb=" O THR A 52 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'A' and resid 67 through 70 removed outlier: 6.550A pdb=" N LEU A 120 " --> pdb=" O GLU A 70 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'A' and resid 161 through 164 Processing sheet with id= 12, first strand: chain 'A' and resid 192 through 196 removed outlier: 3.534A pdb=" N HIS A 202 " --> pdb=" O SER A 195 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'A' and resid 231 through 235 removed outlier: 4.109A pdb=" N ASP A 232 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N LEU A 274 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 14.680A pdb=" N PHE A 295 " --> pdb=" O LEU A 308 " (cutoff:3.500A) removed outlier: 10.457A pdb=" N LEU A 308 " --> pdb=" O PHE A 295 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N LEU A 297 " --> pdb=" O LEU A 306 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LYS A 304 " --> pdb=" O HIS A 299 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'A' and resid 243 through 246 Processing sheet with id= 15, first strand: chain 'A' and resid 329 through 333 Processing sheet with id= 16, first strand: chain 'A' and resid 692 through 697 removed outlier: 6.819A pdb=" N HIS A 692 " --> pdb=" O SER A 795 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG A1637 " --> pdb=" O ILE A1632 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'A' and resid 764 through 770 removed outlier: 3.717A pdb=" N ASP A 753 " --> pdb=" O VAL A 679 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N LYS A 671 " --> pdb=" O LEU A 761 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LYS A 799 " --> pdb=" O ASP A 680 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N CYS A1621 " --> pdb=" O ILE A 798 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLY A1616 " --> pdb=" O ILE A1611 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'A' and resid 777 through 780 Processing sheet with id= 19, first strand: chain 'A' and resid 849 through 852 removed outlier: 5.274A pdb=" N GLN A1211 " --> pdb=" O GLY A 852 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL A1212 " --> pdb=" O VAL A1108 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N GLY A1099 " --> pdb=" O MET A1168 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASP A1160 " --> pdb=" O THR A1107 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'A' and resid 948 through 952 removed outlier: 3.836A pdb=" N HIS A 949 " --> pdb=" O GLU A1065 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU A1065 " --> pdb=" O HIS A 949 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'A' and resid 1147 through 1151 removed outlier: 7.100A pdb=" N ARG A1133 " --> pdb=" O ARG A1119 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLY A1139 " --> pdb=" O MET A1113 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N MET A1113 " --> pdb=" O GLY A1139 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ASP A1112 " --> pdb=" O GLY A1208 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ILE A1087 " --> pdb=" O SER A1252 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N THR A1248 " --> pdb=" O GLU A1091 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N MET A1249 " --> pdb=" O MET A1599 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N LEU A1595 " --> pdb=" O LYS A1253 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'A' and resid 1280 through 1284 removed outlier: 6.284A pdb=" N VAL A1552 " --> pdb=" O PHE A1433 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N PHE A1433 " --> pdb=" O VAL A1552 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N GLY A1558 " --> pdb=" O TYR A1427 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N TYR A1427 " --> pdb=" O GLY A1558 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N SER A1424 " --> pdb=" O ALA A1513 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N LEU A1505 " --> pdb=" O ILE A1432 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU A1517 " --> pdb=" O ASP A1512 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N GLY A1516 " --> pdb=" O VAL A1533 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'A' and resid 1307 through 1310 removed outlier: 4.987A pdb=" N THR A1537 " --> pdb=" O CYS A1310 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N PHE A1301 " --> pdb=" O LEU A1591 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N HIS A1587 " --> pdb=" O SER A1305 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'A' and resid 2741 through 2744 removed outlier: 4.085A pdb=" N GLY A2744 " --> pdb=" O GLN A2754 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ILE A2746 " --> pdb=" O PRO A2755 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'A' and resid 2787 through 2791 removed outlier: 4.674A pdb=" N ARG A2788 " --> pdb=" O SER A2904 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'A' and resid 4132 through 4139 removed outlier: 4.829A pdb=" N PHE A4132 " --> pdb=" O ILE A4152 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'A' and resid 4521 through 4524 Processing sheet with id= 28, first strand: chain 'B' and resid 47 through 52 removed outlier: 3.589A pdb=" N GLU B 50 " --> pdb=" O CYS B 36 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LYS B 34 " --> pdb=" O THR B 52 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'B' and resid 67 through 70 removed outlier: 6.550A pdb=" N LEU B 120 " --> pdb=" O GLU B 70 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'B' and resid 161 through 164 Processing sheet with id= 31, first strand: chain 'B' and resid 192 through 196 removed outlier: 3.534A pdb=" N HIS B 202 " --> pdb=" O SER B 195 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'B' and resid 231 through 235 removed outlier: 4.109A pdb=" N ASP B 232 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N LEU B 274 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 14.681A pdb=" N PHE B 295 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 10.456A pdb=" N LEU B 308 " --> pdb=" O PHE B 295 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N LEU B 297 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LYS B 304 " --> pdb=" O HIS B 299 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'B' and resid 243 through 246 Processing sheet with id= 34, first strand: chain 'B' and resid 329 through 333 Processing sheet with id= 35, first strand: chain 'B' and resid 692 through 697 removed outlier: 6.818A pdb=" N HIS B 692 " --> pdb=" O SER B 795 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG B1637 " --> pdb=" O ILE B1632 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'B' and resid 764 through 770 removed outlier: 3.717A pdb=" N ASP B 753 " --> pdb=" O VAL B 679 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N LYS B 671 " --> pdb=" O LEU B 761 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LYS B 799 " --> pdb=" O ASP B 680 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N CYS B1621 " --> pdb=" O ILE B 798 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N GLY B1616 " --> pdb=" O ILE B1611 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'B' and resid 777 through 780 Processing sheet with id= 38, first strand: chain 'B' and resid 849 through 852 removed outlier: 5.274A pdb=" N GLN B1211 " --> pdb=" O GLY B 852 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL B1212 " --> pdb=" O VAL B1108 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N GLY B1099 " --> pdb=" O MET B1168 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASP B1160 " --> pdb=" O THR B1107 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'B' and resid 948 through 952 removed outlier: 3.836A pdb=" N HIS B 949 " --> pdb=" O GLU B1065 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU B1065 " --> pdb=" O HIS B 949 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'B' and resid 1147 through 1151 removed outlier: 7.100A pdb=" N ARG B1133 " --> pdb=" O ARG B1119 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLY B1139 " --> pdb=" O MET B1113 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N MET B1113 " --> pdb=" O GLY B1139 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ASP B1112 " --> pdb=" O GLY B1208 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ILE B1087 " --> pdb=" O SER B1252 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N THR B1248 " --> pdb=" O GLU B1091 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N MET B1249 " --> pdb=" O MET B1599 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N LEU B1595 " --> pdb=" O LYS B1253 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'B' and resid 1280 through 1284 removed outlier: 6.283A pdb=" N VAL B1552 " --> pdb=" O PHE B1433 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N PHE B1433 " --> pdb=" O VAL B1552 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N GLY B1558 " --> pdb=" O TYR B1427 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N TYR B1427 " --> pdb=" O GLY B1558 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N SER B1424 " --> pdb=" O ALA B1513 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N LEU B1505 " --> pdb=" O ILE B1432 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU B1517 " --> pdb=" O ASP B1512 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N GLY B1516 " --> pdb=" O VAL B1533 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'B' and resid 1307 through 1310 removed outlier: 4.986A pdb=" N THR B1537 " --> pdb=" O CYS B1310 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N PHE B1301 " --> pdb=" O LEU B1591 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N HIS B1587 " --> pdb=" O SER B1305 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'B' and resid 2741 through 2744 removed outlier: 4.086A pdb=" N GLY B2744 " --> pdb=" O GLN B2754 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ILE B2746 " --> pdb=" O PRO B2755 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'B' and resid 2787 through 2791 removed outlier: 4.675A pdb=" N ARG B2788 " --> pdb=" O SER B2904 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'B' and resid 4132 through 4139 removed outlier: 4.830A pdb=" N PHE B4132 " --> pdb=" O ILE B4152 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'B' and resid 4521 through 4524 Processing sheet with id= 47, first strand: chain 'C' and resid 47 through 52 removed outlier: 3.589A pdb=" N GLU C 50 " --> pdb=" O CYS C 36 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LYS C 34 " --> pdb=" O THR C 52 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'C' and resid 67 through 70 removed outlier: 6.549A pdb=" N LEU C 120 " --> pdb=" O GLU C 70 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'C' and resid 161 through 164 Processing sheet with id= 50, first strand: chain 'C' and resid 192 through 196 removed outlier: 3.534A pdb=" N HIS C 202 " --> pdb=" O SER C 195 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'C' and resid 231 through 235 removed outlier: 4.108A pdb=" N ASP C 232 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N LEU C 274 " --> pdb=" O VAL C 300 " (cutoff:3.500A) removed outlier: 14.681A pdb=" N PHE C 295 " --> pdb=" O LEU C 308 " (cutoff:3.500A) removed outlier: 10.456A pdb=" N LEU C 308 " --> pdb=" O PHE C 295 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N LEU C 297 " --> pdb=" O LEU C 306 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LYS C 304 " --> pdb=" O HIS C 299 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'C' and resid 243 through 246 Processing sheet with id= 53, first strand: chain 'C' and resid 329 through 333 Processing sheet with id= 54, first strand: chain 'C' and resid 692 through 697 removed outlier: 6.819A pdb=" N HIS C 692 " --> pdb=" O SER C 795 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG C1637 " --> pdb=" O ILE C1632 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'C' and resid 764 through 770 removed outlier: 3.717A pdb=" N ASP C 753 " --> pdb=" O VAL C 679 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N LYS C 671 " --> pdb=" O LEU C 761 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LYS C 799 " --> pdb=" O ASP C 680 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N CYS C1621 " --> pdb=" O ILE C 798 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLY C1616 " --> pdb=" O ILE C1611 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'C' and resid 777 through 780 Processing sheet with id= 57, first strand: chain 'C' and resid 849 through 852 removed outlier: 5.273A pdb=" N GLN C1211 " --> pdb=" O GLY C 852 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL C1212 " --> pdb=" O VAL C1108 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N GLY C1099 " --> pdb=" O MET C1168 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASP C1160 " --> pdb=" O THR C1107 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'C' and resid 948 through 952 removed outlier: 3.835A pdb=" N HIS C 949 " --> pdb=" O GLU C1065 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU C1065 " --> pdb=" O HIS C 949 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'C' and resid 1147 through 1151 removed outlier: 7.099A pdb=" N ARG C1133 " --> pdb=" O ARG C1119 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLY C1139 " --> pdb=" O MET C1113 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N MET C1113 " --> pdb=" O GLY C1139 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ASP C1112 " --> pdb=" O GLY C1208 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ILE C1087 " --> pdb=" O SER C1252 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N THR C1248 " --> pdb=" O GLU C1091 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N MET C1249 " --> pdb=" O MET C1599 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N LEU C1595 " --> pdb=" O LYS C1253 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'C' and resid 1280 through 1284 removed outlier: 6.284A pdb=" N VAL C1552 " --> pdb=" O PHE C1433 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N PHE C1433 " --> pdb=" O VAL C1552 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N GLY C1558 " --> pdb=" O TYR C1427 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N TYR C1427 " --> pdb=" O GLY C1558 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N SER C1424 " --> pdb=" O ALA C1513 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N LEU C1505 " --> pdb=" O ILE C1432 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU C1517 " --> pdb=" O ASP C1512 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N GLY C1516 " --> pdb=" O VAL C1533 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'C' and resid 1307 through 1310 removed outlier: 4.986A pdb=" N THR C1537 " --> pdb=" O CYS C1310 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N PHE C1301 " --> pdb=" O LEU C1591 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N HIS C1587 " --> pdb=" O SER C1305 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'C' and resid 2741 through 2744 removed outlier: 4.085A pdb=" N GLY C2744 " --> pdb=" O GLN C2754 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ILE C2746 " --> pdb=" O PRO C2755 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'C' and resid 2787 through 2791 removed outlier: 4.675A pdb=" N ARG C2788 " --> pdb=" O SER C2904 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'C' and resid 4132 through 4139 removed outlier: 4.829A pdb=" N PHE C4132 " --> pdb=" O ILE C4152 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'C' and resid 4521 through 4524 Processing sheet with id= 66, first strand: chain 'D' and resid 47 through 52 removed outlier: 3.589A pdb=" N GLU D 50 " --> pdb=" O CYS D 36 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LYS D 34 " --> pdb=" O THR D 52 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'D' and resid 67 through 70 removed outlier: 6.549A pdb=" N LEU D 120 " --> pdb=" O GLU D 70 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'D' and resid 161 through 164 Processing sheet with id= 69, first strand: chain 'D' and resid 192 through 196 removed outlier: 3.533A pdb=" N HIS D 202 " --> pdb=" O SER D 195 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'D' and resid 231 through 235 removed outlier: 4.109A pdb=" N ASP D 232 " --> pdb=" O LEU D 277 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N LEU D 274 " --> pdb=" O VAL D 300 " (cutoff:3.500A) removed outlier: 14.681A pdb=" N PHE D 295 " --> pdb=" O LEU D 308 " (cutoff:3.500A) removed outlier: 10.456A pdb=" N LEU D 308 " --> pdb=" O PHE D 295 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N LEU D 297 " --> pdb=" O LEU D 306 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LYS D 304 " --> pdb=" O HIS D 299 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'D' and resid 243 through 246 Processing sheet with id= 72, first strand: chain 'D' and resid 329 through 333 Processing sheet with id= 73, first strand: chain 'D' and resid 692 through 697 removed outlier: 6.819A pdb=" N HIS D 692 " --> pdb=" O SER D 795 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG D1637 " --> pdb=" O ILE D1632 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'D' and resid 764 through 770 removed outlier: 3.718A pdb=" N ASP D 753 " --> pdb=" O VAL D 679 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N LYS D 671 " --> pdb=" O LEU D 761 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LYS D 799 " --> pdb=" O ASP D 680 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N CYS D1621 " --> pdb=" O ILE D 798 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLY D1616 " --> pdb=" O ILE D1611 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'D' and resid 777 through 780 Processing sheet with id= 76, first strand: chain 'D' and resid 849 through 852 removed outlier: 5.274A pdb=" N GLN D1211 " --> pdb=" O GLY D 852 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL D1212 " --> pdb=" O VAL D1108 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N GLY D1099 " --> pdb=" O MET D1168 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASP D1160 " --> pdb=" O THR D1107 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'D' and resid 948 through 952 removed outlier: 3.836A pdb=" N HIS D 949 " --> pdb=" O GLU D1065 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU D1065 " --> pdb=" O HIS D 949 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'D' and resid 1147 through 1151 removed outlier: 7.099A pdb=" N ARG D1133 " --> pdb=" O ARG D1119 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLY D1139 " --> pdb=" O MET D1113 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N MET D1113 " --> pdb=" O GLY D1139 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ASP D1112 " --> pdb=" O GLY D1208 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ILE D1087 " --> pdb=" O SER D1252 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N THR D1248 " --> pdb=" O GLU D1091 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N MET D1249 " --> pdb=" O MET D1599 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N LEU D1595 " --> pdb=" O LYS D1253 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'D' and resid 1280 through 1284 removed outlier: 6.284A pdb=" N VAL D1552 " --> pdb=" O PHE D1433 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N PHE D1433 " --> pdb=" O VAL D1552 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N GLY D1558 " --> pdb=" O TYR D1427 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N TYR D1427 " --> pdb=" O GLY D1558 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N SER D1424 " --> pdb=" O ALA D1513 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N LEU D1505 " --> pdb=" O ILE D1432 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU D1517 " --> pdb=" O ASP D1512 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N GLY D1516 " --> pdb=" O VAL D1533 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'D' and resid 1307 through 1310 removed outlier: 4.986A pdb=" N THR D1537 " --> pdb=" O CYS D1310 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N PHE D1301 " --> pdb=" O LEU D1591 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N HIS D1587 " --> pdb=" O SER D1305 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain 'D' and resid 2741 through 2744 removed outlier: 4.084A pdb=" N GLY D2744 " --> pdb=" O GLN D2754 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ILE D2746 " --> pdb=" O PRO D2755 " (cutoff:3.500A) Processing sheet with id= 82, first strand: chain 'D' and resid 2787 through 2791 removed outlier: 4.675A pdb=" N ARG D2788 " --> pdb=" O SER D2904 " (cutoff:3.500A) Processing sheet with id= 83, first strand: chain 'D' and resid 4132 through 4139 removed outlier: 4.830A pdb=" N PHE D4132 " --> pdb=" O ILE D4152 " (cutoff:3.500A) Processing sheet with id= 84, first strand: chain 'D' and resid 4521 through 4524 7232 hydrogen bonds defined for protein. 21580 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: 104.84 Time building geometry restraints manager: 46.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.40: 58054 1.40 - 1.62: 82078 1.62 - 1.83: 1516 1.83 - 2.05: 12 2.05 - 2.26: 16 Bond restraints: 141676 Sorted by residual: bond pdb=" CD1 PHE D3117 " pdb=" CE1 PHE D3117 " ideal model delta sigma weight residual 1.382 2.261 -0.879 3.00e-02 1.11e+03 8.59e+02 bond pdb=" CD1 PHE B3117 " pdb=" CE1 PHE B3117 " ideal model delta sigma weight residual 1.382 2.261 -0.879 3.00e-02 1.11e+03 8.59e+02 bond pdb=" CD1 PHE A3117 " pdb=" CE1 PHE A3117 " ideal model delta sigma weight residual 1.382 2.260 -0.878 3.00e-02 1.11e+03 8.57e+02 bond pdb=" CD1 PHE C3117 " pdb=" CE1 PHE C3117 " ideal model delta sigma weight residual 1.382 2.260 -0.878 3.00e-02 1.11e+03 8.56e+02 bond pdb=" CD2 PHE B3117 " pdb=" CE2 PHE B3117 " ideal model delta sigma weight residual 1.382 2.212 -0.830 3.00e-02 1.11e+03 7.66e+02 ... (remaining 141671 not shown) Histogram of bond angle deviations from ideal: 92.03 - 104.65: 2462 104.65 - 117.28: 98451 117.28 - 129.90: 89450 129.90 - 142.53: 1057 142.53 - 155.15: 4 Bond angle restraints: 191424 Sorted by residual: angle pdb=" CD ARG A3043 " pdb=" NE ARG A3043 " pdb=" CZ ARG A3043 " ideal model delta sigma weight residual 124.40 155.15 -30.75 1.40e+00 5.10e-01 4.83e+02 angle pdb=" CD ARG B3043 " pdb=" NE ARG B3043 " pdb=" CZ ARG B3043 " ideal model delta sigma weight residual 124.40 155.15 -30.75 1.40e+00 5.10e-01 4.82e+02 angle pdb=" CD ARG D3043 " pdb=" NE ARG D3043 " pdb=" CZ ARG D3043 " ideal model delta sigma weight residual 124.40 155.13 -30.73 1.40e+00 5.10e-01 4.82e+02 angle pdb=" CD ARG C3043 " pdb=" NE ARG C3043 " pdb=" CZ ARG C3043 " ideal model delta sigma weight residual 124.40 155.13 -30.73 1.40e+00 5.10e-01 4.82e+02 angle pdb=" CG ARG B3043 " pdb=" CD ARG B3043 " pdb=" NE ARG B3043 " ideal model delta sigma weight residual 112.00 136.30 -24.30 2.20e+00 2.07e-01 1.22e+02 ... (remaining 191419 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 76300 17.60 - 35.20: 7177 35.20 - 52.80: 1325 52.80 - 70.40: 458 70.40 - 88.00: 164 Dihedral angle restraints: 85424 sinusoidal: 35064 harmonic: 50360 Sorted by residual: dihedral pdb=" CA PHE B4640 " pdb=" C PHE B4640 " pdb=" N PRO B4641 " pdb=" CA PRO B4641 " ideal model delta harmonic sigma weight residual -180.00 -138.82 -41.18 0 5.00e+00 4.00e-02 6.78e+01 dihedral pdb=" CA PHE C4640 " pdb=" C PHE C4640 " pdb=" N PRO C4641 " pdb=" CA PRO C4641 " ideal model delta harmonic sigma weight residual -180.00 -138.84 -41.16 0 5.00e+00 4.00e-02 6.78e+01 dihedral pdb=" CA PHE A4640 " pdb=" C PHE A4640 " pdb=" N PRO A4641 " pdb=" CA PRO A4641 " ideal model delta harmonic sigma weight residual -180.00 -138.87 -41.13 0 5.00e+00 4.00e-02 6.77e+01 ... (remaining 85421 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 17775 0.058 - 0.115: 2915 0.115 - 0.173: 236 0.173 - 0.231: 54 0.231 - 0.288: 8 Chirality restraints: 20988 Sorted by residual: chirality pdb=" CG LEU A3211 " pdb=" CB LEU A3211 " pdb=" CD1 LEU A3211 " pdb=" CD2 LEU A3211 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" CG LEU C3211 " pdb=" CB LEU C3211 " pdb=" CD1 LEU C3211 " pdb=" CD2 LEU C3211 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" CG LEU B3211 " pdb=" CB LEU B3211 " pdb=" CD1 LEU B3211 " pdb=" CD2 LEU B3211 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.04e+00 ... (remaining 20985 not shown) Planarity restraints: 24592 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A4640 " 0.096 5.00e-02 4.00e+02 1.49e-01 3.56e+01 pdb=" N PRO A4641 " -0.258 5.00e-02 4.00e+02 pdb=" CA PRO A4641 " 0.085 5.00e-02 4.00e+02 pdb=" CD PRO A4641 " 0.076 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE D4640 " -0.096 5.00e-02 4.00e+02 1.49e-01 3.55e+01 pdb=" N PRO D4641 " 0.258 5.00e-02 4.00e+02 pdb=" CA PRO D4641 " -0.085 5.00e-02 4.00e+02 pdb=" CD PRO D4641 " -0.076 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B4640 " 0.096 5.00e-02 4.00e+02 1.49e-01 3.55e+01 pdb=" N PRO B4641 " -0.258 5.00e-02 4.00e+02 pdb=" CA PRO B4641 " 0.085 5.00e-02 4.00e+02 pdb=" CD PRO B4641 " 0.076 5.00e-02 4.00e+02 ... (remaining 24589 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 994 2.53 - 3.12: 108415 3.12 - 3.71: 230882 3.71 - 4.31: 315453 4.31 - 4.90: 514298 Nonbonded interactions: 1170042 Sorted by model distance: nonbonded pdb=" NE ARG D3043 " pdb=" CD2 PHE D3117 " model vdw 1.935 3.420 nonbonded pdb=" NE ARG A3043 " pdb=" CD2 PHE A3117 " model vdw 1.935 3.420 nonbonded pdb=" NE ARG C3043 " pdb=" CD2 PHE C3117 " model vdw 1.935 3.420 nonbonded pdb=" NE ARG B3043 " pdb=" CD2 PHE B3117 " model vdw 1.936 3.420 nonbonded pdb=" NE ARG D3043 " pdb=" CE2 PHE D3117 " model vdw 1.974 3.420 ... (remaining 1170037 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 10 through 2577 or resid 2579 through 2837 or resid 2839 t \ hrough 4967 or resid 5001 through 5005)) selection = (chain 'B' and (resid 10 through 2577 or resid 2579 through 2837 or resid 2839 t \ hrough 4967 or resid 5001 through 5005)) selection = (chain 'C' and (resid 10 through 2577 or resid 2579 through 2837 or resid 2839 t \ hrough 4967 or resid 5001 through 5005)) selection = (chain 'D' and (resid 10 through 2577 or resid 2579 through 2837 or resid 2839 t \ hrough 4967 or resid 5001 through 5005)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.220 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: 0.090 Extract box with map and model: 30.790 Check model and map are aligned: 1.480 Set scattering table: 0.910 Process input model: 437.010 Find NCS groups from input model: 7.410 Set up NCS constraints: 0.890 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 489.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 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 : 0.010 0.879 141676 Z= 0.645 Angle : 0.881 30.752 191424 Z= 0.482 Chirality : 0.043 0.288 20988 Planarity : 0.006 0.198 24592 Dihedral : 14.895 87.996 52936 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.10 % Favored : 96.83 % Rotamer: Outliers : 1.82 % Allowed : 1.14 % Favored : 97.04 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.06), residues: 17212 helix: 1.06 (0.06), residues: 9008 sheet: 0.12 (0.13), residues: 1584 loop : -0.70 (0.08), residues: 6620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.096 0.003 TRP D 902 HIS 0.020 0.001 HIS B4903 PHE 0.050 0.002 PHE B3109 TYR 0.031 0.001 TYR B4818 ARG 0.056 0.001 ARG B3043 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1071 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 276 poor density : 795 time to evaluate : 11.068 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: A 203 VAL cc_start: 0.8749 (OUTLIER) cc_final: 0.8537 (p) REVERT: A 309 MET cc_start: 0.7519 (OUTLIER) cc_final: 0.7138 (mmt) REVERT: A 494 MET cc_start: 0.8650 (OUTLIER) cc_final: 0.8357 (mmm) REVERT: A 893 TRP cc_start: 0.9077 (m-90) cc_final: 0.8517 (m-90) REVERT: A 995 MET cc_start: 0.8700 (mtm) cc_final: 0.8130 (mtt) REVERT: A 1300 MET cc_start: 0.8484 (mmm) cc_final: 0.8255 (mmp) REVERT: A 1494 MET cc_start: 0.7947 (ptm) cc_final: 0.7648 (ttp) REVERT: A 1751 ILE cc_start: 0.9098 (OUTLIER) cc_final: 0.8863 (pt) REVERT: A 1906 MET cc_start: 0.8364 (mmm) cc_final: 0.8149 (mmp) REVERT: A 2248 MET cc_start: 0.7923 (OUTLIER) cc_final: 0.7457 (ttm) REVERT: A 2456 MET cc_start: 0.8454 (ptp) cc_final: 0.8222 (mtp) REVERT: A 2512 MET cc_start: 0.8847 (tpt) cc_final: 0.8514 (tpp) REVERT: A 2605 MET cc_start: 0.8635 (tmm) cc_final: 0.8397 (tmm) REVERT: A 2695 MET cc_start: 0.5312 (mmm) cc_final: 0.4945 (mmm) REVERT: A 2785 TRP cc_start: 0.7822 (t-100) cc_final: 0.6854 (t60) REVERT: A 2844 MET cc_start: 0.8988 (ptp) cc_final: 0.8235 (ptp) REVERT: A 2899 ASN cc_start: 0.8435 (m-40) cc_final: 0.8188 (t0) REVERT: A 2901 TYR cc_start: 0.6963 (m-80) cc_final: 0.6363 (m-10) REVERT: A 3104 MET cc_start: 0.7813 (ppp) cc_final: 0.7230 (ppp) REVERT: A 3277 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8751 (mt) REVERT: A 3819 MET cc_start: 0.5898 (OUTLIER) cc_final: 0.5329 (mtp) REVERT: A 3981 MET cc_start: 0.8227 (OUTLIER) cc_final: 0.7742 (ttp) REVERT: A 4654 MET cc_start: 0.8100 (tpt) cc_final: 0.7733 (tpp) REVERT: A 4748 MET cc_start: 0.7302 (OUTLIER) cc_final: 0.6501 (tpt) REVERT: B 403 ILE cc_start: 0.8616 (OUTLIER) cc_final: 0.8252 (mp) REVERT: B 494 MET cc_start: 0.8541 (OUTLIER) cc_final: 0.8338 (mmm) REVERT: B 893 TRP cc_start: 0.9254 (m-90) cc_final: 0.8775 (m-90) REVERT: B 995 MET cc_start: 0.8331 (mtm) cc_final: 0.7957 (mtt) REVERT: B 1300 MET cc_start: 0.8798 (mmm) cc_final: 0.8264 (mpp) REVERT: B 1751 ILE cc_start: 0.9032 (OUTLIER) cc_final: 0.8641 (pt) REVERT: B 1794 MET cc_start: 0.8549 (mtm) cc_final: 0.8334 (mtp) REVERT: B 2142 MET cc_start: 0.8200 (OUTLIER) cc_final: 0.7864 (mpp) REVERT: B 2279 MET cc_start: 0.8949 (OUTLIER) cc_final: 0.8487 (tmm) REVERT: B 2384 MET cc_start: 0.9114 (mmm) cc_final: 0.8889 (mmm) REVERT: B 2389 MET cc_start: 0.8889 (mtp) cc_final: 0.8425 (mtm) REVERT: B 2468 MET cc_start: 0.8955 (mmm) cc_final: 0.8658 (mmp) REVERT: B 2605 MET cc_start: 0.8704 (tmm) cc_final: 0.8481 (tmm) REVERT: B 2695 MET cc_start: 0.5944 (mmm) cc_final: 0.5709 (mmm) REVERT: B 2720 PHE cc_start: 0.8492 (t80) cc_final: 0.7759 (t80) REVERT: B 2758 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.7862 (ptmm) REVERT: B 2760 TYR cc_start: 0.7786 (t80) cc_final: 0.7124 (t80) REVERT: B 2771 TYR cc_start: 0.8086 (m-80) cc_final: 0.7682 (m-80) REVERT: B 2844 MET cc_start: 0.9012 (ptp) cc_final: 0.8119 (ptp) REVERT: B 2899 ASN cc_start: 0.8355 (m-40) cc_final: 0.7684 (t0) REVERT: B 2901 TYR cc_start: 0.6921 (m-80) cc_final: 0.6616 (m-80) REVERT: B 3104 MET cc_start: 0.7772 (ppp) cc_final: 0.7506 (ppp) REVERT: B 3162 PHE cc_start: 0.7884 (t80) cc_final: 0.7327 (t80) REVERT: B 3246 MET cc_start: 0.7756 (ptt) cc_final: 0.7105 (ppp) REVERT: B 3277 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8603 (mt) REVERT: B 3689 MET cc_start: 0.8427 (mtt) cc_final: 0.8040 (mtm) REVERT: B 3819 MET cc_start: 0.5368 (OUTLIER) cc_final: 0.4735 (mpp) REVERT: B 4502 MET cc_start: 0.8083 (mtm) cc_final: 0.7732 (ptm) REVERT: B 4504 MET cc_start: 0.8340 (tpt) cc_final: 0.8107 (tpt) REVERT: B 4748 MET cc_start: 0.8119 (OUTLIER) cc_final: 0.7890 (mmm) REVERT: B 4817 MET cc_start: 0.8627 (mmm) cc_final: 0.8343 (mmm) REVERT: B 4884 MET cc_start: 0.8467 (OUTLIER) cc_final: 0.8237 (tpt) REVERT: C 893 TRP cc_start: 0.9217 (m-90) cc_final: 0.8730 (m-90) REVERT: C 995 MET cc_start: 0.8720 (mtm) cc_final: 0.8299 (mtt) REVERT: C 1751 ILE cc_start: 0.9285 (OUTLIER) cc_final: 0.9017 (pt) REVERT: C 2162 MET cc_start: 0.8713 (mmp) cc_final: 0.8271 (mmp) REVERT: C 2167 MET cc_start: 0.7552 (mtp) cc_final: 0.7299 (mtp) REVERT: C 2214 MET cc_start: 0.9120 (mmm) cc_final: 0.8919 (mmm) REVERT: C 2279 MET cc_start: 0.8912 (OUTLIER) cc_final: 0.8633 (ptt) REVERT: C 2384 MET cc_start: 0.9343 (mmm) cc_final: 0.9061 (mmm) REVERT: C 2389 MET cc_start: 0.9039 (mtp) cc_final: 0.8671 (mtp) REVERT: C 2456 MET cc_start: 0.8562 (ptp) cc_final: 0.8335 (mtt) REVERT: C 2512 MET cc_start: 0.8913 (tpt) cc_final: 0.8686 (tpp) REVERT: C 2758 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.8485 (ptmm) REVERT: C 2761 LYS cc_start: 0.9008 (OUTLIER) cc_final: 0.8611 (mmtp) REVERT: C 2843 MET cc_start: 0.7087 (tpp) cc_final: 0.6732 (tpp) REVERT: C 2895 PHE cc_start: 0.8020 (t80) cc_final: 0.7649 (t80) REVERT: C 2901 TYR cc_start: 0.7031 (m-80) cc_final: 0.6821 (m-80) REVERT: C 3104 MET cc_start: 0.8033 (ppp) cc_final: 0.7401 (ppp) REVERT: C 3246 MET cc_start: 0.7811 (ptt) cc_final: 0.7468 (ptp) REVERT: C 3277 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8916 (mt) REVERT: C 3819 MET cc_start: 0.6314 (OUTLIER) cc_final: 0.5714 (mtp) REVERT: C 3954 MET cc_start: 0.8576 (OUTLIER) cc_final: 0.8372 (mmm) REVERT: C 4279 MET cc_start: 0.6753 (OUTLIER) cc_final: 0.6504 (tpt) REVERT: C 4491 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.9003 (pp) REVERT: C 4748 MET cc_start: 0.7720 (OUTLIER) cc_final: 0.7435 (mmm) REVERT: D 494 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.8156 (mmm) REVERT: D 893 TRP cc_start: 0.9130 (m-90) cc_final: 0.8590 (m-90) REVERT: D 995 MET cc_start: 0.8696 (mtm) cc_final: 0.8330 (mtt) REVERT: D 1174 MET cc_start: 0.7825 (ptp) cc_final: 0.7391 (ptt) REVERT: D 1300 MET cc_start: 0.8709 (mmm) cc_final: 0.8330 (mmm) REVERT: D 1751 ILE cc_start: 0.9063 (OUTLIER) cc_final: 0.8626 (pt) REVERT: D 2084 MET cc_start: 0.8802 (mtp) cc_final: 0.8596 (mtp) REVERT: D 2142 MET cc_start: 0.8197 (OUTLIER) cc_final: 0.7749 (mpp) REVERT: D 2279 MET cc_start: 0.8963 (OUTLIER) cc_final: 0.8627 (tmm) REVERT: D 2384 MET cc_start: 0.8797 (mmm) cc_final: 0.8587 (mmp) REVERT: D 2468 MET cc_start: 0.8582 (mmm) cc_final: 0.8284 (mmp) REVERT: D 2512 MET cc_start: 0.8959 (tpt) cc_final: 0.8623 (tpp) REVERT: D 2584 MET cc_start: 0.7703 (mtt) cc_final: 0.7419 (mtt) REVERT: D 2720 PHE cc_start: 0.8409 (t80) cc_final: 0.7931 (t80) REVERT: D 2734 MET cc_start: 0.8531 (mpp) cc_final: 0.8187 (mpp) REVERT: D 2758 LYS cc_start: 0.7814 (OUTLIER) cc_final: 0.7530 (ptmm) REVERT: D 2844 MET cc_start: 0.8395 (ptp) cc_final: 0.7735 (ptp) REVERT: D 2848 TYR cc_start: 0.8326 (m-10) cc_final: 0.8018 (m-10) REVERT: D 3060 PHE cc_start: 0.8054 (t80) cc_final: 0.7523 (t80) REVERT: D 3104 MET cc_start: 0.8160 (ppp) cc_final: 0.7751 (ppp) REVERT: D 3201 VAL cc_start: 0.7412 (OUTLIER) cc_final: 0.6977 (t) REVERT: D 3246 MET cc_start: 0.7152 (ptt) cc_final: 0.6331 (ppp) REVERT: D 3277 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.8060 (mt) REVERT: D 3819 MET cc_start: 0.4787 (OUTLIER) cc_final: 0.4349 (mpp) REVERT: D 3981 MET cc_start: 0.7852 (OUTLIER) cc_final: 0.7554 (ttp) REVERT: D 4707 MET cc_start: 0.8464 (OUTLIER) cc_final: 0.8202 (tmm) REVERT: D 4748 MET cc_start: 0.7647 (OUTLIER) cc_final: 0.6775 (tpt) outliers start: 276 outliers final: 72 residues processed: 880 average time/residue: 1.1972 time to fit residues: 1866.1063 Evaluate side-chains 841 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 729 time to evaluate : 11.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 19 LYS Chi-restraints excluded: chain F residue 19 LYS Chi-restraints excluded: chain G residue 19 LYS Chi-restraints excluded: chain H residue 18 LYS Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 469 HIS Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 1564 MET Chi-restraints excluded: chain A residue 1751 ILE Chi-restraints excluded: chain A residue 2066 MET Chi-restraints excluded: chain A residue 2192 MET Chi-restraints excluded: chain A residue 2248 MET Chi-restraints excluded: chain A residue 2681 MET Chi-restraints excluded: chain A residue 2754 GLN Chi-restraints excluded: chain A residue 2772 ARG Chi-restraints excluded: chain A residue 2828 MET Chi-restraints excluded: chain A residue 3235 MET Chi-restraints excluded: chain A residue 3277 LEU Chi-restraints excluded: chain A residue 3819 MET Chi-restraints excluded: chain A residue 3981 MET Chi-restraints excluded: chain A residue 3985 MET Chi-restraints excluded: chain A residue 4626 ILE Chi-restraints excluded: chain A residue 4707 MET Chi-restraints excluded: chain A residue 4726 MET Chi-restraints excluded: chain A residue 4748 MET Chi-restraints excluded: chain A residue 4804 MET Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain B residue 765 SER Chi-restraints excluded: chain B residue 1694 MET Chi-restraints excluded: chain B residue 1751 ILE Chi-restraints excluded: chain B residue 2066 MET Chi-restraints excluded: chain B residue 2142 MET Chi-restraints excluded: chain B residue 2192 MET Chi-restraints excluded: chain B residue 2279 MET Chi-restraints excluded: chain B residue 2347 MET Chi-restraints excluded: chain B residue 2681 MET Chi-restraints excluded: chain B residue 2754 GLN Chi-restraints excluded: chain B residue 2758 LYS Chi-restraints excluded: chain B residue 2772 ARG Chi-restraints excluded: chain B residue 2828 MET Chi-restraints excluded: chain B residue 3235 MET Chi-restraints excluded: chain B residue 3242 LEU Chi-restraints excluded: chain B residue 3277 LEU Chi-restraints excluded: chain B residue 3819 MET Chi-restraints excluded: chain B residue 4626 ILE Chi-restraints excluded: chain B residue 4726 MET Chi-restraints excluded: chain B residue 4748 MET Chi-restraints excluded: chain B residue 4882 GLU Chi-restraints excluded: chain B residue 4884 MET Chi-restraints excluded: chain C residue 309 MET Chi-restraints excluded: chain C residue 393 MET Chi-restraints excluded: chain C residue 469 HIS Chi-restraints excluded: chain C residue 494 MET Chi-restraints excluded: chain C residue 765 SER Chi-restraints excluded: chain C residue 1481 LYS Chi-restraints excluded: chain C residue 1564 MET Chi-restraints excluded: chain C residue 1751 ILE Chi-restraints excluded: chain C residue 2066 MET Chi-restraints excluded: chain C residue 2192 MET Chi-restraints excluded: chain C residue 2248 MET Chi-restraints excluded: chain C residue 2279 MET Chi-restraints excluded: chain C residue 2347 MET Chi-restraints excluded: chain C residue 2681 MET Chi-restraints excluded: chain C residue 2758 LYS Chi-restraints excluded: chain C residue 2761 LYS Chi-restraints excluded: chain C residue 2828 MET Chi-restraints excluded: chain C residue 3242 LEU Chi-restraints excluded: chain C residue 3277 LEU Chi-restraints excluded: chain C residue 3819 MET Chi-restraints excluded: chain C residue 3954 MET Chi-restraints excluded: chain C residue 3985 MET Chi-restraints excluded: chain C residue 4279 MET Chi-restraints excluded: chain C residue 4491 LEU Chi-restraints excluded: chain C residue 4626 ILE Chi-restraints excluded: chain C residue 4707 MET Chi-restraints excluded: chain C residue 4726 MET Chi-restraints excluded: chain C residue 4748 MET Chi-restraints excluded: chain C residue 4804 MET Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 309 MET Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 469 HIS Chi-restraints excluded: chain D residue 494 MET Chi-restraints excluded: chain D residue 1564 MET Chi-restraints excluded: chain D residue 1694 MET Chi-restraints excluded: chain D residue 1751 ILE Chi-restraints excluded: chain D residue 2066 MET Chi-restraints excluded: chain D residue 2142 MET Chi-restraints excluded: chain D residue 2192 MET Chi-restraints excluded: chain D residue 2279 MET Chi-restraints excluded: chain D residue 2681 MET Chi-restraints excluded: chain D residue 2758 LYS Chi-restraints excluded: chain D residue 2761 LYS Chi-restraints excluded: chain D residue 2772 ARG Chi-restraints excluded: chain D residue 2828 MET Chi-restraints excluded: chain D residue 3201 VAL Chi-restraints excluded: chain D residue 3235 MET Chi-restraints excluded: chain D residue 3242 LEU Chi-restraints excluded: chain D residue 3277 LEU Chi-restraints excluded: chain D residue 3819 MET Chi-restraints excluded: chain D residue 3981 MET Chi-restraints excluded: chain D residue 4626 ILE Chi-restraints excluded: chain D residue 4707 MET Chi-restraints excluded: chain D residue 4726 MET Chi-restraints excluded: chain D residue 4748 MET Chi-restraints excluded: chain D residue 4804 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1459 optimal weight: 9.9990 chunk 1309 optimal weight: 9.9990 chunk 726 optimal weight: 20.0000 chunk 447 optimal weight: 0.8980 chunk 883 optimal weight: 9.9990 chunk 699 optimal weight: 0.9990 chunk 1354 optimal weight: 10.0000 chunk 524 optimal weight: 0.3980 chunk 823 optimal weight: 2.9990 chunk 1008 optimal weight: 6.9990 chunk 1569 optimal weight: 20.0000 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 836 HIS ** A 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1691 ASN ** A2654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2727 HIS ** A2830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2849 HIS A2897 GLN ** A3174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2897 GLN C2978 HIS ** C3174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4903 HIS ** D 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1691 ASN ** D2654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2849 HIS D2978 HIS ** D3174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.0969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.907 141676 Z= 0.638 Angle : 0.639 29.525 191424 Z= 0.338 Chirality : 0.041 0.318 20988 Planarity : 0.005 0.129 24592 Dihedral : 6.683 80.985 19343 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.89 % Favored : 97.04 % Rotamer: Outliers : 0.61 % Allowed : 3.55 % Favored : 95.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.06), residues: 17212 helix: 1.40 (0.06), residues: 9000 sheet: 0.07 (0.13), residues: 1556 loop : -0.63 (0.07), residues: 6656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP D 893 HIS 0.009 0.001 HIS C3233 PHE 0.051 0.002 PHE A3319 TYR 0.022 0.001 TYR B4250 ARG 0.026 0.001 ARG D3043 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 849 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 756 time to evaluate : 11.843 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: G 4 GLU cc_start: 0.7540 (pm20) cc_final: 0.7076 (pm20) REVERT: G 14 ARG cc_start: 0.8310 (mtm110) cc_final: 0.8104 (mtm110) REVERT: A 203 VAL cc_start: 0.8795 (OUTLIER) cc_final: 0.8588 (p) REVERT: A 893 TRP cc_start: 0.9034 (m-90) cc_final: 0.8260 (m-90) REVERT: A 964 MET cc_start: 0.3219 (OUTLIER) cc_final: 0.2288 (mpp) REVERT: A 995 MET cc_start: 0.8758 (mtm) cc_final: 0.8157 (mtt) REVERT: A 1300 MET cc_start: 0.8426 (mmm) cc_final: 0.8107 (mmp) REVERT: A 2248 MET cc_start: 0.8022 (ttm) cc_final: 0.7763 (ttm) REVERT: A 2512 MET cc_start: 0.8842 (tpt) cc_final: 0.8473 (tmm) REVERT: A 2681 MET cc_start: 0.7953 (OUTLIER) cc_final: 0.7750 (tpp) REVERT: A 2695 MET cc_start: 0.5892 (mmm) cc_final: 0.5620 (mmm) REVERT: A 2720 PHE cc_start: 0.8508 (t80) cc_final: 0.8257 (t80) REVERT: A 2843 MET cc_start: 0.7938 (ptp) cc_final: 0.6710 (tpt) REVERT: A 3003 MET cc_start: 0.8954 (ptm) cc_final: 0.8510 (ptt) REVERT: A 3104 MET cc_start: 0.7867 (ppp) cc_final: 0.7268 (ppp) REVERT: A 3273 MET cc_start: 0.6733 (ptt) cc_final: 0.5909 (ppp) REVERT: A 3819 MET cc_start: 0.6051 (mtt) cc_final: 0.5424 (mtp) REVERT: A 4246 PHE cc_start: 0.8444 (t80) cc_final: 0.7973 (t80) REVERT: A 4250 TYR cc_start: 0.8430 (t80) cc_final: 0.7668 (m-80) REVERT: A 4256 MET cc_start: 0.8571 (mmp) cc_final: 0.8362 (mmm) REVERT: A 4268 MET cc_start: 0.4294 (tpt) cc_final: 0.3678 (tmm) REVERT: A 4654 MET cc_start: 0.8230 (tpt) cc_final: 0.7968 (tpp) REVERT: A 4748 MET cc_start: 0.7293 (mmm) cc_final: 0.6750 (tpt) REVERT: B 494 MET cc_start: 0.8471 (mmp) cc_final: 0.8155 (mmp) REVERT: B 893 TRP cc_start: 0.9188 (m-90) cc_final: 0.8426 (m-90) REVERT: B 964 MET cc_start: 0.3047 (OUTLIER) cc_final: 0.2617 (mpp) REVERT: B 995 MET cc_start: 0.8359 (mtm) cc_final: 0.7994 (mtt) REVERT: B 1720 MET cc_start: 0.8286 (ppp) cc_final: 0.8046 (ptm) REVERT: B 2192 MET cc_start: 0.8540 (tpt) cc_final: 0.8005 (mmm) REVERT: B 2214 MET cc_start: 0.9002 (mmm) cc_final: 0.8220 (mmm) REVERT: B 2279 MET cc_start: 0.8936 (OUTLIER) cc_final: 0.8458 (tmm) REVERT: B 2456 MET cc_start: 0.8523 (mtp) cc_final: 0.8066 (mtm) REVERT: B 2468 MET cc_start: 0.8967 (mmm) cc_final: 0.8667 (mmp) REVERT: B 2512 MET cc_start: 0.8935 (tpt) cc_final: 0.8623 (tpp) REVERT: B 2695 MET cc_start: 0.6136 (mmm) cc_final: 0.5863 (mmm) REVERT: B 2720 PHE cc_start: 0.8581 (t80) cc_final: 0.8127 (t80) REVERT: B 2771 TYR cc_start: 0.8146 (m-80) cc_final: 0.7741 (m-80) REVERT: B 2785 TRP cc_start: 0.7903 (t-100) cc_final: 0.7599 (t-100) REVERT: B 2840 MET cc_start: 0.7454 (mmt) cc_final: 0.7180 (mmt) REVERT: B 2848 TYR cc_start: 0.7883 (m-10) cc_final: 0.7618 (m-10) REVERT: B 3060 PHE cc_start: 0.7757 (t80) cc_final: 0.6751 (t80) REVERT: B 3104 MET cc_start: 0.7809 (ppp) cc_final: 0.7525 (ppp) REVERT: B 3162 PHE cc_start: 0.8027 (t80) cc_final: 0.7571 (t80) REVERT: B 3171 LEU cc_start: 0.8743 (mt) cc_final: 0.8413 (mt) REVERT: B 3273 MET cc_start: 0.7001 (ptt) cc_final: 0.6035 (ppp) REVERT: B 3277 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8459 (mt) REVERT: B 3295 TRP cc_start: 0.7209 (p-90) cc_final: 0.6844 (p-90) REVERT: B 4186 MET cc_start: 0.9262 (mmt) cc_final: 0.9021 (mmp) REVERT: B 4292 MET cc_start: 0.8147 (mmm) cc_final: 0.7927 (mmm) REVERT: B 4502 MET cc_start: 0.8119 (mtm) cc_final: 0.7649 (ptp) REVERT: B 4504 MET cc_start: 0.8345 (tpt) cc_final: 0.8076 (tpt) REVERT: B 4748 MET cc_start: 0.8317 (mmm) cc_final: 0.8024 (mmm) REVERT: C 393 MET cc_start: 0.7511 (tpt) cc_final: 0.7247 (mmm) REVERT: C 893 TRP cc_start: 0.9113 (m-90) cc_final: 0.8399 (m-90) REVERT: C 964 MET cc_start: 0.3101 (OUTLIER) cc_final: 0.2829 (mpp) REVERT: C 995 MET cc_start: 0.8769 (mtm) cc_final: 0.8322 (mtt) REVERT: C 1168 MET cc_start: 0.8505 (mmm) cc_final: 0.8270 (mmp) REVERT: C 1174 MET cc_start: 0.7957 (ptp) cc_final: 0.7720 (ptt) REVERT: C 1215 MET cc_start: 0.8477 (mtp) cc_final: 0.8135 (ttm) REVERT: C 2162 MET cc_start: 0.8672 (mmp) cc_final: 0.8249 (mmp) REVERT: C 2167 MET cc_start: 0.7612 (mtp) cc_final: 0.7121 (mtp) REVERT: C 2214 MET cc_start: 0.9137 (mmm) cc_final: 0.8664 (mmm) REVERT: C 2234 MET cc_start: 0.8832 (mmm) cc_final: 0.8512 (mtp) REVERT: C 2279 MET cc_start: 0.8926 (OUTLIER) cc_final: 0.8594 (ptt) REVERT: C 2384 MET cc_start: 0.9315 (mmm) cc_final: 0.8960 (mmm) REVERT: C 2512 MET cc_start: 0.8895 (tpt) cc_final: 0.8487 (tmm) REVERT: C 2843 MET cc_start: 0.7110 (tpp) cc_final: 0.6613 (tpp) REVERT: C 2844 MET cc_start: 0.8798 (ptp) cc_final: 0.8289 (ptp) REVERT: C 2895 PHE cc_start: 0.7946 (t80) cc_final: 0.7631 (t80) REVERT: C 3003 MET cc_start: 0.9098 (ptm) cc_final: 0.8702 (ptm) REVERT: C 3104 MET cc_start: 0.8117 (ppp) cc_final: 0.7450 (ppp) REVERT: C 3246 MET cc_start: 0.7425 (ptt) cc_final: 0.7144 (ptp) REVERT: C 3273 MET cc_start: 0.6562 (ptt) cc_final: 0.6322 (ppp) REVERT: C 3277 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8746 (mt) REVERT: C 3819 MET cc_start: 0.6385 (mtt) cc_final: 0.5839 (mtp) REVERT: C 3954 MET cc_start: 0.8698 (tpt) cc_final: 0.8217 (mmm) REVERT: C 4707 MET cc_start: 0.8464 (OUTLIER) cc_final: 0.8111 (tpp) REVERT: D 403 ILE cc_start: 0.8562 (OUTLIER) cc_final: 0.8257 (mp) REVERT: D 893 TRP cc_start: 0.9075 (m-90) cc_final: 0.8419 (m-90) REVERT: D 964 MET cc_start: 0.4908 (OUTLIER) cc_final: 0.3487 (mpp) REVERT: D 995 MET cc_start: 0.8792 (mtm) cc_final: 0.8428 (mtt) REVERT: D 1174 MET cc_start: 0.7816 (ptp) cc_final: 0.7547 (ptt) REVERT: D 2279 MET cc_start: 0.8952 (OUTLIER) cc_final: 0.8618 (tmm) REVERT: D 2384 MET cc_start: 0.8797 (mmm) cc_final: 0.8596 (mmp) REVERT: D 2468 MET cc_start: 0.8648 (mmm) cc_final: 0.8309 (mmp) REVERT: D 2512 MET cc_start: 0.8894 (tpt) cc_final: 0.8507 (tpp) REVERT: D 2584 MET cc_start: 0.7710 (mtt) cc_final: 0.7324 (mtt) REVERT: D 2844 MET cc_start: 0.8586 (ptp) cc_final: 0.7778 (ppp) REVERT: D 2848 TYR cc_start: 0.8412 (m-10) cc_final: 0.8158 (m-10) REVERT: D 2901 TYR cc_start: 0.7135 (m-80) cc_final: 0.6352 (m-80) REVERT: D 3060 PHE cc_start: 0.7996 (t80) cc_final: 0.7668 (t80) REVERT: D 3104 MET cc_start: 0.8177 (ppp) cc_final: 0.7791 (ppp) REVERT: D 3215 MET cc_start: 0.8881 (mtt) cc_final: 0.8654 (ptp) REVERT: D 3235 MET cc_start: 0.7393 (ppp) cc_final: 0.6952 (ppp) REVERT: D 3250 TRP cc_start: 0.7256 (t60) cc_final: 0.6962 (t60) REVERT: D 3277 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7842 (mt) REVERT: D 3295 TRP cc_start: 0.7094 (p-90) cc_final: 0.6706 (p-90) REVERT: D 3719 MET cc_start: 0.8330 (tpp) cc_final: 0.8013 (tpp) REVERT: D 3819 MET cc_start: 0.5282 (mtt) cc_final: 0.4988 (mpp) REVERT: D 3981 MET cc_start: 0.8395 (OUTLIER) cc_final: 0.8189 (ttp) REVERT: D 4654 MET cc_start: 0.8294 (tmm) cc_final: 0.8064 (tmm) REVERT: D 4748 MET cc_start: 0.7620 (mmm) cc_final: 0.6819 (tpt) REVERT: D 4884 MET cc_start: 0.8502 (tpp) cc_final: 0.8087 (tpt) outliers start: 93 outliers final: 34 residues processed: 796 average time/residue: 1.1742 time to fit residues: 1661.0343 Evaluate side-chains 770 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 721 time to evaluate : 11.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 18 LYS Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain G residue 30 MET Chi-restraints excluded: chain A residue 29 HIS Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 949 HIS Chi-restraints excluded: chain A residue 964 MET Chi-restraints excluded: chain A residue 1421 MET Chi-restraints excluded: chain A residue 2681 MET Chi-restraints excluded: chain A residue 2897 GLN Chi-restraints excluded: chain A residue 3277 LEU Chi-restraints excluded: chain A residue 4587 ILE Chi-restraints excluded: chain A residue 4626 ILE Chi-restraints excluded: chain A residue 4672 MET Chi-restraints excluded: chain B residue 29 HIS Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 949 HIS Chi-restraints excluded: chain B residue 964 MET Chi-restraints excluded: chain B residue 2279 MET Chi-restraints excluded: chain B residue 2348 GLU Chi-restraints excluded: chain B residue 2897 GLN Chi-restraints excluded: chain B residue 3277 LEU Chi-restraints excluded: chain B residue 4626 ILE Chi-restraints excluded: chain B residue 4884 MET Chi-restraints excluded: chain C residue 29 HIS Chi-restraints excluded: chain C residue 469 HIS Chi-restraints excluded: chain C residue 949 HIS Chi-restraints excluded: chain C residue 964 MET Chi-restraints excluded: chain C residue 2279 MET Chi-restraints excluded: chain C residue 2348 GLU Chi-restraints excluded: chain C residue 2897 GLN Chi-restraints excluded: chain C residue 3277 LEU Chi-restraints excluded: chain C residue 4587 ILE Chi-restraints excluded: chain C residue 4626 ILE Chi-restraints excluded: chain C residue 4707 MET Chi-restraints excluded: chain C residue 4814 MET Chi-restraints excluded: chain D residue 29 HIS Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 778 MET Chi-restraints excluded: chain D residue 949 HIS Chi-restraints excluded: chain D residue 964 MET Chi-restraints excluded: chain D residue 2279 MET Chi-restraints excluded: chain D residue 2897 GLN Chi-restraints excluded: chain D residue 2954 PHE Chi-restraints excluded: chain D residue 3277 LEU Chi-restraints excluded: chain D residue 3981 MET Chi-restraints excluded: chain D residue 4587 ILE Chi-restraints excluded: chain D residue 4626 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 872 optimal weight: 0.9980 chunk 487 optimal weight: 20.0000 chunk 1306 optimal weight: 30.0000 chunk 1068 optimal weight: 7.9990 chunk 432 optimal weight: 10.0000 chunk 1572 optimal weight: 10.0000 chunk 1698 optimal weight: 20.0000 chunk 1400 optimal weight: 8.9990 chunk 1558 optimal weight: 20.0000 chunk 535 optimal weight: 8.9990 chunk 1261 optimal weight: 9.9990 overall best weight: 7.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 26 HIS F 26 HIS H 26 HIS ** A 608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1691 ASN A2091 GLN ** A2251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2316 ASN ** A2654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2897 GLN ** A2899 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2978 HIS ** A3017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4945 GLN ** B1581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2727 HIS B2978 HIS ** B3017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3850 HIS B4178 ASN ** B4489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4642 ASN B4945 GLN ** C1581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2897 GLN ** C3017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3666 GLN ** C4489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4945 GLN D 836 HIS ** D1581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1691 ASN D2602 HIS ** D2654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2659 GLN ** D2684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2899 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4945 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.901 141676 Z= 0.724 Angle : 0.685 31.322 191424 Z= 0.365 Chirality : 0.043 0.329 20988 Planarity : 0.005 0.124 24592 Dihedral : 5.786 83.959 19072 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.27 % Favored : 96.66 % Rotamer: Outliers : 0.54 % Allowed : 5.06 % Favored : 94.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.06), residues: 17212 helix: 1.50 (0.06), residues: 8980 sheet: -0.32 (0.12), residues: 1612 loop : -0.59 (0.08), residues: 6620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP D 893 HIS 0.012 0.002 HIS A1656 PHE 0.044 0.002 PHE A3854 TYR 0.031 0.002 TYR C3285 ARG 0.031 0.001 ARG B2793 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 842 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 760 time to evaluate : 11.877 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: H 67 MET cc_start: 0.8890 (mtp) cc_final: 0.8689 (mtp) REVERT: A 893 TRP cc_start: 0.9152 (m-90) cc_final: 0.8614 (m-90) REVERT: A 895 MET cc_start: 0.9129 (ptp) cc_final: 0.8761 (ppp) REVERT: A 964 MET cc_start: 0.3032 (mtt) cc_final: 0.2160 (mpp) REVERT: A 995 MET cc_start: 0.8893 (mtm) cc_final: 0.8327 (mtt) REVERT: A 2167 MET cc_start: 0.8117 (mtm) cc_final: 0.7844 (mtm) REVERT: A 2512 MET cc_start: 0.8872 (tpt) cc_final: 0.8478 (tmm) REVERT: A 2695 MET cc_start: 0.6033 (mmm) cc_final: 0.5768 (mmm) REVERT: A 2720 PHE cc_start: 0.8523 (t80) cc_final: 0.8238 (t80) REVERT: A 2732 TRP cc_start: 0.8034 (t-100) cc_final: 0.7822 (t-100) REVERT: A 2773 TRP cc_start: 0.8029 (t-100) cc_final: 0.7693 (t-100) REVERT: A 2798 MET cc_start: 0.7271 (mmm) cc_final: 0.6990 (mmm) REVERT: A 2843 MET cc_start: 0.7971 (ptp) cc_final: 0.6795 (tpt) REVERT: A 2844 MET cc_start: 0.8666 (ptp) cc_final: 0.7900 (ptp) REVERT: A 2848 TYR cc_start: 0.7800 (m-10) cc_final: 0.7382 (m-10) REVERT: A 3104 MET cc_start: 0.7990 (ppp) cc_final: 0.7338 (ppp) REVERT: A 3235 MET cc_start: 0.7246 (ppp) cc_final: 0.7038 (tpt) REVERT: A 3273 MET cc_start: 0.7406 (ptt) cc_final: 0.6773 (ppp) REVERT: A 3819 MET cc_start: 0.6393 (mtt) cc_final: 0.6052 (mtm) REVERT: A 3954 MET cc_start: 0.8352 (mmm) cc_final: 0.7681 (tpp) REVERT: A 3981 MET cc_start: 0.8325 (tmm) cc_final: 0.7685 (ttp) REVERT: A 4256 MET cc_start: 0.8630 (mmp) cc_final: 0.8347 (mmm) REVERT: A 4268 MET cc_start: 0.4285 (tpt) cc_final: 0.3636 (tmm) REVERT: A 4279 MET cc_start: 0.6620 (ttt) cc_final: 0.6258 (tpt) REVERT: A 4558 HIS cc_start: 0.7879 (m-70) cc_final: 0.7525 (m90) REVERT: A 4654 MET cc_start: 0.8175 (tpt) cc_final: 0.7896 (tpp) REVERT: A 4748 MET cc_start: 0.7331 (mmm) cc_final: 0.6911 (tpt) REVERT: A 4804 MET cc_start: 0.9017 (mmm) cc_final: 0.8504 (mmm) REVERT: A 4884 MET cc_start: 0.8409 (tpp) cc_final: 0.7982 (tpt) REVERT: B 964 MET cc_start: 0.2683 (mtt) cc_final: 0.2142 (mpp) REVERT: B 995 MET cc_start: 0.8523 (mtm) cc_final: 0.8100 (mtt) REVERT: B 2142 MET cc_start: 0.8591 (mmt) cc_final: 0.8302 (mmp) REVERT: B 2279 MET cc_start: 0.8917 (OUTLIER) cc_final: 0.8446 (tmm) REVERT: B 2389 MET cc_start: 0.9091 (OUTLIER) cc_final: 0.8818 (mtp) REVERT: B 2468 MET cc_start: 0.8976 (mmm) cc_final: 0.8773 (mmp) REVERT: B 2512 MET cc_start: 0.9015 (tpt) cc_final: 0.8479 (tmm) REVERT: B 2695 MET cc_start: 0.5986 (mmm) cc_final: 0.5759 (mmm) REVERT: B 2732 TRP cc_start: 0.8057 (t-100) cc_final: 0.7830 (t-100) REVERT: B 2771 TYR cc_start: 0.8270 (m-80) cc_final: 0.7894 (m-80) REVERT: B 2782 MET cc_start: 0.8924 (ptt) cc_final: 0.8629 (ppp) REVERT: B 2785 TRP cc_start: 0.7973 (t-100) cc_final: 0.7294 (t-100) REVERT: B 2844 MET cc_start: 0.8583 (ptp) cc_final: 0.7970 (ptp) REVERT: B 2848 TYR cc_start: 0.7845 (m-10) cc_final: 0.7478 (m-10) REVERT: B 2899 ASN cc_start: 0.8389 (m-40) cc_final: 0.8160 (t0) REVERT: B 2901 TYR cc_start: 0.7527 (m-80) cc_final: 0.6244 (m-10) REVERT: B 3060 PHE cc_start: 0.7808 (t80) cc_final: 0.6738 (t80) REVERT: B 3104 MET cc_start: 0.7951 (ppp) cc_final: 0.7580 (ppp) REVERT: B 3215 MET cc_start: 0.8996 (ptp) cc_final: 0.8764 (ptp) REVERT: B 3245 TYR cc_start: 0.7912 (t80) cc_final: 0.7653 (t80) REVERT: B 3246 MET cc_start: 0.7181 (OUTLIER) cc_final: 0.6875 (mtt) REVERT: B 3295 TRP cc_start: 0.7406 (p-90) cc_final: 0.7204 (p-90) REVERT: B 3819 MET cc_start: 0.6200 (mtp) cc_final: 0.5556 (mpp) REVERT: B 3954 MET cc_start: 0.8584 (tpp) cc_final: 0.8245 (tpp) REVERT: B 4292 MET cc_start: 0.8193 (mmm) cc_final: 0.7967 (mmm) REVERT: B 4502 MET cc_start: 0.8260 (mtm) cc_final: 0.7995 (mtm) REVERT: B 4504 MET cc_start: 0.8389 (tpt) cc_final: 0.7961 (mmm) REVERT: B 4728 MET cc_start: 0.8704 (mmm) cc_final: 0.8467 (mmm) REVERT: B 4748 MET cc_start: 0.8286 (mmm) cc_final: 0.7994 (mmm) REVERT: B 4945 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.7634 (mp10) REVERT: C 393 MET cc_start: 0.7744 (tpt) cc_final: 0.7284 (mmm) REVERT: C 964 MET cc_start: 0.3035 (mtt) cc_final: 0.2615 (mpp) REVERT: C 995 MET cc_start: 0.8846 (mtm) cc_final: 0.8380 (mtt) REVERT: C 1174 MET cc_start: 0.7889 (ptp) cc_final: 0.7632 (ptt) REVERT: C 1720 MET cc_start: 0.8561 (ptm) cc_final: 0.8313 (ptm) REVERT: C 2234 MET cc_start: 0.8783 (mmm) cc_final: 0.8495 (mtp) REVERT: C 2512 MET cc_start: 0.8910 (tpt) cc_final: 0.8612 (tmm) REVERT: C 2695 MET cc_start: 0.6421 (mmm) cc_final: 0.5989 (mmt) REVERT: C 2720 PHE cc_start: 0.8635 (t80) cc_final: 0.8320 (t80) REVERT: C 2840 MET cc_start: 0.7976 (mmt) cc_final: 0.7728 (mmt) REVERT: C 2843 MET cc_start: 0.7255 (tpp) cc_final: 0.6751 (tpp) REVERT: C 3003 MET cc_start: 0.9100 (ptm) cc_final: 0.8855 (ptm) REVERT: C 3104 MET cc_start: 0.8230 (ppp) cc_final: 0.7575 (ppp) REVERT: C 3246 MET cc_start: 0.7578 (ptt) cc_final: 0.7239 (ptp) REVERT: C 3273 MET cc_start: 0.7195 (ptt) cc_final: 0.6681 (ppp) REVERT: C 3819 MET cc_start: 0.6498 (mtt) cc_final: 0.6104 (mtm) REVERT: C 3985 MET cc_start: 0.9104 (tpp) cc_final: 0.8596 (tpp) REVERT: C 4279 MET cc_start: 0.6663 (mtt) cc_final: 0.6421 (tpp) REVERT: C 4654 MET cc_start: 0.8263 (tpp) cc_final: 0.7970 (tpp) REVERT: C 4884 MET cc_start: 0.8416 (tpp) cc_final: 0.7985 (tpt) REVERT: D 964 MET cc_start: 0.5136 (OUTLIER) cc_final: 0.3649 (mpp) REVERT: D 995 MET cc_start: 0.8842 (mtm) cc_final: 0.8451 (mtt) REVERT: D 1168 MET cc_start: 0.8143 (tpp) cc_final: 0.7941 (mmm) REVERT: D 1174 MET cc_start: 0.7836 (ptp) cc_final: 0.7562 (ptt) REVERT: D 1300 MET cc_start: 0.8598 (mmm) cc_final: 0.8349 (mmp) REVERT: D 2248 MET cc_start: 0.8456 (tpp) cc_final: 0.7985 (ttm) REVERT: D 2279 MET cc_start: 0.8962 (OUTLIER) cc_final: 0.8570 (tmm) REVERT: D 2384 MET cc_start: 0.9021 (mmm) cc_final: 0.8785 (mmm) REVERT: D 2468 MET cc_start: 0.8843 (mmm) cc_final: 0.8455 (mmp) REVERT: D 2512 MET cc_start: 0.8979 (tpt) cc_final: 0.8420 (tmm) REVERT: D 2584 MET cc_start: 0.8071 (mtt) cc_final: 0.7707 (mtt) REVERT: D 2681 MET cc_start: 0.8063 (mmp) cc_final: 0.7835 (mmm) REVERT: D 2688 MET cc_start: 0.5027 (mtt) cc_final: 0.4290 (pmm) REVERT: D 2724 TYR cc_start: 0.8315 (t80) cc_final: 0.7990 (t80) REVERT: D 2840 MET cc_start: 0.8695 (mmt) cc_final: 0.8454 (mmt) REVERT: D 2844 MET cc_start: 0.8686 (ptp) cc_final: 0.7815 (ppp) REVERT: D 2848 TYR cc_start: 0.8512 (m-10) cc_final: 0.8201 (m-10) REVERT: D 3060 PHE cc_start: 0.7990 (t80) cc_final: 0.7634 (t80) REVERT: D 3104 MET cc_start: 0.8237 (ppp) cc_final: 0.7806 (ppp) REVERT: D 3235 MET cc_start: 0.7423 (ppp) cc_final: 0.7049 (ppp) REVERT: D 3250 TRP cc_start: 0.7527 (t60) cc_final: 0.7163 (t60) REVERT: D 3295 TRP cc_start: 0.7017 (p-90) cc_final: 0.6733 (p-90) REVERT: D 3819 MET cc_start: 0.6132 (mtt) cc_final: 0.5771 (mpp) REVERT: D 4481 TRP cc_start: 0.6093 (m100) cc_final: 0.5889 (m100) REVERT: D 4654 MET cc_start: 0.8378 (tmm) cc_final: 0.8061 (tmm) REVERT: D 4748 MET cc_start: 0.7584 (mmm) cc_final: 0.6980 (tpt) outliers start: 82 outliers final: 41 residues processed: 798 average time/residue: 1.1982 time to fit residues: 1705.8024 Evaluate side-chains 772 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 725 time to evaluate : 11.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 18 LYS Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain G residue 30 MET Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain A residue 29 HIS Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 949 HIS Chi-restraints excluded: chain A residue 1215 MET Chi-restraints excluded: chain A residue 1421 MET Chi-restraints excluded: chain A residue 2162 MET Chi-restraints excluded: chain A residue 2585 MET Chi-restraints excluded: chain A residue 2896 LEU Chi-restraints excluded: chain A residue 3318 HIS Chi-restraints excluded: chain A residue 4626 ILE Chi-restraints excluded: chain A residue 4672 MET Chi-restraints excluded: chain A residue 4945 GLN Chi-restraints excluded: chain B residue 29 HIS Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 949 HIS Chi-restraints excluded: chain B residue 2279 MET Chi-restraints excluded: chain B residue 2389 MET Chi-restraints excluded: chain B residue 2585 MET Chi-restraints excluded: chain B residue 2897 GLN Chi-restraints excluded: chain B residue 3246 MET Chi-restraints excluded: chain B residue 4626 ILE Chi-restraints excluded: chain B residue 4945 GLN Chi-restraints excluded: chain C residue 29 HIS Chi-restraints excluded: chain C residue 469 HIS Chi-restraints excluded: chain C residue 949 HIS Chi-restraints excluded: chain C residue 2897 GLN Chi-restraints excluded: chain C residue 4587 ILE Chi-restraints excluded: chain C residue 4626 ILE Chi-restraints excluded: chain C residue 4814 MET Chi-restraints excluded: chain C residue 4945 GLN Chi-restraints excluded: chain D residue 29 HIS Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 949 HIS Chi-restraints excluded: chain D residue 964 MET Chi-restraints excluded: chain D residue 2279 MET Chi-restraints excluded: chain D residue 2389 MET Chi-restraints excluded: chain D residue 2954 PHE Chi-restraints excluded: chain D residue 4052 MET Chi-restraints excluded: chain D residue 4279 MET Chi-restraints excluded: chain D residue 4626 ILE Chi-restraints excluded: chain D residue 4945 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1553 optimal weight: 50.0000 chunk 1181 optimal weight: 7.9990 chunk 815 optimal weight: 10.0000 chunk 174 optimal weight: 5.9990 chunk 750 optimal weight: 40.0000 chunk 1055 optimal weight: 0.7980 chunk 1577 optimal weight: 0.8980 chunk 1670 optimal weight: 10.0000 chunk 824 optimal weight: 10.0000 chunk 1495 optimal weight: 0.7980 chunk 450 optimal weight: 0.8980 overall best weight: 1.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1691 ASN A2091 GLN A2654 GLN ** A2684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2899 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3017 HIS ** A3174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3850 HIS ** A4629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2654 GLN ** B2684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3017 HIS ** B3174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2654 GLN ** C2684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3017 HIS ** C3174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3666 GLN ** C4629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1691 ASN D2654 GLN ** D2684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3017 HIS ** D3174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.905 141676 Z= 0.627 Angle : 0.598 31.028 191424 Z= 0.317 Chirality : 0.039 0.301 20988 Planarity : 0.004 0.118 24592 Dihedral : 5.444 85.699 19046 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.84 % Favored : 97.09 % Rotamer: Outliers : 0.41 % Allowed : 6.30 % Favored : 93.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.07), residues: 17212 helix: 1.65 (0.06), residues: 9096 sheet: -0.27 (0.12), residues: 1652 loop : -0.53 (0.08), residues: 6464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP C2787 HIS 0.006 0.001 HIS B3034 PHE 0.040 0.001 PHE D3162 TYR 0.055 0.001 TYR B 931 ARG 0.011 0.000 ARG D2793 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 799 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 736 time to evaluate : 11.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 MET cc_start: 0.7265 (mmp) cc_final: 0.6908 (mmt) REVERT: A 895 MET cc_start: 0.9142 (ptp) cc_final: 0.8778 (ppp) REVERT: A 964 MET cc_start: 0.2953 (mtt) cc_final: 0.2205 (mpp) REVERT: A 995 MET cc_start: 0.8841 (mtm) cc_final: 0.8245 (mtt) REVERT: A 2167 MET cc_start: 0.7911 (mtm) cc_final: 0.7605 (mtm) REVERT: A 2468 MET cc_start: 0.8923 (mmm) cc_final: 0.8623 (mmp) REVERT: A 2512 MET cc_start: 0.8791 (tpt) cc_final: 0.8438 (tmm) REVERT: A 2681 MET cc_start: 0.8301 (tpp) cc_final: 0.7783 (tpp) REVERT: A 2695 MET cc_start: 0.5931 (mmm) cc_final: 0.5709 (mmm) REVERT: A 2720 PHE cc_start: 0.8352 (t80) cc_final: 0.8120 (t80) REVERT: A 2732 TRP cc_start: 0.8130 (t-100) cc_final: 0.7880 (t-100) REVERT: A 2772 ARG cc_start: 0.8862 (mtt-85) cc_final: 0.8412 (mtt-85) REVERT: A 2773 TRP cc_start: 0.7985 (t-100) cc_final: 0.7657 (t-100) REVERT: A 2843 MET cc_start: 0.7987 (ptp) cc_final: 0.6810 (tpt) REVERT: A 2848 TYR cc_start: 0.7852 (m-10) cc_final: 0.7542 (m-10) REVERT: A 3003 MET cc_start: 0.9025 (ptm) cc_final: 0.8589 (ptm) REVERT: A 3060 PHE cc_start: 0.7656 (t80) cc_final: 0.6283 (t80) REVERT: A 3104 MET cc_start: 0.8003 (ppp) cc_final: 0.7366 (ppp) REVERT: A 3246 MET cc_start: 0.7414 (ptt) cc_final: 0.7017 (mtt) REVERT: A 3273 MET cc_start: 0.6899 (ptt) cc_final: 0.6468 (ppp) REVERT: A 3819 MET cc_start: 0.6243 (mtt) cc_final: 0.5850 (mtm) REVERT: A 3954 MET cc_start: 0.8386 (mmm) cc_final: 0.7643 (tpp) REVERT: A 4246 PHE cc_start: 0.8428 (t80) cc_final: 0.7862 (t80) REVERT: A 4250 TYR cc_start: 0.8547 (t80) cc_final: 0.7691 (m-80) REVERT: A 4256 MET cc_start: 0.8648 (mmp) cc_final: 0.8405 (mmm) REVERT: A 4268 MET cc_start: 0.4346 (tpt) cc_final: 0.3743 (tmm) REVERT: A 4654 MET cc_start: 0.8197 (tpt) cc_final: 0.7923 (tpp) REVERT: A 4748 MET cc_start: 0.7307 (mmm) cc_final: 0.6877 (tpt) REVERT: A 4884 MET cc_start: 0.8331 (tpp) cc_final: 0.7986 (tpt) REVERT: B 964 MET cc_start: 0.2681 (mtt) cc_final: 0.1773 (mpp) REVERT: B 995 MET cc_start: 0.8448 (mtm) cc_final: 0.8056 (mtt) REVERT: B 1300 MET cc_start: 0.8941 (mmp) cc_final: 0.8730 (mmm) REVERT: B 2142 MET cc_start: 0.8424 (mmt) cc_final: 0.8197 (mmp) REVERT: B 2214 MET cc_start: 0.8841 (mmp) cc_final: 0.8273 (mmm) REVERT: B 2279 MET cc_start: 0.8911 (OUTLIER) cc_final: 0.8397 (tmm) REVERT: B 2512 MET cc_start: 0.8917 (tpt) cc_final: 0.8372 (tmm) REVERT: B 2605 MET cc_start: 0.8883 (tmm) cc_final: 0.8581 (tmm) REVERT: B 2681 MET cc_start: 0.7971 (tpp) cc_final: 0.7413 (tpp) REVERT: B 2771 TYR cc_start: 0.8197 (m-80) cc_final: 0.7849 (m-80) REVERT: B 2782 MET cc_start: 0.8805 (OUTLIER) cc_final: 0.8499 (ppp) REVERT: B 2844 MET cc_start: 0.8612 (ptp) cc_final: 0.7975 (ptp) REVERT: B 2848 TYR cc_start: 0.7823 (m-10) cc_final: 0.7454 (m-10) REVERT: B 2899 ASN cc_start: 0.8491 (m-40) cc_final: 0.8230 (t0) REVERT: B 2901 TYR cc_start: 0.7286 (m-80) cc_final: 0.6230 (m-10) REVERT: B 3060 PHE cc_start: 0.7715 (t80) cc_final: 0.6664 (t80) REVERT: B 3104 MET cc_start: 0.7870 (ppp) cc_final: 0.7478 (ppp) REVERT: B 3162 PHE cc_start: 0.8010 (t80) cc_final: 0.7554 (t80) REVERT: B 3249 TRP cc_start: 0.8173 (m100) cc_final: 0.7932 (m100) REVERT: B 3605 MET cc_start: 0.3749 (ppp) cc_final: 0.3387 (ppp) REVERT: B 3819 MET cc_start: 0.6194 (mtp) cc_final: 0.5613 (mpp) REVERT: B 3954 MET cc_start: 0.8552 (tpp) cc_final: 0.8204 (tpp) REVERT: B 4279 MET cc_start: 0.6541 (ttm) cc_final: 0.5958 (tmm) REVERT: B 4292 MET cc_start: 0.8192 (mmm) cc_final: 0.7949 (mmm) REVERT: B 4502 MET cc_start: 0.8244 (mtm) cc_final: 0.7989 (mtm) REVERT: B 4504 MET cc_start: 0.8307 (tpt) cc_final: 0.7890 (mmm) REVERT: B 4728 MET cc_start: 0.8616 (mmm) cc_final: 0.8330 (mmm) REVERT: B 4748 MET cc_start: 0.8211 (mmm) cc_final: 0.7939 (mmm) REVERT: C 393 MET cc_start: 0.7729 (tpt) cc_final: 0.7196 (mmm) REVERT: C 964 MET cc_start: 0.2938 (mtt) cc_final: 0.2583 (mpp) REVERT: C 995 MET cc_start: 0.8770 (mtm) cc_final: 0.8304 (mtt) REVERT: C 1174 MET cc_start: 0.7860 (ptp) cc_final: 0.7602 (ptt) REVERT: C 1720 MET cc_start: 0.8491 (ptm) cc_final: 0.8232 (ptm) REVERT: C 2167 MET cc_start: 0.8048 (mtm) cc_final: 0.7814 (mtm) REVERT: C 2214 MET cc_start: 0.8752 (mmm) cc_final: 0.8163 (mmm) REVERT: C 2234 MET cc_start: 0.8790 (mmm) cc_final: 0.8482 (mtp) REVERT: C 2384 MET cc_start: 0.9281 (mmm) cc_final: 0.8839 (mmm) REVERT: C 2512 MET cc_start: 0.8837 (tpt) cc_final: 0.8534 (tmm) REVERT: C 2681 MET cc_start: 0.8286 (tpp) cc_final: 0.7774 (tpp) REVERT: C 2720 PHE cc_start: 0.8558 (t80) cc_final: 0.8140 (t80) REVERT: C 2732 TRP cc_start: 0.8177 (t-100) cc_final: 0.7956 (t-100) REVERT: C 2771 TYR cc_start: 0.8525 (m-80) cc_final: 0.8290 (m-80) REVERT: C 2787 TRP cc_start: 0.8070 (m-90) cc_final: 0.7802 (m-90) REVERT: C 2840 MET cc_start: 0.7771 (mmt) cc_final: 0.7014 (mmt) REVERT: C 2843 MET cc_start: 0.7211 (tpp) cc_final: 0.6524 (tpp) REVERT: C 2844 MET cc_start: 0.8847 (ptp) cc_final: 0.8607 (ptp) REVERT: C 2895 PHE cc_start: 0.8072 (t80) cc_final: 0.7760 (t80) REVERT: C 3003 MET cc_start: 0.9051 (ptm) cc_final: 0.8788 (ptm) REVERT: C 3104 MET cc_start: 0.8197 (ppp) cc_final: 0.7537 (ppp) REVERT: C 3246 MET cc_start: 0.7596 (ptt) cc_final: 0.7278 (ptp) REVERT: C 3273 MET cc_start: 0.6814 (ptt) cc_final: 0.6575 (ppp) REVERT: C 3819 MET cc_start: 0.6422 (mtt) cc_final: 0.6063 (mtm) REVERT: C 4279 MET cc_start: 0.6656 (mtt) cc_final: 0.6392 (tmm) REVERT: C 4654 MET cc_start: 0.8247 (tpp) cc_final: 0.7965 (tpp) REVERT: C 4884 MET cc_start: 0.8326 (tpp) cc_final: 0.7977 (tpt) REVERT: D 309 MET cc_start: 0.7497 (mmp) cc_final: 0.7282 (mmp) REVERT: D 964 MET cc_start: 0.4857 (OUTLIER) cc_final: 0.3236 (mpp) REVERT: D 995 MET cc_start: 0.8800 (mtm) cc_final: 0.8476 (mtt) REVERT: D 1174 MET cc_start: 0.7779 (ptp) cc_final: 0.7523 (ptt) REVERT: D 1300 MET cc_start: 0.8614 (mmm) cc_final: 0.8212 (mmp) REVERT: D 2248 MET cc_start: 0.8394 (tpp) cc_final: 0.7842 (ttm) REVERT: D 2279 MET cc_start: 0.8945 (OUTLIER) cc_final: 0.8543 (tmm) REVERT: D 2384 MET cc_start: 0.8935 (mmm) cc_final: 0.8712 (mmm) REVERT: D 2468 MET cc_start: 0.8807 (mmm) cc_final: 0.8489 (mmp) REVERT: D 2512 MET cc_start: 0.8921 (tpt) cc_final: 0.8376 (tmm) REVERT: D 2584 MET cc_start: 0.7935 (mtt) cc_final: 0.7533 (mtt) REVERT: D 2688 MET cc_start: 0.5068 (mtt) cc_final: 0.4402 (pmm) REVERT: D 2724 TYR cc_start: 0.8300 (t80) cc_final: 0.7944 (t80) REVERT: D 2732 TRP cc_start: 0.7747 (t-100) cc_final: 0.7470 (t-100) REVERT: D 2793 ARG cc_start: 0.8433 (mmp-170) cc_final: 0.8230 (mmp80) REVERT: D 2844 MET cc_start: 0.8692 (ptp) cc_final: 0.7867 (ppp) REVERT: D 2848 TYR cc_start: 0.8487 (m-10) cc_final: 0.8184 (m-10) REVERT: D 3060 PHE cc_start: 0.7906 (t80) cc_final: 0.7511 (t80) REVERT: D 3104 MET cc_start: 0.8191 (ppp) cc_final: 0.7755 (ppp) REVERT: D 3115 HIS cc_start: 0.8250 (OUTLIER) cc_final: 0.7890 (t-90) REVERT: D 3215 MET cc_start: 0.8864 (mtt) cc_final: 0.8574 (ptp) REVERT: D 3235 MET cc_start: 0.7345 (ppp) cc_final: 0.6971 (ppp) REVERT: D 3819 MET cc_start: 0.6186 (mtt) cc_final: 0.5892 (mpp) REVERT: D 3972 MET cc_start: 0.8396 (mtp) cc_final: 0.8097 (mtp) REVERT: D 4654 MET cc_start: 0.8417 (tmm) cc_final: 0.8127 (tmm) REVERT: D 4748 MET cc_start: 0.7542 (mmm) cc_final: 0.6979 (tpt) REVERT: D 4817 MET cc_start: 0.8706 (tpp) cc_final: 0.8462 (mmm) REVERT: D 4884 MET cc_start: 0.8559 (tpp) cc_final: 0.8126 (tpt) outliers start: 63 outliers final: 37 residues processed: 768 average time/residue: 1.1889 time to fit residues: 1623.2458 Evaluate side-chains 767 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 725 time to evaluate : 11.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 18 LYS Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain A residue 29 HIS Chi-restraints excluded: chain A residue 949 HIS Chi-restraints excluded: chain A residue 1552 VAL Chi-restraints excluded: chain A residue 1599 MET Chi-restraints excluded: chain A residue 2162 MET Chi-restraints excluded: chain A residue 2585 MET Chi-restraints excluded: chain A residue 3192 ARG Chi-restraints excluded: chain A residue 4587 ILE Chi-restraints excluded: chain A residue 4626 ILE Chi-restraints excluded: chain A residue 4672 MET Chi-restraints excluded: chain B residue 29 HIS Chi-restraints excluded: chain B residue 949 HIS Chi-restraints excluded: chain B residue 1896 MET Chi-restraints excluded: chain B residue 2279 MET Chi-restraints excluded: chain B residue 2585 MET Chi-restraints excluded: chain B residue 2782 MET Chi-restraints excluded: chain B residue 2897 GLN Chi-restraints excluded: chain B residue 3192 ARG Chi-restraints excluded: chain B residue 3283 ILE Chi-restraints excluded: chain B residue 4626 ILE Chi-restraints excluded: chain C residue 29 HIS Chi-restraints excluded: chain C residue 469 HIS Chi-restraints excluded: chain C residue 949 HIS Chi-restraints excluded: chain C residue 1215 MET Chi-restraints excluded: chain C residue 1552 VAL Chi-restraints excluded: chain C residue 2585 MET Chi-restraints excluded: chain C residue 3192 ARG Chi-restraints excluded: chain C residue 4587 ILE Chi-restraints excluded: chain C residue 4626 ILE Chi-restraints excluded: chain C residue 4814 MET Chi-restraints excluded: chain D residue 29 HIS Chi-restraints excluded: chain D residue 964 MET Chi-restraints excluded: chain D residue 2279 MET Chi-restraints excluded: chain D residue 2954 PHE Chi-restraints excluded: chain D residue 3115 HIS Chi-restraints excluded: chain D residue 3192 ARG Chi-restraints excluded: chain D residue 3245 TYR Chi-restraints excluded: chain D residue 4279 MET Chi-restraints excluded: chain D residue 4587 ILE Chi-restraints excluded: chain D residue 4626 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1391 optimal weight: 50.0000 chunk 948 optimal weight: 9.9990 chunk 24 optimal weight: 7.9990 chunk 1243 optimal weight: 1.9990 chunk 689 optimal weight: 30.0000 chunk 1425 optimal weight: 10.0000 chunk 1154 optimal weight: 0.4980 chunk 1 optimal weight: 9.9990 chunk 852 optimal weight: 20.0000 chunk 1499 optimal weight: 9.9990 chunk 421 optimal weight: 20.0000 overall best weight: 6.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 26 HIS ** A1581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1656 HIS A1691 ASN ** A2684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2899 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4642 ASN A4945 GLN ** B1581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1656 HIS ** B2684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4945 GLN C 395 HIS ** C1581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2897 GLN ** C3174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3666 GLN ** C4489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4642 ASN C4945 GLN ** D1581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1691 ASN ** D2684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4642 ASN D4903 HIS D4945 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.899 141676 Z= 0.690 Angle : 0.628 31.347 191424 Z= 0.334 Chirality : 0.041 0.289 20988 Planarity : 0.004 0.117 24592 Dihedral : 5.364 85.743 19044 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.20 % Favored : 96.73 % Rotamer: Outliers : 0.59 % Allowed : 6.81 % Favored : 92.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.62 % 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: 1.02 (0.07), residues: 17212 helix: 1.74 (0.06), residues: 9048 sheet: -0.40 (0.12), residues: 1692 loop : -0.50 (0.08), residues: 6472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP D3295 HIS 0.009 0.001 HIS A3665 PHE 0.037 0.002 PHE A3854 TYR 0.051 0.001 TYR B 931 ARG 0.010 0.001 ARG G 14 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 825 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 735 time to evaluate : 11.727 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: A 309 MET cc_start: 0.7325 (mmp) cc_final: 0.6961 (mmt) REVERT: A 893 TRP cc_start: 0.9139 (m-90) cc_final: 0.8532 (m-90) REVERT: A 895 MET cc_start: 0.9203 (ptp) cc_final: 0.8773 (ppp) REVERT: A 964 MET cc_start: 0.3263 (mtt) cc_final: 0.2436 (mpp) REVERT: A 995 MET cc_start: 0.8881 (mtm) cc_final: 0.8315 (mtt) REVERT: A 1842 ILE cc_start: 0.9054 (OUTLIER) cc_final: 0.8743 (tp) REVERT: A 2167 MET cc_start: 0.7990 (mtm) cc_final: 0.7694 (mtm) REVERT: A 2512 MET cc_start: 0.8852 (tpt) cc_final: 0.8535 (tmm) REVERT: A 2695 MET cc_start: 0.6177 (mmm) cc_final: 0.5917 (mmm) REVERT: A 2720 PHE cc_start: 0.8503 (t80) cc_final: 0.8224 (t80) REVERT: A 2732 TRP cc_start: 0.8161 (t-100) cc_final: 0.7931 (t-100) REVERT: A 2772 ARG cc_start: 0.8849 (mtt-85) cc_final: 0.8409 (mtt-85) REVERT: A 2773 TRP cc_start: 0.8047 (t-100) cc_final: 0.7679 (t-100) REVERT: A 2843 MET cc_start: 0.8012 (ptp) cc_final: 0.6823 (tpt) REVERT: A 2848 TYR cc_start: 0.7847 (m-10) cc_final: 0.7525 (m-10) REVERT: A 3003 MET cc_start: 0.9069 (ptm) cc_final: 0.8637 (ptm) REVERT: A 3060 PHE cc_start: 0.7691 (t80) cc_final: 0.6296 (t80) REVERT: A 3104 MET cc_start: 0.8063 (ppp) cc_final: 0.7419 (ppp) REVERT: A 3246 MET cc_start: 0.7494 (ptt) cc_final: 0.7205 (mtm) REVERT: A 3819 MET cc_start: 0.6388 (mtt) cc_final: 0.6027 (mtm) REVERT: A 3954 MET cc_start: 0.8434 (mmm) cc_final: 0.7714 (tpp) REVERT: A 4268 MET cc_start: 0.4383 (tpt) cc_final: 0.3776 (tmm) REVERT: A 4279 MET cc_start: 0.6604 (ttt) cc_final: 0.6210 (tpt) REVERT: A 4654 MET cc_start: 0.8168 (tpt) cc_final: 0.7878 (tpp) REVERT: A 4707 MET cc_start: 0.8434 (ppp) cc_final: 0.8231 (ppp) REVERT: A 4748 MET cc_start: 0.7451 (mmm) cc_final: 0.6936 (tpt) REVERT: A 4804 MET cc_start: 0.9087 (mmm) cc_final: 0.8597 (mmm) REVERT: A 4884 MET cc_start: 0.8388 (tpp) cc_final: 0.8102 (tpt) REVERT: B 655 MET cc_start: 0.8946 (mmm) cc_final: 0.8650 (mmp) REVERT: B 893 TRP cc_start: 0.9275 (m-90) cc_final: 0.8518 (m-90) REVERT: B 964 MET cc_start: 0.2866 (mtt) cc_final: 0.1952 (mpp) REVERT: B 995 MET cc_start: 0.8529 (mtm) cc_final: 0.8114 (mtt) REVERT: B 1165 MET cc_start: 0.8201 (mtm) cc_final: 0.7918 (mtm) REVERT: B 2142 MET cc_start: 0.8515 (mmt) cc_final: 0.8304 (mmp) REVERT: B 2192 MET cc_start: 0.8420 (tpp) cc_final: 0.8212 (tpp) REVERT: B 2279 MET cc_start: 0.8915 (OUTLIER) cc_final: 0.8382 (tmm) REVERT: B 2512 MET cc_start: 0.8944 (tpt) cc_final: 0.8450 (tmm) REVERT: B 2605 MET cc_start: 0.8939 (tmm) cc_final: 0.8646 (tmm) REVERT: B 2732 TRP cc_start: 0.7952 (t-100) cc_final: 0.7644 (t-100) REVERT: B 2771 TYR cc_start: 0.8242 (m-80) cc_final: 0.7981 (m-80) REVERT: B 2798 MET cc_start: 0.6159 (mmp) cc_final: 0.5814 (mmp) REVERT: B 2840 MET cc_start: 0.7535 (mmt) cc_final: 0.6932 (mmt) REVERT: B 2844 MET cc_start: 0.8647 (ptp) cc_final: 0.8065 (ptp) REVERT: B 2848 TYR cc_start: 0.7897 (m-10) cc_final: 0.7567 (m-10) REVERT: B 3060 PHE cc_start: 0.7694 (t80) cc_final: 0.6626 (t80) REVERT: B 3104 MET cc_start: 0.8014 (ppp) cc_final: 0.7568 (ppp) REVERT: B 3162 PHE cc_start: 0.8109 (t80) cc_final: 0.7629 (t80) REVERT: B 3215 MET cc_start: 0.8750 (ptp) cc_final: 0.8547 (ptp) REVERT: B 3235 MET cc_start: 0.7565 (ppp) cc_final: 0.6952 (tpt) REVERT: B 3249 TRP cc_start: 0.8252 (m100) cc_final: 0.7908 (m100) REVERT: B 3605 MET cc_start: 0.3688 (ppp) cc_final: 0.3391 (ppp) REVERT: B 3819 MET cc_start: 0.6359 (mtp) cc_final: 0.5705 (mpp) REVERT: B 3956 MET cc_start: 0.8413 (mmt) cc_final: 0.8195 (mmt) REVERT: B 4279 MET cc_start: 0.6430 (ttm) cc_final: 0.5820 (tmm) REVERT: B 4292 MET cc_start: 0.8138 (mmm) cc_final: 0.7876 (mmm) REVERT: B 4502 MET cc_start: 0.8300 (mtm) cc_final: 0.8031 (mtm) REVERT: B 4748 MET cc_start: 0.8145 (mmm) cc_final: 0.7856 (mmm) REVERT: B 4814 MET cc_start: 0.8242 (mmm) cc_final: 0.7929 (tpp) REVERT: C 128 MET cc_start: 0.8622 (mtm) cc_final: 0.8316 (mtp) REVERT: C 393 MET cc_start: 0.7758 (tpt) cc_final: 0.7461 (mmm) REVERT: C 893 TRP cc_start: 0.9218 (m-90) cc_final: 0.8540 (m-90) REVERT: C 964 MET cc_start: 0.3140 (mtt) cc_final: 0.2756 (mpp) REVERT: C 995 MET cc_start: 0.8863 (mtm) cc_final: 0.8354 (mtt) REVERT: C 1168 MET cc_start: 0.8476 (mmm) cc_final: 0.8264 (mmp) REVERT: C 1174 MET cc_start: 0.7878 (ptp) cc_final: 0.7643 (ptt) REVERT: C 1720 MET cc_start: 0.8558 (ptm) cc_final: 0.8281 (ptt) REVERT: C 1948 MET cc_start: 0.8593 (ptm) cc_final: 0.8339 (ppp) REVERT: C 2214 MET cc_start: 0.8741 (mmm) cc_final: 0.8266 (mmm) REVERT: C 2234 MET cc_start: 0.8773 (mmm) cc_final: 0.8482 (mtp) REVERT: C 2384 MET cc_start: 0.9342 (mmm) cc_final: 0.8894 (mmm) REVERT: C 2389 MET cc_start: 0.9208 (mtp) cc_final: 0.8846 (mtt) REVERT: C 2512 MET cc_start: 0.8888 (tpt) cc_final: 0.8609 (tmm) REVERT: C 2695 MET cc_start: 0.6385 (mmm) cc_final: 0.5968 (mmt) REVERT: C 2720 PHE cc_start: 0.8607 (t80) cc_final: 0.8217 (t80) REVERT: C 2732 TRP cc_start: 0.8242 (t-100) cc_final: 0.7990 (t-100) REVERT: C 2771 TYR cc_start: 0.8481 (m-80) cc_final: 0.8280 (m-80) REVERT: C 2787 TRP cc_start: 0.8215 (m-90) cc_final: 0.7828 (m-90) REVERT: C 2840 MET cc_start: 0.7751 (mmt) cc_final: 0.6587 (mmt) REVERT: C 2843 MET cc_start: 0.7272 (tpp) cc_final: 0.6615 (tpp) REVERT: C 2844 MET cc_start: 0.8886 (ptp) cc_final: 0.8477 (ptp) REVERT: C 3104 MET cc_start: 0.8263 (ppp) cc_final: 0.7621 (ppp) REVERT: C 3246 MET cc_start: 0.7585 (ptt) cc_final: 0.7299 (mtm) REVERT: C 3273 MET cc_start: 0.7111 (ptt) cc_final: 0.6611 (ppp) REVERT: C 3295 TRP cc_start: 0.7296 (p-90) cc_final: 0.7000 (p-90) REVERT: C 3954 MET cc_start: 0.8669 (mmm) cc_final: 0.8353 (tpp) REVERT: C 4279 MET cc_start: 0.6702 (mtt) cc_final: 0.6432 (tmm) REVERT: C 4654 MET cc_start: 0.8253 (tpp) cc_final: 0.7966 (tpp) REVERT: C 4884 MET cc_start: 0.8376 (tpp) cc_final: 0.8083 (tpt) REVERT: D 893 TRP cc_start: 0.9139 (m-90) cc_final: 0.8462 (m-90) REVERT: D 964 MET cc_start: 0.5078 (OUTLIER) cc_final: 0.3407 (mpp) REVERT: D 981 MET cc_start: 0.8237 (pmm) cc_final: 0.7751 (pmm) REVERT: D 995 MET cc_start: 0.8858 (mtm) cc_final: 0.8455 (mtt) REVERT: D 1174 MET cc_start: 0.7836 (ptp) cc_final: 0.7552 (ptt) REVERT: D 1300 MET cc_start: 0.8644 (mmm) cc_final: 0.8222 (mmp) REVERT: D 2279 MET cc_start: 0.8957 (OUTLIER) cc_final: 0.8526 (tmm) REVERT: D 2468 MET cc_start: 0.8934 (mmm) cc_final: 0.8582 (mmp) REVERT: D 2512 MET cc_start: 0.8970 (tpt) cc_final: 0.8485 (tmm) REVERT: D 2584 MET cc_start: 0.8084 (mtt) cc_final: 0.7824 (mtt) REVERT: D 2688 MET cc_start: 0.5104 (mtt) cc_final: 0.4447 (pmm) REVERT: D 2720 PHE cc_start: 0.8883 (t80) cc_final: 0.8588 (t80) REVERT: D 2844 MET cc_start: 0.8772 (ptp) cc_final: 0.8141 (ppp) REVERT: D 2901 TYR cc_start: 0.7301 (m-80) cc_final: 0.6886 (m-80) REVERT: D 3003 MET cc_start: 0.8708 (ptm) cc_final: 0.8405 (ptm) REVERT: D 3060 PHE cc_start: 0.7942 (t80) cc_final: 0.7533 (t80) REVERT: D 3104 MET cc_start: 0.8225 (ppp) cc_final: 0.7762 (ppp) REVERT: D 3115 HIS cc_start: 0.8235 (OUTLIER) cc_final: 0.7909 (t-170) REVERT: D 3819 MET cc_start: 0.6497 (mtt) cc_final: 0.6293 (mpp) REVERT: D 3972 MET cc_start: 0.8486 (mtp) cc_final: 0.8207 (mtp) REVERT: D 4002 MET cc_start: 0.8550 (tmm) cc_final: 0.8078 (tmm) REVERT: D 4654 MET cc_start: 0.8452 (tmm) cc_final: 0.8145 (tmm) REVERT: D 4748 MET cc_start: 0.7744 (mmm) cc_final: 0.7155 (tpt) REVERT: D 4884 MET cc_start: 0.8562 (tpp) cc_final: 0.8169 (tpt) outliers start: 90 outliers final: 55 residues processed: 782 average time/residue: 1.1694 time to fit residues: 1629.3747 Evaluate side-chains 779 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 719 time to evaluate : 11.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 30 MET Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain A residue 29 HIS Chi-restraints excluded: chain A residue 1215 MET Chi-restraints excluded: chain A residue 1421 MET Chi-restraints excluded: chain A residue 1552 VAL Chi-restraints excluded: chain A residue 1599 MET Chi-restraints excluded: chain A residue 1727 VAL Chi-restraints excluded: chain A residue 1842 ILE Chi-restraints excluded: chain A residue 2162 MET Chi-restraints excluded: chain A residue 2585 MET Chi-restraints excluded: chain A residue 3192 ARG Chi-restraints excluded: chain A residue 3942 ASP Chi-restraints excluded: chain A residue 4587 ILE Chi-restraints excluded: chain A residue 4626 ILE Chi-restraints excluded: chain A residue 4672 MET Chi-restraints excluded: chain A residue 4945 GLN Chi-restraints excluded: chain B residue 29 HIS Chi-restraints excluded: chain B residue 1608 VAL Chi-restraints excluded: chain B residue 1727 VAL Chi-restraints excluded: chain B residue 1896 MET Chi-restraints excluded: chain B residue 2279 MET Chi-restraints excluded: chain B residue 2585 MET Chi-restraints excluded: chain B residue 2782 MET Chi-restraints excluded: chain B residue 2897 GLN Chi-restraints excluded: chain B residue 3115 HIS Chi-restraints excluded: chain B residue 3283 ILE Chi-restraints excluded: chain B residue 3318 HIS Chi-restraints excluded: chain B residue 4626 ILE Chi-restraints excluded: chain B residue 4945 GLN Chi-restraints excluded: chain C residue 29 HIS Chi-restraints excluded: chain C residue 469 HIS Chi-restraints excluded: chain C residue 1215 MET Chi-restraints excluded: chain C residue 1552 VAL Chi-restraints excluded: chain C residue 1727 VAL Chi-restraints excluded: chain C residue 2585 MET Chi-restraints excluded: chain C residue 2897 GLN Chi-restraints excluded: chain C residue 3115 HIS Chi-restraints excluded: chain C residue 3192 ARG Chi-restraints excluded: chain C residue 4587 ILE Chi-restraints excluded: chain C residue 4626 ILE Chi-restraints excluded: chain C residue 4814 MET Chi-restraints excluded: chain C residue 4945 GLN Chi-restraints excluded: chain D residue 29 HIS Chi-restraints excluded: chain D residue 778 MET Chi-restraints excluded: chain D residue 949 HIS Chi-restraints excluded: chain D residue 964 MET Chi-restraints excluded: chain D residue 1165 MET Chi-restraints excluded: chain D residue 1727 VAL Chi-restraints excluded: chain D residue 2279 MET Chi-restraints excluded: chain D residue 3115 HIS Chi-restraints excluded: chain D residue 3192 ARG Chi-restraints excluded: chain D residue 3245 TYR Chi-restraints excluded: chain D residue 4279 MET Chi-restraints excluded: chain D residue 4626 ILE Chi-restraints excluded: chain D residue 4945 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 561 optimal weight: 30.0000 chunk 1504 optimal weight: 0.9990 chunk 330 optimal weight: 40.0000 chunk 980 optimal weight: 30.0000 chunk 412 optimal weight: 20.0000 chunk 1671 optimal weight: 6.9990 chunk 1387 optimal weight: 0.5980 chunk 774 optimal weight: 6.9990 chunk 139 optimal weight: 4.9990 chunk 553 optimal weight: 0.0040 chunk 877 optimal weight: 0.0370 overall best weight: 1.3274 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1691 ASN A2091 GLN ** A2684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2899 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2091 GLN ** B2684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4088 HIS ** B4629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1691 ASN ** C2684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2897 GLN C2899 ASN ** C3174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3666 GLN ** C4629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 364 GLN ** D 808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1691 ASN ** D2684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.909 141676 Z= 0.625 Angle : 0.584 31.210 191424 Z= 0.308 Chirality : 0.039 0.297 20988 Planarity : 0.004 0.114 24592 Dihedral : 5.216 85.895 19044 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.86 % Favored : 97.07 % Rotamer: Outliers : 0.53 % Allowed : 7.40 % Favored : 92.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.62 % 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: 1.13 (0.07), residues: 17212 helix: 1.81 (0.06), residues: 9076 sheet: -0.25 (0.12), residues: 1668 loop : -0.45 (0.08), residues: 6468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP B3295 HIS 0.027 0.001 HIS G 26 PHE 0.044 0.001 PHE D3162 TYR 0.045 0.001 TYR B 931 ARG 0.011 0.000 ARG G 14 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 809 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 729 time to evaluate : 11.989 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: H 67 MET cc_start: 0.8806 (mtp) cc_final: 0.8472 (mtp) REVERT: A 111 ARG cc_start: 0.7372 (OUTLIER) cc_final: 0.7147 (mtt90) REVERT: A 309 MET cc_start: 0.7294 (mmp) cc_final: 0.6958 (mmt) REVERT: A 893 TRP cc_start: 0.9099 (m-90) cc_final: 0.8510 (m-90) REVERT: A 895 MET cc_start: 0.9174 (ptp) cc_final: 0.8737 (ppp) REVERT: A 964 MET cc_start: 0.2799 (mtt) cc_final: 0.2061 (mpp) REVERT: A 995 MET cc_start: 0.8810 (mtm) cc_final: 0.8204 (mtt) REVERT: A 2167 MET cc_start: 0.7870 (mtm) cc_final: 0.7567 (mtm) REVERT: A 2512 MET cc_start: 0.8808 (tpt) cc_final: 0.8474 (tmm) REVERT: A 2681 MET cc_start: 0.8252 (tpp) cc_final: 0.7778 (tpp) REVERT: A 2720 PHE cc_start: 0.8439 (t80) cc_final: 0.8175 (t80) REVERT: A 2732 TRP cc_start: 0.8194 (t-100) cc_final: 0.7974 (t-100) REVERT: A 2772 ARG cc_start: 0.8855 (mtt-85) cc_final: 0.8399 (mtt-85) REVERT: A 2773 TRP cc_start: 0.8021 (t-100) cc_final: 0.7644 (t-100) REVERT: A 2843 MET cc_start: 0.7978 (ptp) cc_final: 0.6777 (tpt) REVERT: A 2848 TYR cc_start: 0.7882 (m-10) cc_final: 0.7567 (m-10) REVERT: A 3003 MET cc_start: 0.9015 (ptm) cc_final: 0.8579 (ptm) REVERT: A 3060 PHE cc_start: 0.7604 (t80) cc_final: 0.6244 (t80) REVERT: A 3104 MET cc_start: 0.8073 (ppp) cc_final: 0.7419 (ppp) REVERT: A 3246 MET cc_start: 0.7507 (ptt) cc_final: 0.7190 (mtm) REVERT: A 3273 MET cc_start: 0.7069 (ptp) cc_final: 0.6856 (ppp) REVERT: A 3819 MET cc_start: 0.6461 (mtt) cc_final: 0.6221 (mtm) REVERT: A 3954 MET cc_start: 0.8427 (mmm) cc_final: 0.7691 (tpp) REVERT: A 4246 PHE cc_start: 0.8498 (t80) cc_final: 0.7897 (t80) REVERT: A 4250 TYR cc_start: 0.8589 (t80) cc_final: 0.7683 (m-80) REVERT: A 4268 MET cc_start: 0.4385 (tpt) cc_final: 0.3803 (tmm) REVERT: A 4279 MET cc_start: 0.6417 (ttt) cc_final: 0.5989 (tpt) REVERT: A 4654 MET cc_start: 0.8164 (tpt) cc_final: 0.7848 (tpp) REVERT: A 4707 MET cc_start: 0.8408 (ppp) cc_final: 0.8181 (ppp) REVERT: A 4748 MET cc_start: 0.7406 (mmm) cc_final: 0.6917 (tpt) REVERT: A 4804 MET cc_start: 0.9014 (mmm) cc_final: 0.8536 (mmm) REVERT: A 4884 MET cc_start: 0.8307 (tpp) cc_final: 0.8076 (tpt) REVERT: B 655 MET cc_start: 0.8908 (mmm) cc_final: 0.8681 (mmp) REVERT: B 893 TRP cc_start: 0.9252 (m-90) cc_final: 0.8671 (m-90) REVERT: B 895 MET cc_start: 0.8571 (ptp) cc_final: 0.8164 (ppp) REVERT: B 964 MET cc_start: 0.2636 (mtt) cc_final: 0.1738 (mpp) REVERT: B 995 MET cc_start: 0.8431 (mtm) cc_final: 0.8037 (mtt) REVERT: B 1165 MET cc_start: 0.8166 (mtm) cc_final: 0.7889 (mtm) REVERT: B 2192 MET cc_start: 0.8391 (tpp) cc_final: 0.8139 (tpp) REVERT: B 2214 MET cc_start: 0.8714 (mmt) cc_final: 0.8109 (mmm) REVERT: B 2279 MET cc_start: 0.8884 (OUTLIER) cc_final: 0.8274 (tmm) REVERT: B 2512 MET cc_start: 0.8886 (tpt) cc_final: 0.8383 (tmm) REVERT: B 2605 MET cc_start: 0.8913 (tmm) cc_final: 0.8652 (tmm) REVERT: B 2681 MET cc_start: 0.8045 (tpp) cc_final: 0.7512 (tpp) REVERT: B 2727 HIS cc_start: 0.8021 (m90) cc_final: 0.7612 (m90) REVERT: B 2732 TRP cc_start: 0.7944 (t-100) cc_final: 0.7720 (t-100) REVERT: B 2771 TYR cc_start: 0.8207 (m-80) cc_final: 0.7947 (m-80) REVERT: B 2782 MET cc_start: 0.8814 (OUTLIER) cc_final: 0.8490 (ppp) REVERT: B 2798 MET cc_start: 0.5789 (mmp) cc_final: 0.5456 (mmp) REVERT: B 2840 MET cc_start: 0.7590 (mmt) cc_final: 0.6908 (mmt) REVERT: B 2844 MET cc_start: 0.8653 (ptp) cc_final: 0.8071 (ptp) REVERT: B 2848 TYR cc_start: 0.7820 (m-10) cc_final: 0.7509 (m-10) REVERT: B 3060 PHE cc_start: 0.7608 (t80) cc_final: 0.6515 (t80) REVERT: B 3104 MET cc_start: 0.7937 (ppp) cc_final: 0.7498 (ppp) REVERT: B 3162 PHE cc_start: 0.8082 (t80) cc_final: 0.7596 (t80) REVERT: B 3235 MET cc_start: 0.7572 (ppp) cc_final: 0.6929 (tpt) REVERT: B 3249 TRP cc_start: 0.8088 (m100) cc_final: 0.7572 (m100) REVERT: B 3295 TRP cc_start: 0.7193 (p-90) cc_final: 0.6904 (p-90) REVERT: B 3605 MET cc_start: 0.3583 (ppp) cc_final: 0.3306 (ppp) REVERT: B 3689 MET cc_start: 0.8766 (mmp) cc_final: 0.8409 (mmp) REVERT: B 3819 MET cc_start: 0.6257 (mtp) cc_final: 0.5632 (mpp) REVERT: B 4186 MET cc_start: 0.9317 (mmp) cc_final: 0.8471 (mmt) REVERT: B 4279 MET cc_start: 0.6380 (ttm) cc_final: 0.5806 (tmm) REVERT: B 4292 MET cc_start: 0.8220 (mmm) cc_final: 0.7955 (mmm) REVERT: B 4502 MET cc_start: 0.8235 (mtm) cc_final: 0.7998 (mtm) REVERT: B 4654 MET cc_start: 0.8111 (tmm) cc_final: 0.7756 (tmm) REVERT: B 4728 MET cc_start: 0.8722 (mmm) cc_final: 0.8371 (mmm) REVERT: B 4748 MET cc_start: 0.8068 (mmm) cc_final: 0.7798 (mmm) REVERT: B 4814 MET cc_start: 0.8290 (mmm) cc_final: 0.8033 (mmm) REVERT: C 128 MET cc_start: 0.8556 (mtm) cc_final: 0.8319 (mtp) REVERT: C 309 MET cc_start: 0.7719 (mmp) cc_final: 0.7491 (mmp) REVERT: C 893 TRP cc_start: 0.9221 (m-90) cc_final: 0.8600 (m-90) REVERT: C 964 MET cc_start: 0.2984 (mtt) cc_final: 0.2595 (mpp) REVERT: C 995 MET cc_start: 0.8790 (mtm) cc_final: 0.8303 (mtt) REVERT: C 1168 MET cc_start: 0.8504 (mmm) cc_final: 0.8255 (mmp) REVERT: C 1174 MET cc_start: 0.7860 (ptp) cc_final: 0.7630 (ptt) REVERT: C 1720 MET cc_start: 0.8485 (ptm) cc_final: 0.8188 (ptt) REVERT: C 1948 MET cc_start: 0.8569 (ptm) cc_final: 0.8330 (ppp) REVERT: C 2214 MET cc_start: 0.8714 (mmm) cc_final: 0.8139 (mmm) REVERT: C 2234 MET cc_start: 0.8760 (mmm) cc_final: 0.8482 (mtp) REVERT: C 2389 MET cc_start: 0.9154 (mtp) cc_final: 0.8866 (mtp) REVERT: C 2512 MET cc_start: 0.8809 (tpt) cc_final: 0.8522 (tmm) REVERT: C 2681 MET cc_start: 0.8198 (tpp) cc_final: 0.7409 (tpp) REVERT: C 2695 MET cc_start: 0.6439 (mmm) cc_final: 0.6072 (mmt) REVERT: C 2720 PHE cc_start: 0.8554 (t80) cc_final: 0.7649 (t80) REVERT: C 2787 TRP cc_start: 0.8063 (m-90) cc_final: 0.7811 (m-90) REVERT: C 2840 MET cc_start: 0.7695 (mmt) cc_final: 0.6530 (mmt) REVERT: C 2843 MET cc_start: 0.7270 (tpp) cc_final: 0.6623 (tpp) REVERT: C 2844 MET cc_start: 0.8812 (ptp) cc_final: 0.8529 (ptp) REVERT: C 2895 PHE cc_start: 0.8372 (t80) cc_final: 0.7625 (t80) REVERT: C 3003 MET cc_start: 0.9164 (ptt) cc_final: 0.8678 (ptm) REVERT: C 3104 MET cc_start: 0.8251 (ppp) cc_final: 0.7583 (ppp) REVERT: C 3246 MET cc_start: 0.7501 (ptt) cc_final: 0.7246 (mtm) REVERT: C 3273 MET cc_start: 0.6846 (ptt) cc_final: 0.6539 (ppp) REVERT: C 3295 TRP cc_start: 0.7166 (p-90) cc_final: 0.6950 (p-90) REVERT: C 3819 MET cc_start: 0.6387 (mtp) cc_final: 0.5784 (mtm) REVERT: C 3954 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.8308 (tpp) REVERT: C 4279 MET cc_start: 0.6704 (mtt) cc_final: 0.6443 (tmm) REVERT: C 4641 PRO cc_start: 0.8075 (OUTLIER) cc_final: 0.7777 (Cg_endo) REVERT: C 4654 MET cc_start: 0.8248 (tpp) cc_final: 0.7970 (tpp) REVERT: C 4884 MET cc_start: 0.8275 (tpp) cc_final: 0.8034 (tpt) REVERT: C 4923 MET cc_start: 0.8800 (ttp) cc_final: 0.8576 (ttp) REVERT: D 893 TRP cc_start: 0.9115 (m-90) cc_final: 0.8442 (m-90) REVERT: D 964 MET cc_start: 0.4856 (OUTLIER) cc_final: 0.3118 (mpp) REVERT: D 981 MET cc_start: 0.8020 (pmm) cc_final: 0.7706 (pmm) REVERT: D 995 MET cc_start: 0.8797 (mtm) cc_final: 0.8394 (mtt) REVERT: D 1174 MET cc_start: 0.7739 (ptp) cc_final: 0.7518 (ptt) REVERT: D 1300 MET cc_start: 0.8627 (mmm) cc_final: 0.8256 (mmp) REVERT: D 1842 ILE cc_start: 0.9012 (OUTLIER) cc_final: 0.8763 (pt) REVERT: D 2279 MET cc_start: 0.8941 (OUTLIER) cc_final: 0.8499 (tmm) REVERT: D 2456 MET cc_start: 0.8824 (pmm) cc_final: 0.8243 (mpp) REVERT: D 2468 MET cc_start: 0.8911 (mmm) cc_final: 0.8597 (mmp) REVERT: D 2512 MET cc_start: 0.8932 (tpt) cc_final: 0.8364 (tmm) REVERT: D 2584 MET cc_start: 0.7978 (mtt) cc_final: 0.7776 (mtt) REVERT: D 2688 MET cc_start: 0.5083 (mtt) cc_final: 0.4490 (pmm) REVERT: D 2720 PHE cc_start: 0.8840 (t80) cc_final: 0.8440 (t80) REVERT: D 2724 TYR cc_start: 0.8192 (t80) cc_final: 0.7963 (t80) REVERT: D 2844 MET cc_start: 0.8701 (ptp) cc_final: 0.8158 (ppp) REVERT: D 2901 TYR cc_start: 0.7227 (m-80) cc_final: 0.6878 (m-80) REVERT: D 3060 PHE cc_start: 0.7877 (t80) cc_final: 0.7471 (t80) REVERT: D 3104 MET cc_start: 0.8190 (ppp) cc_final: 0.7734 (ppp) REVERT: D 3115 HIS cc_start: 0.8179 (OUTLIER) cc_final: 0.7812 (t-170) REVERT: D 3215 MET cc_start: 0.8893 (mtt) cc_final: 0.8621 (ptp) REVERT: D 3235 MET cc_start: 0.7312 (ppp) cc_final: 0.7104 (ppp) REVERT: D 3246 MET cc_start: 0.5556 (mtm) cc_final: 0.5333 (mtm) REVERT: D 3819 MET cc_start: 0.6571 (mtt) cc_final: 0.6332 (mpp) REVERT: D 4002 MET cc_start: 0.8554 (tmm) cc_final: 0.8070 (tmm) REVERT: D 4654 MET cc_start: 0.8436 (tmm) cc_final: 0.8107 (tmm) REVERT: D 4748 MET cc_start: 0.7687 (mmm) cc_final: 0.7147 (tpt) REVERT: D 4884 MET cc_start: 0.8528 (tpp) cc_final: 0.8160 (tpt) outliers start: 80 outliers final: 45 residues processed: 773 average time/residue: 1.1785 time to fit residues: 1627.1882 Evaluate side-chains 774 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 720 time to evaluate : 11.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 30 MET Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain A residue 29 HIS Chi-restraints excluded: chain A residue 111 ARG Chi-restraints excluded: chain A residue 1215 MET Chi-restraints excluded: chain A residue 1552 VAL Chi-restraints excluded: chain A residue 1599 MET Chi-restraints excluded: chain A residue 1608 VAL Chi-restraints excluded: chain A residue 1727 VAL Chi-restraints excluded: chain A residue 2162 MET Chi-restraints excluded: chain A residue 2585 MET Chi-restraints excluded: chain A residue 3192 ARG Chi-restraints excluded: chain A residue 3942 ASP Chi-restraints excluded: chain A residue 4587 ILE Chi-restraints excluded: chain A residue 4626 ILE Chi-restraints excluded: chain A residue 4672 MET Chi-restraints excluded: chain B residue 29 HIS Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 1608 VAL Chi-restraints excluded: chain B residue 1727 VAL Chi-restraints excluded: chain B residue 1896 MET Chi-restraints excluded: chain B residue 2279 MET Chi-restraints excluded: chain B residue 2585 MET Chi-restraints excluded: chain B residue 2782 MET Chi-restraints excluded: chain B residue 3043 ARG Chi-restraints excluded: chain B residue 3115 HIS Chi-restraints excluded: chain B residue 3283 ILE Chi-restraints excluded: chain B residue 3942 ASP Chi-restraints excluded: chain B residue 4626 ILE Chi-restraints excluded: chain C residue 29 HIS Chi-restraints excluded: chain C residue 469 HIS Chi-restraints excluded: chain C residue 1215 MET Chi-restraints excluded: chain C residue 1552 VAL Chi-restraints excluded: chain C residue 1727 VAL Chi-restraints excluded: chain C residue 2585 MET Chi-restraints excluded: chain C residue 2899 ASN Chi-restraints excluded: chain C residue 3115 HIS Chi-restraints excluded: chain C residue 3192 ARG Chi-restraints excluded: chain C residue 3954 MET Chi-restraints excluded: chain C residue 4587 ILE Chi-restraints excluded: chain C residue 4626 ILE Chi-restraints excluded: chain C residue 4641 PRO Chi-restraints excluded: chain D residue 29 HIS Chi-restraints excluded: chain D residue 778 MET Chi-restraints excluded: chain D residue 964 MET Chi-restraints excluded: chain D residue 1727 VAL Chi-restraints excluded: chain D residue 1842 ILE Chi-restraints excluded: chain D residue 2279 MET Chi-restraints excluded: chain D residue 3115 HIS Chi-restraints excluded: chain D residue 3192 ARG Chi-restraints excluded: chain D residue 3245 TYR Chi-restraints excluded: chain D residue 4279 MET Chi-restraints excluded: chain D residue 4587 ILE Chi-restraints excluded: chain D residue 4626 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1611 optimal weight: 8.9990 chunk 188 optimal weight: 4.9990 chunk 952 optimal weight: 10.0000 chunk 1220 optimal weight: 6.9990 chunk 945 optimal weight: 10.0000 chunk 1407 optimal weight: 20.0000 chunk 933 optimal weight: 6.9990 chunk 1665 optimal weight: 4.9990 chunk 1042 optimal weight: 9.9990 chunk 1015 optimal weight: 9.9990 chunk 768 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 26 HIS ** A 608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1691 ASN A2091 GLN ** A2684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2899 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3850 HIS ** A4629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1046 ASN ** B1581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2091 GLN ** B2684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2722 ASN ** B3174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1691 ASN ** C2684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2899 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3666 GLN ** C4489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1046 ASN ** D1581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1656 HIS D1691 ASN ** D2684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.910 141676 Z= 0.708 Angle : 0.627 30.562 191424 Z= 0.332 Chirality : 0.041 0.281 20988 Planarity : 0.005 0.168 24592 Dihedral : 5.209 85.578 19044 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.31 % Favored : 96.62 % Rotamer: Outliers : 0.61 % Allowed : 7.58 % Favored : 91.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.62 % 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: 1.13 (0.07), residues: 17212 helix: 1.84 (0.06), residues: 9044 sheet: -0.26 (0.13), residues: 1632 loop : -0.50 (0.08), residues: 6536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.002 TRP D3295 HIS 0.009 0.001 HIS A3665 PHE 0.052 0.002 PHE A3117 TYR 0.042 0.001 TYR B 931 ARG 0.038 0.001 ARG C3043 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 823 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 731 time to evaluate : 11.623 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: A 111 ARG cc_start: 0.7758 (OUTLIER) cc_final: 0.7524 (mtt90) REVERT: A 309 MET cc_start: 0.7338 (mmp) cc_final: 0.7004 (mmt) REVERT: A 893 TRP cc_start: 0.9122 (m-10) cc_final: 0.8554 (m-90) REVERT: A 895 MET cc_start: 0.9225 (ptp) cc_final: 0.8777 (ppp) REVERT: A 964 MET cc_start: 0.3178 (mtt) cc_final: 0.2361 (mpp) REVERT: A 995 MET cc_start: 0.8884 (mtm) cc_final: 0.8317 (mtt) REVERT: A 1842 ILE cc_start: 0.9057 (OUTLIER) cc_final: 0.8752 (tp) REVERT: A 2167 MET cc_start: 0.7968 (mtm) cc_final: 0.7656 (mtm) REVERT: A 2248 MET cc_start: 0.8099 (tpp) cc_final: 0.7670 (ttp) REVERT: A 2512 MET cc_start: 0.8879 (tpt) cc_final: 0.8526 (tmm) REVERT: A 2681 MET cc_start: 0.8501 (tpp) cc_final: 0.8050 (tpp) REVERT: A 2695 MET cc_start: 0.5866 (mmm) cc_final: 0.5655 (mmt) REVERT: A 2720 PHE cc_start: 0.8504 (t80) cc_final: 0.8216 (t80) REVERT: A 2732 TRP cc_start: 0.8206 (t-100) cc_final: 0.7970 (t-100) REVERT: A 2772 ARG cc_start: 0.8867 (mtt-85) cc_final: 0.8406 (mtt-85) REVERT: A 2773 TRP cc_start: 0.8075 (t-100) cc_final: 0.7676 (t-100) REVERT: A 2843 MET cc_start: 0.8010 (ptp) cc_final: 0.6805 (tpt) REVERT: A 2848 TYR cc_start: 0.7922 (m-10) cc_final: 0.7591 (m-10) REVERT: A 2939 TYR cc_start: 0.8822 (m-80) cc_final: 0.8506 (m-80) REVERT: A 3060 PHE cc_start: 0.7673 (t80) cc_final: 0.6300 (t80) REVERT: A 3104 MET cc_start: 0.8130 (ppp) cc_final: 0.7474 (ppp) REVERT: A 3246 MET cc_start: 0.7525 (ptt) cc_final: 0.7191 (mtm) REVERT: A 3819 MET cc_start: 0.6510 (mtt) cc_final: 0.6233 (mtm) REVERT: A 3954 MET cc_start: 0.8457 (mmm) cc_final: 0.7976 (tpp) REVERT: A 4246 PHE cc_start: 0.8489 (t80) cc_final: 0.7883 (t80) REVERT: A 4250 TYR cc_start: 0.8659 (t80) cc_final: 0.7710 (m-80) REVERT: A 4268 MET cc_start: 0.4415 (tpt) cc_final: 0.3846 (tmm) REVERT: A 4641 PRO cc_start: 0.8265 (OUTLIER) cc_final: 0.7918 (Cg_endo) REVERT: A 4654 MET cc_start: 0.8168 (tpt) cc_final: 0.7870 (tpp) REVERT: A 4707 MET cc_start: 0.8391 (ppp) cc_final: 0.8173 (ppp) REVERT: A 4748 MET cc_start: 0.7479 (mmm) cc_final: 0.6644 (tpt) REVERT: B 964 MET cc_start: 0.3000 (mtt) cc_final: 0.2176 (mpp) REVERT: B 995 MET cc_start: 0.8544 (mtm) cc_final: 0.8140 (mtt) REVERT: B 1165 MET cc_start: 0.8227 (mtm) cc_final: 0.7872 (mtm) REVERT: B 2142 MET cc_start: 0.8536 (mpp) cc_final: 0.8038 (mpp) REVERT: B 2214 MET cc_start: 0.8721 (mmt) cc_final: 0.8346 (mmm) REVERT: B 2279 MET cc_start: 0.8892 (OUTLIER) cc_final: 0.8251 (tmm) REVERT: B 2512 MET cc_start: 0.8953 (tpt) cc_final: 0.8482 (tmm) REVERT: B 2605 MET cc_start: 0.8966 (tmm) cc_final: 0.8691 (tmm) REVERT: B 2681 MET cc_start: 0.8318 (tpp) cc_final: 0.7833 (tpp) REVERT: B 2727 HIS cc_start: 0.8040 (m90) cc_final: 0.7586 (m90) REVERT: B 2732 TRP cc_start: 0.8013 (t-100) cc_final: 0.7790 (t-100) REVERT: B 2771 TYR cc_start: 0.8269 (m-80) cc_final: 0.7580 (m-80) REVERT: B 2782 MET cc_start: 0.8824 (OUTLIER) cc_final: 0.8487 (ppp) REVERT: B 2798 MET cc_start: 0.5982 (mmp) cc_final: 0.5751 (mmp) REVERT: B 2840 MET cc_start: 0.7634 (mmt) cc_final: 0.6748 (mmt) REVERT: B 2844 MET cc_start: 0.8657 (ptp) cc_final: 0.8075 (ptp) REVERT: B 2848 TYR cc_start: 0.7882 (m-10) cc_final: 0.7560 (m-10) REVERT: B 3060 PHE cc_start: 0.7680 (t80) cc_final: 0.6585 (t80) REVERT: B 3104 MET cc_start: 0.8072 (ppp) cc_final: 0.7614 (ppp) REVERT: B 3235 MET cc_start: 0.7585 (ppp) cc_final: 0.6990 (tpt) REVERT: B 3249 TRP cc_start: 0.8174 (m100) cc_final: 0.7718 (m100) REVERT: B 3605 MET cc_start: 0.3682 (ppp) cc_final: 0.3459 (ppp) REVERT: B 3819 MET cc_start: 0.6710 (mtp) cc_final: 0.6143 (mpp) REVERT: B 4186 MET cc_start: 0.9350 (mmp) cc_final: 0.8401 (mmt) REVERT: B 4279 MET cc_start: 0.6387 (ttm) cc_final: 0.5712 (tmm) REVERT: B 4292 MET cc_start: 0.8183 (mmm) cc_final: 0.7912 (mmm) REVERT: B 4502 MET cc_start: 0.8271 (mtm) cc_final: 0.8016 (mtm) REVERT: B 4654 MET cc_start: 0.8173 (tmm) cc_final: 0.7807 (tmm) REVERT: B 4748 MET cc_start: 0.8108 (mmm) cc_final: 0.7812 (mmm) REVERT: B 4814 MET cc_start: 0.8293 (mmm) cc_final: 0.7919 (mmm) REVERT: C 309 MET cc_start: 0.7730 (mmp) cc_final: 0.7467 (mmp) REVERT: C 393 MET cc_start: 0.7760 (mmt) cc_final: 0.7437 (mmm) REVERT: C 964 MET cc_start: 0.3235 (mtt) cc_final: 0.2702 (mpp) REVERT: C 995 MET cc_start: 0.8840 (mtm) cc_final: 0.8349 (mtt) REVERT: C 1168 MET cc_start: 0.8435 (mmm) cc_final: 0.8172 (mmp) REVERT: C 1174 MET cc_start: 0.7875 (ptp) cc_final: 0.7653 (ptt) REVERT: C 1720 MET cc_start: 0.8565 (ptm) cc_final: 0.8296 (ptt) REVERT: C 2142 MET cc_start: 0.8360 (mtp) cc_final: 0.8147 (mpp) REVERT: C 2214 MET cc_start: 0.8751 (mmm) cc_final: 0.8297 (mmm) REVERT: C 2234 MET cc_start: 0.8756 (mmm) cc_final: 0.8475 (mtp) REVERT: C 2384 MET cc_start: 0.9307 (mmm) cc_final: 0.8937 (mmm) REVERT: C 2389 MET cc_start: 0.9203 (mtp) cc_final: 0.8917 (mtp) REVERT: C 2512 MET cc_start: 0.8903 (tpt) cc_final: 0.8527 (tmm) REVERT: C 2681 MET cc_start: 0.8540 (tpp) cc_final: 0.7865 (tpp) REVERT: C 2695 MET cc_start: 0.6460 (mmm) cc_final: 0.6111 (mmt) REVERT: C 2766 LYS cc_start: 0.9466 (mmmt) cc_final: 0.9263 (mmmt) REVERT: C 2840 MET cc_start: 0.7740 (mmt) cc_final: 0.6254 (mmt) REVERT: C 2843 MET cc_start: 0.7276 (tpp) cc_final: 0.6622 (tpp) REVERT: C 2844 MET cc_start: 0.8860 (ptp) cc_final: 0.8392 (ptp) REVERT: C 2895 PHE cc_start: 0.8273 (t80) cc_final: 0.7862 (t80) REVERT: C 3003 MET cc_start: 0.9221 (ptt) cc_final: 0.8725 (ptm) REVERT: C 3104 MET cc_start: 0.8286 (ppp) cc_final: 0.7607 (ppp) REVERT: C 3246 MET cc_start: 0.7539 (ptt) cc_final: 0.7257 (mtm) REVERT: C 3273 MET cc_start: 0.6982 (ptt) cc_final: 0.6502 (ppp) REVERT: C 3819 MET cc_start: 0.6470 (mtp) cc_final: 0.5872 (mtm) REVERT: C 4279 MET cc_start: 0.6664 (mtt) cc_final: 0.6427 (tmm) REVERT: C 4641 PRO cc_start: 0.8233 (OUTLIER) cc_final: 0.7935 (Cg_endo) REVERT: C 4654 MET cc_start: 0.8241 (tpp) cc_final: 0.7940 (tpp) REVERT: D 964 MET cc_start: 0.5090 (OUTLIER) cc_final: 0.3260 (mpp) REVERT: D 981 MET cc_start: 0.8068 (pmm) cc_final: 0.7717 (pmm) REVERT: D 995 MET cc_start: 0.8860 (mtm) cc_final: 0.8462 (mtt) REVERT: D 1174 MET cc_start: 0.7828 (ptp) cc_final: 0.7596 (ptt) REVERT: D 1300 MET cc_start: 0.8651 (mmm) cc_final: 0.8244 (mmp) REVERT: D 1842 ILE cc_start: 0.9040 (OUTLIER) cc_final: 0.8787 (pt) REVERT: D 2279 MET cc_start: 0.8956 (OUTLIER) cc_final: 0.8550 (tmm) REVERT: D 2468 MET cc_start: 0.8962 (mmm) cc_final: 0.8654 (mmp) REVERT: D 2512 MET cc_start: 0.8986 (tpt) cc_final: 0.8508 (tmm) REVERT: D 2688 MET cc_start: 0.5279 (mtt) cc_final: 0.4713 (pmm) REVERT: D 2720 PHE cc_start: 0.8858 (t80) cc_final: 0.8562 (t80) REVERT: D 2724 TYR cc_start: 0.8242 (t80) cc_final: 0.7997 (t80) REVERT: D 2844 MET cc_start: 0.8715 (ptp) cc_final: 0.8199 (ppp) REVERT: D 2901 TYR cc_start: 0.7339 (m-80) cc_final: 0.6922 (m-80) REVERT: D 3003 MET cc_start: 0.8791 (ptm) cc_final: 0.8495 (ptm) REVERT: D 3060 PHE cc_start: 0.7933 (t80) cc_final: 0.7510 (t80) REVERT: D 3104 MET cc_start: 0.8219 (ppp) cc_final: 0.7729 (ppp) REVERT: D 3115 HIS cc_start: 0.8249 (OUTLIER) cc_final: 0.7864 (t-170) REVERT: D 3215 MET cc_start: 0.8885 (mtt) cc_final: 0.8614 (ptp) REVERT: D 3246 MET cc_start: 0.5524 (mtm) cc_final: 0.4962 (mmm) REVERT: D 3249 TRP cc_start: 0.7898 (m-90) cc_final: 0.7615 (m-90) REVERT: D 3819 MET cc_start: 0.6617 (mtt) cc_final: 0.6386 (mpp) REVERT: D 4002 MET cc_start: 0.8505 (tmm) cc_final: 0.8069 (tmm) REVERT: D 4641 PRO cc_start: 0.8524 (OUTLIER) cc_final: 0.8233 (Cg_endo) REVERT: D 4654 MET cc_start: 0.8460 (tmm) cc_final: 0.8117 (tmm) REVERT: D 4748 MET cc_start: 0.7734 (mmm) cc_final: 0.7197 (tpt) REVERT: D 4884 MET cc_start: 0.8533 (tpp) cc_final: 0.8190 (tpt) outliers start: 92 outliers final: 57 residues processed: 782 average time/residue: 1.2124 time to fit residues: 1691.0356 Evaluate side-chains 789 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 721 time to evaluate : 11.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 30 MET Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain A residue 29 HIS Chi-restraints excluded: chain A residue 111 ARG Chi-restraints excluded: chain A residue 949 HIS Chi-restraints excluded: chain A residue 1165 MET Chi-restraints excluded: chain A residue 1215 MET Chi-restraints excluded: chain A residue 1552 VAL Chi-restraints excluded: chain A residue 1599 MET Chi-restraints excluded: chain A residue 1608 VAL Chi-restraints excluded: chain A residue 1727 VAL Chi-restraints excluded: chain A residue 1842 ILE Chi-restraints excluded: chain A residue 2162 MET Chi-restraints excluded: chain A residue 2585 MET Chi-restraints excluded: chain A residue 3117 PHE Chi-restraints excluded: chain A residue 3942 ASP Chi-restraints excluded: chain A residue 4587 ILE Chi-restraints excluded: chain A residue 4626 ILE Chi-restraints excluded: chain A residue 4641 PRO Chi-restraints excluded: chain A residue 4672 MET Chi-restraints excluded: chain B residue 29 HIS Chi-restraints excluded: chain B residue 111 ARG Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 1608 VAL Chi-restraints excluded: chain B residue 1727 VAL Chi-restraints excluded: chain B residue 1896 MET Chi-restraints excluded: chain B residue 2279 MET Chi-restraints excluded: chain B residue 2585 MET Chi-restraints excluded: chain B residue 2782 MET Chi-restraints excluded: chain B residue 3043 ARG Chi-restraints excluded: chain B residue 3115 HIS Chi-restraints excluded: chain B residue 3283 ILE Chi-restraints excluded: chain B residue 3318 HIS Chi-restraints excluded: chain B residue 3942 ASP Chi-restraints excluded: chain B residue 4256 MET Chi-restraints excluded: chain B residue 4626 ILE Chi-restraints excluded: chain C residue 29 HIS Chi-restraints excluded: chain C residue 1215 MET Chi-restraints excluded: chain C residue 1552 VAL Chi-restraints excluded: chain C residue 1727 VAL Chi-restraints excluded: chain C residue 2585 MET Chi-restraints excluded: chain C residue 3115 HIS Chi-restraints excluded: chain C residue 3215 MET Chi-restraints excluded: chain C residue 3954 MET Chi-restraints excluded: chain C residue 4587 ILE Chi-restraints excluded: chain C residue 4626 ILE Chi-restraints excluded: chain C residue 4641 PRO Chi-restraints excluded: chain D residue 29 HIS Chi-restraints excluded: chain D residue 778 MET Chi-restraints excluded: chain D residue 919 VAL Chi-restraints excluded: chain D residue 949 HIS Chi-restraints excluded: chain D residue 964 MET Chi-restraints excluded: chain D residue 1165 MET Chi-restraints excluded: chain D residue 1251 LEU Chi-restraints excluded: chain D residue 1727 VAL Chi-restraints excluded: chain D residue 1842 ILE Chi-restraints excluded: chain D residue 2279 MET Chi-restraints excluded: chain D residue 3115 HIS Chi-restraints excluded: chain D residue 3245 TYR Chi-restraints excluded: chain D residue 3318 HIS Chi-restraints excluded: chain D residue 4279 MET Chi-restraints excluded: chain D residue 4587 ILE Chi-restraints excluded: chain D residue 4626 ILE Chi-restraints excluded: chain D residue 4641 PRO Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1030 optimal weight: 5.9990 chunk 665 optimal weight: 10.0000 chunk 994 optimal weight: 2.9990 chunk 501 optimal weight: 5.9990 chunk 327 optimal weight: 9.9990 chunk 322 optimal weight: 4.9990 chunk 1058 optimal weight: 10.0000 chunk 1134 optimal weight: 8.9990 chunk 823 optimal weight: 6.9990 chunk 155 optimal weight: 10.0000 chunk 1309 optimal weight: 8.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 26 HIS A 398 HIS ** A 608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1691 ASN ** A2684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2899 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2899 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2899 ASN C3666 GLN C4088 HIS C4178 ASN D 608 HIS ** D1581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2729 HIS ** D3174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3230 GLN ** D4629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.908 141676 Z= 0.675 Angle : 0.618 29.541 191424 Z= 0.325 Chirality : 0.040 0.267 20988 Planarity : 0.005 0.210 24592 Dihedral : 5.209 85.739 19042 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.20 % Favored : 96.74 % Rotamer: Outliers : 0.55 % Allowed : 7.92 % Favored : 91.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.62 % 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: 1.11 (0.07), residues: 17212 helix: 1.83 (0.06), residues: 9072 sheet: -0.29 (0.12), residues: 1632 loop : -0.52 (0.08), residues: 6508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.097 0.002 TRP B3295 HIS 0.030 0.001 HIS G 26 PHE 0.057 0.002 PHE A3117 TYR 0.040 0.001 TYR A 931 ARG 0.051 0.001 ARG A3043 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 806 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 722 time to evaluate : 11.732 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: H 67 MET cc_start: 0.8841 (mtp) cc_final: 0.8536 (mtp) REVERT: A 309 MET cc_start: 0.7365 (mmp) cc_final: 0.7018 (mmt) REVERT: A 893 TRP cc_start: 0.9103 (m-10) cc_final: 0.8542 (m-90) REVERT: A 895 MET cc_start: 0.9225 (ptp) cc_final: 0.8789 (ppp) REVERT: A 964 MET cc_start: 0.3221 (mtt) cc_final: 0.2401 (mpp) REVERT: A 995 MET cc_start: 0.8876 (mtm) cc_final: 0.8312 (mtt) REVERT: A 1113 MET cc_start: 0.8149 (mtt) cc_final: 0.7784 (mtt) REVERT: A 1842 ILE cc_start: 0.9049 (OUTLIER) cc_final: 0.8737 (tp) REVERT: A 2167 MET cc_start: 0.7938 (mtm) cc_final: 0.7634 (mtm) REVERT: A 2248 MET cc_start: 0.8134 (tpp) cc_final: 0.7662 (ttp) REVERT: A 2468 MET cc_start: 0.8899 (mmm) cc_final: 0.8614 (mmm) REVERT: A 2512 MET cc_start: 0.8841 (tpt) cc_final: 0.8553 (tmm) REVERT: A 2681 MET cc_start: 0.8479 (tpp) cc_final: 0.8034 (tpp) REVERT: A 2720 PHE cc_start: 0.8470 (t80) cc_final: 0.8173 (t80) REVERT: A 2732 TRP cc_start: 0.8193 (t-100) cc_final: 0.7959 (t-100) REVERT: A 2772 ARG cc_start: 0.8850 (mtt-85) cc_final: 0.8367 (mtt-85) REVERT: A 2773 TRP cc_start: 0.8061 (t-100) cc_final: 0.7673 (t-100) REVERT: A 2843 MET cc_start: 0.7975 (ptp) cc_final: 0.6777 (tpt) REVERT: A 2848 TYR cc_start: 0.7926 (m-10) cc_final: 0.7604 (m-10) REVERT: A 3003 MET cc_start: 0.9075 (ptm) cc_final: 0.8636 (ptm) REVERT: A 3060 PHE cc_start: 0.7596 (t80) cc_final: 0.6249 (t80) REVERT: A 3104 MET cc_start: 0.8139 (ppp) cc_final: 0.7506 (ppp) REVERT: A 3246 MET cc_start: 0.7528 (ptt) cc_final: 0.7211 (mtm) REVERT: A 3273 MET cc_start: 0.7250 (ptp) cc_final: 0.6942 (ppp) REVERT: A 3819 MET cc_start: 0.6532 (mtt) cc_final: 0.6290 (mtm) REVERT: A 3954 MET cc_start: 0.8451 (mmm) cc_final: 0.7943 (tpp) REVERT: A 4256 MET cc_start: 0.8590 (mmp) cc_final: 0.8311 (mmm) REVERT: A 4268 MET cc_start: 0.4416 (tpt) cc_final: 0.3853 (tmm) REVERT: A 4641 PRO cc_start: 0.8255 (OUTLIER) cc_final: 0.7926 (Cg_endo) REVERT: A 4654 MET cc_start: 0.8154 (tpt) cc_final: 0.7868 (tpp) REVERT: A 4707 MET cc_start: 0.8390 (ppp) cc_final: 0.8169 (ppp) REVERT: A 4748 MET cc_start: 0.7462 (mmm) cc_final: 0.6652 (tpt) REVERT: A 4804 MET cc_start: 0.9097 (mmm) cc_final: 0.8729 (mmm) REVERT: A 4817 MET cc_start: 0.8709 (tpp) cc_final: 0.8503 (mmm) REVERT: A 4884 MET cc_start: 0.8400 (tpp) cc_final: 0.7983 (tpt) REVERT: B 494 MET cc_start: 0.8687 (mmp) cc_final: 0.8430 (mmp) REVERT: B 895 MET cc_start: 0.8762 (ptp) cc_final: 0.8544 (mpp) REVERT: B 964 MET cc_start: 0.2970 (mtt) cc_final: 0.1984 (mpp) REVERT: B 995 MET cc_start: 0.8564 (mtm) cc_final: 0.8146 (mtt) REVERT: B 1165 MET cc_start: 0.8220 (mtm) cc_final: 0.7914 (mtm) REVERT: B 2142 MET cc_start: 0.8500 (mpp) cc_final: 0.8017 (mpp) REVERT: B 2162 MET cc_start: 0.8620 (mmp) cc_final: 0.8306 (mmp) REVERT: B 2192 MET cc_start: 0.8417 (tpp) cc_final: 0.8114 (tpp) REVERT: B 2214 MET cc_start: 0.8728 (mmt) cc_final: 0.8331 (mmm) REVERT: B 2279 MET cc_start: 0.8892 (ttt) cc_final: 0.8251 (tmm) REVERT: B 2512 MET cc_start: 0.8936 (tpt) cc_final: 0.8450 (tmm) REVERT: B 2605 MET cc_start: 0.8943 (tmm) cc_final: 0.8644 (tmm) REVERT: B 2681 MET cc_start: 0.8260 (tpp) cc_final: 0.7778 (tpp) REVERT: B 2727 HIS cc_start: 0.8044 (m90) cc_final: 0.7577 (m90) REVERT: B 2732 TRP cc_start: 0.8005 (t-100) cc_final: 0.7772 (t-100) REVERT: B 2771 TYR cc_start: 0.8353 (m-80) cc_final: 0.8088 (m-80) REVERT: B 2782 MET cc_start: 0.8812 (OUTLIER) cc_final: 0.8510 (ppp) REVERT: B 2840 MET cc_start: 0.7706 (mmt) cc_final: 0.6746 (mmt) REVERT: B 2844 MET cc_start: 0.8665 (ptp) cc_final: 0.8072 (ptp) REVERT: B 2848 TYR cc_start: 0.7859 (m-10) cc_final: 0.7536 (m-10) REVERT: B 3060 PHE cc_start: 0.7654 (t80) cc_final: 0.6545 (t80) REVERT: B 3104 MET cc_start: 0.8048 (ppp) cc_final: 0.7593 (ppp) REVERT: B 3235 MET cc_start: 0.7687 (ppp) cc_final: 0.7084 (tpt) REVERT: B 3245 TYR cc_start: 0.7963 (t80) cc_final: 0.7761 (m-80) REVERT: B 3249 TRP cc_start: 0.8161 (m100) cc_final: 0.7952 (m100) REVERT: B 3295 TRP cc_start: 0.7467 (p-90) cc_final: 0.7171 (p-90) REVERT: B 3605 MET cc_start: 0.3710 (ppp) cc_final: 0.3507 (ppp) REVERT: B 3819 MET cc_start: 0.6771 (mtp) cc_final: 0.6321 (mpp) REVERT: B 4186 MET cc_start: 0.9360 (mmp) cc_final: 0.8415 (mmt) REVERT: B 4279 MET cc_start: 0.6322 (ttm) cc_final: 0.5746 (tmm) REVERT: B 4292 MET cc_start: 0.8180 (mmm) cc_final: 0.7905 (mmm) REVERT: B 4502 MET cc_start: 0.8279 (mtm) cc_final: 0.7973 (mtm) REVERT: B 4654 MET cc_start: 0.8189 (tmm) cc_final: 0.7805 (tmm) REVERT: B 4728 MET cc_start: 0.8755 (mmm) cc_final: 0.8334 (mmm) REVERT: B 4748 MET cc_start: 0.8027 (mmm) cc_final: 0.7632 (mmm) REVERT: B 4814 MET cc_start: 0.8282 (mmm) cc_final: 0.8027 (mmm) REVERT: C 309 MET cc_start: 0.7722 (mmp) cc_final: 0.7478 (mmp) REVERT: C 393 MET cc_start: 0.7745 (mmt) cc_final: 0.7467 (mmm) REVERT: C 895 MET cc_start: 0.9199 (ptp) cc_final: 0.8833 (ppp) REVERT: C 964 MET cc_start: 0.3174 (mtt) cc_final: 0.2298 (mpp) REVERT: C 995 MET cc_start: 0.8861 (mtm) cc_final: 0.8339 (mtt) REVERT: C 1168 MET cc_start: 0.8413 (mmm) cc_final: 0.8139 (mmp) REVERT: C 1174 MET cc_start: 0.7877 (ptp) cc_final: 0.7646 (ptt) REVERT: C 1720 MET cc_start: 0.8554 (ptm) cc_final: 0.8294 (ptt) REVERT: C 1896 MET cc_start: 0.8580 (ttm) cc_final: 0.8355 (ttt) REVERT: C 2214 MET cc_start: 0.8753 (mmm) cc_final: 0.8294 (mmm) REVERT: C 2234 MET cc_start: 0.8754 (mmm) cc_final: 0.8470 (mtp) REVERT: C 2384 MET cc_start: 0.9317 (mmm) cc_final: 0.8932 (mmm) REVERT: C 2389 MET cc_start: 0.9196 (mtp) cc_final: 0.8905 (mtp) REVERT: C 2456 MET cc_start: 0.8662 (mtm) cc_final: 0.8134 (mpp) REVERT: C 2512 MET cc_start: 0.8838 (tpt) cc_final: 0.8557 (tmm) REVERT: C 2681 MET cc_start: 0.8579 (tpp) cc_final: 0.7925 (tpp) REVERT: C 2695 MET cc_start: 0.6409 (mmm) cc_final: 0.6077 (mmt) REVERT: C 2766 LYS cc_start: 0.9474 (mmmt) cc_final: 0.9269 (mmmt) REVERT: C 2787 TRP cc_start: 0.8290 (m-90) cc_final: 0.7674 (m-90) REVERT: C 2840 MET cc_start: 0.7779 (mmt) cc_final: 0.6423 (mmt) REVERT: C 2843 MET cc_start: 0.7288 (tpp) cc_final: 0.6655 (tpp) REVERT: C 2844 MET cc_start: 0.8824 (ptp) cc_final: 0.8508 (ptp) REVERT: C 2895 PHE cc_start: 0.8325 (t80) cc_final: 0.7913 (t80) REVERT: C 3003 MET cc_start: 0.9216 (ptt) cc_final: 0.8872 (ttp) REVERT: C 3104 MET cc_start: 0.8257 (ppp) cc_final: 0.7590 (ppp) REVERT: C 3235 MET cc_start: 0.7497 (ppp) cc_final: 0.7153 (tpt) REVERT: C 3246 MET cc_start: 0.7482 (ptt) cc_final: 0.7224 (mtm) REVERT: C 3273 MET cc_start: 0.6997 (ptt) cc_final: 0.6592 (ppp) REVERT: C 3295 TRP cc_start: 0.7480 (p-90) cc_final: 0.6993 (p-90) REVERT: C 3819 MET cc_start: 0.6402 (mtp) cc_final: 0.5998 (mtm) REVERT: C 4279 MET cc_start: 0.6647 (mtt) cc_final: 0.6417 (tpp) REVERT: C 4641 PRO cc_start: 0.8209 (OUTLIER) cc_final: 0.7915 (Cg_endo) REVERT: C 4654 MET cc_start: 0.8231 (tpp) cc_final: 0.7928 (tpp) REVERT: D 964 MET cc_start: 0.5030 (OUTLIER) cc_final: 0.3248 (mpp) REVERT: D 981 MET cc_start: 0.8001 (pmm) cc_final: 0.7797 (pmm) REVERT: D 995 MET cc_start: 0.8842 (mtm) cc_final: 0.8465 (mtt) REVERT: D 1174 MET cc_start: 0.7815 (ptp) cc_final: 0.7581 (ptt) REVERT: D 1300 MET cc_start: 0.8648 (mmm) cc_final: 0.8244 (mmp) REVERT: D 1842 ILE cc_start: 0.9007 (OUTLIER) cc_final: 0.8760 (pt) REVERT: D 2142 MET cc_start: 0.8372 (mmt) cc_final: 0.8167 (mmt) REVERT: D 2162 MET cc_start: 0.8686 (mmp) cc_final: 0.8275 (mmp) REVERT: D 2279 MET cc_start: 0.8966 (OUTLIER) cc_final: 0.8577 (tmm) REVERT: D 2468 MET cc_start: 0.8965 (mmm) cc_final: 0.8680 (mmp) REVERT: D 2512 MET cc_start: 0.8983 (tpt) cc_final: 0.8499 (tmm) REVERT: D 2605 MET cc_start: 0.9031 (ttp) cc_final: 0.8598 (tmm) REVERT: D 2688 MET cc_start: 0.5353 (mtt) cc_final: 0.4822 (pmm) REVERT: D 2695 MET cc_start: 0.5624 (mmm) cc_final: 0.5369 (mmm) REVERT: D 2720 PHE cc_start: 0.8859 (t80) cc_final: 0.8553 (t80) REVERT: D 2724 TYR cc_start: 0.8241 (t80) cc_final: 0.8012 (t80) REVERT: D 2844 MET cc_start: 0.8707 (ptp) cc_final: 0.8176 (ppp) REVERT: D 2848 TYR cc_start: 0.8819 (t80) cc_final: 0.8533 (t80) REVERT: D 2901 TYR cc_start: 0.7353 (m-80) cc_final: 0.6925 (m-80) REVERT: D 3060 PHE cc_start: 0.7951 (t80) cc_final: 0.7521 (t80) REVERT: D 3104 MET cc_start: 0.8214 (ppp) cc_final: 0.7720 (ppp) REVERT: D 3115 HIS cc_start: 0.8234 (OUTLIER) cc_final: 0.7862 (t-170) REVERT: D 3215 MET cc_start: 0.8909 (mtt) cc_final: 0.8619 (ptp) REVERT: D 3246 MET cc_start: 0.5667 (mtm) cc_final: 0.5022 (mmm) REVERT: D 3819 MET cc_start: 0.6636 (mtt) cc_final: 0.6305 (mpp) REVERT: D 4002 MET cc_start: 0.8501 (tmm) cc_final: 0.8070 (tmm) REVERT: D 4641 PRO cc_start: 0.8488 (OUTLIER) cc_final: 0.8212 (Cg_endo) REVERT: D 4654 MET cc_start: 0.8463 (tmm) cc_final: 0.8121 (tmm) REVERT: D 4748 MET cc_start: 0.7730 (mmm) cc_final: 0.7188 (tpt) REVERT: D 4884 MET cc_start: 0.8508 (tpp) cc_final: 0.8177 (tpt) outliers start: 84 outliers final: 57 residues processed: 774 average time/residue: 1.2092 time to fit residues: 1675.3126 Evaluate side-chains 788 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 722 time to evaluate : 11.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 30 MET Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain A residue 29 HIS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 949 HIS Chi-restraints excluded: chain A residue 1165 MET Chi-restraints excluded: chain A residue 1215 MET Chi-restraints excluded: chain A residue 1552 VAL Chi-restraints excluded: chain A residue 1599 MET Chi-restraints excluded: chain A residue 1608 VAL Chi-restraints excluded: chain A residue 1619 VAL Chi-restraints excluded: chain A residue 1727 VAL Chi-restraints excluded: chain A residue 1842 ILE Chi-restraints excluded: chain A residue 2162 MET Chi-restraints excluded: chain A residue 2585 MET Chi-restraints excluded: chain A residue 3117 PHE Chi-restraints excluded: chain A residue 3942 ASP Chi-restraints excluded: chain A residue 4587 ILE Chi-restraints excluded: chain A residue 4626 ILE Chi-restraints excluded: chain A residue 4641 PRO Chi-restraints excluded: chain A residue 4672 MET Chi-restraints excluded: chain B residue 29 HIS Chi-restraints excluded: chain B residue 1608 VAL Chi-restraints excluded: chain B residue 1727 VAL Chi-restraints excluded: chain B residue 1896 MET Chi-restraints excluded: chain B residue 2585 MET Chi-restraints excluded: chain B residue 2782 MET Chi-restraints excluded: chain B residue 3043 ARG Chi-restraints excluded: chain B residue 3115 HIS Chi-restraints excluded: chain B residue 3283 ILE Chi-restraints excluded: chain B residue 3318 HIS Chi-restraints excluded: chain B residue 3942 ASP Chi-restraints excluded: chain B residue 4256 MET Chi-restraints excluded: chain B residue 4626 ILE Chi-restraints excluded: chain C residue 29 HIS Chi-restraints excluded: chain C residue 1215 MET Chi-restraints excluded: chain C residue 1552 VAL Chi-restraints excluded: chain C residue 1727 VAL Chi-restraints excluded: chain C residue 2585 MET Chi-restraints excluded: chain C residue 2899 ASN Chi-restraints excluded: chain C residue 3115 HIS Chi-restraints excluded: chain C residue 3215 MET Chi-restraints excluded: chain C residue 3942 ASP Chi-restraints excluded: chain C residue 4587 ILE Chi-restraints excluded: chain C residue 4626 ILE Chi-restraints excluded: chain C residue 4641 PRO Chi-restraints excluded: chain D residue 29 HIS Chi-restraints excluded: chain D residue 778 MET Chi-restraints excluded: chain D residue 949 HIS Chi-restraints excluded: chain D residue 964 MET Chi-restraints excluded: chain D residue 1251 LEU Chi-restraints excluded: chain D residue 1727 VAL Chi-restraints excluded: chain D residue 1842 ILE Chi-restraints excluded: chain D residue 2279 MET Chi-restraints excluded: chain D residue 2585 MET Chi-restraints excluded: chain D residue 3115 HIS Chi-restraints excluded: chain D residue 3245 TYR Chi-restraints excluded: chain D residue 3318 HIS Chi-restraints excluded: chain D residue 3942 ASP Chi-restraints excluded: chain D residue 4279 MET Chi-restraints excluded: chain D residue 4587 ILE Chi-restraints excluded: chain D residue 4626 ILE Chi-restraints excluded: chain D residue 4641 PRO Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1515 optimal weight: 0.9990 chunk 1595 optimal weight: 30.0000 chunk 1455 optimal weight: 10.0000 chunk 1552 optimal weight: 0.2980 chunk 934 optimal weight: 7.9990 chunk 676 optimal weight: 9.9990 chunk 1218 optimal weight: 6.9990 chunk 476 optimal weight: 5.9990 chunk 1402 optimal weight: 30.0000 chunk 1467 optimal weight: 0.0570 chunk 1546 optimal weight: 8.9990 overall best weight: 2.8704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 26 HIS ** A 608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2899 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4945 GLN ** B 608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2091 GLN ** B2684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2899 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2899 ASN ** C4629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4945 GLN ** D 808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2091 GLN ** D2684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.908 141676 Z= 0.638 Angle : 0.594 29.502 191424 Z= 0.312 Chirality : 0.039 0.269 20988 Planarity : 0.004 0.192 24592 Dihedral : 5.126 85.884 19039 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.15 % Favored : 96.79 % Rotamer: Outliers : 0.54 % Allowed : 8.03 % Favored : 91.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.01 % 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: 1.17 (0.07), residues: 17212 helix: 1.88 (0.06), residues: 9044 sheet: -0.22 (0.13), residues: 1640 loop : -0.48 (0.08), residues: 6528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.081 0.002 TRP B3295 HIS 0.009 0.001 HIS G 26 PHE 0.051 0.001 PHE A3117 TYR 0.038 0.001 TYR A 931 ARG 0.051 0.000 ARG A3043 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 807 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 725 time to evaluate : 11.611 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: A 309 MET cc_start: 0.7317 (mmp) cc_final: 0.6976 (mmt) REVERT: A 895 MET cc_start: 0.9206 (ptp) cc_final: 0.8777 (ppp) REVERT: A 964 MET cc_start: 0.2981 (mtt) cc_final: 0.2207 (mpp) REVERT: A 995 MET cc_start: 0.8834 (mtm) cc_final: 0.8255 (mtt) REVERT: A 1842 ILE cc_start: 0.9038 (OUTLIER) cc_final: 0.8716 (tp) REVERT: A 2142 MET cc_start: 0.8121 (OUTLIER) cc_final: 0.7887 (tpp) REVERT: A 2167 MET cc_start: 0.7890 (mtm) cc_final: 0.7620 (mtm) REVERT: A 2468 MET cc_start: 0.8914 (mmm) cc_final: 0.8629 (mmm) REVERT: A 2512 MET cc_start: 0.8813 (tpt) cc_final: 0.8516 (tmm) REVERT: A 2681 MET cc_start: 0.8458 (tpp) cc_final: 0.7998 (tpp) REVERT: A 2695 MET cc_start: 0.6732 (mmt) cc_final: 0.6159 (mmm) REVERT: A 2720 PHE cc_start: 0.8460 (t80) cc_final: 0.8152 (t80) REVERT: A 2732 TRP cc_start: 0.8180 (t-100) cc_final: 0.7945 (t-100) REVERT: A 2772 ARG cc_start: 0.8847 (mtt-85) cc_final: 0.8350 (mtt-85) REVERT: A 2773 TRP cc_start: 0.8048 (t-100) cc_final: 0.7646 (t-100) REVERT: A 2843 MET cc_start: 0.7977 (ptp) cc_final: 0.6784 (tpt) REVERT: A 2844 MET cc_start: 0.8587 (ptp) cc_final: 0.7883 (ptp) REVERT: A 2848 TYR cc_start: 0.7916 (m-10) cc_final: 0.7566 (m-10) REVERT: A 3003 MET cc_start: 0.9052 (ptm) cc_final: 0.8614 (ptm) REVERT: A 3060 PHE cc_start: 0.7566 (t80) cc_final: 0.6242 (t80) REVERT: A 3104 MET cc_start: 0.8114 (ppp) cc_final: 0.7468 (ppp) REVERT: A 3235 MET cc_start: 0.7444 (ppp) cc_final: 0.6820 (ppp) REVERT: A 3246 MET cc_start: 0.7490 (ptt) cc_final: 0.7135 (mtm) REVERT: A 3273 MET cc_start: 0.7174 (ptp) cc_final: 0.6967 (ppp) REVERT: A 3819 MET cc_start: 0.6508 (mtt) cc_final: 0.6299 (mtm) REVERT: A 3954 MET cc_start: 0.8447 (mmm) cc_final: 0.7762 (tpp) REVERT: A 4186 MET cc_start: 0.9337 (mmm) cc_final: 0.8568 (mmm) REVERT: A 4246 PHE cc_start: 0.8511 (t80) cc_final: 0.8073 (t80) REVERT: A 4250 TYR cc_start: 0.8643 (t80) cc_final: 0.7695 (m-80) REVERT: A 4256 MET cc_start: 0.8615 (mmp) cc_final: 0.8409 (mmm) REVERT: A 4268 MET cc_start: 0.4404 (tpt) cc_final: 0.3843 (tmm) REVERT: A 4641 PRO cc_start: 0.8230 (OUTLIER) cc_final: 0.7919 (Cg_endo) REVERT: A 4654 MET cc_start: 0.8146 (tpt) cc_final: 0.7874 (tpp) REVERT: A 4707 MET cc_start: 0.8393 (ppp) cc_final: 0.8162 (ppp) REVERT: A 4748 MET cc_start: 0.7454 (mmm) cc_final: 0.7042 (tpt) REVERT: A 4804 MET cc_start: 0.9089 (mmm) cc_final: 0.8718 (mmm) REVERT: A 4884 MET cc_start: 0.8342 (tpp) cc_final: 0.7927 (tpt) REVERT: B 469 HIS cc_start: 0.8043 (m-70) cc_final: 0.7733 (m90) REVERT: B 494 MET cc_start: 0.8684 (mmp) cc_final: 0.8415 (mmp) REVERT: B 964 MET cc_start: 0.2837 (mtt) cc_final: 0.1919 (mpp) REVERT: B 995 MET cc_start: 0.8520 (mtm) cc_final: 0.8095 (mtt) REVERT: B 1165 MET cc_start: 0.8201 (mtm) cc_final: 0.7898 (mtm) REVERT: B 1215 MET cc_start: 0.8675 (mmm) cc_final: 0.7723 (mtp) REVERT: B 2142 MET cc_start: 0.8485 (mpp) cc_final: 0.8009 (mpp) REVERT: B 2162 MET cc_start: 0.8568 (mmp) cc_final: 0.8276 (mmp) REVERT: B 2192 MET cc_start: 0.8385 (tpp) cc_final: 0.8077 (tpp) REVERT: B 2214 MET cc_start: 0.8712 (mmt) cc_final: 0.8288 (mmm) REVERT: B 2279 MET cc_start: 0.8894 (ttt) cc_final: 0.8246 (tmm) REVERT: B 2512 MET cc_start: 0.8893 (tpt) cc_final: 0.8446 (tmm) REVERT: B 2605 MET cc_start: 0.8938 (tmm) cc_final: 0.8640 (tmm) REVERT: B 2681 MET cc_start: 0.8249 (tpp) cc_final: 0.7749 (tpp) REVERT: B 2695 MET cc_start: 0.6645 (mmt) cc_final: 0.6287 (mmm) REVERT: B 2727 HIS cc_start: 0.8023 (m90) cc_final: 0.7560 (m90) REVERT: B 2732 TRP cc_start: 0.7998 (t-100) cc_final: 0.7767 (t-100) REVERT: B 2771 TYR cc_start: 0.8422 (m-80) cc_final: 0.8182 (m-80) REVERT: B 2782 MET cc_start: 0.8795 (OUTLIER) cc_final: 0.8493 (ppp) REVERT: B 2840 MET cc_start: 0.7675 (mmt) cc_final: 0.6646 (mmt) REVERT: B 2844 MET cc_start: 0.8652 (ptp) cc_final: 0.8050 (ptp) REVERT: B 2848 TYR cc_start: 0.7834 (m-10) cc_final: 0.7522 (m-10) REVERT: B 3060 PHE cc_start: 0.7623 (t80) cc_final: 0.6510 (t80) REVERT: B 3104 MET cc_start: 0.8019 (ppp) cc_final: 0.7560 (ppp) REVERT: B 3235 MET cc_start: 0.7606 (ppp) cc_final: 0.7058 (tpt) REVERT: B 3249 TRP cc_start: 0.8084 (m100) cc_final: 0.7867 (m100) REVERT: B 3295 TRP cc_start: 0.7350 (p-90) cc_final: 0.7111 (p-90) REVERT: B 3689 MET cc_start: 0.8795 (mmp) cc_final: 0.8494 (mmp) REVERT: B 3819 MET cc_start: 0.6721 (mtp) cc_final: 0.6278 (mpp) REVERT: B 4279 MET cc_start: 0.6199 (ttm) cc_final: 0.5561 (tmm) REVERT: B 4292 MET cc_start: 0.8200 (mmm) cc_final: 0.7932 (mmm) REVERT: B 4502 MET cc_start: 0.8244 (mtm) cc_final: 0.7946 (mtm) REVERT: B 4654 MET cc_start: 0.8191 (tmm) cc_final: 0.7801 (tmm) REVERT: B 4728 MET cc_start: 0.8740 (mmm) cc_final: 0.8311 (mmm) REVERT: B 4748 MET cc_start: 0.7992 (mmm) cc_final: 0.7608 (mmm) REVERT: B 4804 MET cc_start: 0.9029 (tpp) cc_final: 0.8435 (mmm) REVERT: B 4814 MET cc_start: 0.8284 (mmm) cc_final: 0.8042 (mmm) REVERT: C 393 MET cc_start: 0.7701 (mmt) cc_final: 0.7438 (mmm) REVERT: C 895 MET cc_start: 0.9184 (ptp) cc_final: 0.8858 (ppp) REVERT: C 964 MET cc_start: 0.2867 (mtt) cc_final: 0.2416 (mpp) REVERT: C 995 MET cc_start: 0.8824 (mtm) cc_final: 0.8290 (mtt) REVERT: C 1168 MET cc_start: 0.8418 (mmm) cc_final: 0.8141 (mmp) REVERT: C 1174 MET cc_start: 0.7856 (ptp) cc_final: 0.7647 (ptt) REVERT: C 1720 MET cc_start: 0.8511 (ptm) cc_final: 0.8241 (ptt) REVERT: C 2214 MET cc_start: 0.8721 (mmm) cc_final: 0.8192 (mmm) REVERT: C 2234 MET cc_start: 0.8764 (mmm) cc_final: 0.8468 (mtp) REVERT: C 2384 MET cc_start: 0.9304 (mmm) cc_final: 0.8893 (mmm) REVERT: C 2389 MET cc_start: 0.9177 (mtp) cc_final: 0.8883 (mtp) REVERT: C 2456 MET cc_start: 0.8649 (mtm) cc_final: 0.8102 (mpp) REVERT: C 2512 MET cc_start: 0.8800 (tpt) cc_final: 0.8523 (tmm) REVERT: C 2681 MET cc_start: 0.8578 (tpp) cc_final: 0.7925 (tpp) REVERT: C 2695 MET cc_start: 0.6334 (mmm) cc_final: 0.6003 (mmt) REVERT: C 2787 TRP cc_start: 0.8262 (m-90) cc_final: 0.7973 (m-90) REVERT: C 2840 MET cc_start: 0.7869 (mmt) cc_final: 0.7484 (mmt) REVERT: C 2843 MET cc_start: 0.7299 (tpp) cc_final: 0.6578 (tpp) REVERT: C 2895 PHE cc_start: 0.8277 (t80) cc_final: 0.7841 (t80) REVERT: C 3003 MET cc_start: 0.9188 (ptt) cc_final: 0.8866 (ttp) REVERT: C 3104 MET cc_start: 0.8250 (ppp) cc_final: 0.7569 (ppp) REVERT: C 3235 MET cc_start: 0.7518 (ppp) cc_final: 0.7156 (tpt) REVERT: C 3246 MET cc_start: 0.7452 (ptt) cc_final: 0.7100 (ptp) REVERT: C 3273 MET cc_start: 0.6852 (ptt) cc_final: 0.6538 (ppp) REVERT: C 3277 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8757 (pp) REVERT: C 3295 TRP cc_start: 0.7450 (p-90) cc_final: 0.7134 (p-90) REVERT: C 3819 MET cc_start: 0.6322 (mtp) cc_final: 0.5426 (mtp) REVERT: C 4279 MET cc_start: 0.6597 (mtt) cc_final: 0.6357 (tpp) REVERT: C 4626 ILE cc_start: 0.9163 (OUTLIER) cc_final: 0.8923 (tp) REVERT: C 4641 PRO cc_start: 0.8195 (OUTLIER) cc_final: 0.7914 (Cg_endo) REVERT: C 4654 MET cc_start: 0.8228 (tpp) cc_final: 0.7922 (tpp) REVERT: D 895 MET cc_start: 0.9289 (ptp) cc_final: 0.8930 (ppp) REVERT: D 995 MET cc_start: 0.8836 (mtm) cc_final: 0.8451 (mtt) REVERT: D 1174 MET cc_start: 0.7825 (ptp) cc_final: 0.7581 (ptt) REVERT: D 1215 MET cc_start: 0.8383 (mtp) cc_final: 0.8034 (mtp) REVERT: D 1300 MET cc_start: 0.8644 (mmm) cc_final: 0.8255 (mmp) REVERT: D 1842 ILE cc_start: 0.9020 (OUTLIER) cc_final: 0.8768 (pt) REVERT: D 2162 MET cc_start: 0.8706 (mmp) cc_final: 0.8339 (mmp) REVERT: D 2279 MET cc_start: 0.8981 (ttt) cc_final: 0.8541 (tmm) REVERT: D 2456 MET cc_start: 0.8798 (pmm) cc_final: 0.8313 (mpp) REVERT: D 2468 MET cc_start: 0.8973 (mmm) cc_final: 0.8701 (mmp) REVERT: D 2512 MET cc_start: 0.8963 (tpt) cc_final: 0.8434 (tmm) REVERT: D 2605 MET cc_start: 0.9033 (ttp) cc_final: 0.8584 (tmm) REVERT: D 2688 MET cc_start: 0.5374 (mtt) cc_final: 0.4341 (pmm) REVERT: D 2720 PHE cc_start: 0.8826 (t80) cc_final: 0.8504 (t80) REVERT: D 2724 TYR cc_start: 0.8240 (t80) cc_final: 0.8025 (t80) REVERT: D 2844 MET cc_start: 0.8717 (ptp) cc_final: 0.8174 (ppp) REVERT: D 2848 TYR cc_start: 0.8813 (t80) cc_final: 0.8537 (t80) REVERT: D 2901 TYR cc_start: 0.7294 (m-80) cc_final: 0.6890 (m-80) REVERT: D 3003 MET cc_start: 0.8795 (ptm) cc_final: 0.8506 (ptm) REVERT: D 3060 PHE cc_start: 0.7914 (t80) cc_final: 0.7483 (t80) REVERT: D 3104 MET cc_start: 0.8198 (ppp) cc_final: 0.7701 (ppp) REVERT: D 3215 MET cc_start: 0.8947 (mtt) cc_final: 0.8676 (ptp) REVERT: D 3246 MET cc_start: 0.5459 (mtm) cc_final: 0.4832 (mmm) REVERT: D 3819 MET cc_start: 0.6634 (mtt) cc_final: 0.6322 (mpp) REVERT: D 4002 MET cc_start: 0.8496 (tmm) cc_final: 0.8059 (tmm) REVERT: D 4641 PRO cc_start: 0.8441 (OUTLIER) cc_final: 0.8144 (Cg_endo) REVERT: D 4654 MET cc_start: 0.8449 (tmm) cc_final: 0.8099 (tmm) REVERT: D 4748 MET cc_start: 0.7719 (mmm) cc_final: 0.7238 (tpt) REVERT: D 4884 MET cc_start: 0.8470 (tpp) cc_final: 0.8146 (tpt) outliers start: 82 outliers final: 56 residues processed: 780 average time/residue: 1.1786 time to fit residues: 1642.1177 Evaluate side-chains 784 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 719 time to evaluate : 11.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 30 MET Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain A residue 29 HIS Chi-restraints excluded: chain A residue 949 HIS Chi-restraints excluded: chain A residue 1165 MET Chi-restraints excluded: chain A residue 1215 MET Chi-restraints excluded: chain A residue 1552 VAL Chi-restraints excluded: chain A residue 1599 MET Chi-restraints excluded: chain A residue 1608 VAL Chi-restraints excluded: chain A residue 1727 VAL Chi-restraints excluded: chain A residue 1842 ILE Chi-restraints excluded: chain A residue 2142 MET Chi-restraints excluded: chain A residue 2162 MET Chi-restraints excluded: chain A residue 2585 MET Chi-restraints excluded: chain A residue 3117 PHE Chi-restraints excluded: chain A residue 3942 ASP Chi-restraints excluded: chain A residue 4587 ILE Chi-restraints excluded: chain A residue 4626 ILE Chi-restraints excluded: chain A residue 4641 PRO Chi-restraints excluded: chain A residue 4945 GLN Chi-restraints excluded: chain B residue 29 HIS Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 1608 VAL Chi-restraints excluded: chain B residue 1727 VAL Chi-restraints excluded: chain B residue 1896 MET Chi-restraints excluded: chain B residue 2585 MET Chi-restraints excluded: chain B residue 2782 MET Chi-restraints excluded: chain B residue 3043 ARG Chi-restraints excluded: chain B residue 3115 HIS Chi-restraints excluded: chain B residue 3283 ILE Chi-restraints excluded: chain B residue 3739 MET Chi-restraints excluded: chain B residue 3942 ASP Chi-restraints excluded: chain B residue 4256 MET Chi-restraints excluded: chain B residue 4626 ILE Chi-restraints excluded: chain C residue 29 HIS Chi-restraints excluded: chain C residue 938 GLU Chi-restraints excluded: chain C residue 1215 MET Chi-restraints excluded: chain C residue 1727 VAL Chi-restraints excluded: chain C residue 2585 MET Chi-restraints excluded: chain C residue 2899 ASN Chi-restraints excluded: chain C residue 3115 HIS Chi-restraints excluded: chain C residue 3215 MET Chi-restraints excluded: chain C residue 3277 LEU Chi-restraints excluded: chain C residue 3942 ASP Chi-restraints excluded: chain C residue 3954 MET Chi-restraints excluded: chain C residue 4587 ILE Chi-restraints excluded: chain C residue 4626 ILE Chi-restraints excluded: chain C residue 4641 PRO Chi-restraints excluded: chain C residue 4945 GLN Chi-restraints excluded: chain D residue 29 HIS Chi-restraints excluded: chain D residue 778 MET Chi-restraints excluded: chain D residue 949 HIS Chi-restraints excluded: chain D residue 1251 LEU Chi-restraints excluded: chain D residue 1727 VAL Chi-restraints excluded: chain D residue 1842 ILE Chi-restraints excluded: chain D residue 2585 MET Chi-restraints excluded: chain D residue 3115 HIS Chi-restraints excluded: chain D residue 3245 TYR Chi-restraints excluded: chain D residue 3318 HIS Chi-restraints excluded: chain D residue 3942 ASP Chi-restraints excluded: chain D residue 4626 ILE Chi-restraints excluded: chain D residue 4641 PRO Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1019 optimal weight: 10.0000 chunk 1641 optimal weight: 0.9980 chunk 1001 optimal weight: 10.0000 chunk 778 optimal weight: 10.0000 chunk 1140 optimal weight: 30.0000 chunk 1721 optimal weight: 0.1980 chunk 1584 optimal weight: 7.9990 chunk 1370 optimal weight: 8.9990 chunk 142 optimal weight: 8.9990 chunk 1058 optimal weight: 7.9990 chunk 840 optimal weight: 9.9990 overall best weight: 5.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2899 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4945 GLN ** B 608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2899 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2899 ASN ** C4629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4945 GLN ** D 808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.930 141676 Z= 0.664 Angle : 0.678 59.200 191424 Z= 0.370 Chirality : 0.040 0.496 20988 Planarity : 0.005 0.227 24592 Dihedral : 5.118 85.887 19036 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.14 % Favored : 96.79 % Rotamer: Outliers : 0.52 % Allowed : 8.10 % Favored : 91.38 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.62 % 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: 1.16 (0.07), residues: 17212 helix: 1.87 (0.06), residues: 9044 sheet: -0.21 (0.12), residues: 1640 loop : -0.49 (0.08), residues: 6528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.148 0.002 TRP A3295 HIS 0.196 0.001 HIS G 26 PHE 0.075 0.001 PHE B3170 TYR 0.038 0.001 TYR A 931 ARG 0.061 0.000 ARG D3043 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 799 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 720 time to evaluate : 12.003 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: A 309 MET cc_start: 0.7319 (mmp) cc_final: 0.6977 (mmt) REVERT: A 895 MET cc_start: 0.9210 (ptp) cc_final: 0.8766 (ppp) REVERT: A 964 MET cc_start: 0.2985 (mtt) cc_final: 0.2211 (mpp) REVERT: A 995 MET cc_start: 0.8836 (mtm) cc_final: 0.8258 (mtt) REVERT: A 1842 ILE cc_start: 0.9035 (OUTLIER) cc_final: 0.8719 (tp) REVERT: A 2142 MET cc_start: 0.8118 (OUTLIER) cc_final: 0.7888 (tpp) REVERT: A 2167 MET cc_start: 0.7889 (mtm) cc_final: 0.7619 (mtm) REVERT: A 2468 MET cc_start: 0.8926 (mmm) cc_final: 0.8648 (mmm) REVERT: A 2512 MET cc_start: 0.8810 (tpt) cc_final: 0.8516 (tmm) REVERT: A 2681 MET cc_start: 0.8463 (tpp) cc_final: 0.7997 (tpp) REVERT: A 2695 MET cc_start: 0.6691 (mmt) cc_final: 0.6131 (mmm) REVERT: A 2720 PHE cc_start: 0.8369 (t80) cc_final: 0.8150 (t80) REVERT: A 2732 TRP cc_start: 0.8181 (t-100) cc_final: 0.7945 (t-100) REVERT: A 2772 ARG cc_start: 0.8848 (mtt-85) cc_final: 0.8341 (mtt-85) REVERT: A 2773 TRP cc_start: 0.8051 (t-100) cc_final: 0.7648 (t-100) REVERT: A 2843 MET cc_start: 0.7979 (ptp) cc_final: 0.6781 (tpt) REVERT: A 2848 TYR cc_start: 0.7919 (m-10) cc_final: 0.7585 (m-10) REVERT: A 3003 MET cc_start: 0.9053 (ptm) cc_final: 0.8617 (ptm) REVERT: A 3060 PHE cc_start: 0.7569 (t80) cc_final: 0.6244 (t80) REVERT: A 3104 MET cc_start: 0.8117 (ppp) cc_final: 0.7470 (ppp) REVERT: A 3235 MET cc_start: 0.7389 (ppp) cc_final: 0.7053 (ppp) REVERT: A 3246 MET cc_start: 0.7494 (ptt) cc_final: 0.7135 (mtm) REVERT: A 3273 MET cc_start: 0.7179 (ptp) cc_final: 0.6978 (ppp) REVERT: A 3295 TRP cc_start: 0.5887 (p-90) cc_final: 0.5683 (p-90) REVERT: A 3819 MET cc_start: 0.6508 (mtt) cc_final: 0.6300 (mtm) REVERT: A 3954 MET cc_start: 0.8450 (mmm) cc_final: 0.7766 (tpp) REVERT: A 4186 MET cc_start: 0.9336 (mmm) cc_final: 0.8569 (mmm) REVERT: A 4246 PHE cc_start: 0.8512 (t80) cc_final: 0.8082 (t80) REVERT: A 4250 TYR cc_start: 0.8643 (t80) cc_final: 0.7694 (m-80) REVERT: A 4256 MET cc_start: 0.8620 (mmp) cc_final: 0.8408 (mmm) REVERT: A 4268 MET cc_start: 0.4404 (tpt) cc_final: 0.3845 (tmm) REVERT: A 4641 PRO cc_start: 0.8233 (OUTLIER) cc_final: 0.7931 (Cg_endo) REVERT: A 4654 MET cc_start: 0.8147 (tpt) cc_final: 0.7877 (tpp) REVERT: A 4707 MET cc_start: 0.8394 (ppp) cc_final: 0.8163 (ppp) REVERT: A 4748 MET cc_start: 0.7456 (mmm) cc_final: 0.7044 (tpt) REVERT: A 4804 MET cc_start: 0.9090 (mmm) cc_final: 0.8721 (mmm) REVERT: A 4884 MET cc_start: 0.8343 (tpp) cc_final: 0.7937 (tpt) REVERT: B 469 HIS cc_start: 0.8045 (m-70) cc_final: 0.7736 (m90) REVERT: B 655 MET cc_start: 0.8980 (mmm) cc_final: 0.8618 (mmp) REVERT: B 964 MET cc_start: 0.2714 (mtt) cc_final: 0.1924 (mpp) REVERT: B 995 MET cc_start: 0.8524 (mtm) cc_final: 0.8098 (mtt) REVERT: B 1165 MET cc_start: 0.8202 (mtm) cc_final: 0.7901 (mtm) REVERT: B 1215 MET cc_start: 0.8676 (mmm) cc_final: 0.7728 (mtp) REVERT: B 2142 MET cc_start: 0.8461 (mpp) cc_final: 0.7968 (mpp) REVERT: B 2162 MET cc_start: 0.8570 (mmp) cc_final: 0.8274 (mmp) REVERT: B 2192 MET cc_start: 0.8407 (tpp) cc_final: 0.8097 (tpp) REVERT: B 2214 MET cc_start: 0.8704 (OUTLIER) cc_final: 0.8295 (mmm) REVERT: B 2279 MET cc_start: 0.8895 (ttt) cc_final: 0.8247 (tmm) REVERT: B 2512 MET cc_start: 0.8897 (tpt) cc_final: 0.8450 (tmm) REVERT: B 2605 MET cc_start: 0.8941 (tmm) cc_final: 0.8644 (tmm) REVERT: B 2695 MET cc_start: 0.6648 (mmt) cc_final: 0.6289 (mmm) REVERT: B 2727 HIS cc_start: 0.8035 (m90) cc_final: 0.7575 (m90) REVERT: B 2732 TRP cc_start: 0.8009 (t-100) cc_final: 0.7774 (t-100) REVERT: B 2771 TYR cc_start: 0.8423 (m-80) cc_final: 0.8183 (m-80) REVERT: B 2782 MET cc_start: 0.8793 (OUTLIER) cc_final: 0.8496 (ppp) REVERT: B 2840 MET cc_start: 0.7674 (mmt) cc_final: 0.6665 (mmt) REVERT: B 2844 MET cc_start: 0.8654 (ptp) cc_final: 0.8051 (ptp) REVERT: B 2848 TYR cc_start: 0.7836 (m-10) cc_final: 0.7524 (m-10) REVERT: B 3060 PHE cc_start: 0.7626 (t80) cc_final: 0.6513 (t80) REVERT: B 3104 MET cc_start: 0.8036 (ppp) cc_final: 0.7574 (ppp) REVERT: B 3235 MET cc_start: 0.7609 (ppp) cc_final: 0.7054 (tpt) REVERT: B 3249 TRP cc_start: 0.8305 (m100) cc_final: 0.8000 (m100) REVERT: B 3605 MET cc_start: 0.3948 (ppp) cc_final: 0.3583 (ppp) REVERT: B 3689 MET cc_start: 0.8798 (mmp) cc_final: 0.8499 (mmp) REVERT: B 3819 MET cc_start: 0.6722 (mtp) cc_final: 0.6279 (mpp) REVERT: B 4186 MET cc_start: 0.9411 (mmp) cc_final: 0.8563 (mmt) REVERT: B 4279 MET cc_start: 0.6201 (ttm) cc_final: 0.5561 (tmm) REVERT: B 4292 MET cc_start: 0.8201 (mmm) cc_final: 0.7932 (mmm) REVERT: B 4502 MET cc_start: 0.8246 (mtm) cc_final: 0.7949 (mtm) REVERT: B 4654 MET cc_start: 0.8192 (tmm) cc_final: 0.7804 (tmm) REVERT: B 4728 MET cc_start: 0.8742 (mmm) cc_final: 0.8312 (mmm) REVERT: B 4748 MET cc_start: 0.7992 (mmm) cc_final: 0.7613 (mmm) REVERT: B 4804 MET cc_start: 0.9031 (tpp) cc_final: 0.8439 (mmm) REVERT: B 4814 MET cc_start: 0.8286 (mmm) cc_final: 0.8046 (mmm) REVERT: C 393 MET cc_start: 0.7704 (mmt) cc_final: 0.7441 (mmm) REVERT: C 895 MET cc_start: 0.9181 (ptp) cc_final: 0.8864 (ppp) REVERT: C 964 MET cc_start: 0.2870 (mtt) cc_final: 0.2420 (mpp) REVERT: C 995 MET cc_start: 0.8836 (mtm) cc_final: 0.8299 (mtt) REVERT: C 1168 MET cc_start: 0.8420 (mmm) cc_final: 0.8140 (mmp) REVERT: C 1174 MET cc_start: 0.7858 (ptp) cc_final: 0.7649 (ptt) REVERT: C 1720 MET cc_start: 0.8509 (ptm) cc_final: 0.8244 (ptt) REVERT: C 2214 MET cc_start: 0.8721 (mmm) cc_final: 0.8195 (mmm) REVERT: C 2234 MET cc_start: 0.8763 (mmm) cc_final: 0.8470 (mtp) REVERT: C 2384 MET cc_start: 0.9305 (mmm) cc_final: 0.8891 (mmm) REVERT: C 2389 MET cc_start: 0.9179 (mtp) cc_final: 0.8885 (mtp) REVERT: C 2456 MET cc_start: 0.8653 (mtm) cc_final: 0.8105 (mpp) REVERT: C 2512 MET cc_start: 0.8803 (tpt) cc_final: 0.8528 (tmm) REVERT: C 2681 MET cc_start: 0.8567 (tpp) cc_final: 0.7908 (tpp) REVERT: C 2695 MET cc_start: 0.6333 (mmm) cc_final: 0.6002 (mmt) REVERT: C 2720 PHE cc_start: 0.8606 (t80) cc_final: 0.7987 (t80) REVERT: C 2787 TRP cc_start: 0.8263 (m-90) cc_final: 0.7971 (m-90) REVERT: C 2840 MET cc_start: 0.7872 (mmt) cc_final: 0.7490 (mmt) REVERT: C 2843 MET cc_start: 0.7305 (tpp) cc_final: 0.6575 (tpp) REVERT: C 2895 PHE cc_start: 0.8067 (t80) cc_final: 0.7554 (t80) REVERT: C 3003 MET cc_start: 0.9190 (ptt) cc_final: 0.8868 (ttp) REVERT: C 3104 MET cc_start: 0.8253 (ppp) cc_final: 0.7568 (ppp) REVERT: C 3235 MET cc_start: 0.7517 (ppp) cc_final: 0.7161 (tpt) REVERT: C 3246 MET cc_start: 0.7454 (ptt) cc_final: 0.7101 (ptp) REVERT: C 3273 MET cc_start: 0.6857 (ptt) cc_final: 0.6541 (ppp) REVERT: C 3277 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8758 (pp) REVERT: C 3295 TRP cc_start: 0.7493 (p-90) cc_final: 0.7093 (p-90) REVERT: C 3819 MET cc_start: 0.6299 (mtp) cc_final: 0.5439 (mtp) REVERT: C 4279 MET cc_start: 0.6599 (mtt) cc_final: 0.6358 (tpp) REVERT: C 4626 ILE cc_start: 0.9164 (OUTLIER) cc_final: 0.8924 (tp) REVERT: C 4641 PRO cc_start: 0.8196 (OUTLIER) cc_final: 0.7915 (Cg_endo) REVERT: C 4654 MET cc_start: 0.8229 (tpp) cc_final: 0.7924 (tpp) REVERT: D 895 MET cc_start: 0.9288 (ptp) cc_final: 0.8924 (ppp) REVERT: D 995 MET cc_start: 0.8838 (mtm) cc_final: 0.8454 (mtt) REVERT: D 1174 MET cc_start: 0.7827 (ptp) cc_final: 0.7583 (ptt) REVERT: D 1215 MET cc_start: 0.8382 (mtp) cc_final: 0.8032 (mtp) REVERT: D 1300 MET cc_start: 0.8646 (mmm) cc_final: 0.8255 (mmp) REVERT: D 1842 ILE cc_start: 0.9021 (OUTLIER) cc_final: 0.8769 (pt) REVERT: D 2162 MET cc_start: 0.8699 (mmp) cc_final: 0.8338 (mmp) REVERT: D 2279 MET cc_start: 0.8981 (ttt) cc_final: 0.8542 (tmm) REVERT: D 2456 MET cc_start: 0.8800 (pmm) cc_final: 0.8455 (mpp) REVERT: D 2468 MET cc_start: 0.8974 (mmm) cc_final: 0.8703 (mmp) REVERT: D 2512 MET cc_start: 0.8966 (tpt) cc_final: 0.8470 (tmm) REVERT: D 2585 MET cc_start: 0.8802 (OUTLIER) cc_final: 0.8590 (ppp) REVERT: D 2605 MET cc_start: 0.9035 (ttp) cc_final: 0.8589 (tmm) REVERT: D 2688 MET cc_start: 0.5375 (mtt) cc_final: 0.4340 (pmm) REVERT: D 2720 PHE cc_start: 0.8827 (t80) cc_final: 0.8505 (t80) REVERT: D 2724 TYR cc_start: 0.8229 (t80) cc_final: 0.8017 (t80) REVERT: D 2844 MET cc_start: 0.8722 (ptp) cc_final: 0.8176 (ppp) REVERT: D 2848 TYR cc_start: 0.8815 (t80) cc_final: 0.8535 (t80) REVERT: D 2901 TYR cc_start: 0.7298 (m-80) cc_final: 0.6893 (m-80) REVERT: D 3060 PHE cc_start: 0.7917 (t80) cc_final: 0.7485 (t80) REVERT: D 3104 MET cc_start: 0.8200 (ppp) cc_final: 0.7703 (ppp) REVERT: D 3215 MET cc_start: 0.8950 (mtt) cc_final: 0.8698 (ptp) REVERT: D 3246 MET cc_start: 0.5471 (mtm) cc_final: 0.4839 (mmm) REVERT: D 3819 MET cc_start: 0.6636 (mtt) cc_final: 0.6323 (mpp) REVERT: D 4002 MET cc_start: 0.8494 (tmm) cc_final: 0.8056 (tmm) REVERT: D 4641 PRO cc_start: 0.8460 (OUTLIER) cc_final: 0.8163 (Cg_endo) REVERT: D 4654 MET cc_start: 0.8450 (tmm) cc_final: 0.8102 (tmm) REVERT: D 4748 MET cc_start: 0.7721 (mmm) cc_final: 0.7241 (tpt) REVERT: D 4884 MET cc_start: 0.8472 (tpp) cc_final: 0.8152 (tpt) outliers start: 79 outliers final: 58 residues processed: 768 average time/residue: 1.1688 time to fit residues: 1612.6293 Evaluate side-chains 788 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 719 time to evaluate : 11.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain G residue 30 MET Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain A residue 29 HIS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 949 HIS Chi-restraints excluded: chain A residue 1165 MET Chi-restraints excluded: chain A residue 1215 MET Chi-restraints excluded: chain A residue 1487 MET Chi-restraints excluded: chain A residue 1552 VAL Chi-restraints excluded: chain A residue 1599 MET Chi-restraints excluded: chain A residue 1608 VAL Chi-restraints excluded: chain A residue 1619 VAL Chi-restraints excluded: chain A residue 1727 VAL Chi-restraints excluded: chain A residue 1842 ILE Chi-restraints excluded: chain A residue 2142 MET Chi-restraints excluded: chain A residue 2162 MET Chi-restraints excluded: chain A residue 2585 MET Chi-restraints excluded: chain A residue 3117 PHE Chi-restraints excluded: chain A residue 3942 ASP Chi-restraints excluded: chain A residue 4587 ILE Chi-restraints excluded: chain A residue 4626 ILE Chi-restraints excluded: chain A residue 4641 PRO Chi-restraints excluded: chain B residue 29 HIS Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 1608 VAL Chi-restraints excluded: chain B residue 1727 VAL Chi-restraints excluded: chain B residue 1896 MET Chi-restraints excluded: chain B residue 2214 MET Chi-restraints excluded: chain B residue 2585 MET Chi-restraints excluded: chain B residue 2782 MET Chi-restraints excluded: chain B residue 3115 HIS Chi-restraints excluded: chain B residue 3283 ILE Chi-restraints excluded: chain B residue 3739 MET Chi-restraints excluded: chain B residue 3942 ASP Chi-restraints excluded: chain B residue 4256 MET Chi-restraints excluded: chain B residue 4294 LEU Chi-restraints excluded: chain B residue 4626 ILE Chi-restraints excluded: chain C residue 29 HIS Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 938 GLU Chi-restraints excluded: chain C residue 1215 MET Chi-restraints excluded: chain C residue 1727 VAL Chi-restraints excluded: chain C residue 2585 MET Chi-restraints excluded: chain C residue 2858 MET Chi-restraints excluded: chain C residue 3115 HIS Chi-restraints excluded: chain C residue 3215 MET Chi-restraints excluded: chain C residue 3277 LEU Chi-restraints excluded: chain C residue 3942 ASP Chi-restraints excluded: chain C residue 3954 MET Chi-restraints excluded: chain C residue 4587 ILE Chi-restraints excluded: chain C residue 4626 ILE Chi-restraints excluded: chain C residue 4641 PRO Chi-restraints excluded: chain D residue 29 HIS Chi-restraints excluded: chain D residue 778 MET Chi-restraints excluded: chain D residue 949 HIS Chi-restraints excluded: chain D residue 1251 LEU Chi-restraints excluded: chain D residue 1727 VAL Chi-restraints excluded: chain D residue 1842 ILE Chi-restraints excluded: chain D residue 2585 MET Chi-restraints excluded: chain D residue 2858 MET Chi-restraints excluded: chain D residue 3115 HIS Chi-restraints excluded: chain D residue 3245 TYR Chi-restraints excluded: chain D residue 3318 HIS Chi-restraints excluded: chain D residue 3942 ASP Chi-restraints excluded: chain D residue 4587 ILE Chi-restraints excluded: chain D residue 4626 ILE Chi-restraints excluded: chain D residue 4641 PRO Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1088 optimal weight: 3.9990 chunk 1460 optimal weight: 5.9990 chunk 419 optimal weight: 10.0000 chunk 1264 optimal weight: 8.9990 chunk 202 optimal weight: 8.9990 chunk 380 optimal weight: 0.9990 chunk 1373 optimal weight: 0.0470 chunk 574 optimal weight: 20.0000 chunk 1409 optimal weight: 40.0000 chunk 173 optimal weight: 5.9990 chunk 252 optimal weight: 2.9990 overall best weight: 2.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2899 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2899 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2899 ASN ** C4629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.039496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.029582 restraints weight = 2088803.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.030915 restraints weight = 867986.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.031099 restraints weight = 454491.947| |-----------------------------------------------------------------------------| r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3010 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3010 r_free = 0.3010 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3010 r_free = 0.3010 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3010 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.930 141676 Z= 0.664 Angle : 0.678 59.199 191424 Z= 0.370 Chirality : 0.040 0.496 20988 Planarity : 0.005 0.227 24592 Dihedral : 5.118 85.887 19036 Min Nonbonded Distance : 1.285 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.14 % Favored : 96.79 % Rotamer: Outliers : 0.45 % Allowed : 8.11 % Favored : 91.44 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.62 % 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: 1.16 (0.07), residues: 17212 helix: 1.87 (0.06), residues: 9044 sheet: -0.21 (0.12), residues: 1640 loop : -0.49 (0.08), residues: 6528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.148 0.002 TRP A3295 HIS 0.196 0.001 HIS G 26 PHE 0.075 0.001 PHE B3170 TYR 0.038 0.001 TYR A 931 ARG 0.061 0.000 ARG D3043 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 29053.03 seconds wall clock time: 513 minutes 34.00 seconds (30814.00 seconds total)