Starting phenix.real_space_refine on Mon Mar 18 18:03:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u9x_26409/03_2024/7u9x_26409_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u9x_26409/03_2024/7u9x_26409.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u9x_26409/03_2024/7u9x_26409.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u9x_26409/03_2024/7u9x_26409.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u9x_26409/03_2024/7u9x_26409_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u9x_26409/03_2024/7u9x_26409_updated.pdb" } resolution = 2.58 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= 0.011 sd= 0.036 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: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 24 5.49 5 S 936 5.16 5 C 88196 2.51 5 N 23584 2.21 5 O 25844 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 311": "OD1" <-> "OD2" Residue "A ASP 680": "OD1" <-> "OD2" Residue "A TYR 703": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 706": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1131": "OD1" <-> "OD2" Residue "A GLU 1150": "OE1" <-> "OE2" Residue "A GLU 1170": "OE1" <-> "OE2" Residue "A TYR 1302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1471": "OD1" <-> "OD2" Residue "A PHE 1603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1623": "OD1" <-> "OD2" Residue "A PHE 2199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2743": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2821": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 3119": "OE1" <-> "OE2" Residue "A TYR 3138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 3172": "OE1" <-> "OE2" Residue "A TYR 3228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 3291": "OD1" <-> "OD2" Residue "A PHE 3686": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 3822": "OE1" <-> "OE2" Residue "A PHE 4020": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 4080": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 4846": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 311": "OD1" <-> "OD2" Residue "B ASP 680": "OD1" <-> "OD2" Residue "B TYR 703": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 706": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1131": "OD1" <-> "OD2" Residue "B GLU 1150": "OE1" <-> "OE2" Residue "B GLU 1170": "OE1" <-> "OE2" Residue "B TYR 1302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1471": "OD1" <-> "OD2" Residue "B PHE 1603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1623": "OD1" <-> "OD2" Residue "B PHE 2199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 2743": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 2821": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 3119": "OE1" <-> "OE2" Residue "B TYR 3138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 3172": "OE1" <-> "OE2" Residue "B TYR 3228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 3291": "OD1" <-> "OD2" Residue "B PHE 3686": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 3822": "OE1" <-> "OE2" Residue "B PHE 4020": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 4080": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 4846": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 311": "OD1" <-> "OD2" Residue "C ASP 680": "OD1" <-> "OD2" Residue "C TYR 703": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 706": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1131": "OD1" <-> "OD2" Residue "C GLU 1150": "OE1" <-> "OE2" Residue "C GLU 1170": "OE1" <-> "OE2" Residue "C TYR 1302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1471": "OD1" <-> "OD2" Residue "C PHE 1603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1623": "OD1" <-> "OD2" Residue "C PHE 2199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 2743": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 2821": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 3119": "OE1" <-> "OE2" Residue "C TYR 3138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 3172": "OE1" <-> "OE2" Residue "C TYR 3228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 3291": "OD1" <-> "OD2" Residue "C PHE 3686": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 3822": "OE1" <-> "OE2" Residue "C PHE 4020": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 4080": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 4846": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 311": "OD1" <-> "OD2" Residue "D ASP 680": "OD1" <-> "OD2" Residue "D TYR 703": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 706": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1131": "OD1" <-> "OD2" Residue "D GLU 1150": "OE1" <-> "OE2" Residue "D GLU 1170": "OE1" <-> "OE2" Residue "D TYR 1302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1471": "OD1" <-> "OD2" Residue "D PHE 1603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1623": "OD1" <-> "OD2" Residue "D PHE 2199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 2630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 2743": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 2821": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 3119": "OE1" <-> "OE2" Residue "D TYR 3138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 3172": "OE1" <-> "OE2" Residue "D TYR 3228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 3291": "OD1" <-> "OD2" Residue "D PHE 3686": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 3822": "OE1" <-> "OE2" Residue "D PHE 4020": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 4080": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 4846": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.37s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 138588 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 33766 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4224, 33758 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, 33758 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: 34480 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: "B" Number of atoms: 33766 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4224, 33758 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, 33758 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: 34480 Chain: "C" Number of atoms: 33766 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4224, 33758 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, 33758 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: 34480 Chain: "D" Number of atoms: 33766 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4224, 33758 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, 33758 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: 34480 Chain: "A" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' ZN': 1, 'ATP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' ZN': 1, 'ATP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' ZN': 1, 'ATP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' ZN': 1, 'ATP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 33087 SG CYS A4888 168.327 193.461 121.892 1.00 67.30 S ATOM 33112 SG CYS A4891 168.826 190.862 119.088 1.00 66.59 S ATOM 70125 SG CYS B4888 193.467 198.002 121.885 1.00 67.51 S ATOM 70150 SG CYS B4891 190.869 197.503 119.081 1.00 66.78 S ATOM A0303 SG CYS C4888 198.026 172.884 121.884 1.00 67.35 S ATOM A030S SG CYS C4891 197.528 175.482 119.080 1.00 66.53 S ATOM A0T21 SG CYS D4888 172.860 168.336 121.884 1.00 67.27 S ATOM A0T2Q SG CYS D4891 175.458 168.834 119.080 1.00 66.57 S Time building chain proxies: 93.34, per 1000 atoms: 0.67 Number of scatterers: 138588 At special positions: 0 Unit cell: (367.744, 367.744, 209.664, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 936 16.00 P 24 15.00 O 25844 8.00 N 23584 7.00 C 88196 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A4806 " - pdb=" SG CYS A4812 " distance=2.03 Simple disulfide: pdb=" SG CYS B4806 " - pdb=" SG CYS B4812 " distance=2.03 Simple disulfide: pdb=" SG CYS C4806 " - pdb=" SG CYS C4812 " 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: 40.01 Conformation dependent library (CDL) restraints added in 33.1 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: 680 helices and 80 sheets defined 58.6% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 40.93 Creating SS restraints... Processing helix chain 'A' and resid 61 through 66 removed outlier: 3.772A 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 253 through 259 removed outlier: 4.663A pdb=" N THR A 259 " --> pdb=" O GLU A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 271 removed outlier: 5.091A pdb=" N ALA A 271 " --> pdb=" O VAL A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 439 Processing helix chain 'A' and resid 441 through 446 removed outlier: 5.083A 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: 3.616A pdb=" N VAL A 507 " --> pdb=" O ASP A 503 " (cutoff:3.500A) removed outlier: 5.093A 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: 4.707A pdb=" N LYS A 527 " --> pdb=" O GLY A 523 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N SER A 528 " --> pdb=" O GLU A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 556 removed outlier: 4.701A pdb=" N GLY A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N SER A 554 " --> pdb=" O GLN A 550 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ASP A 556 " --> pdb=" O SER A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 563 removed outlier: 4.414A pdb=" N ARG A 561 " --> pdb=" O TRP A 557 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LEU A 562 " --> pdb=" O LEU A 558 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N GLU A 563 " --> pdb=" O ILE A 559 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 557 through 563' Processing helix chain 'A' and resid 567 through 582 Processing helix chain 'A' and resid 583 through 589 removed outlier: 3.673A pdb=" N ILE A 588 " --> pdb=" O GLU A 584 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE A 589 " --> pdb=" O ALA A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 604 Processing helix chain 'A' and resid 607 through 620 removed outlier: 3.718A pdb=" N LEU A 611 " --> pdb=" O ASN A 607 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N CYS A 620 " --> pdb=" O SER A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 640 Proline residue: A 638 - end of helix Processing helix chain 'A' and resid 821 through 826 removed outlier: 4.664A pdb=" N ALA A 825 " --> pdb=" O PRO A 821 " (cutoff:3.500A) removed outlier: 4.844A 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 857 through 862 removed outlier: 4.556A pdb=" N ALA A 861 " --> pdb=" O LEU A 857 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N PHE A 862 " --> pdb=" O THR A 858 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 857 through 862' Processing helix chain 'A' and resid 875 through 901 removed outlier: 3.693A pdb=" N LYS A 884 " --> pdb=" O ARG A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 946 Processing helix chain 'A' and resid 954 through 961 removed outlier: 3.989A 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: 3.641A pdb=" N LEU A1057 " --> pdb=" O ALA A1053 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLY A1061 " --> pdb=" O LEU A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1230 through 1235 removed outlier: 7.021A pdb=" N GLU A1234 " --> pdb=" O CYS A1230 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY A1235 " --> pdb=" O GLY A1231 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1230 through 1235' Processing helix chain 'A' and resid 1416 through 1423 Processing helix chain 'A' and resid 1437 through 1442 removed outlier: 3.822A pdb=" N VAL A1441 " --> pdb=" O GLU A1437 " (cutoff:3.500A) removed outlier: 5.152A 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: 4.066A pdb=" N SER A1495 " --> pdb=" O GLY A1491 " (cutoff:3.500A) Processing helix chain 'A' and resid 1565 through 1571 removed outlier: 3.790A pdb=" N GLY A1569 " --> pdb=" O PRO A1565 " (cutoff:3.500A) Processing helix chain 'A' and resid 1640 through 1647 removed outlier: 4.368A pdb=" N LEU A1644 " --> pdb=" O ASP A1640 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N THR A1645 " --> pdb=" O ILE A1641 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N GLU A1646 " --> pdb=" O LEU A1642 " (cutoff:3.500A) Processing helix chain 'A' and resid 1648 through 1666 Processing helix chain 'A' and resid 1669 through 1680 removed outlier: 3.821A pdb=" N SER A1678 " --> pdb=" O HIS A1674 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N HIS A1679 " --> pdb=" O ALA A1675 " (cutoff:3.500A) Processing helix chain 'A' and resid 1681 through 1691 Processing helix chain 'A' and resid 1695 through 1710 Processing helix chain 'A' and resid 1711 through 1723 removed outlier: 4.597A pdb=" N ASN A1723 " --> pdb=" O LEU A1719 " (cutoff:3.500A) Processing helix chain 'A' and resid 1730 through 1736 removed outlier: 3.633A pdb=" N ILE A1736 " --> pdb=" O GLU A1732 " (cutoff:3.500A) Processing helix chain 'A' and resid 1773 through 1778 removed outlier: 4.410A pdb=" N GLN A1777 " --> pdb=" O ASN A1773 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N TYR A1778 " --> pdb=" O GLU A1774 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1773 through 1778' Processing helix chain 'A' and resid 1783 through 1802 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: 3.981A pdb=" N MET A1896 " --> pdb=" O GLY A1892 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N LYS A1897 " --> pdb=" O LEU A1893 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1892 through 1897' Processing helix chain 'A' and resid 1899 through 1948 removed outlier: 3.973A pdb=" N ASP A1931 " --> pdb=" O ALA A1927 " (cutoff:3.500A) Processing helix chain 'A' and resid 1950 through 1955 Processing helix chain 'A' and resid 1956 through 1967 removed outlier: 5.056A pdb=" N ARG A1960 " --> pdb=" O ALA A1956 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N GLU A1964 " --> pdb=" O ARG A1960 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N PHE A1965 " --> pdb=" O LYS A1961 " (cutoff:3.500A) Processing helix chain 'A' and resid 1968 through 1979 removed outlier: 3.772A pdb=" N ASN A1978 " --> pdb=" O ASN A1974 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N PHE A1979 " --> pdb=" O MET A1975 " (cutoff:3.500A) Processing helix chain 'A' and resid 1989 through 2008 removed outlier: 3.947A pdb=" N GLN A1995 " --> pdb=" O GLU A1991 " (cutoff:3.500A) Processing helix chain 'A' and resid 2057 through 2073 Processing helix chain 'A' and resid 2077 through 2094 removed outlier: 3.541A 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: 3.884A pdb=" N VAL A2113 " --> pdb=" O ASN A2109 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N GLU A2114 " --> pdb=" O GLY A2110 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ASP A2115 " --> pdb=" O VAL A2111 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N SER A2131 " --> pdb=" O ARG A2127 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N VAL A2132 " --> pdb=" O SER A2128 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N ARG A2133 " --> pdb=" O LEU A2129 " (cutoff:3.500A) Processing helix chain 'A' and resid 2135 through 2152 Processing helix chain 'A' and resid 2153 through 2158 Processing helix chain 'A' and resid 2159 through 2166 Processing helix chain 'A' and resid 2167 through 2183 removed outlier: 4.915A pdb=" N GLY A2182 " --> pdb=" O VAL A2178 " (cutoff:3.500A) Processing helix chain 'A' and resid 2189 through 2208 removed outlier: 3.592A pdb=" N VAL A2193 " --> pdb=" O PHE A2189 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N SER A2207 " --> pdb=" O PHE A2203 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N ARG A2208 " --> pdb=" O CYS A2204 " (cutoff:3.500A) Processing helix chain 'A' and resid 2209 through 2219 removed outlier: 3.637A pdb=" N ASP A2216 " --> pdb=" O LYS A2212 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N HIS A2217 " --> pdb=" O ALA A2213 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LEU A2218 " --> pdb=" O MET A2214 " (cutoff:3.500A) removed outlier: 5.429A 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: 3.608A pdb=" N LEU A2262 " --> pdb=" O ARG A2258 " (cutoff:3.500A) Processing helix chain 'A' and resid 2277 through 2284 Processing helix chain 'A' and resid 2291 through 2307 removed outlier: 3.628A pdb=" N ARG A2297 " --> pdb=" O VAL A2293 " (cutoff:3.500A) Processing helix chain 'A' and resid 2313 through 2328 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 2383 through 2403 Processing helix chain 'A' and resid 2405 through 2412 Processing helix chain 'A' and resid 2413 through 2428 Proline residue: A2428 - end of helix Processing helix chain 'A' and resid 2429 through 2438 Processing helix chain 'A' and resid 2455 through 2460 removed outlier: 3.811A pdb=" N GLY A2459 " --> pdb=" O ASP A2455 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N PHE A2460 " --> pdb=" O MET A2456 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2455 through 2460' Processing helix chain 'A' and resid 2461 through 2475 removed outlier: 3.972A pdb=" N LYS A2465 " --> pdb=" O CYS A2461 " (cutoff:3.500A) Processing helix chain 'A' and resid 2480 through 2491 Processing helix chain 'A' and resid 2492 through 2503 removed outlier: 3.870A pdb=" N ASP A2503 " --> pdb=" O ALA A2499 " (cutoff:3.500A) Processing helix chain 'A' and resid 2504 through 2510 removed outlier: 4.650A pdb=" N ALA A2509 " --> pdb=" O ALA A2505 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N THR A2510 " --> pdb=" O ALA A2506 " (cutoff:3.500A) Processing helix chain 'A' and resid 2511 through 2532 removed outlier: 5.394A 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 2558 removed outlier: 4.884A pdb=" N GLY A2558 " --> pdb=" O ARG A2554 " (cutoff:3.500A) Processing helix chain 'A' and resid 2562 through 2580 removed outlier: 3.576A pdb=" N GLN A2579 " --> pdb=" O SER A2575 " (cutoff:3.500A) Processing helix chain 'A' and resid 2581 through 2596 removed outlier: 3.992A pdb=" N MET A2585 " --> pdb=" O ARG A2581 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N GLN A2586 " --> pdb=" O PRO A2582 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N HIS A2587 " --> pdb=" O SER A2583 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N LEU A2588 " --> pdb=" O MET A2584 " (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: 6.226A 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 2714 through 2740 removed outlier: 4.090A pdb=" N GLU A2718 " --> pdb=" O PRO A2714 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N TYR A2719 " --> pdb=" O GLU A2715 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N PHE A2720 " --> pdb=" O LYS A2716 " (cutoff:3.500A) Processing helix chain 'A' and resid 2759 through 2764 removed outlier: 5.049A pdb=" N SER A2764 " --> pdb=" O TYR A2760 " (cutoff:3.500A) Processing helix chain 'A' and resid 2768 through 2784 Proline residue: A2774 - end of helix Processing helix chain 'A' and resid 2792 through 2802 removed outlier: 4.032A 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: 5.271A pdb=" N THR A2878 " --> pdb=" O TYR A2874 " (cutoff:3.500A) Processing helix chain 'A' and resid 2879 through 2900 removed outlier: 4.656A pdb=" N LYS A2884 " --> pdb=" O LYS A2880 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ASP A2885 " --> pdb=" O GLU A2881 " (cutoff:3.500A) Processing helix chain 'A' and resid 2916 through 2947 removed outlier: 4.453A pdb=" N ARG A2920 " --> pdb=" O SER A2916 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N PHE A2921 " --> pdb=" O ILE A2917 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ALA A2922 " --> pdb=" O GLU A2918 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N TYR A2923 " --> pdb=" O LYS A2919 " (cutoff:3.500A) Processing helix chain 'A' and resid 2956 through 2979 removed outlier: 4.662A pdb=" N LEU A2968 " --> pdb=" O ALA A2964 " (cutoff:3.500A) Proline residue: A2969 - end of helix removed outlier: 3.756A pdb=" N ARG A2979 " --> pdb=" O PHE A2975 " (cutoff:3.500A) Processing helix chain 'A' and resid 2997 through 3016 Processing helix chain 'A' and resid 3018 through 3023 Processing helix chain 'A' and resid 3024 through 3040 removed outlier: 4.231A pdb=" N SER A3028 " --> pdb=" O ASN A3024 " (cutoff:3.500A) Processing helix chain 'A' and resid 3041 through 3048 Processing helix chain 'A' and resid 3050 through 3078 Processing helix chain 'A' and resid 3088 through 3116 removed outlier: 5.001A 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 3122 Processing helix chain 'A' and resid 3124 through 3143 Processing helix chain 'A' and resid 3145 through 3152 removed outlier: 4.013A pdb=" N ARG A3150 " --> pdb=" O ILE A3146 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLN A3151 " --> pdb=" O TYR A3147 " (cutoff:3.500A) Processing helix chain 'A' and resid 3153 through 3166 Processing helix chain 'A' and resid 3172 through 3177 removed outlier: 4.147A pdb=" N ASP A3176 " --> pdb=" O GLU A3172 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N LYS A3177 " --> pdb=" O THR A3173 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3172 through 3177' Processing helix chain 'A' and resid 3182 through 3187 Processing helix chain 'A' and resid 3188 through 3196 removed outlier: 4.422A pdb=" N SER A3196 " --> pdb=" O ARG A3192 " (cutoff:3.500A) Processing helix chain 'A' and resid 3200 through 3206 removed outlier: 4.876A 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 removed outlier: 4.337A pdb=" N ALA A3222 " --> pdb=" O ILE A3218 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLU A3223 " --> pdb=" O VAL A3219 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N GLY A3225 " --> pdb=" O LEU A3221 " (cutoff:3.500A) Processing helix chain 'A' and resid 3227 through 3232 removed outlier: 3.765A pdb=" N MET A3231 " --> pdb=" O ARG A3227 " (cutoff:3.500A) Proline residue: A3232 - end of helix No H-bonds generated for 'chain 'A' and resid 3227 through 3232' Processing helix chain 'A' and resid 3233 through 3250 removed outlier: 5.615A pdb=" N LEU A3239 " --> pdb=" O MET A3235 " (cutoff:3.500A) Proline residue: A3240 - end of helix 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: 4.679A pdb=" N GLY A3289 " --> pdb=" O TYR A3285 " (cutoff:3.500A) Processing helix chain 'A' and resid 3294 through 3307 Proline residue: A3305 - end of helix Processing helix chain 'A' and resid 3313 through 3327 removed outlier: 5.017A pdb=" N THR A3317 " --> pdb=" O GLN A3313 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LEU A3320 " --> pdb=" O LYS A3316 " (cutoff:3.500A) Proline residue: A3321 - end of helix removed outlier: 3.880A pdb=" N LYS A3327 " --> pdb=" O MET A3323 " (cutoff:3.500A) Processing helix chain 'A' and resid 3599 through 3605 Processing helix chain 'A' and resid 3612 through 3632 removed outlier: 3.770A pdb=" N ILE A3629 " --> pdb=" O GLU A3625 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N GLU A3630 " --> pdb=" O LYS A3626 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N THR A3631 " --> pdb=" O SER A3627 " (cutoff:3.500A) Processing helix chain 'A' and resid 3636 through 3647 removed outlier: 3.517A pdb=" N LYS A3646 " --> pdb=" O GLU A3642 " (cutoff:3.500A) Proline residue: A3647 - end of helix Processing helix chain 'A' and resid 3649 through 3654 Processing helix chain 'A' and resid 3662 through 3677 Processing helix chain 'A' and resid 3685 through 3701 removed outlier: 3.561A pdb=" N CYS A3699 " --> pdb=" O MET A3695 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N HIS A3700 " --> pdb=" O ALA A3696 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASP A3701 " --> pdb=" O LYS A3697 " (cutoff:3.500A) Processing helix chain 'A' and resid 3713 through 3733 removed outlier: 3.745A pdb=" N LEU A3731 " --> pdb=" O GLN A3727 " (cutoff:3.500A) Processing helix chain 'A' and resid 3735 through 3748 removed outlier: 3.882A 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: 3.997A 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: 3.592A pdb=" N CYS A3847 " --> pdb=" O LEU A3843 " (cutoff:3.500A) Processing helix chain 'A' and resid 3851 through 3860 removed outlier: 4.583A pdb=" N ARG A3859 " --> pdb=" O GLN A3855 " (cutoff:3.500A) Processing helix chain 'A' and resid 3869 through 3894 removed outlier: 4.716A 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 3938 Processing helix chain 'A' and resid 3939 through 3962 removed outlier: 3.684A pdb=" N ALA A3943 " --> pdb=" O ARG A3939 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N MET A3956 " --> pdb=" O ALA A3952 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLN A3960 " --> pdb=" O MET A3956 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ASP A3961 " --> pdb=" O LYS A3957 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N SER A3962 " --> pdb=" O LEU A3958 " (cutoff:3.500A) Processing helix chain 'A' and resid 3964 through 3987 Processing helix chain 'A' and resid 3993 through 4007 Processing helix chain 'A' and resid 4008 through 4029 removed outlier: 4.163A pdb=" N LYS A4024 " --> pdb=" O PHE A4020 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASP A4025 " --> pdb=" O LEU A4021 " (cutoff:3.500A) Processing helix chain 'A' and resid 4030 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 4070 Processing helix chain 'A' and resid 4079 through 4110 removed outlier: 4.533A pdb=" N GLU A4089 " --> pdb=" O LYS A4085 " (cutoff:3.500A) Proline residue: A4090 - end of helix removed outlier: 3.677A pdb=" N ASN A4097 " --> pdb=" O ASP A4093 " (cutoff:3.500A) Proline residue: A4110 - end of helix Processing helix chain 'A' and resid 4112 through 4123 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 4184 through 4208 removed outlier: 4.907A pdb=" N GLU A4208 " --> pdb=" O ALA A4204 " (cutoff:3.500A) Processing helix chain 'A' and resid 4237 through 4272 removed outlier: 4.240A pdb=" N LEU A4261 " --> pdb=" O ARG A4257 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N LYS A4262 " --> pdb=" O MET A4258 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N SER A4263 " --> pdb=" O LEU A4259 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LEU A4264 " --> pdb=" O SER A4260 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LYS A4265 " --> pdb=" O LEU A4261 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LYS A4266 " --> pdb=" O LYS A4262 " (cutoff:3.500A) Processing helix chain 'A' and resid 4275 through 4310 removed outlier: 3.841A pdb=" N TYR A4287 " --> pdb=" O PHE A4283 " (cutoff:3.500A) Processing helix chain 'A' and resid 4480 through 4499 Processing helix chain 'A' and resid 4500 through 4520 removed outlier: 4.280A pdb=" N PHE A4519 " --> pdb=" O PHE A4515 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N TYR A4520 " --> pdb=" O ILE A4516 " (cutoff:3.500A) Processing helix chain 'A' and resid 4568 through 4612 removed outlier: 4.078A 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: 4.037A pdb=" N ARG A4632 " --> pdb=" O GLY A4628 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N LEU A4633 " --> pdb=" O GLN A4629 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N VAL A4634 " --> pdb=" O TRP A4630 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE A4635 " --> pdb=" O ASP A4631 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ASN A4636 " --> pdb=" O ARG A4632 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N THR A4637 " --> pdb=" O LEU A4633 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N GLN A4638 " --> pdb=" O VAL A4634 " (cutoff:3.500A) Processing helix chain 'A' and resid 4648 through 4657 Processing helix chain 'A' and resid 4662 through 4671 removed outlier: 3.769A pdb=" N SER A4667 " --> pdb=" O ARG A4663 " (cutoff:3.500A) Processing helix chain 'A' and resid 4675 through 4683 Processing helix chain 'A' and resid 4693 through 4702 removed outlier: 5.720A pdb=" N ASP A4702 " --> pdb=" O LEU A4698 " (cutoff:3.500A) Processing helix chain 'A' and resid 4703 through 4716 Processing helix chain 'A' and resid 4717 through 4735 removed outlier: 3.883A pdb=" N HIS A4733 " --> pdb=" O SER A4729 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N TYR A4734 " --> pdb=" O VAL A4730 " (cutoff:3.500A) Processing helix chain 'A' and resid 4736 through 4750 removed outlier: 4.635A pdb=" N ALA A4740 " --> pdb=" O ASN A4736 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ALA A4741 " --> pdb=" O PHE A4737 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N HIS A4742 " --> pdb=" O PHE A4738 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LEU A4743 " --> pdb=" O PHE A4739 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LEU A4744 " --> pdb=" O ALA A4740 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ASP A4745 " --> pdb=" O ALA A4741 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N ILE A4746 " --> pdb=" O HIS A4742 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N ALA A4747 " --> pdb=" O LEU A4743 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N MET A4748 " --> pdb=" O LEU A4744 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE A4750 " --> pdb=" O ILE A4746 " (cutoff:3.500A) Processing helix chain 'A' and resid 4751 through 4762 removed outlier: 3.760A pdb=" N SER A4759 " --> pdb=" O THR A4755 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL A4760 " --> pdb=" O ILE A4756 " (cutoff:3.500A) Processing helix chain 'A' and resid 4763 through 4788 Processing helix chain 'A' and resid 4789 through 4794 removed outlier: 4.238A pdb=" N TYR A4793 " --> pdb=" O PHE A4789 " (cutoff:3.500A) removed outlier: 4.835A 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: 4.269A pdb=" N VAL A4821 " --> pdb=" O MET A4817 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ARG A4822 " --> pdb=" O TYR A4818 " (cutoff:3.500A) Processing helix chain 'A' and resid 4826 through 4832 removed outlier: 4.511A pdb=" N GLU A4830 " --> pdb=" O GLY A4826 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE A4831 " --> pdb=" O ILE A4827 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N GLU A4832 " --> pdb=" O GLY A4828 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4826 through 4832' 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 4900 removed outlier: 3.891A pdb=" N PHE A4898 " --> pdb=" O GLY A4894 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N THR A4900 " --> pdb=" O ASP A4896 " (cutoff:3.500A) Processing helix chain 'A' and resid 4903 through 4911 Processing helix chain 'A' and resid 4914 through 4928 Processing helix chain 'A' and resid 4934 through 4947 Processing helix chain 'A' and resid 4957 through 4963 Processing helix chain 'A' and resid 4614 through 4619 Processing helix chain 'B' and resid 61 through 66 removed outlier: 3.772A 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 253 through 259 removed outlier: 4.663A pdb=" N THR B 259 " --> pdb=" O GLU B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 271 removed outlier: 5.091A pdb=" N ALA B 271 " --> pdb=" O VAL B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 439 Processing helix chain 'B' and resid 441 through 446 removed outlier: 5.082A 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: 3.616A pdb=" N VAL B 507 " --> pdb=" O ASP B 503 " (cutoff:3.500A) removed outlier: 5.093A 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: 4.707A pdb=" N LYS B 527 " --> pdb=" O GLY B 523 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N SER B 528 " --> pdb=" O GLU B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 556 removed outlier: 4.701A pdb=" N GLY B 553 " --> pdb=" O ALA B 549 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N SER B 554 " --> pdb=" O GLN B 550 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ASP B 556 " --> pdb=" O SER B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 563 removed outlier: 4.415A pdb=" N ARG B 561 " --> pdb=" O TRP B 557 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LEU B 562 " --> pdb=" O LEU B 558 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N GLU B 563 " --> pdb=" O ILE B 559 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 557 through 563' Processing helix chain 'B' and resid 567 through 582 Processing helix chain 'B' and resid 583 through 589 removed outlier: 3.673A pdb=" N ILE B 588 " --> pdb=" O GLU B 584 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE B 589 " --> pdb=" O ALA B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 604 Processing helix chain 'B' and resid 607 through 620 removed outlier: 3.718A pdb=" N LEU B 611 " --> pdb=" O ASN B 607 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N CYS B 620 " --> pdb=" O SER B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 640 Proline residue: B 638 - end of helix Processing helix chain 'B' and resid 821 through 826 removed outlier: 4.664A pdb=" N ALA B 825 " --> pdb=" O PRO B 821 " (cutoff:3.500A) removed outlier: 4.844A 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 857 through 862 removed outlier: 4.557A pdb=" N ALA B 861 " --> pdb=" O LEU B 857 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N PHE B 862 " --> pdb=" O THR B 858 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 857 through 862' Processing helix chain 'B' and resid 875 through 901 removed outlier: 3.693A pdb=" N LYS B 884 " --> pdb=" O ARG B 880 " (cutoff:3.500A) Processing helix chain 'B' and resid 925 through 946 Processing helix chain 'B' and resid 954 through 961 removed outlier: 3.989A 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: 3.640A pdb=" N LEU B1057 " --> pdb=" O ALA B1053 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLY B1061 " --> pdb=" O LEU B1057 " (cutoff:3.500A) Processing helix chain 'B' and resid 1230 through 1235 removed outlier: 7.020A pdb=" N GLU B1234 " --> pdb=" O CYS B1230 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY B1235 " --> pdb=" O GLY B1231 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1230 through 1235' Processing helix chain 'B' and resid 1416 through 1423 Processing helix chain 'B' and resid 1437 through 1442 removed outlier: 3.822A pdb=" N VAL B1441 " --> pdb=" O GLU B1437 " (cutoff:3.500A) removed outlier: 5.152A 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: 4.065A pdb=" N SER B1495 " --> pdb=" O GLY B1491 " (cutoff:3.500A) Processing helix chain 'B' and resid 1565 through 1571 removed outlier: 3.790A pdb=" N GLY B1569 " --> pdb=" O PRO B1565 " (cutoff:3.500A) Processing helix chain 'B' and resid 1640 through 1647 removed outlier: 4.367A pdb=" N LEU B1644 " --> pdb=" O ASP B1640 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N THR B1645 " --> pdb=" O ILE B1641 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N GLU B1646 " --> pdb=" O LEU B1642 " (cutoff:3.500A) Processing helix chain 'B' and resid 1648 through 1666 Processing helix chain 'B' and resid 1669 through 1680 removed outlier: 3.822A pdb=" N SER B1678 " --> pdb=" O HIS B1674 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N HIS B1679 " --> pdb=" O ALA B1675 " (cutoff:3.500A) Processing helix chain 'B' and resid 1681 through 1691 Processing helix chain 'B' and resid 1695 through 1710 Processing helix chain 'B' and resid 1711 through 1723 removed outlier: 4.597A pdb=" N ASN B1723 " --> pdb=" O LEU B1719 " (cutoff:3.500A) Processing helix chain 'B' and resid 1730 through 1736 removed outlier: 3.634A pdb=" N ILE B1736 " --> pdb=" O GLU B1732 " (cutoff:3.500A) Processing helix chain 'B' and resid 1773 through 1778 removed outlier: 4.409A pdb=" N GLN B1777 " --> pdb=" O ASN B1773 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N TYR B1778 " --> pdb=" O GLU B1774 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1773 through 1778' Processing helix chain 'B' and resid 1783 through 1802 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: 3.980A pdb=" N MET B1896 " --> pdb=" O GLY B1892 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N LYS B1897 " --> pdb=" O LEU B1893 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1892 through 1897' Processing helix chain 'B' and resid 1899 through 1948 removed outlier: 3.972A pdb=" N ASP B1931 " --> pdb=" O ALA B1927 " (cutoff:3.500A) Processing helix chain 'B' and resid 1950 through 1955 Processing helix chain 'B' and resid 1956 through 1967 removed outlier: 5.056A pdb=" N ARG B1960 " --> pdb=" O ALA B1956 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N GLU B1964 " --> pdb=" O ARG B1960 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N PHE B1965 " --> pdb=" O LYS B1961 " (cutoff:3.500A) Processing helix chain 'B' and resid 1968 through 1979 removed outlier: 3.772A pdb=" N ASN B1978 " --> pdb=" O ASN B1974 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N PHE B1979 " --> pdb=" O MET B1975 " (cutoff:3.500A) Processing helix chain 'B' and resid 1989 through 2008 removed outlier: 3.947A pdb=" N GLN B1995 " --> pdb=" O GLU B1991 " (cutoff:3.500A) Processing helix chain 'B' and resid 2057 through 2073 Processing helix chain 'B' and resid 2077 through 2094 removed outlier: 3.541A 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: 3.883A pdb=" N VAL B2113 " --> pdb=" O ASN B2109 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N GLU B2114 " --> pdb=" O GLY B2110 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ASP B2115 " --> pdb=" O VAL B2111 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N SER B2131 " --> pdb=" O ARG B2127 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N VAL B2132 " --> pdb=" O SER B2128 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N ARG B2133 " --> pdb=" O LEU B2129 " (cutoff:3.500A) Processing helix chain 'B' and resid 2135 through 2152 Processing helix chain 'B' and resid 2153 through 2158 Processing helix chain 'B' and resid 2159 through 2166 Processing helix chain 'B' and resid 2167 through 2183 removed outlier: 4.915A pdb=" N GLY B2182 " --> pdb=" O VAL B2178 " (cutoff:3.500A) Processing helix chain 'B' and resid 2189 through 2208 removed outlier: 3.592A pdb=" N VAL B2193 " --> pdb=" O PHE B2189 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N SER B2207 " --> pdb=" O PHE B2203 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N ARG B2208 " --> pdb=" O CYS B2204 " (cutoff:3.500A) Processing helix chain 'B' and resid 2209 through 2219 removed outlier: 3.637A pdb=" N ASP B2216 " --> pdb=" O LYS B2212 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N HIS B2217 " --> pdb=" O ALA B2213 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LEU B2218 " --> pdb=" O MET B2214 " (cutoff:3.500A) removed outlier: 5.429A 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: 3.607A pdb=" N LEU B2262 " --> pdb=" O ARG B2258 " (cutoff:3.500A) Processing helix chain 'B' and resid 2277 through 2284 Processing helix chain 'B' and resid 2291 through 2307 removed outlier: 3.629A pdb=" N ARG B2297 " --> pdb=" O VAL B2293 " (cutoff:3.500A) Processing helix chain 'B' and resid 2313 through 2328 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 2383 through 2403 Processing helix chain 'B' and resid 2405 through 2412 Processing helix chain 'B' and resid 2413 through 2428 Proline residue: B2428 - end of helix Processing helix chain 'B' and resid 2429 through 2438 Processing helix chain 'B' and resid 2455 through 2460 removed outlier: 3.810A pdb=" N GLY B2459 " --> pdb=" O ASP B2455 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N PHE B2460 " --> pdb=" O MET B2456 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2455 through 2460' Processing helix chain 'B' and resid 2461 through 2475 removed outlier: 3.972A pdb=" N LYS B2465 " --> pdb=" O CYS B2461 " (cutoff:3.500A) Processing helix chain 'B' and resid 2480 through 2491 Processing helix chain 'B' and resid 2492 through 2503 removed outlier: 3.870A pdb=" N ASP B2503 " --> pdb=" O ALA B2499 " (cutoff:3.500A) Processing helix chain 'B' and resid 2504 through 2510 removed outlier: 4.651A pdb=" N ALA B2509 " --> pdb=" O ALA B2505 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N THR B2510 " --> pdb=" O ALA B2506 " (cutoff:3.500A) Processing helix chain 'B' and resid 2511 through 2532 removed outlier: 5.394A 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 2558 removed outlier: 4.884A pdb=" N GLY B2558 " --> pdb=" O ARG B2554 " (cutoff:3.500A) Processing helix chain 'B' and resid 2562 through 2580 removed outlier: 3.577A pdb=" N GLN B2579 " --> pdb=" O SER B2575 " (cutoff:3.500A) Processing helix chain 'B' and resid 2581 through 2596 removed outlier: 3.992A pdb=" N MET B2585 " --> pdb=" O ARG B2581 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N GLN B2586 " --> pdb=" O PRO B2582 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N HIS B2587 " --> pdb=" O SER B2583 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N LEU B2588 " --> pdb=" O MET B2584 " (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: 6.225A 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 2714 through 2740 removed outlier: 4.090A pdb=" N GLU B2718 " --> pdb=" O PRO B2714 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N TYR B2719 " --> pdb=" O GLU B2715 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N PHE B2720 " --> pdb=" O LYS B2716 " (cutoff:3.500A) Processing helix chain 'B' and resid 2759 through 2764 removed outlier: 5.049A pdb=" N SER B2764 " --> pdb=" O TYR B2760 " (cutoff:3.500A) Processing helix chain 'B' and resid 2768 through 2784 Proline residue: B2774 - end of helix Processing helix chain 'B' and resid 2792 through 2802 removed outlier: 4.032A 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: 5.271A pdb=" N THR B2878 " --> pdb=" O TYR B2874 " (cutoff:3.500A) Processing helix chain 'B' and resid 2879 through 2900 removed outlier: 4.656A pdb=" N LYS B2884 " --> pdb=" O LYS B2880 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ASP B2885 " --> pdb=" O GLU B2881 " (cutoff:3.500A) Processing helix chain 'B' and resid 2916 through 2947 removed outlier: 4.453A pdb=" N ARG B2920 " --> pdb=" O SER B2916 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N PHE B2921 " --> pdb=" O ILE B2917 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ALA B2922 " --> pdb=" O GLU B2918 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N TYR B2923 " --> pdb=" O LYS B2919 " (cutoff:3.500A) Processing helix chain 'B' and resid 2956 through 2979 removed outlier: 4.662A pdb=" N LEU B2968 " --> pdb=" O ALA B2964 " (cutoff:3.500A) Proline residue: B2969 - end of helix removed outlier: 3.757A pdb=" N ARG B2979 " --> pdb=" O PHE B2975 " (cutoff:3.500A) Processing helix chain 'B' and resid 2997 through 3016 Processing helix chain 'B' and resid 3018 through 3023 Processing helix chain 'B' and resid 3024 through 3040 removed outlier: 4.231A pdb=" N SER B3028 " --> pdb=" O ASN B3024 " (cutoff:3.500A) Processing helix chain 'B' and resid 3041 through 3048 Processing helix chain 'B' and resid 3050 through 3078 Processing helix chain 'B' and resid 3088 through 3116 removed outlier: 5.002A 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 3122 Processing helix chain 'B' and resid 3124 through 3143 Processing helix chain 'B' and resid 3145 through 3152 removed outlier: 4.013A pdb=" N ARG B3150 " --> pdb=" O ILE B3146 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLN B3151 " --> pdb=" O TYR B3147 " (cutoff:3.500A) Processing helix chain 'B' and resid 3153 through 3166 Processing helix chain 'B' and resid 3172 through 3177 removed outlier: 4.147A pdb=" N ASP B3176 " --> pdb=" O GLU B3172 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N LYS B3177 " --> pdb=" O THR B3173 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3172 through 3177' Processing helix chain 'B' and resid 3182 through 3187 Processing helix chain 'B' and resid 3188 through 3196 removed outlier: 4.422A pdb=" N SER B3196 " --> pdb=" O ARG B3192 " (cutoff:3.500A) Processing helix chain 'B' and resid 3200 through 3206 removed outlier: 4.876A 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 removed outlier: 4.338A pdb=" N ALA B3222 " --> pdb=" O ILE B3218 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLU B3223 " --> pdb=" O VAL B3219 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N GLY B3225 " --> pdb=" O LEU B3221 " (cutoff:3.500A) Processing helix chain 'B' and resid 3227 through 3232 removed outlier: 3.766A pdb=" N MET B3231 " --> pdb=" O ARG B3227 " (cutoff:3.500A) Proline residue: B3232 - end of helix No H-bonds generated for 'chain 'B' and resid 3227 through 3232' Processing helix chain 'B' and resid 3233 through 3250 removed outlier: 5.615A pdb=" N LEU B3239 " --> pdb=" O MET B3235 " (cutoff:3.500A) Proline residue: B3240 - end of helix 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: 4.679A pdb=" N GLY B3289 " --> pdb=" O TYR B3285 " (cutoff:3.500A) Processing helix chain 'B' and resid 3294 through 3307 Proline residue: B3305 - end of helix Processing helix chain 'B' and resid 3313 through 3327 removed outlier: 5.016A pdb=" N THR B3317 " --> pdb=" O GLN B3313 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LEU B3320 " --> pdb=" O LYS B3316 " (cutoff:3.500A) Proline residue: B3321 - end of helix removed outlier: 3.880A pdb=" N LYS B3327 " --> pdb=" O MET B3323 " (cutoff:3.500A) Processing helix chain 'B' and resid 3599 through 3605 Processing helix chain 'B' and resid 3612 through 3632 removed outlier: 3.771A pdb=" N ILE B3629 " --> pdb=" O GLU B3625 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N GLU B3630 " --> pdb=" O LYS B3626 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N THR B3631 " --> pdb=" O SER B3627 " (cutoff:3.500A) Processing helix chain 'B' and resid 3636 through 3647 removed outlier: 3.516A pdb=" N LYS B3646 " --> pdb=" O GLU B3642 " (cutoff:3.500A) Proline residue: B3647 - end of helix Processing helix chain 'B' and resid 3649 through 3654 Processing helix chain 'B' and resid 3662 through 3677 Processing helix chain 'B' and resid 3685 through 3701 removed outlier: 3.561A pdb=" N CYS B3699 " --> pdb=" O MET B3695 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N HIS B3700 " --> pdb=" O ALA B3696 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASP B3701 " --> pdb=" O LYS B3697 " (cutoff:3.500A) Processing helix chain 'B' and resid 3713 through 3733 removed outlier: 3.746A pdb=" N LEU B3731 " --> pdb=" O GLN B3727 " (cutoff:3.500A) Processing helix chain 'B' and resid 3735 through 3748 removed outlier: 3.881A 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: 3.996A 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: 3.592A pdb=" N CYS B3847 " --> pdb=" O LEU B3843 " (cutoff:3.500A) Processing helix chain 'B' and resid 3851 through 3860 removed outlier: 4.584A pdb=" N ARG B3859 " --> pdb=" O GLN B3855 " (cutoff:3.500A) Processing helix chain 'B' and resid 3869 through 3894 removed outlier: 4.716A 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 3938 Processing helix chain 'B' and resid 3939 through 3962 removed outlier: 3.685A pdb=" N ALA B3943 " --> pdb=" O ARG B3939 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N MET B3956 " --> pdb=" O ALA B3952 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLN B3960 " --> pdb=" O MET B3956 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ASP B3961 " --> pdb=" O LYS B3957 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N SER B3962 " --> pdb=" O LEU B3958 " (cutoff:3.500A) Processing helix chain 'B' and resid 3964 through 3987 Processing helix chain 'B' and resid 3993 through 4007 Processing helix chain 'B' and resid 4008 through 4029 removed outlier: 4.163A pdb=" N LYS B4024 " --> pdb=" O PHE B4020 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASP B4025 " --> pdb=" O LEU B4021 " (cutoff:3.500A) Processing helix chain 'B' and resid 4030 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 4070 Processing helix chain 'B' and resid 4079 through 4110 removed outlier: 4.533A pdb=" N GLU B4089 " --> pdb=" O LYS B4085 " (cutoff:3.500A) Proline residue: B4090 - end of helix removed outlier: 3.677A pdb=" N ASN B4097 " --> pdb=" O ASP B4093 " (cutoff:3.500A) Proline residue: B4110 - end of helix Processing helix chain 'B' and resid 4112 through 4123 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 4184 through 4208 removed outlier: 4.907A pdb=" N GLU B4208 " --> pdb=" O ALA B4204 " (cutoff:3.500A) Processing helix chain 'B' and resid 4237 through 4272 removed outlier: 4.240A pdb=" N LEU B4261 " --> pdb=" O ARG B4257 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N LYS B4262 " --> pdb=" O MET B4258 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N SER B4263 " --> pdb=" O LEU B4259 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LEU B4264 " --> pdb=" O SER B4260 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LYS B4265 " --> pdb=" O LEU B4261 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LYS B4266 " --> pdb=" O LYS B4262 " (cutoff:3.500A) Processing helix chain 'B' and resid 4275 through 4310 removed outlier: 3.843A pdb=" N TYR B4287 " --> pdb=" O PHE B4283 " (cutoff:3.500A) Processing helix chain 'B' and resid 4480 through 4499 Processing helix chain 'B' and resid 4500 through 4520 removed outlier: 4.280A pdb=" N PHE B4519 " --> pdb=" O PHE B4515 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N TYR B4520 " --> pdb=" O ILE B4516 " (cutoff:3.500A) Processing helix chain 'B' and resid 4568 through 4612 removed outlier: 4.078A 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: 4.037A pdb=" N ARG B4632 " --> pdb=" O GLY B4628 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N LEU B4633 " --> pdb=" O GLN B4629 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N VAL B4634 " --> pdb=" O TRP B4630 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE B4635 " --> pdb=" O ASP B4631 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ASN B4636 " --> pdb=" O ARG B4632 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N THR B4637 " --> pdb=" O LEU B4633 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N GLN B4638 " --> pdb=" O VAL B4634 " (cutoff:3.500A) Processing helix chain 'B' and resid 4648 through 4657 Processing helix chain 'B' and resid 4662 through 4671 removed outlier: 3.769A pdb=" N SER B4667 " --> pdb=" O ARG B4663 " (cutoff:3.500A) Processing helix chain 'B' and resid 4675 through 4683 Processing helix chain 'B' and resid 4693 through 4702 removed outlier: 5.720A pdb=" N ASP B4702 " --> pdb=" O LEU B4698 " (cutoff:3.500A) Processing helix chain 'B' and resid 4703 through 4716 Processing helix chain 'B' and resid 4717 through 4735 removed outlier: 3.883A pdb=" N HIS B4733 " --> pdb=" O SER B4729 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N TYR B4734 " --> pdb=" O VAL B4730 " (cutoff:3.500A) Processing helix chain 'B' and resid 4736 through 4750 removed outlier: 4.635A pdb=" N ALA B4740 " --> pdb=" O ASN B4736 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ALA B4741 " --> pdb=" O PHE B4737 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N HIS B4742 " --> pdb=" O PHE B4738 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LEU B4743 " --> pdb=" O PHE B4739 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LEU B4744 " --> pdb=" O ALA B4740 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ASP B4745 " --> pdb=" O ALA B4741 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N ILE B4746 " --> pdb=" O HIS B4742 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N ALA B4747 " --> pdb=" O LEU B4743 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N MET B4748 " --> pdb=" O LEU B4744 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE B4750 " --> pdb=" O ILE B4746 " (cutoff:3.500A) Processing helix chain 'B' and resid 4751 through 4762 removed outlier: 3.760A pdb=" N SER B4759 " --> pdb=" O THR B4755 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL B4760 " --> pdb=" O ILE B4756 " (cutoff:3.500A) Processing helix chain 'B' and resid 4763 through 4788 Processing helix chain 'B' and resid 4789 through 4794 removed outlier: 4.238A pdb=" N TYR B4793 " --> pdb=" O PHE B4789 " (cutoff:3.500A) removed outlier: 4.836A 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: 4.269A pdb=" N VAL B4821 " --> pdb=" O MET B4817 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ARG B4822 " --> pdb=" O TYR B4818 " (cutoff:3.500A) Processing helix chain 'B' and resid 4826 through 4832 removed outlier: 4.512A pdb=" N GLU B4830 " --> pdb=" O GLY B4826 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE B4831 " --> pdb=" O ILE B4827 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N GLU B4832 " --> pdb=" O GLY B4828 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4826 through 4832' 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 4900 removed outlier: 3.892A pdb=" N PHE B4898 " --> pdb=" O GLY B4894 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N THR B4900 " --> pdb=" O ASP B4896 " (cutoff:3.500A) Processing helix chain 'B' and resid 4903 through 4911 Processing helix chain 'B' and resid 4914 through 4928 Processing helix chain 'B' and resid 4934 through 4947 Processing helix chain 'B' and resid 4957 through 4963 Processing helix chain 'B' and resid 4614 through 4619 Processing helix chain 'C' and resid 61 through 66 removed outlier: 3.772A 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 253 through 259 removed outlier: 4.663A pdb=" N THR C 259 " --> pdb=" O GLU C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 271 removed outlier: 5.092A pdb=" N ALA C 271 " --> pdb=" O VAL C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 439 Processing helix chain 'C' and resid 441 through 446 removed outlier: 5.083A 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: 3.615A pdb=" N VAL C 507 " --> pdb=" O ASP C 503 " (cutoff:3.500A) removed outlier: 5.093A 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: 4.708A pdb=" N LYS C 527 " --> pdb=" O GLY C 523 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N SER C 528 " --> pdb=" O GLU C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 556 removed outlier: 4.701A pdb=" N GLY C 553 " --> pdb=" O ALA C 549 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N SER C 554 " --> pdb=" O GLN C 550 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ASP C 556 " --> pdb=" O SER C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 563 removed outlier: 4.415A pdb=" N ARG C 561 " --> pdb=" O TRP C 557 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LEU C 562 " --> pdb=" O LEU C 558 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N GLU C 563 " --> pdb=" O ILE C 559 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 557 through 563' Processing helix chain 'C' and resid 567 through 582 Processing helix chain 'C' and resid 583 through 589 removed outlier: 3.673A pdb=" N ILE C 588 " --> pdb=" O GLU C 584 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE C 589 " --> pdb=" O ALA C 585 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 604 Processing helix chain 'C' and resid 607 through 620 removed outlier: 3.718A pdb=" N LEU C 611 " --> pdb=" O ASN C 607 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N CYS C 620 " --> pdb=" O SER C 616 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 640 Proline residue: C 638 - end of helix Processing helix chain 'C' and resid 821 through 826 removed outlier: 4.664A pdb=" N ALA C 825 " --> pdb=" O PRO C 821 " (cutoff:3.500A) removed outlier: 4.844A 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 857 through 862 removed outlier: 4.556A pdb=" N ALA C 861 " --> pdb=" O LEU C 857 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N PHE C 862 " --> pdb=" O THR C 858 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 857 through 862' Processing helix chain 'C' and resid 875 through 901 removed outlier: 3.693A pdb=" N LYS C 884 " --> pdb=" O ARG C 880 " (cutoff:3.500A) Processing helix chain 'C' and resid 925 through 946 Processing helix chain 'C' and resid 954 through 961 removed outlier: 3.989A 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: 3.641A pdb=" N LEU C1057 " --> pdb=" O ALA C1053 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLY C1061 " --> pdb=" O LEU C1057 " (cutoff:3.500A) Processing helix chain 'C' and resid 1230 through 1235 removed outlier: 7.021A pdb=" N GLU C1234 " --> pdb=" O CYS C1230 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY C1235 " --> pdb=" O GLY C1231 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1230 through 1235' Processing helix chain 'C' and resid 1416 through 1423 Processing helix chain 'C' and resid 1437 through 1442 removed outlier: 3.822A pdb=" N VAL C1441 " --> pdb=" O GLU C1437 " (cutoff:3.500A) removed outlier: 5.153A 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: 4.066A pdb=" N SER C1495 " --> pdb=" O GLY C1491 " (cutoff:3.500A) Processing helix chain 'C' and resid 1565 through 1571 removed outlier: 3.790A pdb=" N GLY C1569 " --> pdb=" O PRO C1565 " (cutoff:3.500A) Processing helix chain 'C' and resid 1640 through 1647 removed outlier: 4.367A pdb=" N LEU C1644 " --> pdb=" O ASP C1640 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N THR C1645 " --> pdb=" O ILE C1641 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N GLU C1646 " --> pdb=" O LEU C1642 " (cutoff:3.500A) Processing helix chain 'C' and resid 1648 through 1666 Processing helix chain 'C' and resid 1669 through 1680 removed outlier: 3.822A pdb=" N SER C1678 " --> pdb=" O HIS C1674 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N HIS C1679 " --> pdb=" O ALA C1675 " (cutoff:3.500A) Processing helix chain 'C' and resid 1681 through 1691 Processing helix chain 'C' and resid 1695 through 1710 Processing helix chain 'C' and resid 1711 through 1723 removed outlier: 4.597A pdb=" N ASN C1723 " --> pdb=" O LEU C1719 " (cutoff:3.500A) Processing helix chain 'C' and resid 1730 through 1736 removed outlier: 3.633A pdb=" N ILE C1736 " --> pdb=" O GLU C1732 " (cutoff:3.500A) Processing helix chain 'C' and resid 1773 through 1778 removed outlier: 4.410A pdb=" N GLN C1777 " --> pdb=" O ASN C1773 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N TYR C1778 " --> pdb=" O GLU C1774 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1773 through 1778' Processing helix chain 'C' and resid 1783 through 1802 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: 3.981A pdb=" N MET C1896 " --> pdb=" O GLY C1892 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N LYS C1897 " --> pdb=" O LEU C1893 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1892 through 1897' Processing helix chain 'C' and resid 1899 through 1948 removed outlier: 3.972A pdb=" N ASP C1931 " --> pdb=" O ALA C1927 " (cutoff:3.500A) Processing helix chain 'C' and resid 1950 through 1955 Processing helix chain 'C' and resid 1956 through 1967 removed outlier: 5.056A pdb=" N ARG C1960 " --> pdb=" O ALA C1956 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N GLU C1964 " --> pdb=" O ARG C1960 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N PHE C1965 " --> pdb=" O LYS C1961 " (cutoff:3.500A) Processing helix chain 'C' and resid 1968 through 1979 removed outlier: 3.772A pdb=" N ASN C1978 " --> pdb=" O ASN C1974 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N PHE C1979 " --> pdb=" O MET C1975 " (cutoff:3.500A) Processing helix chain 'C' and resid 1989 through 2008 removed outlier: 3.946A pdb=" N GLN C1995 " --> pdb=" O GLU C1991 " (cutoff:3.500A) Processing helix chain 'C' and resid 2057 through 2073 Processing helix chain 'C' and resid 2077 through 2094 removed outlier: 3.541A 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: 3.884A pdb=" N VAL C2113 " --> pdb=" O ASN C2109 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N GLU C2114 " --> pdb=" O GLY C2110 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ASP C2115 " --> pdb=" O VAL C2111 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N SER C2131 " --> pdb=" O ARG C2127 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N VAL C2132 " --> pdb=" O SER C2128 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N ARG C2133 " --> pdb=" O LEU C2129 " (cutoff:3.500A) Processing helix chain 'C' and resid 2135 through 2152 Processing helix chain 'C' and resid 2153 through 2158 Processing helix chain 'C' and resid 2159 through 2166 Processing helix chain 'C' and resid 2167 through 2183 removed outlier: 4.915A pdb=" N GLY C2182 " --> pdb=" O VAL C2178 " (cutoff:3.500A) Processing helix chain 'C' and resid 2189 through 2208 removed outlier: 3.593A pdb=" N VAL C2193 " --> pdb=" O PHE C2189 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N SER C2207 " --> pdb=" O PHE C2203 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N ARG C2208 " --> pdb=" O CYS C2204 " (cutoff:3.500A) Processing helix chain 'C' and resid 2209 through 2219 removed outlier: 3.637A pdb=" N ASP C2216 " --> pdb=" O LYS C2212 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N HIS C2217 " --> pdb=" O ALA C2213 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LEU C2218 " --> pdb=" O MET C2214 " (cutoff:3.500A) removed outlier: 5.430A 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: 3.607A pdb=" N LEU C2262 " --> pdb=" O ARG C2258 " (cutoff:3.500A) Processing helix chain 'C' and resid 2277 through 2284 Processing helix chain 'C' and resid 2291 through 2307 removed outlier: 3.628A pdb=" N ARG C2297 " --> pdb=" O VAL C2293 " (cutoff:3.500A) Processing helix chain 'C' and resid 2313 through 2328 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 2383 through 2403 Processing helix chain 'C' and resid 2405 through 2412 Processing helix chain 'C' and resid 2413 through 2428 Proline residue: C2428 - end of helix Processing helix chain 'C' and resid 2429 through 2438 Processing helix chain 'C' and resid 2455 through 2460 removed outlier: 3.810A pdb=" N GLY C2459 " --> pdb=" O ASP C2455 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N PHE C2460 " --> pdb=" O MET C2456 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2455 through 2460' Processing helix chain 'C' and resid 2461 through 2475 removed outlier: 3.971A pdb=" N LYS C2465 " --> pdb=" O CYS C2461 " (cutoff:3.500A) Processing helix chain 'C' and resid 2480 through 2491 Processing helix chain 'C' and resid 2492 through 2503 removed outlier: 3.869A pdb=" N ASP C2503 " --> pdb=" O ALA C2499 " (cutoff:3.500A) Processing helix chain 'C' and resid 2504 through 2510 removed outlier: 4.650A pdb=" N ALA C2509 " --> pdb=" O ALA C2505 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N THR C2510 " --> pdb=" O ALA C2506 " (cutoff:3.500A) Processing helix chain 'C' and resid 2511 through 2532 removed outlier: 5.393A 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 2558 removed outlier: 4.884A pdb=" N GLY C2558 " --> pdb=" O ARG C2554 " (cutoff:3.500A) Processing helix chain 'C' and resid 2562 through 2580 removed outlier: 3.576A pdb=" N GLN C2579 " --> pdb=" O SER C2575 " (cutoff:3.500A) Processing helix chain 'C' and resid 2581 through 2596 removed outlier: 3.992A pdb=" N MET C2585 " --> pdb=" O ARG C2581 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N GLN C2586 " --> pdb=" O PRO C2582 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N HIS C2587 " --> pdb=" O SER C2583 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N LEU C2588 " --> pdb=" O MET C2584 " (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: 6.225A 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 2714 through 2740 removed outlier: 4.089A pdb=" N GLU C2718 " --> pdb=" O PRO C2714 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N TYR C2719 " --> pdb=" O GLU C2715 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N PHE C2720 " --> pdb=" O LYS C2716 " (cutoff:3.500A) Processing helix chain 'C' and resid 2759 through 2764 removed outlier: 5.049A pdb=" N SER C2764 " --> pdb=" O TYR C2760 " (cutoff:3.500A) Processing helix chain 'C' and resid 2768 through 2784 Proline residue: C2774 - end of helix Processing helix chain 'C' and resid 2792 through 2802 removed outlier: 4.032A 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: 5.272A pdb=" N THR C2878 " --> pdb=" O TYR C2874 " (cutoff:3.500A) Processing helix chain 'C' and resid 2879 through 2900 removed outlier: 4.656A pdb=" N LYS C2884 " --> pdb=" O LYS C2880 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ASP C2885 " --> pdb=" O GLU C2881 " (cutoff:3.500A) Processing helix chain 'C' and resid 2916 through 2947 removed outlier: 4.453A pdb=" N ARG C2920 " --> pdb=" O SER C2916 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N PHE C2921 " --> pdb=" O ILE C2917 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ALA C2922 " --> pdb=" O GLU C2918 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N TYR C2923 " --> pdb=" O LYS C2919 " (cutoff:3.500A) Processing helix chain 'C' and resid 2956 through 2979 removed outlier: 4.661A pdb=" N LEU C2968 " --> pdb=" O ALA C2964 " (cutoff:3.500A) Proline residue: C2969 - end of helix removed outlier: 3.756A pdb=" N ARG C2979 " --> pdb=" O PHE C2975 " (cutoff:3.500A) Processing helix chain 'C' and resid 2997 through 3016 Processing helix chain 'C' and resid 3018 through 3023 Processing helix chain 'C' and resid 3024 through 3040 removed outlier: 4.232A pdb=" N SER C3028 " --> pdb=" O ASN C3024 " (cutoff:3.500A) Processing helix chain 'C' and resid 3041 through 3048 Processing helix chain 'C' and resid 3050 through 3078 Processing helix chain 'C' and resid 3088 through 3116 removed outlier: 5.002A 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 3122 Processing helix chain 'C' and resid 3124 through 3143 Processing helix chain 'C' and resid 3145 through 3152 removed outlier: 4.013A pdb=" N ARG C3150 " --> pdb=" O ILE C3146 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N GLN C3151 " --> pdb=" O TYR C3147 " (cutoff:3.500A) Processing helix chain 'C' and resid 3153 through 3166 Processing helix chain 'C' and resid 3172 through 3177 removed outlier: 4.148A pdb=" N ASP C3176 " --> pdb=" O GLU C3172 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N LYS C3177 " --> pdb=" O THR C3173 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 3172 through 3177' Processing helix chain 'C' and resid 3182 through 3187 Processing helix chain 'C' and resid 3188 through 3196 removed outlier: 4.422A pdb=" N SER C3196 " --> pdb=" O ARG C3192 " (cutoff:3.500A) Processing helix chain 'C' and resid 3200 through 3206 removed outlier: 4.875A 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 removed outlier: 4.338A pdb=" N ALA C3222 " --> pdb=" O ILE C3218 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLU C3223 " --> pdb=" O VAL C3219 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N GLY C3225 " --> pdb=" O LEU C3221 " (cutoff:3.500A) Processing helix chain 'C' and resid 3227 through 3232 removed outlier: 3.767A pdb=" N MET C3231 " --> pdb=" O ARG C3227 " (cutoff:3.500A) Proline residue: C3232 - end of helix No H-bonds generated for 'chain 'C' and resid 3227 through 3232' Processing helix chain 'C' and resid 3233 through 3250 removed outlier: 5.615A pdb=" N LEU C3239 " --> pdb=" O MET C3235 " (cutoff:3.500A) Proline residue: C3240 - end of helix 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: 4.679A pdb=" N GLY C3289 " --> pdb=" O TYR C3285 " (cutoff:3.500A) Processing helix chain 'C' and resid 3294 through 3307 Proline residue: C3305 - end of helix Processing helix chain 'C' and resid 3313 through 3327 removed outlier: 5.016A pdb=" N THR C3317 " --> pdb=" O GLN C3313 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LEU C3320 " --> pdb=" O LYS C3316 " (cutoff:3.500A) Proline residue: C3321 - end of helix removed outlier: 3.880A pdb=" N LYS C3327 " --> pdb=" O MET C3323 " (cutoff:3.500A) Processing helix chain 'C' and resid 3599 through 3605 Processing helix chain 'C' and resid 3612 through 3632 removed outlier: 3.770A pdb=" N ILE C3629 " --> pdb=" O GLU C3625 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N GLU C3630 " --> pdb=" O LYS C3626 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N THR C3631 " --> pdb=" O SER C3627 " (cutoff:3.500A) Processing helix chain 'C' and resid 3636 through 3647 removed outlier: 3.517A pdb=" N LYS C3646 " --> pdb=" O GLU C3642 " (cutoff:3.500A) Proline residue: C3647 - end of helix Processing helix chain 'C' and resid 3649 through 3654 Processing helix chain 'C' and resid 3662 through 3677 Processing helix chain 'C' and resid 3685 through 3701 removed outlier: 3.560A pdb=" N CYS C3699 " --> pdb=" O MET C3695 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N HIS C3700 " --> pdb=" O ALA C3696 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASP C3701 " --> pdb=" O LYS C3697 " (cutoff:3.500A) Processing helix chain 'C' and resid 3713 through 3733 removed outlier: 3.746A pdb=" N LEU C3731 " --> pdb=" O GLN C3727 " (cutoff:3.500A) Processing helix chain 'C' and resid 3735 through 3748 removed outlier: 3.882A 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: 3.997A 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: 3.593A pdb=" N CYS C3847 " --> pdb=" O LEU C3843 " (cutoff:3.500A) Processing helix chain 'C' and resid 3851 through 3860 removed outlier: 4.583A pdb=" N ARG C3859 " --> pdb=" O GLN C3855 " (cutoff:3.500A) Processing helix chain 'C' and resid 3869 through 3894 removed outlier: 4.716A 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 3938 Processing helix chain 'C' and resid 3939 through 3962 removed outlier: 3.685A pdb=" N ALA C3943 " --> pdb=" O ARG C3939 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N MET C3956 " --> pdb=" O ALA C3952 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLN C3960 " --> pdb=" O MET C3956 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ASP C3961 " --> pdb=" O LYS C3957 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N SER C3962 " --> pdb=" O LEU C3958 " (cutoff:3.500A) Processing helix chain 'C' and resid 3964 through 3987 Processing helix chain 'C' and resid 3993 through 4007 Processing helix chain 'C' and resid 4008 through 4029 removed outlier: 4.165A pdb=" N LYS C4024 " --> pdb=" O PHE C4020 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASP C4025 " --> pdb=" O LEU C4021 " (cutoff:3.500A) Processing helix chain 'C' and resid 4030 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 4070 Processing helix chain 'C' and resid 4079 through 4110 removed outlier: 4.533A pdb=" N GLU C4089 " --> pdb=" O LYS C4085 " (cutoff:3.500A) Proline residue: C4090 - end of helix removed outlier: 3.676A pdb=" N ASN C4097 " --> pdb=" O ASP C4093 " (cutoff:3.500A) Proline residue: C4110 - end of helix Processing helix chain 'C' and resid 4112 through 4123 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 4184 through 4208 removed outlier: 4.908A pdb=" N GLU C4208 " --> pdb=" O ALA C4204 " (cutoff:3.500A) Processing helix chain 'C' and resid 4237 through 4272 removed outlier: 4.240A pdb=" N LEU C4261 " --> pdb=" O ARG C4257 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N LYS C4262 " --> pdb=" O MET C4258 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N SER C4263 " --> pdb=" O LEU C4259 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LEU C4264 " --> pdb=" O SER C4260 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LYS C4265 " --> pdb=" O LEU C4261 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LYS C4266 " --> pdb=" O LYS C4262 " (cutoff:3.500A) Processing helix chain 'C' and resid 4275 through 4310 removed outlier: 3.842A pdb=" N TYR C4287 " --> pdb=" O PHE C4283 " (cutoff:3.500A) Processing helix chain 'C' and resid 4480 through 4499 Processing helix chain 'C' and resid 4500 through 4520 removed outlier: 4.280A pdb=" N PHE C4519 " --> pdb=" O PHE C4515 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N TYR C4520 " --> pdb=" O ILE C4516 " (cutoff:3.500A) Processing helix chain 'C' and resid 4568 through 4612 removed outlier: 4.077A 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: 4.037A pdb=" N ARG C4632 " --> pdb=" O GLY C4628 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N LEU C4633 " --> pdb=" O GLN C4629 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N VAL C4634 " --> pdb=" O TRP C4630 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE C4635 " --> pdb=" O ASP C4631 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ASN C4636 " --> pdb=" O ARG C4632 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N THR C4637 " --> pdb=" O LEU C4633 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N GLN C4638 " --> pdb=" O VAL C4634 " (cutoff:3.500A) Processing helix chain 'C' and resid 4648 through 4657 Processing helix chain 'C' and resid 4662 through 4671 removed outlier: 3.770A pdb=" N SER C4667 " --> pdb=" O ARG C4663 " (cutoff:3.500A) Processing helix chain 'C' and resid 4675 through 4683 Processing helix chain 'C' and resid 4693 through 4702 removed outlier: 5.720A pdb=" N ASP C4702 " --> pdb=" O LEU C4698 " (cutoff:3.500A) Processing helix chain 'C' and resid 4703 through 4716 Processing helix chain 'C' and resid 4717 through 4735 removed outlier: 3.882A pdb=" N HIS C4733 " --> pdb=" O SER C4729 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N TYR C4734 " --> pdb=" O VAL C4730 " (cutoff:3.500A) Processing helix chain 'C' and resid 4736 through 4750 removed outlier: 4.636A pdb=" N ALA C4740 " --> pdb=" O ASN C4736 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ALA C4741 " --> pdb=" O PHE C4737 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N HIS C4742 " --> pdb=" O PHE C4738 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LEU C4743 " --> pdb=" O PHE C4739 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LEU C4744 " --> pdb=" O ALA C4740 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ASP C4745 " --> pdb=" O ALA C4741 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N ILE C4746 " --> pdb=" O HIS C4742 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N ALA C4747 " --> pdb=" O LEU C4743 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N MET C4748 " --> pdb=" O LEU C4744 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE C4750 " --> pdb=" O ILE C4746 " (cutoff:3.500A) Processing helix chain 'C' and resid 4751 through 4762 removed outlier: 3.759A pdb=" N SER C4759 " --> pdb=" O THR C4755 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL C4760 " --> pdb=" O ILE C4756 " (cutoff:3.500A) Processing helix chain 'C' and resid 4763 through 4788 Processing helix chain 'C' and resid 4789 through 4794 removed outlier: 4.238A pdb=" N TYR C4793 " --> pdb=" O PHE C4789 " (cutoff:3.500A) removed outlier: 4.836A 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: 4.269A pdb=" N VAL C4821 " --> pdb=" O MET C4817 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ARG C4822 " --> pdb=" O TYR C4818 " (cutoff:3.500A) Processing helix chain 'C' and resid 4826 through 4832 removed outlier: 4.511A pdb=" N GLU C4830 " --> pdb=" O GLY C4826 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE C4831 " --> pdb=" O ILE C4827 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N GLU C4832 " --> pdb=" O GLY C4828 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 4826 through 4832' 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 4900 removed outlier: 3.892A pdb=" N PHE C4898 " --> pdb=" O GLY C4894 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N THR C4900 " --> pdb=" O ASP C4896 " (cutoff:3.500A) Processing helix chain 'C' and resid 4903 through 4911 Processing helix chain 'C' and resid 4914 through 4928 Processing helix chain 'C' and resid 4934 through 4947 Processing helix chain 'C' and resid 4957 through 4963 Processing helix chain 'C' and resid 4614 through 4619 Processing helix chain 'D' and resid 61 through 66 removed outlier: 3.772A 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 253 through 259 removed outlier: 4.664A pdb=" N THR D 259 " --> pdb=" O GLU D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 271 removed outlier: 5.091A pdb=" N ALA D 271 " --> pdb=" O VAL D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 439 Processing helix chain 'D' and resid 441 through 446 removed outlier: 5.083A 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: 3.616A pdb=" N VAL D 507 " --> pdb=" O ASP D 503 " (cutoff:3.500A) removed outlier: 5.094A 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: 4.707A pdb=" N LYS D 527 " --> pdb=" O GLY D 523 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N SER D 528 " --> pdb=" O GLU D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 544 through 556 removed outlier: 4.701A pdb=" N GLY D 553 " --> pdb=" O ALA D 549 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N SER D 554 " --> pdb=" O GLN D 550 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ASP D 556 " --> pdb=" O SER D 552 " (cutoff:3.500A) Processing helix chain 'D' and resid 557 through 563 removed outlier: 4.415A pdb=" N ARG D 561 " --> pdb=" O TRP D 557 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LEU D 562 " --> pdb=" O LEU D 558 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N GLU D 563 " --> pdb=" O ILE D 559 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 557 through 563' Processing helix chain 'D' and resid 567 through 582 Processing helix chain 'D' and resid 583 through 589 removed outlier: 3.674A pdb=" N ILE D 588 " --> pdb=" O GLU D 584 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE D 589 " --> pdb=" O ALA D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 590 through 604 Processing helix chain 'D' and resid 607 through 620 removed outlier: 3.718A pdb=" N LEU D 611 " --> pdb=" O ASN D 607 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N CYS D 620 " --> pdb=" O SER D 616 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 640 Proline residue: D 638 - end of helix Processing helix chain 'D' and resid 821 through 826 removed outlier: 4.664A pdb=" N ALA D 825 " --> pdb=" O PRO D 821 " (cutoff:3.500A) removed outlier: 4.844A 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 857 through 862 removed outlier: 4.557A pdb=" N ALA D 861 " --> pdb=" O LEU D 857 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N PHE D 862 " --> pdb=" O THR D 858 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 857 through 862' Processing helix chain 'D' and resid 875 through 901 removed outlier: 3.694A pdb=" N LYS D 884 " --> pdb=" O ARG D 880 " (cutoff:3.500A) Processing helix chain 'D' and resid 925 through 946 Processing helix chain 'D' and resid 954 through 961 removed outlier: 3.989A 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: 3.641A pdb=" N LEU D1057 " --> pdb=" O ALA D1053 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLY D1061 " --> pdb=" O LEU D1057 " (cutoff:3.500A) Processing helix chain 'D' and resid 1230 through 1235 removed outlier: 7.022A pdb=" N GLU D1234 " --> pdb=" O CYS D1230 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY D1235 " --> pdb=" O GLY D1231 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1230 through 1235' Processing helix chain 'D' and resid 1416 through 1423 Processing helix chain 'D' and resid 1437 through 1442 removed outlier: 3.823A pdb=" N VAL D1441 " --> pdb=" O GLU D1437 " (cutoff:3.500A) removed outlier: 5.151A 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: 4.066A pdb=" N SER D1495 " --> pdb=" O GLY D1491 " (cutoff:3.500A) Processing helix chain 'D' and resid 1565 through 1571 removed outlier: 3.790A pdb=" N GLY D1569 " --> pdb=" O PRO D1565 " (cutoff:3.500A) Processing helix chain 'D' and resid 1640 through 1647 removed outlier: 4.367A pdb=" N LEU D1644 " --> pdb=" O ASP D1640 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N THR D1645 " --> pdb=" O ILE D1641 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N GLU D1646 " --> pdb=" O LEU D1642 " (cutoff:3.500A) Processing helix chain 'D' and resid 1648 through 1666 Processing helix chain 'D' and resid 1669 through 1680 removed outlier: 3.821A pdb=" N SER D1678 " --> pdb=" O HIS D1674 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N HIS D1679 " --> pdb=" O ALA D1675 " (cutoff:3.500A) Processing helix chain 'D' and resid 1681 through 1691 Processing helix chain 'D' and resid 1695 through 1710 Processing helix chain 'D' and resid 1711 through 1723 removed outlier: 4.597A pdb=" N ASN D1723 " --> pdb=" O LEU D1719 " (cutoff:3.500A) Processing helix chain 'D' and resid 1730 through 1736 removed outlier: 3.634A pdb=" N ILE D1736 " --> pdb=" O GLU D1732 " (cutoff:3.500A) Processing helix chain 'D' and resid 1773 through 1778 removed outlier: 4.410A pdb=" N GLN D1777 " --> pdb=" O ASN D1773 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N TYR D1778 " --> pdb=" O GLU D1774 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1773 through 1778' Processing helix chain 'D' and resid 1783 through 1802 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: 3.981A pdb=" N MET D1896 " --> pdb=" O GLY D1892 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N LYS D1897 " --> pdb=" O LEU D1893 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1892 through 1897' Processing helix chain 'D' and resid 1899 through 1948 removed outlier: 3.972A pdb=" N ASP D1931 " --> pdb=" O ALA D1927 " (cutoff:3.500A) Processing helix chain 'D' and resid 1950 through 1955 Processing helix chain 'D' and resid 1956 through 1967 removed outlier: 5.055A pdb=" N ARG D1960 " --> pdb=" O ALA D1956 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N GLU D1964 " --> pdb=" O ARG D1960 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N PHE D1965 " --> pdb=" O LYS D1961 " (cutoff:3.500A) Processing helix chain 'D' and resid 1968 through 1979 removed outlier: 3.773A pdb=" N ASN D1978 " --> pdb=" O ASN D1974 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N PHE D1979 " --> pdb=" O MET D1975 " (cutoff:3.500A) Processing helix chain 'D' and resid 1989 through 2008 removed outlier: 3.947A pdb=" N GLN D1995 " --> pdb=" O GLU D1991 " (cutoff:3.500A) Processing helix chain 'D' and resid 2057 through 2073 Processing helix chain 'D' and resid 2077 through 2094 removed outlier: 3.542A 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: 3.884A pdb=" N VAL D2113 " --> pdb=" O ASN D2109 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N GLU D2114 " --> pdb=" O GLY D2110 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ASP D2115 " --> pdb=" O VAL D2111 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N SER D2131 " --> pdb=" O ARG D2127 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N VAL D2132 " --> pdb=" O SER D2128 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N ARG D2133 " --> pdb=" O LEU D2129 " (cutoff:3.500A) Processing helix chain 'D' and resid 2135 through 2152 Processing helix chain 'D' and resid 2153 through 2158 Processing helix chain 'D' and resid 2159 through 2166 Processing helix chain 'D' and resid 2167 through 2183 removed outlier: 4.916A pdb=" N GLY D2182 " --> pdb=" O VAL D2178 " (cutoff:3.500A) Processing helix chain 'D' and resid 2189 through 2208 removed outlier: 3.592A pdb=" N VAL D2193 " --> pdb=" O PHE D2189 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N SER D2207 " --> pdb=" O PHE D2203 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N ARG D2208 " --> pdb=" O CYS D2204 " (cutoff:3.500A) Processing helix chain 'D' and resid 2209 through 2219 removed outlier: 3.637A pdb=" N ASP D2216 " --> pdb=" O LYS D2212 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N HIS D2217 " --> pdb=" O ALA D2213 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LEU D2218 " --> pdb=" O MET D2214 " (cutoff:3.500A) removed outlier: 5.430A 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: 3.607A pdb=" N LEU D2262 " --> pdb=" O ARG D2258 " (cutoff:3.500A) Processing helix chain 'D' and resid 2277 through 2284 Processing helix chain 'D' and resid 2291 through 2307 removed outlier: 3.629A pdb=" N ARG D2297 " --> pdb=" O VAL D2293 " (cutoff:3.500A) Processing helix chain 'D' and resid 2313 through 2328 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 2383 through 2403 Processing helix chain 'D' and resid 2405 through 2412 Processing helix chain 'D' and resid 2413 through 2428 Proline residue: D2428 - end of helix Processing helix chain 'D' and resid 2429 through 2438 Processing helix chain 'D' and resid 2455 through 2460 removed outlier: 3.811A pdb=" N GLY D2459 " --> pdb=" O ASP D2455 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N PHE D2460 " --> pdb=" O MET D2456 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2455 through 2460' Processing helix chain 'D' and resid 2461 through 2475 removed outlier: 3.972A pdb=" N LYS D2465 " --> pdb=" O CYS D2461 " (cutoff:3.500A) Processing helix chain 'D' and resid 2480 through 2491 Processing helix chain 'D' and resid 2492 through 2503 removed outlier: 3.869A pdb=" N ASP D2503 " --> pdb=" O ALA D2499 " (cutoff:3.500A) Processing helix chain 'D' and resid 2504 through 2510 removed outlier: 4.650A pdb=" N ALA D2509 " --> pdb=" O ALA D2505 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N THR D2510 " --> pdb=" O ALA D2506 " (cutoff:3.500A) Processing helix chain 'D' and resid 2511 through 2532 removed outlier: 5.393A 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 2558 removed outlier: 4.883A pdb=" N GLY D2558 " --> pdb=" O ARG D2554 " (cutoff:3.500A) Processing helix chain 'D' and resid 2562 through 2580 removed outlier: 3.576A pdb=" N GLN D2579 " --> pdb=" O SER D2575 " (cutoff:3.500A) Processing helix chain 'D' and resid 2581 through 2596 removed outlier: 3.992A pdb=" N MET D2585 " --> pdb=" O ARG D2581 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N GLN D2586 " --> pdb=" O PRO D2582 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N HIS D2587 " --> pdb=" O SER D2583 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N LEU D2588 " --> pdb=" O MET D2584 " (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: 6.225A 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 2714 through 2740 removed outlier: 4.090A pdb=" N GLU D2718 " --> pdb=" O PRO D2714 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N TYR D2719 " --> pdb=" O GLU D2715 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N PHE D2720 " --> pdb=" O LYS D2716 " (cutoff:3.500A) Processing helix chain 'D' and resid 2759 through 2764 removed outlier: 5.050A pdb=" N SER D2764 " --> pdb=" O TYR D2760 " (cutoff:3.500A) Processing helix chain 'D' and resid 2768 through 2784 Proline residue: D2774 - end of helix Processing helix chain 'D' and resid 2792 through 2802 removed outlier: 4.032A 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: 5.271A pdb=" N THR D2878 " --> pdb=" O TYR D2874 " (cutoff:3.500A) Processing helix chain 'D' and resid 2879 through 2900 removed outlier: 4.656A pdb=" N LYS D2884 " --> pdb=" O LYS D2880 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ASP D2885 " --> pdb=" O GLU D2881 " (cutoff:3.500A) Processing helix chain 'D' and resid 2916 through 2947 removed outlier: 4.453A pdb=" N ARG D2920 " --> pdb=" O SER D2916 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N PHE D2921 " --> pdb=" O ILE D2917 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ALA D2922 " --> pdb=" O GLU D2918 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N TYR D2923 " --> pdb=" O LYS D2919 " (cutoff:3.500A) Processing helix chain 'D' and resid 2956 through 2979 removed outlier: 4.662A pdb=" N LEU D2968 " --> pdb=" O ALA D2964 " (cutoff:3.500A) Proline residue: D2969 - end of helix removed outlier: 3.756A pdb=" N ARG D2979 " --> pdb=" O PHE D2975 " (cutoff:3.500A) Processing helix chain 'D' and resid 2997 through 3016 Processing helix chain 'D' and resid 3018 through 3023 Processing helix chain 'D' and resid 3024 through 3040 removed outlier: 4.231A pdb=" N SER D3028 " --> pdb=" O ASN D3024 " (cutoff:3.500A) Processing helix chain 'D' and resid 3041 through 3048 Processing helix chain 'D' and resid 3050 through 3078 Processing helix chain 'D' and resid 3088 through 3116 removed outlier: 5.002A 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 3122 Processing helix chain 'D' and resid 3124 through 3143 Processing helix chain 'D' and resid 3145 through 3152 removed outlier: 4.013A pdb=" N ARG D3150 " --> pdb=" O ILE D3146 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLN D3151 " --> pdb=" O TYR D3147 " (cutoff:3.500A) Processing helix chain 'D' and resid 3153 through 3166 Processing helix chain 'D' and resid 3172 through 3177 removed outlier: 4.148A pdb=" N ASP D3176 " --> pdb=" O GLU D3172 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N LYS D3177 " --> pdb=" O THR D3173 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 3172 through 3177' Processing helix chain 'D' and resid 3182 through 3187 Processing helix chain 'D' and resid 3188 through 3196 removed outlier: 4.422A pdb=" N SER D3196 " --> pdb=" O ARG D3192 " (cutoff:3.500A) Processing helix chain 'D' and resid 3200 through 3206 removed outlier: 4.876A 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 removed outlier: 4.338A pdb=" N ALA D3222 " --> pdb=" O ILE D3218 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N GLU D3223 " --> pdb=" O VAL D3219 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N GLY D3225 " --> pdb=" O LEU D3221 " (cutoff:3.500A) Processing helix chain 'D' and resid 3227 through 3232 removed outlier: 3.766A pdb=" N MET D3231 " --> pdb=" O ARG D3227 " (cutoff:3.500A) Proline residue: D3232 - end of helix No H-bonds generated for 'chain 'D' and resid 3227 through 3232' Processing helix chain 'D' and resid 3233 through 3250 removed outlier: 5.615A pdb=" N LEU D3239 " --> pdb=" O MET D3235 " (cutoff:3.500A) Proline residue: D3240 - end of helix 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: 4.679A pdb=" N GLY D3289 " --> pdb=" O TYR D3285 " (cutoff:3.500A) Processing helix chain 'D' and resid 3294 through 3307 Proline residue: D3305 - end of helix Processing helix chain 'D' and resid 3313 through 3327 removed outlier: 5.016A pdb=" N THR D3317 " --> pdb=" O GLN D3313 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LEU D3320 " --> pdb=" O LYS D3316 " (cutoff:3.500A) Proline residue: D3321 - end of helix removed outlier: 3.879A pdb=" N LYS D3327 " --> pdb=" O MET D3323 " (cutoff:3.500A) Processing helix chain 'D' and resid 3599 through 3605 Processing helix chain 'D' and resid 3612 through 3632 removed outlier: 3.770A pdb=" N ILE D3629 " --> pdb=" O GLU D3625 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N GLU D3630 " --> pdb=" O LYS D3626 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N THR D3631 " --> pdb=" O SER D3627 " (cutoff:3.500A) Processing helix chain 'D' and resid 3636 through 3647 removed outlier: 3.516A pdb=" N LYS D3646 " --> pdb=" O GLU D3642 " (cutoff:3.500A) Proline residue: D3647 - end of helix Processing helix chain 'D' and resid 3649 through 3654 Processing helix chain 'D' and resid 3662 through 3677 Processing helix chain 'D' and resid 3685 through 3701 removed outlier: 3.560A pdb=" N CYS D3699 " --> pdb=" O MET D3695 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N HIS D3700 " --> pdb=" O ALA D3696 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASP D3701 " --> pdb=" O LYS D3697 " (cutoff:3.500A) Processing helix chain 'D' and resid 3713 through 3733 removed outlier: 3.744A pdb=" N LEU D3731 " --> pdb=" O GLN D3727 " (cutoff:3.500A) Processing helix chain 'D' and resid 3735 through 3748 removed outlier: 3.882A 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: 3.996A 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: 3.592A pdb=" N CYS D3847 " --> pdb=" O LEU D3843 " (cutoff:3.500A) Processing helix chain 'D' and resid 3851 through 3860 removed outlier: 4.583A pdb=" N ARG D3859 " --> pdb=" O GLN D3855 " (cutoff:3.500A) Processing helix chain 'D' and resid 3869 through 3894 removed outlier: 4.716A 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 3938 Processing helix chain 'D' and resid 3939 through 3962 removed outlier: 3.684A pdb=" N ALA D3943 " --> pdb=" O ARG D3939 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N MET D3956 " --> pdb=" O ALA D3952 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLN D3960 " --> pdb=" O MET D3956 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ASP D3961 " --> pdb=" O LYS D3957 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N SER D3962 " --> pdb=" O LEU D3958 " (cutoff:3.500A) Processing helix chain 'D' and resid 3964 through 3987 Processing helix chain 'D' and resid 3993 through 4007 Processing helix chain 'D' and resid 4008 through 4029 removed outlier: 4.163A pdb=" N LYS D4024 " --> pdb=" O PHE D4020 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASP D4025 " --> pdb=" O LEU D4021 " (cutoff:3.500A) Processing helix chain 'D' and resid 4030 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 4070 Processing helix chain 'D' and resid 4079 through 4110 removed outlier: 4.532A pdb=" N GLU D4089 " --> pdb=" O LYS D4085 " (cutoff:3.500A) Proline residue: D4090 - end of helix removed outlier: 3.677A pdb=" N ASN D4097 " --> pdb=" O ASP D4093 " (cutoff:3.500A) Proline residue: D4110 - end of helix Processing helix chain 'D' and resid 4112 through 4123 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 4184 through 4208 removed outlier: 4.907A pdb=" N GLU D4208 " --> pdb=" O ALA D4204 " (cutoff:3.500A) Processing helix chain 'D' and resid 4237 through 4272 removed outlier: 4.240A pdb=" N LEU D4261 " --> pdb=" O ARG D4257 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N LYS D4262 " --> pdb=" O MET D4258 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N SER D4263 " --> pdb=" O LEU D4259 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LEU D4264 " --> pdb=" O SER D4260 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LYS D4265 " --> pdb=" O LEU D4261 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LYS D4266 " --> pdb=" O LYS D4262 " (cutoff:3.500A) Processing helix chain 'D' and resid 4275 through 4310 removed outlier: 3.842A pdb=" N TYR D4287 " --> pdb=" O PHE D4283 " (cutoff:3.500A) Processing helix chain 'D' and resid 4480 through 4499 Processing helix chain 'D' and resid 4500 through 4520 removed outlier: 4.280A pdb=" N PHE D4519 " --> pdb=" O PHE D4515 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N TYR D4520 " --> pdb=" O ILE D4516 " (cutoff:3.500A) Processing helix chain 'D' and resid 4568 through 4612 removed outlier: 4.078A 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: 4.037A pdb=" N ARG D4632 " --> pdb=" O GLY D4628 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N LEU D4633 " --> pdb=" O GLN D4629 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N VAL D4634 " --> pdb=" O TRP D4630 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE D4635 " --> pdb=" O ASP D4631 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ASN D4636 " --> pdb=" O ARG D4632 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N THR D4637 " --> pdb=" O LEU D4633 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N GLN D4638 " --> pdb=" O VAL D4634 " (cutoff:3.500A) Processing helix chain 'D' and resid 4648 through 4657 Processing helix chain 'D' and resid 4662 through 4671 removed outlier: 3.769A pdb=" N SER D4667 " --> pdb=" O ARG D4663 " (cutoff:3.500A) Processing helix chain 'D' and resid 4675 through 4683 Processing helix chain 'D' and resid 4693 through 4702 removed outlier: 5.720A pdb=" N ASP D4702 " --> pdb=" O LEU D4698 " (cutoff:3.500A) Processing helix chain 'D' and resid 4703 through 4716 Processing helix chain 'D' and resid 4717 through 4735 removed outlier: 3.882A pdb=" N HIS D4733 " --> pdb=" O SER D4729 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N TYR D4734 " --> pdb=" O VAL D4730 " (cutoff:3.500A) Processing helix chain 'D' and resid 4736 through 4750 removed outlier: 4.635A pdb=" N ALA D4740 " --> pdb=" O ASN D4736 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ALA D4741 " --> pdb=" O PHE D4737 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N HIS D4742 " --> pdb=" O PHE D4738 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LEU D4743 " --> pdb=" O PHE D4739 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LEU D4744 " --> pdb=" O ALA D4740 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ASP D4745 " --> pdb=" O ALA D4741 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N ILE D4746 " --> pdb=" O HIS D4742 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N ALA D4747 " --> pdb=" O LEU D4743 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N MET D4748 " --> pdb=" O LEU D4744 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE D4750 " --> pdb=" O ILE D4746 " (cutoff:3.500A) Processing helix chain 'D' and resid 4751 through 4762 removed outlier: 3.760A pdb=" N SER D4759 " --> pdb=" O THR D4755 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL D4760 " --> pdb=" O ILE D4756 " (cutoff:3.500A) Processing helix chain 'D' and resid 4763 through 4788 Processing helix chain 'D' and resid 4789 through 4794 removed outlier: 4.238A pdb=" N TYR D4793 " --> pdb=" O PHE D4789 " (cutoff:3.500A) removed outlier: 4.836A 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: 4.269A pdb=" N VAL D4821 " --> pdb=" O MET D4817 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ARG D4822 " --> pdb=" O TYR D4818 " (cutoff:3.500A) Processing helix chain 'D' and resid 4826 through 4832 removed outlier: 4.512A pdb=" N GLU D4830 " --> pdb=" O GLY D4826 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE D4831 " --> pdb=" O ILE D4827 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N GLU D4832 " --> pdb=" O GLY D4828 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 4826 through 4832' 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 4900 removed outlier: 3.892A pdb=" N PHE D4898 " --> pdb=" O GLY D4894 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N THR D4900 " --> pdb=" O ASP D4896 " (cutoff:3.500A) Processing helix chain 'D' and resid 4903 through 4911 Processing helix chain 'D' and resid 4914 through 4928 Processing helix chain 'D' and resid 4934 through 4947 Processing helix chain 'D' and resid 4957 through 4963 Processing helix chain 'D' and resid 4614 through 4619 Processing helix chain 'E' and resid 39 through 44 removed outlier: 3.804A pdb=" N ARG E 43 " --> pdb=" O SER E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 68 removed outlier: 3.867A pdb=" N MET E 67 " --> pdb=" O GLY E 63 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N SER E 68 " --> pdb=" O ALA E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 83 removed outlier: 4.029A pdb=" N TYR E 83 " --> pdb=" O PRO E 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 39 through 44 removed outlier: 3.804A pdb=" N ARG F 43 " --> pdb=" O SER F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 68 removed outlier: 3.867A pdb=" N MET F 67 " --> pdb=" O GLY F 63 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N SER F 68 " --> pdb=" O ALA F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 83 removed outlier: 4.028A pdb=" N TYR F 83 " --> pdb=" O PRO F 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 44 removed outlier: 3.805A pdb=" N ARG G 43 " --> pdb=" O SER G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 68 removed outlier: 3.866A pdb=" N MET G 67 " --> pdb=" O GLY G 63 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N SER G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 83 removed outlier: 4.029A pdb=" N TYR G 83 " --> pdb=" O PRO G 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 39 through 44 removed outlier: 3.804A pdb=" N ARG H 43 " --> pdb=" O SER H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 68 removed outlier: 3.867A pdb=" N MET H 67 " --> pdb=" O GLY H 63 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N SER H 68 " --> pdb=" O ALA H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 83 removed outlier: 4.029A pdb=" N TYR H 83 " --> pdb=" O PRO H 79 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'A' and resid 47 through 52 removed outlier: 6.342A pdb=" N LYS A 34 " --> pdb=" O THR A 52 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N LEU A 22 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 10.346A pdb=" N ALA A 39 " --> pdb=" O VAL A 20 " (cutoff:3.500A) removed outlier: 13.387A pdb=" N VAL A 20 " --> pdb=" O ALA A 39 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 67 through 70 removed outlier: 6.725A pdb=" N LEU A 120 " --> pdb=" O GLU A 70 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N LEU A 121 " --> pdb=" O LEU A 130 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N MET A 128 " --> pdb=" O HIS A 123 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 181 through 186 No H-bonds generated for sheet with id= 3 Processing sheet with id= 4, first strand: chain 'A' and resid 243 through 246 Processing sheet with id= 5, first strand: chain 'A' and resid 303 through 306 removed outlier: 3.683A pdb=" N LYS A 304 " --> pdb=" O HIS A 299 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N LEU A 297 " --> pdb=" O LEU A 306 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N LEU A 274 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASP A 232 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N VAL A 233 " --> pdb=" O SER A 408 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'A' and resid 329 through 333 Processing sheet with id= 7, first strand: chain 'A' and resid 737 through 741 removed outlier: 5.519A pdb=" N LEU A 730 " --> pdb=" O VAL A 741 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N HIS A 731 " --> pdb=" O ASP A 728 " (cutoff:3.500A) removed outlier: 5.680A 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= 8, first strand: chain 'A' and resid 764 through 770 removed outlier: 3.859A pdb=" N ASP A 753 " --> pdb=" O VAL A 679 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LYS A 799 " --> pdb=" O ASP A 680 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N GLY A1616 " --> pdb=" O ILE A1611 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'A' and resid 776 through 780 removed outlier: 5.461A pdb=" N GLN A 776 " --> pdb=" O GLY A1470 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'A' and resid 1016 through 1019 removed outlier: 7.447A pdb=" N GLN A1021 " --> pdb=" O PRO A1030 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'A' and resid 1148 through 1152 removed outlier: 4.365A pdb=" N GLY A1148 " --> pdb=" O HIS A1146 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N ALA A1142 " --> pdb=" O TYR A1152 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ARG A1133 " --> pdb=" O ARG A1119 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLY A1139 " --> pdb=" O MET A1113 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N MET A1113 " --> pdb=" O GLY A1139 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ASP A1112 " --> pdb=" O GLY A1208 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ILE A1087 " --> pdb=" O SER A1252 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N THR A1248 " --> pdb=" O GLU A1091 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'A' and resid 1171 through 1177 removed outlier: 3.806A pdb=" N ASP A1160 " --> pdb=" O THR A1107 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N GLY A1099 " --> pdb=" O MET A1168 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL A1212 " --> pdb=" O VAL A1108 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'A' and resid 1280 through 1286 removed outlier: 7.085A pdb=" N VAL A1552 " --> pdb=" O PHE A1433 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE A1433 " --> pdb=" O VAL A1552 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N GLY A1558 " --> pdb=" O TYR A1427 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N TYR A1427 " --> pdb=" O GLY A1558 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N SER A1424 " --> pdb=" O ALA A1513 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N GLY A1516 " --> pdb=" O VAL A1533 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'A' and resid 1307 through 1310 removed outlier: 4.853A pdb=" N THR A1537 " --> pdb=" O CYS A1310 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N PHE A1301 " --> pdb=" O LEU A1591 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'A' and resid 2787 through 2791 Processing sheet with id= 16, first strand: chain 'A' and resid 4132 through 4139 removed outlier: 4.769A pdb=" N PHE A4132 " --> pdb=" O ILE A4152 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'A' and resid 4521 through 4524 Processing sheet with id= 18, first strand: chain 'A' and resid 117 through 120 removed outlier: 4.142A pdb=" N HIS A 117 " --> pdb=" O ILE A 162 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'B' and resid 47 through 52 removed outlier: 6.342A pdb=" N LYS B 34 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N LEU B 22 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 10.347A pdb=" N ALA B 39 " --> pdb=" O VAL B 20 " (cutoff:3.500A) removed outlier: 13.388A pdb=" N VAL B 20 " --> pdb=" O ALA B 39 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'B' and resid 67 through 70 removed outlier: 6.725A pdb=" N LEU B 120 " --> pdb=" O GLU B 70 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N LEU B 121 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N MET B 128 " --> pdb=" O HIS B 123 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'B' and resid 181 through 186 No H-bonds generated for sheet with id= 21 Processing sheet with id= 22, first strand: chain 'B' and resid 243 through 246 Processing sheet with id= 23, first strand: chain 'B' and resid 303 through 306 removed outlier: 3.683A pdb=" N LYS B 304 " --> pdb=" O HIS B 299 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N LEU B 297 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N LEU B 274 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASP B 232 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N VAL B 233 " --> pdb=" O SER B 408 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'B' and resid 329 through 333 Processing sheet with id= 25, first strand: chain 'B' and resid 737 through 741 removed outlier: 5.519A pdb=" N LEU B 730 " --> pdb=" O VAL B 741 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N HIS B 731 " --> pdb=" O ASP B 728 " (cutoff:3.500A) removed outlier: 5.680A 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= 26, first strand: chain 'B' and resid 764 through 770 removed outlier: 3.859A pdb=" N ASP B 753 " --> pdb=" O VAL B 679 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LYS B 799 " --> pdb=" O ASP B 680 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N GLY B1616 " --> pdb=" O ILE B1611 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'B' and resid 776 through 780 removed outlier: 5.459A pdb=" N GLN B 776 " --> pdb=" O GLY B1470 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'B' and resid 1016 through 1019 removed outlier: 7.447A pdb=" N GLN B1021 " --> pdb=" O PRO B1030 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'B' and resid 1148 through 1152 removed outlier: 4.365A pdb=" N GLY B1148 " --> pdb=" O HIS B1146 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N ALA B1142 " --> pdb=" O TYR B1152 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ARG B1133 " --> pdb=" O ARG B1119 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLY B1139 " --> pdb=" O MET B1113 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N MET B1113 " --> pdb=" O GLY B1139 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ASP B1112 " --> pdb=" O GLY B1208 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ILE B1087 " --> pdb=" O SER B1252 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N THR B1248 " --> pdb=" O GLU B1091 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'B' and resid 1171 through 1177 removed outlier: 3.806A pdb=" N ASP B1160 " --> pdb=" O THR B1107 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N GLY B1099 " --> pdb=" O MET B1168 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL B1212 " --> pdb=" O VAL B1108 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'B' and resid 1280 through 1286 removed outlier: 7.085A pdb=" N VAL B1552 " --> pdb=" O PHE B1433 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE B1433 " --> pdb=" O VAL B1552 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N GLY B1558 " --> pdb=" O TYR B1427 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N TYR B1427 " --> pdb=" O GLY B1558 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N SER B1424 " --> pdb=" O ALA B1513 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N GLY B1516 " --> pdb=" O VAL B1533 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'B' and resid 1307 through 1310 removed outlier: 4.853A pdb=" N THR B1537 " --> pdb=" O CYS B1310 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N PHE B1301 " --> pdb=" O LEU B1591 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'B' and resid 2787 through 2791 Processing sheet with id= 34, first strand: chain 'B' and resid 4132 through 4139 removed outlier: 4.769A pdb=" N PHE B4132 " --> pdb=" O ILE B4152 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'B' and resid 4521 through 4524 Processing sheet with id= 36, first strand: chain 'B' and resid 117 through 120 removed outlier: 4.141A pdb=" N HIS B 117 " --> pdb=" O ILE B 162 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'C' and resid 47 through 52 removed outlier: 6.341A pdb=" N LYS C 34 " --> pdb=" O THR C 52 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N LEU C 22 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 10.347A pdb=" N ALA C 39 " --> pdb=" O VAL C 20 " (cutoff:3.500A) removed outlier: 13.387A pdb=" N VAL C 20 " --> pdb=" O ALA C 39 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'C' and resid 67 through 70 removed outlier: 6.725A pdb=" N LEU C 120 " --> pdb=" O GLU C 70 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N LEU C 121 " --> pdb=" O LEU C 130 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N MET C 128 " --> pdb=" O HIS C 123 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'C' and resid 181 through 186 No H-bonds generated for sheet with id= 39 Processing sheet with id= 40, first strand: chain 'C' and resid 243 through 246 Processing sheet with id= 41, first strand: chain 'C' and resid 303 through 306 removed outlier: 3.683A pdb=" N LYS C 304 " --> pdb=" O HIS C 299 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N LEU C 297 " --> pdb=" O LEU C 306 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N LEU C 274 " --> pdb=" O VAL C 300 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASP C 232 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N VAL C 233 " --> pdb=" O SER C 408 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'C' and resid 329 through 333 Processing sheet with id= 43, first strand: chain 'C' and resid 737 through 741 removed outlier: 5.520A pdb=" N LEU C 730 " --> pdb=" O VAL C 741 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N HIS C 731 " --> pdb=" O ASP C 728 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N HIS C 692 " --> pdb=" O SER C 795 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG C1637 " --> pdb=" O ILE C1632 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'C' and resid 764 through 770 removed outlier: 3.860A pdb=" N ASP C 753 " --> pdb=" O VAL C 679 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LYS C 799 " --> pdb=" O ASP C 680 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N GLY C1616 " --> pdb=" O ILE C1611 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'C' and resid 776 through 780 removed outlier: 5.459A pdb=" N GLN C 776 " --> pdb=" O GLY C1470 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'C' and resid 1016 through 1019 removed outlier: 7.446A pdb=" N GLN C1021 " --> pdb=" O PRO C1030 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'C' and resid 1148 through 1152 removed outlier: 4.364A pdb=" N GLY C1148 " --> pdb=" O HIS C1146 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N ALA C1142 " --> pdb=" O TYR C1152 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ARG C1133 " --> pdb=" O ARG C1119 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLY C1139 " --> pdb=" O MET C1113 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N MET C1113 " --> pdb=" O GLY C1139 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ASP C1112 " --> pdb=" O GLY C1208 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ILE C1087 " --> pdb=" O SER C1252 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N THR C1248 " --> pdb=" O GLU C1091 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'C' and resid 1171 through 1177 removed outlier: 3.806A pdb=" N ASP C1160 " --> pdb=" O THR C1107 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N GLY C1099 " --> pdb=" O MET C1168 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL C1212 " --> pdb=" O VAL C1108 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'C' and resid 1280 through 1286 removed outlier: 7.085A pdb=" N VAL C1552 " --> pdb=" O PHE C1433 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE C1433 " --> pdb=" O VAL C1552 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N GLY C1558 " --> pdb=" O TYR C1427 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N TYR C1427 " --> pdb=" O GLY C1558 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N SER C1424 " --> pdb=" O ALA C1513 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N GLY C1516 " --> pdb=" O VAL C1533 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'C' and resid 1307 through 1310 removed outlier: 4.854A pdb=" N THR C1537 " --> pdb=" O CYS C1310 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N PHE C1301 " --> pdb=" O LEU C1591 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'C' and resid 2787 through 2791 Processing sheet with id= 52, first strand: chain 'C' and resid 4132 through 4139 removed outlier: 4.768A pdb=" N PHE C4132 " --> pdb=" O ILE C4152 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'C' and resid 4521 through 4524 Processing sheet with id= 54, first strand: chain 'C' and resid 117 through 120 removed outlier: 4.141A pdb=" N HIS C 117 " --> pdb=" O ILE C 162 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'D' and resid 47 through 52 removed outlier: 6.342A pdb=" N LYS D 34 " --> pdb=" O THR D 52 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N LEU D 22 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 10.347A pdb=" N ALA D 39 " --> pdb=" O VAL D 20 " (cutoff:3.500A) removed outlier: 13.387A pdb=" N VAL D 20 " --> pdb=" O ALA D 39 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'D' and resid 67 through 70 removed outlier: 6.725A pdb=" N LEU D 120 " --> pdb=" O GLU D 70 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N LEU D 121 " --> pdb=" O LEU D 130 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N MET D 128 " --> pdb=" O HIS D 123 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'D' and resid 181 through 186 No H-bonds generated for sheet with id= 57 Processing sheet with id= 58, first strand: chain 'D' and resid 243 through 246 Processing sheet with id= 59, first strand: chain 'D' and resid 303 through 306 removed outlier: 3.683A pdb=" N LYS D 304 " --> pdb=" O HIS D 299 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N LEU D 297 " --> pdb=" O LEU D 306 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N LEU D 274 " --> pdb=" O VAL D 300 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASP D 232 " --> pdb=" O LEU D 277 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N VAL D 233 " --> pdb=" O SER D 408 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'D' and resid 329 through 333 Processing sheet with id= 61, first strand: chain 'D' and resid 737 through 741 removed outlier: 5.519A pdb=" N LEU D 730 " --> pdb=" O VAL D 741 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N HIS D 731 " --> pdb=" O ASP D 728 " (cutoff:3.500A) removed outlier: 5.681A 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= 62, first strand: chain 'D' and resid 764 through 770 removed outlier: 3.860A pdb=" N ASP D 753 " --> pdb=" O VAL D 679 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LYS D 799 " --> pdb=" O ASP D 680 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N GLY D1616 " --> pdb=" O ILE D1611 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'D' and resid 776 through 780 removed outlier: 5.461A pdb=" N GLN D 776 " --> pdb=" O GLY D1470 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'D' and resid 1016 through 1019 removed outlier: 7.446A pdb=" N GLN D1021 " --> pdb=" O PRO D1030 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'D' and resid 1148 through 1152 removed outlier: 4.365A pdb=" N GLY D1148 " --> pdb=" O HIS D1146 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N ALA D1142 " --> pdb=" O TYR D1152 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ARG D1133 " --> pdb=" O ARG D1119 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLY D1139 " --> pdb=" O MET D1113 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N MET D1113 " --> pdb=" O GLY D1139 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ASP D1112 " --> pdb=" O GLY D1208 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ILE D1087 " --> pdb=" O SER D1252 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N THR D1248 " --> pdb=" O GLU D1091 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'D' and resid 1171 through 1177 removed outlier: 3.806A pdb=" N ASP D1160 " --> pdb=" O THR D1107 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N GLY D1099 " --> pdb=" O MET D1168 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL D1212 " --> pdb=" O VAL D1108 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'D' and resid 1280 through 1286 removed outlier: 7.085A pdb=" N VAL D1552 " --> pdb=" O PHE D1433 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE D1433 " --> pdb=" O VAL D1552 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N GLY D1558 " --> pdb=" O TYR D1427 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N TYR D1427 " --> pdb=" O GLY D1558 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N SER D1424 " --> pdb=" O ALA D1513 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N GLY D1516 " --> pdb=" O VAL D1533 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'D' and resid 1307 through 1310 removed outlier: 4.853A pdb=" N THR D1537 " --> pdb=" O CYS D1310 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N PHE D1301 " --> pdb=" O LEU D1591 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'D' and resid 2787 through 2791 Processing sheet with id= 70, first strand: chain 'D' and resid 4132 through 4139 removed outlier: 4.769A pdb=" N PHE D4132 " --> pdb=" O ILE D4152 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'D' and resid 4521 through 4524 Processing sheet with id= 72, first strand: chain 'D' and resid 117 through 120 removed outlier: 4.141A pdb=" N HIS D 117 " --> pdb=" O ILE D 162 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'E' and resid 3 through 8 removed outlier: 6.645A pdb=" N ARG E 72 " --> pdb=" O ILE E 8 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLN E 71 " --> pdb=" O LEU E 104 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'E' and resid 22 through 25 Processing sheet with id= 75, first strand: chain 'F' and resid 3 through 8 removed outlier: 6.646A pdb=" N ARG F 72 " --> pdb=" O ILE F 8 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLN F 71 " --> pdb=" O LEU F 104 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'F' and resid 22 through 25 Processing sheet with id= 77, first strand: chain 'G' and resid 3 through 8 removed outlier: 6.645A pdb=" N ARG G 72 " --> pdb=" O ILE G 8 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLN G 71 " --> pdb=" O LEU G 104 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'G' and resid 22 through 25 Processing sheet with id= 79, first strand: chain 'H' and resid 3 through 8 removed outlier: 6.645A pdb=" N ARG H 72 " --> pdb=" O ILE H 8 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLN H 71 " --> pdb=" O LEU H 104 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'H' and resid 22 through 25 7452 hydrogen bonds defined for protein. 22252 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: 105.82 Time building geometry restraints manager: 44.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 45197 1.34 - 1.46: 21693 1.46 - 1.58: 73158 1.58 - 1.69: 48 1.69 - 1.81: 1512 Bond restraints: 141608 Sorted by residual: bond pdb=" CA VAL A1819 " pdb=" CB VAL A1819 " ideal model delta sigma weight residual 1.539 1.511 0.028 5.40e-03 3.43e+04 2.65e+01 bond pdb=" CA VAL D1819 " pdb=" CB VAL D1819 " ideal model delta sigma weight residual 1.539 1.511 0.028 5.40e-03 3.43e+04 2.60e+01 bond pdb=" CA VAL B1819 " pdb=" CB VAL B1819 " ideal model delta sigma weight residual 1.539 1.511 0.028 5.40e-03 3.43e+04 2.60e+01 bond pdb=" CA VAL C1819 " pdb=" CB VAL C1819 " ideal model delta sigma weight residual 1.539 1.512 0.027 5.40e-03 3.43e+04 2.51e+01 bond pdb=" CA PRO A 816 " pdb=" C PRO A 816 " ideal model delta sigma weight residual 1.514 1.494 0.020 5.50e-03 3.31e+04 1.33e+01 ... (remaining 141603 not shown) Histogram of bond angle deviations from ideal: 95.88 - 104.69: 2337 104.69 - 113.50: 78054 113.50 - 122.31: 92073 122.31 - 131.11: 18211 131.11 - 139.92: 657 Bond angle restraints: 191332 Sorted by residual: angle pdb=" CA GLU C3202 " pdb=" CB GLU C3202 " pdb=" CG GLU C3202 " ideal model delta sigma weight residual 114.10 125.36 -11.26 2.00e+00 2.50e-01 3.17e+01 angle pdb=" CA GLU B3202 " pdb=" CB GLU B3202 " pdb=" CG GLU B3202 " ideal model delta sigma weight residual 114.10 125.36 -11.26 2.00e+00 2.50e-01 3.17e+01 angle pdb=" CA GLU A3202 " pdb=" CB GLU A3202 " pdb=" CG GLU A3202 " ideal model delta sigma weight residual 114.10 125.33 -11.23 2.00e+00 2.50e-01 3.15e+01 angle pdb=" CA GLU D3202 " pdb=" CB GLU D3202 " pdb=" CG GLU D3202 " ideal model delta sigma weight residual 114.10 125.31 -11.21 2.00e+00 2.50e-01 3.14e+01 angle pdb=" N MET C2234 " pdb=" CA MET C2234 " pdb=" C MET C2234 " ideal model delta sigma weight residual 113.16 107.39 5.77 1.24e+00 6.50e-01 2.17e+01 ... (remaining 191327 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 77186 17.86 - 35.71: 6503 35.71 - 53.57: 1191 53.57 - 71.42: 353 71.42 - 89.28: 163 Dihedral angle restraints: 85396 sinusoidal: 35036 harmonic: 50360 Sorted by residual: dihedral pdb=" CA GLY D3926 " pdb=" C GLY D3926 " pdb=" N PRO D3927 " pdb=" CA PRO D3927 " ideal model delta harmonic sigma weight residual -180.00 -140.76 -39.24 0 5.00e+00 4.00e-02 6.16e+01 dihedral pdb=" CA GLY C3926 " pdb=" C GLY C3926 " pdb=" N PRO C3927 " pdb=" CA PRO C3927 " ideal model delta harmonic sigma weight residual -180.00 -140.80 -39.20 0 5.00e+00 4.00e-02 6.15e+01 dihedral pdb=" CA GLY A3926 " pdb=" C GLY A3926 " pdb=" N PRO A3927 " pdb=" CA PRO A3927 " ideal model delta harmonic sigma weight residual -180.00 -140.80 -39.20 0 5.00e+00 4.00e-02 6.15e+01 ... (remaining 85393 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 17256 0.052 - 0.104: 3211 0.104 - 0.157: 493 0.157 - 0.209: 16 0.209 - 0.261: 12 Chirality restraints: 20988 Sorted by residual: chirality pdb=" CA TRP D 902 " pdb=" N TRP D 902 " pdb=" C TRP D 902 " pdb=" CB TRP D 902 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CB ILE B1842 " pdb=" CA ILE B1842 " pdb=" CG1 ILE B1842 " pdb=" CG2 ILE B1842 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA TRP C 902 " pdb=" N TRP C 902 " pdb=" C TRP C 902 " pdb=" CB TRP C 902 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.68e+00 ... (remaining 20985 not shown) Planarity restraints: 24584 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B2635 " 0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C GLU B2635 " -0.056 2.00e-02 2.50e+03 pdb=" O GLU B2635 " 0.021 2.00e-02 2.50e+03 pdb=" N GLU B2636 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU C2635 " 0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C GLU C2635 " -0.056 2.00e-02 2.50e+03 pdb=" O GLU C2635 " 0.021 2.00e-02 2.50e+03 pdb=" N GLU C2636 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU D2635 " 0.016 2.00e-02 2.50e+03 3.17e-02 1.01e+01 pdb=" C GLU D2635 " -0.055 2.00e-02 2.50e+03 pdb=" O GLU D2635 " 0.021 2.00e-02 2.50e+03 pdb=" N GLU D2636 " 0.018 2.00e-02 2.50e+03 ... (remaining 24581 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 1460 2.64 - 3.21: 128434 3.21 - 3.77: 226678 3.77 - 4.34: 312356 4.34 - 4.90: 499342 Nonbonded interactions: 1168270 Sorted by model distance: nonbonded pdb=" OH TYR B2285 " pdb=" O ASP B2380 " model vdw 2.080 2.440 nonbonded pdb=" OH TYR A2285 " pdb=" O ASP A2380 " model vdw 2.080 2.440 nonbonded pdb=" OH TYR C2285 " pdb=" O ASP C2380 " model vdw 2.081 2.440 nonbonded pdb=" OH TYR D2285 " pdb=" O ASP D2380 " model vdw 2.081 2.440 nonbonded pdb=" OH TYR G 83 " pdb=" O PHE C1768 " model vdw 2.083 2.440 ... (remaining 1168265 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 5003)) selection = (chain 'B' and (resid 10 through 2577 or resid 2579 through 2837 or resid 2839 t \ hrough 4967 or resid 5001 through 5003)) selection = (chain 'C' and (resid 10 through 2577 or resid 2579 through 2837 or resid 2839 t \ hrough 4967 or resid 5001 through 5003)) selection = (chain 'D' and (resid 10 through 2577 or resid 2579 through 2837 or resid 2839 t \ hrough 4967 or resid 5001 through 5003)) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.090 Extract box with map and model: 30.510 Check model and map are aligned: 1.480 Set scattering table: 0.930 Process input model: 440.930 Find NCS groups from input model: 7.030 Set up NCS constraints: 0.930 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:10.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 499.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 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 : 0.003 0.076 141608 Z= 0.178 Angle : 0.614 11.263 191332 Z= 0.337 Chirality : 0.041 0.261 20988 Planarity : 0.005 0.077 24584 Dihedral : 14.381 89.278 52920 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.28 % Favored : 97.70 % Rotamer: Outliers : 0.11 % Allowed : 0.26 % Favored : 99.63 % 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: 1.30 (0.06), residues: 17212 helix: 1.90 (0.05), residues: 8960 sheet: 0.07 (0.13), residues: 1684 loop : -0.32 (0.07), residues: 6568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP B1156 HIS 0.012 0.001 HIS B2550 PHE 0.029 0.002 PHE C4511 TYR 0.037 0.002 TYR A2939 ARG 0.013 0.001 ARG C2336 *********************** 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 1047 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 1031 time to evaluate : 11.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 943 LEU cc_start: 0.9133 (mt) cc_final: 0.8912 (mt) REVERT: A 995 MET cc_start: 0.8116 (tmm) cc_final: 0.7620 (tmm) REVERT: A 3147 TYR cc_start: 0.8128 (m-80) cc_final: 0.7917 (m-10) REVERT: A 3286 ASN cc_start: 0.8372 (m-40) cc_final: 0.8061 (m-40) REVERT: A 3304 GLN cc_start: 0.8917 (tp-100) cc_final: 0.8611 (tm-30) REVERT: A 3978 MET cc_start: 0.8733 (ttp) cc_final: 0.8390 (ttp) REVERT: A 4258 MET cc_start: 0.7713 (ttt) cc_final: 0.7284 (tmt) REVERT: A 4279 MET cc_start: 0.7830 (mtp) cc_final: 0.7363 (ttp) REVERT: A 4292 MET cc_start: 0.8337 (mmm) cc_final: 0.8116 (mmm) REVERT: A 4303 ARG cc_start: 0.6114 (mmp-170) cc_final: 0.5668 (mmt180) REVERT: A 4707 MET cc_start: 0.7930 (ttp) cc_final: 0.7700 (ttm) REVERT: E 3 VAL cc_start: 0.8470 (t) cc_final: 0.7830 (p) REVERT: F 3 VAL cc_start: 0.8286 (t) cc_final: 0.7525 (p) REVERT: H 50 ARG cc_start: 0.7942 (ttp-110) cc_final: 0.7574 (ttp80) REVERT: B 309 MET cc_start: 0.6628 (mmt) cc_final: 0.6394 (tpp) REVERT: B 943 LEU cc_start: 0.9020 (mt) cc_final: 0.8773 (mt) REVERT: B 995 MET cc_start: 0.8030 (tmm) cc_final: 0.7790 (tpp) REVERT: B 999 LEU cc_start: 0.8678 (tt) cc_final: 0.8444 (tm) REVERT: B 2710 ASN cc_start: 0.8468 (p0) cc_final: 0.8075 (p0) REVERT: B 3072 MET cc_start: 0.8349 (ttp) cc_final: 0.8144 (ttm) REVERT: B 3147 TYR cc_start: 0.8146 (m-80) cc_final: 0.7886 (m-10) REVERT: B 3162 PHE cc_start: 0.8402 (t80) cc_final: 0.8119 (t80) REVERT: B 3286 ASN cc_start: 0.8439 (m-40) cc_final: 0.8140 (m-40) REVERT: B 3304 GLN cc_start: 0.9045 (tp-100) cc_final: 0.8695 (tm-30) REVERT: B 4258 MET cc_start: 0.7692 (ttt) cc_final: 0.7292 (tmt) REVERT: B 4707 MET cc_start: 0.8085 (ttp) cc_final: 0.7839 (ttm) REVERT: B 4748 MET cc_start: 0.6814 (mpp) cc_final: 0.6608 (mpt) REVERT: C 309 MET cc_start: 0.6656 (mmt) cc_final: 0.6431 (tpp) REVERT: C 943 LEU cc_start: 0.8940 (mt) cc_final: 0.8699 (mt) REVERT: C 995 MET cc_start: 0.8061 (tmm) cc_final: 0.7647 (tmm) REVERT: C 1694 MET cc_start: 0.9024 (tpt) cc_final: 0.8497 (tpt) REVERT: C 3095 ASN cc_start: 0.8597 (m110) cc_final: 0.7942 (m110) REVERT: C 3147 TYR cc_start: 0.7954 (m-80) cc_final: 0.7713 (m-10) REVERT: C 3304 GLN cc_start: 0.8919 (tp-100) cc_final: 0.8444 (tp-100) REVERT: C 4258 MET cc_start: 0.7498 (ttt) cc_final: 0.7162 (tmt) REVERT: C 4307 ARG cc_start: 0.7750 (mtt90) cc_final: 0.7482 (mtt90) REVERT: C 4707 MET cc_start: 0.8026 (ttp) cc_final: 0.7707 (ttm) REVERT: D 202 HIS cc_start: 0.6620 (m-70) cc_final: 0.6414 (m170) REVERT: D 943 LEU cc_start: 0.9049 (mt) cc_final: 0.8830 (mt) REVERT: D 995 MET cc_start: 0.8218 (tmm) cc_final: 0.7682 (tmm) REVERT: D 3286 ASN cc_start: 0.8649 (m-40) cc_final: 0.8363 (m-40) REVERT: D 3304 GLN cc_start: 0.8784 (tp-100) cc_final: 0.8432 (tm-30) REVERT: D 3978 MET cc_start: 0.8720 (ttp) cc_final: 0.8428 (ttp) REVERT: D 4258 MET cc_start: 0.7573 (ttt) cc_final: 0.7153 (tmt) REVERT: D 4292 MET cc_start: 0.8298 (mmm) cc_final: 0.8056 (mmm) REVERT: D 4303 ARG cc_start: 0.5987 (mmp-170) cc_final: 0.5601 (mmt180) outliers start: 16 outliers final: 6 residues processed: 1037 average time/residue: 2.1133 time to fit residues: 3101.2261 Evaluate side-chains 900 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 894 time to evaluate : 11.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3202 GLU Chi-restraints excluded: chain B residue 3202 GLU Chi-restraints excluded: chain C residue 1948 MET Chi-restraints excluded: chain C residue 3202 GLU Chi-restraints excluded: chain C residue 3739 MET Chi-restraints excluded: chain D residue 3202 GLU 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: 10.0000 chunk 726 optimal weight: 10.0000 chunk 447 optimal weight: 8.9990 chunk 883 optimal weight: 7.9990 chunk 699 optimal weight: 4.9990 chunk 1354 optimal weight: 9.9990 chunk 524 optimal weight: 10.0000 chunk 823 optimal weight: 5.9990 chunk 1008 optimal weight: 7.9990 chunk 1569 optimal weight: 9.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1974 ASN A2550 HIS ** A2830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3811 GLN A3955 GLN A3975 GLN ** A4057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 26 HIS G 26 HIS H 26 HIS B 225 GLN ** B 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2251 ASN B2309 ASN B2550 HIS ** B3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3955 GLN B3975 GLN ** B4057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4164 GLN C 225 GLN ** C 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2217 HIS C2251 ASN C2309 ASN C2550 HIS ** C3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3955 GLN C3975 GLN C4493 ASN D 313 ASN ** D 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1147 GLN ** D1501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1974 ASN D2550 HIS ** D2830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3955 GLN D3975 GLN ** D4057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4493 ASN ** D4636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.109 141608 Z= 0.596 Angle : 0.727 14.258 191332 Z= 0.378 Chirality : 0.049 0.308 20988 Planarity : 0.006 0.153 24584 Dihedral : 6.566 98.783 19042 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.56 % Allowed : 4.85 % Favored : 94.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.06), residues: 17212 helix: 1.81 (0.05), residues: 8976 sheet: 0.05 (0.12), residues: 1724 loop : -0.34 (0.08), residues: 6512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.003 TRP A1156 HIS 0.020 0.002 HIS B 123 PHE 0.051 0.003 PHE B3888 TYR 0.045 0.003 TYR C3285 ARG 0.018 0.001 ARG H 14 *********************** 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 1062 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 977 time to evaluate : 11.808 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: A 943 LEU cc_start: 0.9202 (mt) cc_final: 0.8913 (mm) REVERT: A 995 MET cc_start: 0.8201 (tmm) cc_final: 0.7835 (tmm) REVERT: A 2688 MET cc_start: 0.4513 (tmm) cc_final: 0.4269 (tmm) REVERT: A 2689 MET cc_start: 0.2316 (tmm) cc_final: 0.1719 (mmm) REVERT: A 3092 GLN cc_start: 0.7911 (tp40) cc_final: 0.7628 (tp-100) REVERT: A 3142 THR cc_start: 0.8632 (m) cc_final: 0.8334 (p) REVERT: A 3286 ASN cc_start: 0.8495 (m-40) cc_final: 0.8142 (m-40) REVERT: A 3297 LYS cc_start: 0.6504 (mmpt) cc_final: 0.5891 (mmtt) REVERT: A 3304 GLN cc_start: 0.8985 (tp-100) cc_final: 0.8569 (tp-100) REVERT: A 4258 MET cc_start: 0.7775 (ttt) cc_final: 0.7342 (tmt) REVERT: A 4292 MET cc_start: 0.8432 (mmm) cc_final: 0.8216 (mmp) REVERT: A 4303 ARG cc_start: 0.6061 (mmp-170) cc_final: 0.5733 (mmt180) REVERT: A 4307 ARG cc_start: 0.7385 (mtm-85) cc_final: 0.7166 (mtm110) REVERT: A 4707 MET cc_start: 0.8176 (ttp) cc_final: 0.7894 (ttm) REVERT: E 74 LYS cc_start: 0.8894 (ttpt) cc_final: 0.8673 (tttp) REVERT: F 30 MET cc_start: 0.7405 (OUTLIER) cc_final: 0.6807 (mpt) REVERT: F 53 LYS cc_start: 0.8951 (OUTLIER) cc_final: 0.8746 (mtpp) REVERT: B 678 MET cc_start: 0.7721 (tpp) cc_final: 0.7403 (ttp) REVERT: B 943 LEU cc_start: 0.9101 (mt) cc_final: 0.8839 (mt) REVERT: B 995 MET cc_start: 0.8109 (tmm) cc_final: 0.7830 (tpp) REVERT: B 1113 MET cc_start: 0.8694 (mtp) cc_final: 0.8474 (mtm) REVERT: B 2710 ASN cc_start: 0.8615 (p0) cc_final: 0.8176 (p0) REVERT: B 3215 MET cc_start: 0.9160 (mmt) cc_final: 0.8877 (mmm) REVERT: B 3265 CYS cc_start: 0.7973 (m) cc_final: 0.7700 (m) REVERT: B 3286 ASN cc_start: 0.8570 (m-40) cc_final: 0.8232 (m-40) REVERT: B 3304 GLN cc_start: 0.9065 (tp-100) cc_final: 0.8599 (tp-100) REVERT: B 4035 TYR cc_start: 0.7947 (m-80) cc_final: 0.7722 (m-80) REVERT: B 4258 MET cc_start: 0.7739 (ttt) cc_final: 0.7352 (tmt) REVERT: B 4707 MET cc_start: 0.8197 (ttp) cc_final: 0.7910 (ttm) REVERT: C 943 LEU cc_start: 0.9099 (mt) cc_final: 0.8812 (mt) REVERT: C 995 MET cc_start: 0.8140 (tmm) cc_final: 0.7710 (tmm) REVERT: C 3147 TYR cc_start: 0.8087 (m-80) cc_final: 0.7835 (m-10) REVERT: C 3304 GLN cc_start: 0.9001 (tp-100) cc_final: 0.8475 (tp-100) REVERT: C 4258 MET cc_start: 0.7594 (ttt) cc_final: 0.7203 (tmt) REVERT: C 4707 MET cc_start: 0.8135 (ttp) cc_final: 0.7830 (ttm) REVERT: D 241 MET cc_start: 0.5813 (tpt) cc_final: 0.5552 (tpp) REVERT: D 943 LEU cc_start: 0.9164 (mt) cc_final: 0.8874 (mt) REVERT: D 995 MET cc_start: 0.8237 (tmm) cc_final: 0.7683 (tmm) REVERT: D 3003 MET cc_start: 0.8926 (mtm) cc_final: 0.8365 (mtm) REVERT: D 3273 MET cc_start: 0.9120 (OUTLIER) cc_final: 0.8680 (mtp) REVERT: D 3286 ASN cc_start: 0.8679 (m-40) cc_final: 0.8379 (m-40) REVERT: D 3288 LEU cc_start: 0.7990 (mt) cc_final: 0.7728 (mt) REVERT: D 3297 LYS cc_start: 0.6405 (mmtt) cc_final: 0.5523 (mmtt) REVERT: D 3304 GLN cc_start: 0.8928 (tp-100) cc_final: 0.8417 (tp-100) REVERT: D 3310 VAL cc_start: 0.9419 (t) cc_final: 0.9196 (m) REVERT: D 3315 LEU cc_start: 0.8716 (tp) cc_final: 0.8471 (tm) REVERT: D 4258 MET cc_start: 0.7689 (ttt) cc_final: 0.7204 (tmt) REVERT: D 4292 MET cc_start: 0.8355 (mmm) cc_final: 0.8147 (mmp) REVERT: D 4303 ARG cc_start: 0.6180 (mmp-170) cc_final: 0.5761 (mmt180) outliers start: 85 outliers final: 23 residues processed: 998 average time/residue: 2.1264 time to fit residues: 3024.0337 Evaluate side-chains 947 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 921 time to evaluate : 11.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 931 TYR Chi-restraints excluded: chain A residue 2142 MET Chi-restraints excluded: chain A residue 3050 LEU Chi-restraints excluded: chain A residue 3197 LEU Chi-restraints excluded: chain A residue 3202 GLU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain F residue 30 MET Chi-restraints excluded: chain F residue 53 LYS Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain B residue 931 TYR Chi-restraints excluded: chain B residue 1599 MET Chi-restraints excluded: chain B residue 2142 MET Chi-restraints excluded: chain B residue 3150 ARG Chi-restraints excluded: chain B residue 3189 SER Chi-restraints excluded: chain B residue 3201 VAL Chi-restraints excluded: chain B residue 3202 GLU Chi-restraints excluded: chain C residue 931 TYR Chi-restraints excluded: chain C residue 1599 MET Chi-restraints excluded: chain C residue 1720 MET Chi-restraints excluded: chain C residue 3201 VAL Chi-restraints excluded: chain C residue 3202 GLU Chi-restraints excluded: chain D residue 931 TYR Chi-restraints excluded: chain D residue 2142 MET Chi-restraints excluded: chain D residue 3202 GLU Chi-restraints excluded: chain D residue 3273 MET 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: 3.9990 chunk 1306 optimal weight: 10.0000 chunk 1068 optimal weight: 3.9990 chunk 432 optimal weight: 3.9990 chunk 1572 optimal weight: 20.0000 chunk 1698 optimal weight: 9.9990 chunk 1400 optimal weight: 5.9990 chunk 1558 optimal weight: 4.9990 chunk 535 optimal weight: 0.9980 chunk 1261 optimal weight: 9.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1554 GLN A1974 ASN ** A3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 26 HIS E 32 GLN ** H 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 GLN ** B 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 932 ASN ** B 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1554 GLN B3151 GLN ** B3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 225 GLN ** C 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 932 ASN ** C 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1554 GLN ** C3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3811 GLN C3955 GLN C3975 GLN C4493 ASN D 225 GLN ** D 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1147 GLN ** D1501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1554 GLN D1974 ASN ** D3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3811 GLN D3955 GLN D3975 GLN D4493 ASN ** D4636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 141608 Z= 0.261 Angle : 0.588 18.793 191332 Z= 0.302 Chirality : 0.041 0.276 20988 Planarity : 0.004 0.080 24584 Dihedral : 6.259 99.537 19036 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.60 % Allowed : 6.53 % Favored : 92.87 % 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: 1.42 (0.06), residues: 17212 helix: 2.04 (0.06), residues: 8936 sheet: -0.04 (0.12), residues: 1764 loop : -0.29 (0.08), residues: 6512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP A 893 HIS 0.015 0.001 HIS C3318 PHE 0.022 0.002 PHE C3888 TYR 0.034 0.002 TYR C2801 ARG 0.012 0.000 ARG H 14 *********************** 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 1038 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 947 time to evaluate : 11.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 ASN cc_start: 0.7867 (t0) cc_final: 0.7601 (m-40) REVERT: A 317 MET cc_start: 0.7397 (ppp) cc_final: 0.7136 (pp-130) REVERT: A 943 LEU cc_start: 0.9153 (mt) cc_final: 0.8889 (mt) REVERT: A 995 MET cc_start: 0.8130 (tmm) cc_final: 0.7782 (tmm) REVERT: A 2192 MET cc_start: 0.8291 (tpp) cc_final: 0.8037 (tpp) REVERT: A 2689 MET cc_start: 0.2379 (tmm) cc_final: 0.1847 (mmm) REVERT: A 2940 ILE cc_start: 0.8783 (OUTLIER) cc_final: 0.8422 (tt) REVERT: A 3092 GLN cc_start: 0.7880 (tp40) cc_final: 0.7676 (tp40) REVERT: A 3142 THR cc_start: 0.8590 (m) cc_final: 0.8307 (p) REVERT: A 3215 MET cc_start: 0.9139 (mmt) cc_final: 0.8823 (mmm) REVERT: A 3286 ASN cc_start: 0.8441 (m-40) cc_final: 0.8074 (m-40) REVERT: A 3304 GLN cc_start: 0.8944 (tp-100) cc_final: 0.8408 (tp-100) REVERT: A 4258 MET cc_start: 0.7737 (ttt) cc_final: 0.7287 (tmt) REVERT: A 4292 MET cc_start: 0.8410 (mmm) cc_final: 0.8181 (mmp) REVERT: A 4303 ARG cc_start: 0.6105 (mmp-170) cc_final: 0.5761 (mmt180) REVERT: A 4707 MET cc_start: 0.8167 (ttp) cc_final: 0.7874 (ttm) REVERT: F 30 MET cc_start: 0.7365 (OUTLIER) cc_final: 0.6837 (mpt) REVERT: G 18 LYS cc_start: 0.9031 (mppt) cc_final: 0.8754 (mttp) REVERT: H 18 LYS cc_start: 0.8998 (mppt) cc_final: 0.8714 (mttp) REVERT: H 30 MET cc_start: 0.7393 (OUTLIER) cc_final: 0.6816 (mpt) REVERT: B 943 LEU cc_start: 0.9117 (mt) cc_final: 0.8788 (mt) REVERT: B 995 MET cc_start: 0.8074 (tmm) cc_final: 0.7796 (tpp) REVERT: B 1975 MET cc_start: 0.7623 (mtp) cc_final: 0.7350 (mtm) REVERT: B 2710 ASN cc_start: 0.8619 (p0) cc_final: 0.8159 (p0) REVERT: B 2940 ILE cc_start: 0.8823 (OUTLIER) cc_final: 0.8468 (pp) REVERT: B 3215 MET cc_start: 0.9182 (mmt) cc_final: 0.8893 (mmm) REVERT: B 3265 CYS cc_start: 0.7882 (m) cc_final: 0.7610 (m) REVERT: B 3286 ASN cc_start: 0.8481 (m-40) cc_final: 0.8201 (m-40) REVERT: B 3304 GLN cc_start: 0.9019 (tp-100) cc_final: 0.8530 (tp-100) REVERT: B 4035 TYR cc_start: 0.7834 (m-80) cc_final: 0.7627 (m-80) REVERT: B 4258 MET cc_start: 0.7712 (ttt) cc_final: 0.7301 (tmt) REVERT: B 4707 MET cc_start: 0.8199 (ttp) cc_final: 0.7922 (ttm) REVERT: C 111 ARG cc_start: 0.7669 (mmt180) cc_final: 0.7415 (mmp80) REVERT: C 943 LEU cc_start: 0.9063 (mt) cc_final: 0.8778 (mt) REVERT: C 983 LEU cc_start: 0.8115 (mm) cc_final: 0.7680 (mm) REVERT: C 995 MET cc_start: 0.8108 (tmm) cc_final: 0.7645 (tmm) REVERT: C 2939 TYR cc_start: 0.7959 (m-10) cc_final: 0.7580 (m-80) REVERT: C 2940 ILE cc_start: 0.8843 (OUTLIER) cc_final: 0.8535 (pp) REVERT: C 3147 TYR cc_start: 0.8020 (m-80) cc_final: 0.7768 (m-10) REVERT: C 3286 ASN cc_start: 0.8660 (m-40) cc_final: 0.8351 (m-40) REVERT: C 3304 GLN cc_start: 0.8964 (tp-100) cc_final: 0.8420 (tp-100) REVERT: C 3605 MET cc_start: 0.4733 (tmm) cc_final: 0.4488 (ppp) REVERT: C 4258 MET cc_start: 0.7598 (ttt) cc_final: 0.7216 (tmt) REVERT: C 4707 MET cc_start: 0.8121 (ttp) cc_final: 0.7817 (ttm) REVERT: D 241 MET cc_start: 0.5729 (tpt) cc_final: 0.5494 (tpp) REVERT: D 943 LEU cc_start: 0.9120 (mt) cc_final: 0.8821 (mt) REVERT: D 983 LEU cc_start: 0.8147 (mm) cc_final: 0.7781 (mm) REVERT: D 995 MET cc_start: 0.8147 (tmm) cc_final: 0.7548 (tmm) REVERT: D 2688 MET cc_start: 0.5115 (tmm) cc_final: 0.4901 (tmm) REVERT: D 2940 ILE cc_start: 0.8762 (OUTLIER) cc_final: 0.8432 (tt) REVERT: D 3273 MET cc_start: 0.9135 (OUTLIER) cc_final: 0.8848 (mmt) REVERT: D 3286 ASN cc_start: 0.8648 (m-40) cc_final: 0.8326 (m-40) REVERT: D 3304 GLN cc_start: 0.8899 (tp-100) cc_final: 0.8392 (tp-100) REVERT: D 3310 VAL cc_start: 0.9426 (t) cc_final: 0.9220 (m) REVERT: D 4258 MET cc_start: 0.7678 (ttt) cc_final: 0.7228 (tmt) REVERT: D 4292 MET cc_start: 0.8364 (mmm) cc_final: 0.8154 (mmp) REVERT: D 4303 ARG cc_start: 0.6197 (mmp-170) cc_final: 0.5723 (mmt180) REVERT: D 4878 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.7270 (mt-10) outliers start: 91 outliers final: 28 residues processed: 989 average time/residue: 2.1541 time to fit residues: 3029.9051 Evaluate side-chains 960 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 924 time to evaluate : 11.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 2142 MET Chi-restraints excluded: chain A residue 2940 ILE Chi-restraints excluded: chain A residue 3150 ARG Chi-restraints excluded: chain A residue 3653 GLU Chi-restraints excluded: chain A residue 3739 MET Chi-restraints excluded: chain A residue 4878 GLU Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain F residue 30 MET Chi-restraints excluded: chain H residue 30 MET Chi-restraints excluded: chain B residue 776 GLN Chi-restraints excluded: chain B residue 1599 MET Chi-restraints excluded: chain B residue 1948 MET Chi-restraints excluded: chain B residue 2142 MET Chi-restraints excluded: chain B residue 2234 MET Chi-restraints excluded: chain B residue 2456 MET Chi-restraints excluded: chain B residue 2940 ILE Chi-restraints excluded: chain B residue 3150 ARG Chi-restraints excluded: chain B residue 3189 SER Chi-restraints excluded: chain B residue 3290 ILE Chi-restraints excluded: chain B residue 3653 GLU Chi-restraints excluded: chain B residue 4878 GLU Chi-restraints excluded: chain C residue 776 GLN Chi-restraints excluded: chain C residue 1599 MET Chi-restraints excluded: chain C residue 2940 ILE Chi-restraints excluded: chain C residue 3150 ARG Chi-restraints excluded: chain C residue 3653 GLU Chi-restraints excluded: chain C residue 4878 GLU Chi-restraints excluded: chain D residue 776 GLN Chi-restraints excluded: chain D residue 931 TYR Chi-restraints excluded: chain D residue 2142 MET Chi-restraints excluded: chain D residue 2940 ILE Chi-restraints excluded: chain D residue 3273 MET Chi-restraints excluded: chain D residue 3653 GLU Chi-restraints excluded: chain D residue 3739 MET Chi-restraints excluded: chain D residue 4878 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1553 optimal weight: 10.0000 chunk 1181 optimal weight: 20.0000 chunk 815 optimal weight: 40.0000 chunk 174 optimal weight: 6.9990 chunk 750 optimal weight: 9.9990 chunk 1055 optimal weight: 0.9980 chunk 1577 optimal weight: 10.0000 chunk 1670 optimal weight: 4.9990 chunk 824 optimal weight: 9.9990 chunk 1495 optimal weight: 6.9990 chunk 450 optimal weight: 8.9990 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 ASN ** A 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1974 ASN ** A3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4493 ASN E 26 HIS G 26 HIS H 26 HIS B 225 GLN B 469 HIS ** B 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2684 ASN ** B3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4493 ASN C 225 GLN ** C 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3955 GLN C3975 GLN C4493 ASN D 198 ASN ** D 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1974 ASN ** D3151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3955 GLN D3975 GLN D4493 ASN ** D4636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 141608 Z= 0.472 Angle : 0.643 15.884 191332 Z= 0.330 Chirality : 0.045 0.343 20988 Planarity : 0.005 0.105 24584 Dihedral : 6.140 78.580 19024 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.74 % Allowed : 7.67 % Favored : 91.59 % 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: 1.37 (0.06), residues: 17212 helix: 1.98 (0.05), residues: 9004 sheet: -0.10 (0.12), residues: 1832 loop : -0.29 (0.08), residues: 6376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.087 0.002 TRP B 893 HIS 0.015 0.001 HIS C3318 PHE 0.027 0.002 PHE C3888 TYR 0.037 0.002 TYR C2801 ARG 0.014 0.001 ARG F 14 *********************** 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 1054 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 942 time to evaluate : 11.729 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: A 313 ASN cc_start: 0.7889 (t0) cc_final: 0.7533 (m-40) REVERT: A 317 MET cc_start: 0.7474 (ppp) cc_final: 0.7249 (ppp) REVERT: A 943 LEU cc_start: 0.9176 (mt) cc_final: 0.8922 (mt) REVERT: A 995 MET cc_start: 0.8172 (tmm) cc_final: 0.7607 (tmm) REVERT: A 2538 THR cc_start: 0.8401 (OUTLIER) cc_final: 0.8138 (t) REVERT: A 2689 MET cc_start: 0.2481 (tmm) cc_final: 0.2153 (mmm) REVERT: A 2940 ILE cc_start: 0.8806 (OUTLIER) cc_final: 0.8441 (tt) REVERT: A 3092 GLN cc_start: 0.7928 (tp40) cc_final: 0.7718 (tp40) REVERT: A 3121 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8601 (tp) REVERT: A 3142 THR cc_start: 0.8619 (m) cc_final: 0.8361 (p) REVERT: A 3215 MET cc_start: 0.9176 (mmt) cc_final: 0.8840 (mmm) REVERT: A 3286 ASN cc_start: 0.8441 (m-40) cc_final: 0.8077 (m-40) REVERT: A 3297 LYS cc_start: 0.6509 (OUTLIER) cc_final: 0.6113 (mptt) REVERT: A 3304 GLN cc_start: 0.8969 (tp-100) cc_final: 0.8447 (tp-100) REVERT: A 4258 MET cc_start: 0.7776 (ttt) cc_final: 0.7303 (tmt) REVERT: A 4292 MET cc_start: 0.8405 (mmm) cc_final: 0.8192 (mmp) REVERT: A 4303 ARG cc_start: 0.6203 (mmp-170) cc_final: 0.5783 (mmt180) REVERT: A 4707 MET cc_start: 0.8165 (ttp) cc_final: 0.7871 (ttm) REVERT: F 30 MET cc_start: 0.7457 (OUTLIER) cc_final: 0.6842 (mpt) REVERT: G 18 LYS cc_start: 0.9051 (mppt) cc_final: 0.8778 (mttp) REVERT: H 18 LYS cc_start: 0.9009 (mppt) cc_final: 0.8744 (mttp) REVERT: B 655 MET cc_start: 0.8622 (mmm) cc_final: 0.8377 (mmm) REVERT: B 943 LEU cc_start: 0.9153 (mt) cc_final: 0.8819 (mt) REVERT: B 995 MET cc_start: 0.8130 (tmm) cc_final: 0.7671 (tmm) REVERT: B 2279 MET cc_start: 0.8006 (ttp) cc_final: 0.7698 (tmm) REVERT: B 2538 THR cc_start: 0.8368 (OUTLIER) cc_final: 0.8133 (t) REVERT: B 2627 TRP cc_start: 0.8477 (OUTLIER) cc_final: 0.7751 (m-10) REVERT: B 2940 ILE cc_start: 0.8852 (OUTLIER) cc_final: 0.8496 (pp) REVERT: B 3150 ARG cc_start: 0.7724 (tpm-80) cc_final: 0.7519 (OUTLIER) REVERT: B 3215 MET cc_start: 0.9209 (mmt) cc_final: 0.8898 (mmm) REVERT: B 3265 CYS cc_start: 0.7922 (m) cc_final: 0.7680 (m) REVERT: B 3286 ASN cc_start: 0.8499 (m-40) cc_final: 0.8182 (m-40) REVERT: B 3304 GLN cc_start: 0.9016 (tp-100) cc_final: 0.8528 (tp-100) REVERT: B 4035 TYR cc_start: 0.7827 (m-80) cc_final: 0.7609 (m-80) REVERT: B 4258 MET cc_start: 0.7761 (ttt) cc_final: 0.7351 (tmt) REVERT: B 4303 ARG cc_start: 0.6187 (mmp-170) cc_final: 0.5776 (mmt90) REVERT: B 4502 MET cc_start: 0.7887 (OUTLIER) cc_final: 0.7606 (mtp) REVERT: B 4707 MET cc_start: 0.8183 (ttp) cc_final: 0.7922 (ttm) REVERT: C 943 LEU cc_start: 0.9116 (mt) cc_final: 0.8827 (mt) REVERT: C 983 LEU cc_start: 0.8348 (mm) cc_final: 0.7959 (mm) REVERT: C 995 MET cc_start: 0.8139 (tmm) cc_final: 0.7658 (tmm) REVERT: C 1421 MET cc_start: 0.8676 (mmp) cc_final: 0.8476 (mmp) REVERT: C 2940 ILE cc_start: 0.8831 (OUTLIER) cc_final: 0.8505 (tt) REVERT: C 3147 TYR cc_start: 0.8066 (m-80) cc_final: 0.7794 (m-80) REVERT: C 3304 GLN cc_start: 0.8978 (tp-100) cc_final: 0.8442 (tp-100) REVERT: C 4258 MET cc_start: 0.7629 (ttt) cc_final: 0.7244 (tmt) REVERT: C 4307 ARG cc_start: 0.7535 (mtt90) cc_final: 0.7298 (mtt90) REVERT: C 4502 MET cc_start: 0.7901 (mtm) cc_final: 0.7633 (mtp) REVERT: C 4878 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.7243 (mt-10) REVERT: D 198 ASN cc_start: 0.4753 (OUTLIER) cc_final: 0.3906 (p0) REVERT: D 202 HIS cc_start: 0.6568 (m170) cc_final: 0.6058 (m90) REVERT: D 241 MET cc_start: 0.5703 (tpt) cc_final: 0.5478 (tpp) REVERT: D 317 MET cc_start: 0.7451 (ppp) cc_final: 0.7068 (ppp) REVERT: D 943 LEU cc_start: 0.9167 (mt) cc_final: 0.8875 (mt) REVERT: D 983 LEU cc_start: 0.8313 (mm) cc_final: 0.8013 (mm) REVERT: D 995 MET cc_start: 0.8168 (tmm) cc_final: 0.7580 (tmm) REVERT: D 2538 THR cc_start: 0.8296 (OUTLIER) cc_final: 0.8051 (t) REVERT: D 2940 ILE cc_start: 0.8771 (OUTLIER) cc_final: 0.8458 (tt) REVERT: D 3003 MET cc_start: 0.8863 (mtm) cc_final: 0.8338 (mtm) REVERT: D 3273 MET cc_start: 0.9145 (OUTLIER) cc_final: 0.8881 (mmt) REVERT: D 3286 ASN cc_start: 0.8660 (m-40) cc_final: 0.8323 (m-40) REVERT: D 3297 LYS cc_start: 0.6378 (mmtt) cc_final: 0.5272 (mmtt) REVERT: D 3304 GLN cc_start: 0.8937 (tp-100) cc_final: 0.8432 (tp-100) REVERT: D 3310 VAL cc_start: 0.9440 (t) cc_final: 0.9218 (m) REVERT: D 4258 MET cc_start: 0.7673 (ttt) cc_final: 0.7194 (tmt) REVERT: D 4292 MET cc_start: 0.8365 (mmm) cc_final: 0.8155 (mmp) REVERT: D 4303 ARG cc_start: 0.6157 (mmp-170) cc_final: 0.5699 (mmt180) REVERT: D 4502 MET cc_start: 0.7899 (mtm) cc_final: 0.7653 (mtp) REVERT: D 4707 MET cc_start: 0.8135 (ttp) cc_final: 0.7911 (ttm) REVERT: D 4878 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.7244 (mt-10) outliers start: 112 outliers final: 42 residues processed: 1003 average time/residue: 2.1439 time to fit residues: 3074.3297 Evaluate side-chains 976 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 919 time to evaluate : 11.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 1896 MET Chi-restraints excluded: chain A residue 2142 MET Chi-restraints excluded: chain A residue 2234 MET Chi-restraints excluded: chain A residue 2538 THR Chi-restraints excluded: chain A residue 2844 MET Chi-restraints excluded: chain A residue 2940 ILE Chi-restraints excluded: chain A residue 2943 PHE Chi-restraints excluded: chain A residue 3050 LEU Chi-restraints excluded: chain A residue 3121 LEU Chi-restraints excluded: chain A residue 3150 ARG Chi-restraints excluded: chain A residue 3297 LYS Chi-restraints excluded: chain A residue 3653 GLU Chi-restraints excluded: chain A residue 3854 PHE Chi-restraints excluded: chain A residue 3954 MET Chi-restraints excluded: chain A residue 4878 GLU Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain F residue 30 MET Chi-restraints excluded: chain G residue 30 MET Chi-restraints excluded: chain H residue 30 MET Chi-restraints excluded: chain B residue 776 GLN Chi-restraints excluded: chain B residue 1599 MET Chi-restraints excluded: chain B residue 1948 MET Chi-restraints excluded: chain B residue 2142 MET Chi-restraints excluded: chain B residue 2234 MET Chi-restraints excluded: chain B residue 2538 THR Chi-restraints excluded: chain B residue 2627 TRP Chi-restraints excluded: chain B residue 2844 MET Chi-restraints excluded: chain B residue 2940 ILE Chi-restraints excluded: chain B residue 3201 VAL Chi-restraints excluded: chain B residue 3290 ILE Chi-restraints excluded: chain B residue 3653 GLU Chi-restraints excluded: chain B residue 3854 PHE Chi-restraints excluded: chain B residue 4502 MET Chi-restraints excluded: chain B residue 4878 GLU Chi-restraints excluded: chain C residue 776 GLN Chi-restraints excluded: chain C residue 931 TYR Chi-restraints excluded: chain C residue 1599 MET Chi-restraints excluded: chain C residue 2234 MET Chi-restraints excluded: chain C residue 2940 ILE Chi-restraints excluded: chain C residue 3150 ARG Chi-restraints excluded: chain C residue 3201 VAL Chi-restraints excluded: chain C residue 3653 GLU Chi-restraints excluded: chain C residue 3854 PHE Chi-restraints excluded: chain C residue 4878 GLU Chi-restraints excluded: chain D residue 198 ASN Chi-restraints excluded: chain D residue 776 GLN Chi-restraints excluded: chain D residue 1720 MET Chi-restraints excluded: chain D residue 2142 MET Chi-restraints excluded: chain D residue 2538 THR Chi-restraints excluded: chain D residue 2844 MET Chi-restraints excluded: chain D residue 2940 ILE Chi-restraints excluded: chain D residue 3150 ARG Chi-restraints excluded: chain D residue 3273 MET Chi-restraints excluded: chain D residue 3739 MET Chi-restraints excluded: chain D residue 3854 PHE Chi-restraints excluded: chain D residue 4878 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1391 optimal weight: 9.9990 chunk 948 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 1243 optimal weight: 1.9990 chunk 689 optimal weight: 1.9990 chunk 1425 optimal weight: 8.9990 chunk 1154 optimal weight: 40.0000 chunk 1 optimal weight: 6.9990 chunk 852 optimal weight: 1.9990 chunk 1499 optimal weight: 2.9990 chunk 421 optimal weight: 6.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 914 GLN ** A1501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2684 ASN ** A3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4493 ASN E 26 HIS G 26 HIS H 26 HIS B 225 GLN ** B1501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3955 GLN B3975 GLN B4493 ASN C 225 GLN ** C 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 934 GLN ** C1501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3955 GLN C3975 GLN C4493 ASN ** C4636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 914 GLN D 934 GLN ** D1501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1974 ASN D2684 ASN D3151 GLN ** D3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4493 ASN ** D4636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 141608 Z= 0.214 Angle : 0.584 16.488 191332 Z= 0.297 Chirality : 0.040 0.352 20988 Planarity : 0.004 0.142 24584 Dihedral : 6.054 163.407 19024 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.70 % Allowed : 8.37 % Favored : 90.92 % 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: 1.54 (0.07), residues: 17212 helix: 2.16 (0.06), residues: 8944 sheet: -0.05 (0.12), residues: 1824 loop : -0.24 (0.08), residues: 6444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.079 0.001 TRP A 893 HIS 0.016 0.001 HIS C3318 PHE 0.020 0.001 PHE C4508 TYR 0.031 0.001 TYR C2801 ARG 0.015 0.000 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 1030 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 923 time to evaluate : 11.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 ASN cc_start: 0.4686 (OUTLIER) cc_final: 0.4146 (m110) REVERT: A 313 ASN cc_start: 0.7899 (t0) cc_final: 0.7548 (m-40) REVERT: A 317 MET cc_start: 0.7502 (ppp) cc_final: 0.7073 (ppp) REVERT: A 943 LEU cc_start: 0.9167 (mt) cc_final: 0.8901 (mt) REVERT: A 995 MET cc_start: 0.8154 (tmm) cc_final: 0.7559 (tmm) REVERT: A 1057 LEU cc_start: 0.9323 (mm) cc_final: 0.9072 (mt) REVERT: A 2538 THR cc_start: 0.8200 (OUTLIER) cc_final: 0.7896 (t) REVERT: A 2627 TRP cc_start: 0.8342 (OUTLIER) cc_final: 0.7454 (m-10) REVERT: A 2939 TYR cc_start: 0.7881 (m-10) cc_final: 0.7642 (m-80) REVERT: A 2940 ILE cc_start: 0.8855 (OUTLIER) cc_final: 0.8504 (tt) REVERT: A 3121 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8579 (tp) REVERT: A 3142 THR cc_start: 0.8567 (m) cc_final: 0.8305 (p) REVERT: A 3215 MET cc_start: 0.9198 (mmt) cc_final: 0.8848 (mmm) REVERT: A 3286 ASN cc_start: 0.8388 (m-40) cc_final: 0.8024 (m-40) REVERT: A 3304 GLN cc_start: 0.8932 (tp-100) cc_final: 0.8470 (tp-100) REVERT: A 4258 MET cc_start: 0.7715 (ttt) cc_final: 0.7267 (tmt) REVERT: A 4292 MET cc_start: 0.8405 (mmm) cc_final: 0.8195 (mmp) REVERT: A 4303 ARG cc_start: 0.6214 (mmp-170) cc_final: 0.5834 (mmt180) REVERT: A 4502 MET cc_start: 0.7818 (mtm) cc_final: 0.7612 (mtp) REVERT: A 4707 MET cc_start: 0.8164 (ttp) cc_final: 0.7864 (ttm) REVERT: A 4878 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.7267 (mt-10) REVERT: E 53 LYS cc_start: 0.8789 (mmmm) cc_final: 0.8453 (mmmm) REVERT: G 18 LYS cc_start: 0.9060 (mppt) cc_final: 0.8798 (mttp) REVERT: G 30 MET cc_start: 0.7332 (OUTLIER) cc_final: 0.6743 (mpp) REVERT: H 18 LYS cc_start: 0.9023 (mppt) cc_final: 0.8777 (mttp) REVERT: H 30 MET cc_start: 0.7356 (OUTLIER) cc_final: 0.6741 (mpp) REVERT: B 198 ASN cc_start: 0.5064 (OUTLIER) cc_final: 0.4612 (m110) REVERT: B 655 MET cc_start: 0.8589 (mmm) cc_final: 0.8334 (mmm) REVERT: B 943 LEU cc_start: 0.9126 (mt) cc_final: 0.8812 (mt) REVERT: B 995 MET cc_start: 0.8098 (tmm) cc_final: 0.7632 (tmm) REVERT: B 2279 MET cc_start: 0.7950 (ttp) cc_final: 0.7674 (tmm) REVERT: B 2538 THR cc_start: 0.8213 (OUTLIER) cc_final: 0.7951 (t) REVERT: B 2594 PHE cc_start: 0.8174 (t80) cc_final: 0.7907 (t80) REVERT: B 2940 ILE cc_start: 0.8839 (OUTLIER) cc_final: 0.8494 (tt) REVERT: B 3150 ARG cc_start: 0.7650 (tpm-80) cc_final: 0.7435 (OUTLIER) REVERT: B 3215 MET cc_start: 0.9192 (mmt) cc_final: 0.8895 (mmm) REVERT: B 3265 CYS cc_start: 0.7912 (m) cc_final: 0.7640 (m) REVERT: B 3286 ASN cc_start: 0.8471 (m-40) cc_final: 0.8133 (m-40) REVERT: B 3304 GLN cc_start: 0.8982 (tp-100) cc_final: 0.8481 (tp-100) REVERT: B 4035 TYR cc_start: 0.7801 (m-80) cc_final: 0.7567 (m-80) REVERT: B 4258 MET cc_start: 0.7740 (ttt) cc_final: 0.7328 (tmt) REVERT: B 4303 ARG cc_start: 0.6238 (mmp-170) cc_final: 0.5764 (mmt90) REVERT: B 4502 MET cc_start: 0.7790 (mtm) cc_final: 0.7575 (mtp) REVERT: B 4707 MET cc_start: 0.8175 (ttp) cc_final: 0.7880 (ttm) REVERT: C 317 MET cc_start: 0.7382 (ppp) cc_final: 0.7146 (ppp) REVERT: C 943 LEU cc_start: 0.9087 (mt) cc_final: 0.8781 (mt) REVERT: C 983 LEU cc_start: 0.8344 (mm) cc_final: 0.7942 (mm) REVERT: C 995 MET cc_start: 0.8105 (tmm) cc_final: 0.7571 (tmm) REVERT: C 2279 MET cc_start: 0.8040 (ttp) cc_final: 0.7781 (tmm) REVERT: C 2939 TYR cc_start: 0.7987 (m-10) cc_final: 0.7563 (m-80) REVERT: C 2940 ILE cc_start: 0.8818 (OUTLIER) cc_final: 0.8500 (tt) REVERT: C 3121 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8537 (tp) REVERT: C 3215 MET cc_start: 0.9119 (mmt) cc_final: 0.8746 (mmm) REVERT: C 3304 GLN cc_start: 0.8940 (tp-100) cc_final: 0.8413 (tp-100) REVERT: C 3605 MET cc_start: 0.4741 (tmm) cc_final: 0.4452 (ppp) REVERT: C 4258 MET cc_start: 0.7608 (ttt) cc_final: 0.7218 (tmt) REVERT: C 4502 MET cc_start: 0.7813 (mtm) cc_final: 0.7585 (mtp) REVERT: C 4707 MET cc_start: 0.8158 (ttp) cc_final: 0.7853 (ttm) REVERT: C 4878 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.7262 (mt-10) REVERT: D 317 MET cc_start: 0.7467 (ppp) cc_final: 0.7118 (ppp) REVERT: D 943 LEU cc_start: 0.9149 (mt) cc_final: 0.8834 (mt) REVERT: D 983 LEU cc_start: 0.8367 (mm) cc_final: 0.8091 (mm) REVERT: D 995 MET cc_start: 0.8109 (tmm) cc_final: 0.7503 (tmm) REVERT: D 2150 MET cc_start: 0.8390 (mtp) cc_final: 0.8170 (mtt) REVERT: D 2538 THR cc_start: 0.7988 (OUTLIER) cc_final: 0.7750 (t) REVERT: D 2939 TYR cc_start: 0.7946 (m-10) cc_final: 0.7609 (m-80) REVERT: D 2940 ILE cc_start: 0.8761 (OUTLIER) cc_final: 0.8436 (tt) REVERT: D 3003 MET cc_start: 0.8785 (mtm) cc_final: 0.8285 (mtm) REVERT: D 3273 MET cc_start: 0.9114 (OUTLIER) cc_final: 0.8846 (mmt) REVERT: D 3286 ASN cc_start: 0.8611 (m-40) cc_final: 0.8252 (m-40) REVERT: D 3297 LYS cc_start: 0.6270 (mmtt) cc_final: 0.5260 (mmtt) REVERT: D 3304 GLN cc_start: 0.8899 (tp-100) cc_final: 0.8390 (tp-100) REVERT: D 3605 MET cc_start: 0.4106 (ppp) cc_final: 0.2574 (ppp) REVERT: D 4258 MET cc_start: 0.7647 (ttt) cc_final: 0.7183 (tmt) REVERT: D 4292 MET cc_start: 0.8384 (mmm) cc_final: 0.8178 (mmp) REVERT: D 4303 ARG cc_start: 0.6116 (mmp-170) cc_final: 0.5759 (mmt180) REVERT: D 4502 MET cc_start: 0.7812 (mtm) cc_final: 0.7560 (mtp) REVERT: D 4707 MET cc_start: 0.8129 (ttp) cc_final: 0.7914 (ttm) outliers start: 107 outliers final: 38 residues processed: 982 average time/residue: 2.1217 time to fit residues: 2974.9369 Evaluate side-chains 960 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 906 time to evaluate : 11.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 ASN Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 2142 MET Chi-restraints excluded: chain A residue 2234 MET Chi-restraints excluded: chain A residue 2538 THR Chi-restraints excluded: chain A residue 2627 TRP Chi-restraints excluded: chain A residue 2940 ILE Chi-restraints excluded: chain A residue 3121 LEU Chi-restraints excluded: chain A residue 3150 ARG Chi-restraints excluded: chain A residue 3281 LEU Chi-restraints excluded: chain A residue 3288 LEU Chi-restraints excluded: chain A residue 3297 LYS Chi-restraints excluded: chain A residue 3653 GLU Chi-restraints excluded: chain A residue 3854 PHE Chi-restraints excluded: chain A residue 4878 GLU Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 30 MET Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 30 MET Chi-restraints excluded: chain B residue 198 ASN Chi-restraints excluded: chain B residue 776 GLN Chi-restraints excluded: chain B residue 1599 MET Chi-restraints excluded: chain B residue 1896 MET Chi-restraints excluded: chain B residue 2142 MET Chi-restraints excluded: chain B residue 2234 MET Chi-restraints excluded: chain B residue 2538 THR Chi-restraints excluded: chain B residue 2940 ILE Chi-restraints excluded: chain B residue 3121 LEU Chi-restraints excluded: chain B residue 3290 ILE Chi-restraints excluded: chain B residue 3653 GLU Chi-restraints excluded: chain B residue 3854 PHE Chi-restraints excluded: chain B residue 4878 GLU Chi-restraints excluded: chain C residue 776 GLN Chi-restraints excluded: chain C residue 1599 MET Chi-restraints excluded: chain C residue 1896 MET Chi-restraints excluded: chain C residue 2234 MET Chi-restraints excluded: chain C residue 2940 ILE Chi-restraints excluded: chain C residue 3121 LEU Chi-restraints excluded: chain C residue 3150 ARG Chi-restraints excluded: chain C residue 3290 ILE Chi-restraints excluded: chain C residue 3310 VAL Chi-restraints excluded: chain C residue 3653 GLU Chi-restraints excluded: chain C residue 3854 PHE Chi-restraints excluded: chain C residue 4878 GLU Chi-restraints excluded: chain D residue 776 GLN Chi-restraints excluded: chain D residue 2142 MET Chi-restraints excluded: chain D residue 2234 MET Chi-restraints excluded: chain D residue 2538 THR Chi-restraints excluded: chain D residue 2940 ILE Chi-restraints excluded: chain D residue 3273 MET Chi-restraints excluded: chain D residue 3739 MET Chi-restraints excluded: chain D residue 3854 PHE Chi-restraints excluded: chain D residue 4878 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 561 optimal weight: 0.3980 chunk 1504 optimal weight: 8.9990 chunk 330 optimal weight: 50.0000 chunk 980 optimal weight: 10.0000 chunk 412 optimal weight: 8.9990 chunk 1671 optimal weight: 6.9990 chunk 1387 optimal weight: 6.9990 chunk 774 optimal weight: 10.0000 chunk 139 optimal weight: 1.9990 chunk 553 optimal weight: 0.9990 chunk 877 optimal weight: 10.0000 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4493 ASN E 26 HIS G 26 HIS H 26 HIS B 225 GLN B 469 HIS ** B1501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3955 GLN B3975 GLN B4493 ASN ** C 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2684 ASN ** C3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3955 GLN C3975 GLN C4493 ASN ** C4636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1974 ASN ** D3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4493 ASN ** D4636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 141608 Z= 0.310 Angle : 0.608 18.751 191332 Z= 0.307 Chirality : 0.042 0.387 20988 Planarity : 0.004 0.080 24584 Dihedral : 6.040 178.164 19024 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.74 % Allowed : 8.81 % Favored : 90.44 % 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: 1.55 (0.07), residues: 17212 helix: 2.17 (0.06), residues: 8924 sheet: -0.05 (0.12), residues: 1832 loop : -0.22 (0.08), residues: 6456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.083 0.002 TRP A 893 HIS 0.015 0.001 HIS G 26 PHE 0.023 0.002 PHE B2594 TYR 0.033 0.002 TYR C2801 ARG 0.016 0.000 ARG E 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 1028 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 915 time to evaluate : 11.682 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: A 198 ASN cc_start: 0.4773 (OUTLIER) cc_final: 0.4158 (m110) REVERT: A 313 ASN cc_start: 0.7931 (t0) cc_final: 0.7572 (m-40) REVERT: A 317 MET cc_start: 0.7523 (ppp) cc_final: 0.7123 (pp-130) REVERT: A 943 LEU cc_start: 0.9175 (mt) cc_final: 0.8911 (mt) REVERT: A 995 MET cc_start: 0.8166 (tmm) cc_final: 0.7587 (tmm) REVERT: A 1057 LEU cc_start: 0.9335 (mm) cc_final: 0.9076 (mt) REVERT: A 2279 MET cc_start: 0.8058 (ttp) cc_final: 0.7814 (tmm) REVERT: A 2538 THR cc_start: 0.8078 (OUTLIER) cc_final: 0.7841 (t) REVERT: A 2627 TRP cc_start: 0.8392 (OUTLIER) cc_final: 0.7498 (m-10) REVERT: A 2939 TYR cc_start: 0.7904 (m-10) cc_final: 0.7643 (m-80) REVERT: A 2940 ILE cc_start: 0.8840 (OUTLIER) cc_final: 0.8497 (tt) REVERT: A 3046 MET cc_start: 0.9081 (mmm) cc_final: 0.8866 (mmp) REVERT: A 3104 MET cc_start: 0.8193 (mtp) cc_final: 0.7917 (mtm) REVERT: A 3121 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8558 (tp) REVERT: A 3142 THR cc_start: 0.8567 (m) cc_final: 0.8302 (p) REVERT: A 3215 MET cc_start: 0.9202 (mmt) cc_final: 0.8849 (mmm) REVERT: A 3286 ASN cc_start: 0.8495 (m-40) cc_final: 0.8191 (m-40) REVERT: A 3304 GLN cc_start: 0.8934 (tp-100) cc_final: 0.8477 (tp-100) REVERT: A 4258 MET cc_start: 0.7717 (ttt) cc_final: 0.7258 (tmt) REVERT: A 4292 MET cc_start: 0.8403 (mmm) cc_final: 0.8191 (mmp) REVERT: A 4303 ARG cc_start: 0.6237 (mmp-170) cc_final: 0.5841 (mmt180) REVERT: A 4502 MET cc_start: 0.7859 (mtm) cc_final: 0.7624 (mtp) REVERT: A 4707 MET cc_start: 0.8178 (ttp) cc_final: 0.7871 (ttm) REVERT: A 4878 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.7257 (mt-10) REVERT: G 18 LYS cc_start: 0.9056 (mppt) cc_final: 0.8799 (mttp) REVERT: H 18 LYS cc_start: 0.9021 (mppt) cc_final: 0.8782 (mttp) REVERT: B 198 ASN cc_start: 0.4869 (OUTLIER) cc_final: 0.4355 (m110) REVERT: B 313 ASN cc_start: 0.7713 (t0) cc_final: 0.7496 (m-40) REVERT: B 655 MET cc_start: 0.8598 (mmm) cc_final: 0.8377 (mmm) REVERT: B 943 LEU cc_start: 0.9141 (mt) cc_final: 0.8832 (mt) REVERT: B 964 MET cc_start: 0.7630 (pmt) cc_final: 0.7403 (pmm) REVERT: B 995 MET cc_start: 0.8130 (tmm) cc_final: 0.7665 (tmm) REVERT: B 2279 MET cc_start: 0.7969 (ttp) cc_final: 0.7683 (tmm) REVERT: B 2538 THR cc_start: 0.8195 (OUTLIER) cc_final: 0.7946 (t) REVERT: B 2940 ILE cc_start: 0.8848 (OUTLIER) cc_final: 0.8507 (tt) REVERT: B 3104 MET cc_start: 0.8200 (mtp) cc_final: 0.7919 (mtm) REVERT: B 3150 ARG cc_start: 0.7697 (tpm-80) cc_final: 0.7461 (OUTLIER) REVERT: B 3215 MET cc_start: 0.9197 (mmt) cc_final: 0.8905 (mmm) REVERT: B 3286 ASN cc_start: 0.8483 (m-40) cc_final: 0.8157 (m-40) REVERT: B 3304 GLN cc_start: 0.8979 (tp-100) cc_final: 0.8476 (tp-100) REVERT: B 4035 TYR cc_start: 0.7782 (m-80) cc_final: 0.7560 (m-80) REVERT: B 4258 MET cc_start: 0.7746 (ttt) cc_final: 0.7334 (tmt) REVERT: B 4274 MET cc_start: 0.4673 (ptp) cc_final: 0.4390 (ptp) REVERT: B 4303 ARG cc_start: 0.6319 (mmp-170) cc_final: 0.5781 (mmt90) REVERT: B 4502 MET cc_start: 0.7786 (OUTLIER) cc_final: 0.7585 (mtp) REVERT: B 4707 MET cc_start: 0.8171 (ttp) cc_final: 0.7880 (ttm) REVERT: B 4878 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.7243 (mt-10) REVERT: C 317 MET cc_start: 0.7462 (ppp) cc_final: 0.7198 (ppp) REVERT: C 943 LEU cc_start: 0.9123 (mt) cc_final: 0.8817 (mt) REVERT: C 983 LEU cc_start: 0.8422 (mm) cc_final: 0.8040 (mm) REVERT: C 995 MET cc_start: 0.8121 (tmm) cc_final: 0.7591 (tmm) REVERT: C 1975 MET cc_start: 0.7537 (mtp) cc_final: 0.7259 (mtm) REVERT: C 2279 MET cc_start: 0.8085 (ttp) cc_final: 0.7806 (tmm) REVERT: C 2627 TRP cc_start: 0.8550 (OUTLIER) cc_final: 0.7935 (m-10) REVERT: C 2939 TYR cc_start: 0.7993 (m-10) cc_final: 0.7601 (m-80) REVERT: C 2940 ILE cc_start: 0.8820 (OUTLIER) cc_final: 0.8500 (tt) REVERT: C 3121 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8538 (tp) REVERT: C 3215 MET cc_start: 0.9152 (mmt) cc_final: 0.8800 (mmm) REVERT: C 3304 GLN cc_start: 0.8944 (tp-100) cc_final: 0.8431 (tp-100) REVERT: C 4258 MET cc_start: 0.7617 (ttt) cc_final: 0.7222 (tmt) REVERT: C 4303 ARG cc_start: 0.6220 (mmp-170) cc_final: 0.5817 (mpt180) REVERT: C 4502 MET cc_start: 0.7830 (mtm) cc_final: 0.7604 (mtp) REVERT: C 4707 MET cc_start: 0.8159 (ttp) cc_final: 0.7866 (ttm) REVERT: D 317 MET cc_start: 0.7502 (ppp) cc_final: 0.7130 (ppp) REVERT: D 943 LEU cc_start: 0.9165 (mt) cc_final: 0.8863 (mt) REVERT: D 964 MET cc_start: 0.7262 (pmt) cc_final: 0.6983 (pmm) REVERT: D 983 LEU cc_start: 0.8500 (mm) cc_final: 0.8164 (mm) REVERT: D 995 MET cc_start: 0.8122 (tmm) cc_final: 0.7542 (tmm) REVERT: D 2150 MET cc_start: 0.8400 (mtp) cc_final: 0.8195 (mtp) REVERT: D 2538 THR cc_start: 0.8186 (OUTLIER) cc_final: 0.7930 (t) REVERT: D 2627 TRP cc_start: 0.8487 (OUTLIER) cc_final: 0.7636 (m-10) REVERT: D 2939 TYR cc_start: 0.7976 (m-10) cc_final: 0.7634 (m-80) REVERT: D 2940 ILE cc_start: 0.8767 (OUTLIER) cc_final: 0.8451 (tt) REVERT: D 3003 MET cc_start: 0.8800 (mtm) cc_final: 0.8325 (mtm) REVERT: D 3273 MET cc_start: 0.9118 (OUTLIER) cc_final: 0.8852 (mmt) REVERT: D 3286 ASN cc_start: 0.8617 (m-40) cc_final: 0.8263 (m-40) REVERT: D 3304 GLN cc_start: 0.8912 (tp-100) cc_final: 0.8410 (tp-100) REVERT: D 3605 MET cc_start: 0.4178 (ppp) cc_final: 0.2568 (ppp) REVERT: D 4258 MET cc_start: 0.7645 (ttt) cc_final: 0.7169 (tmt) REVERT: D 4292 MET cc_start: 0.8382 (mmm) cc_final: 0.8147 (mmp) REVERT: D 4303 ARG cc_start: 0.6097 (mmp-170) cc_final: 0.5759 (mmt180) REVERT: D 4878 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.7218 (mt-10) outliers start: 113 outliers final: 43 residues processed: 983 average time/residue: 2.1457 time to fit residues: 3004.8318 Evaluate side-chains 962 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 901 time to evaluate : 11.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 198 ASN Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 1896 MET Chi-restraints excluded: chain A residue 2142 MET Chi-restraints excluded: chain A residue 2234 MET Chi-restraints excluded: chain A residue 2538 THR Chi-restraints excluded: chain A residue 2627 TRP Chi-restraints excluded: chain A residue 2940 ILE Chi-restraints excluded: chain A residue 3121 LEU Chi-restraints excluded: chain A residue 3150 ARG Chi-restraints excluded: chain A residue 3297 LYS Chi-restraints excluded: chain A residue 3653 GLU Chi-restraints excluded: chain A residue 3854 PHE Chi-restraints excluded: chain A residue 4878 GLU Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain G residue 44 ASN Chi-restraints excluded: chain B residue 198 ASN Chi-restraints excluded: chain B residue 776 GLN Chi-restraints excluded: chain B residue 1599 MET Chi-restraints excluded: chain B residue 1896 MET Chi-restraints excluded: chain B residue 2095 ILE Chi-restraints excluded: chain B residue 2142 MET Chi-restraints excluded: chain B residue 2234 MET Chi-restraints excluded: chain B residue 2538 THR Chi-restraints excluded: chain B residue 2940 ILE Chi-restraints excluded: chain B residue 3121 LEU Chi-restraints excluded: chain B residue 3290 ILE Chi-restraints excluded: chain B residue 3653 GLU Chi-restraints excluded: chain B residue 3854 PHE Chi-restraints excluded: chain B residue 4502 MET Chi-restraints excluded: chain B residue 4558 HIS Chi-restraints excluded: chain B residue 4878 GLU Chi-restraints excluded: chain C residue 776 GLN Chi-restraints excluded: chain C residue 931 TYR Chi-restraints excluded: chain C residue 1599 MET Chi-restraints excluded: chain C residue 1896 MET Chi-restraints excluded: chain C residue 2234 MET Chi-restraints excluded: chain C residue 2627 TRP Chi-restraints excluded: chain C residue 2940 ILE Chi-restraints excluded: chain C residue 3121 LEU Chi-restraints excluded: chain C residue 3150 ARG Chi-restraints excluded: chain C residue 3290 ILE Chi-restraints excluded: chain C residue 3310 VAL Chi-restraints excluded: chain C residue 3653 GLU Chi-restraints excluded: chain C residue 3854 PHE Chi-restraints excluded: chain C residue 4878 GLU Chi-restraints excluded: chain D residue 776 GLN Chi-restraints excluded: chain D residue 1896 MET Chi-restraints excluded: chain D residue 2142 MET Chi-restraints excluded: chain D residue 2234 MET Chi-restraints excluded: chain D residue 2538 THR Chi-restraints excluded: chain D residue 2627 TRP Chi-restraints excluded: chain D residue 2844 MET Chi-restraints excluded: chain D residue 2940 ILE Chi-restraints excluded: chain D residue 3273 MET Chi-restraints excluded: chain D residue 3739 MET Chi-restraints excluded: chain D residue 3854 PHE Chi-restraints excluded: chain D residue 4485 ILE Chi-restraints excluded: chain D residue 4558 HIS Chi-restraints excluded: chain D residue 4878 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1611 optimal weight: 10.0000 chunk 188 optimal weight: 4.9990 chunk 952 optimal weight: 7.9990 chunk 1220 optimal weight: 5.9990 chunk 945 optimal weight: 4.9990 chunk 1407 optimal weight: 5.9990 chunk 933 optimal weight: 0.9980 chunk 1665 optimal weight: 0.0060 chunk 1042 optimal weight: 6.9990 chunk 1015 optimal weight: 10.0000 chunk 768 optimal weight: 20.0000 overall best weight: 3.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 GLN A 896 ASN ** A1501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4493 ASN E 26 HIS G 26 HIS H 26 HIS B 225 GLN B 896 ASN ** B1501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1974 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4493 ASN ** C 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3318 HIS C3955 GLN C3975 GLN C4493 ASN ** C4636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3318 HIS ** D4636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 141608 Z= 0.303 Angle : 0.615 22.450 191332 Z= 0.309 Chirality : 0.042 0.411 20988 Planarity : 0.004 0.079 24584 Dihedral : 6.005 179.010 19024 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.72 % Allowed : 9.15 % Favored : 90.12 % 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: 1.57 (0.07), residues: 17212 helix: 2.18 (0.06), residues: 8920 sheet: -0.03 (0.12), residues: 1832 loop : -0.22 (0.08), residues: 6460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.085 0.002 TRP A 893 HIS 0.014 0.001 HIS C3318 PHE 0.020 0.002 PHE C4508 TYR 0.030 0.002 TYR C2801 ARG 0.017 0.000 ARG G 14 *********************** 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 1026 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 916 time to evaluate : 11.669 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: A 313 ASN cc_start: 0.7923 (t0) cc_final: 0.7557 (m-40) REVERT: A 317 MET cc_start: 0.7535 (ppp) cc_final: 0.7154 (pp-130) REVERT: A 943 LEU cc_start: 0.9168 (mt) cc_final: 0.8896 (mt) REVERT: A 964 MET cc_start: 0.7475 (pmt) cc_final: 0.7165 (pmm) REVERT: A 995 MET cc_start: 0.8163 (tmm) cc_final: 0.7618 (tmm) REVERT: A 1057 LEU cc_start: 0.9326 (mm) cc_final: 0.9066 (mt) REVERT: A 2279 MET cc_start: 0.8054 (ttp) cc_final: 0.7813 (tmm) REVERT: A 2538 THR cc_start: 0.8175 (OUTLIER) cc_final: 0.7923 (t) REVERT: A 2627 TRP cc_start: 0.8386 (OUTLIER) cc_final: 0.7466 (m-10) REVERT: A 2939 TYR cc_start: 0.7910 (m-10) cc_final: 0.7601 (m-80) REVERT: A 2940 ILE cc_start: 0.8839 (OUTLIER) cc_final: 0.8501 (tt) REVERT: A 3104 MET cc_start: 0.8193 (mtp) cc_final: 0.7908 (ptt) REVERT: A 3121 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8546 (tp) REVERT: A 3142 THR cc_start: 0.8576 (m) cc_final: 0.8312 (p) REVERT: A 3215 MET cc_start: 0.9197 (mmt) cc_final: 0.8857 (mmm) REVERT: A 3286 ASN cc_start: 0.8452 (m-40) cc_final: 0.8107 (m-40) REVERT: A 3304 GLN cc_start: 0.8934 (tp-100) cc_final: 0.8483 (tp-100) REVERT: A 3888 PHE cc_start: 0.9108 (OUTLIER) cc_final: 0.8663 (m-80) REVERT: A 4258 MET cc_start: 0.7715 (ttt) cc_final: 0.7263 (tmt) REVERT: A 4292 MET cc_start: 0.8401 (mmm) cc_final: 0.8184 (mmp) REVERT: A 4303 ARG cc_start: 0.6226 (mmp-170) cc_final: 0.5822 (mmt180) REVERT: A 4502 MET cc_start: 0.7843 (mtm) cc_final: 0.7593 (mtp) REVERT: A 4707 MET cc_start: 0.8177 (ttp) cc_final: 0.7869 (ttm) REVERT: A 4878 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.7268 (mt-10) REVERT: E 58 LYS cc_start: 0.8618 (ptmt) cc_final: 0.8362 (ptmm) REVERT: G 18 LYS cc_start: 0.9075 (mppt) cc_final: 0.8818 (mttp) REVERT: G 30 MET cc_start: 0.7354 (OUTLIER) cc_final: 0.6760 (mpp) REVERT: H 18 LYS cc_start: 0.9028 (mppt) cc_final: 0.8806 (mttp) REVERT: H 30 MET cc_start: 0.7380 (OUTLIER) cc_final: 0.6878 (mpt) REVERT: B 198 ASN cc_start: 0.4773 (OUTLIER) cc_final: 0.4290 (m110) REVERT: B 313 ASN cc_start: 0.7760 (t0) cc_final: 0.7524 (m-40) REVERT: B 655 MET cc_start: 0.8595 (mmm) cc_final: 0.8374 (mmm) REVERT: B 943 LEU cc_start: 0.9132 (mt) cc_final: 0.8811 (mt) REVERT: B 995 MET cc_start: 0.8135 (tmm) cc_final: 0.7567 (tmm) REVERT: B 1975 MET cc_start: 0.7574 (mtp) cc_final: 0.7284 (mtm) REVERT: B 2279 MET cc_start: 0.7966 (ttp) cc_final: 0.7689 (tmm) REVERT: B 2538 THR cc_start: 0.8134 (OUTLIER) cc_final: 0.7885 (t) REVERT: B 2627 TRP cc_start: 0.8399 (OUTLIER) cc_final: 0.7577 (m-10) REVERT: B 2940 ILE cc_start: 0.8846 (OUTLIER) cc_final: 0.8506 (tt) REVERT: B 3150 ARG cc_start: 0.7651 (tpm-80) cc_final: 0.7432 (OUTLIER) REVERT: B 3241 MET cc_start: 0.8826 (ttm) cc_final: 0.8612 (ttm) REVERT: B 3286 ASN cc_start: 0.8498 (m-40) cc_final: 0.8184 (m-40) REVERT: B 3304 GLN cc_start: 0.8968 (tp-100) cc_final: 0.8485 (tp-100) REVERT: B 3888 PHE cc_start: 0.9110 (OUTLIER) cc_final: 0.8666 (m-80) REVERT: B 4035 TYR cc_start: 0.7788 (m-80) cc_final: 0.7579 (m-80) REVERT: B 4258 MET cc_start: 0.7741 (ttt) cc_final: 0.7329 (tmt) REVERT: B 4303 ARG cc_start: 0.6294 (mmp-170) cc_final: 0.5810 (mmt90) REVERT: B 4707 MET cc_start: 0.8175 (ttp) cc_final: 0.7877 (ttm) REVERT: B 4878 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.7245 (mt-10) REVERT: C 241 MET cc_start: 0.5567 (tpt) cc_final: 0.5324 (mmm) REVERT: C 317 MET cc_start: 0.7504 (ppp) cc_final: 0.7214 (ppp) REVERT: C 943 LEU cc_start: 0.9144 (mt) cc_final: 0.8827 (mt) REVERT: C 983 LEU cc_start: 0.8427 (mm) cc_final: 0.8041 (mm) REVERT: C 995 MET cc_start: 0.8120 (tmm) cc_final: 0.7555 (tmm) REVERT: C 2279 MET cc_start: 0.8087 (ttp) cc_final: 0.7824 (tmm) REVERT: C 2627 TRP cc_start: 0.8496 (OUTLIER) cc_final: 0.7838 (m-10) REVERT: C 2939 TYR cc_start: 0.8018 (m-10) cc_final: 0.7618 (m-80) REVERT: C 2940 ILE cc_start: 0.8810 (OUTLIER) cc_final: 0.8495 (tt) REVERT: C 3104 MET cc_start: 0.8183 (ptm) cc_final: 0.7805 (ptt) REVERT: C 3121 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8540 (tp) REVERT: C 4258 MET cc_start: 0.7616 (ttt) cc_final: 0.7186 (tmt) REVERT: C 4878 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.7234 (mt-10) REVERT: D 241 MET cc_start: 0.5617 (tpt) cc_final: 0.5387 (tpp) REVERT: D 317 MET cc_start: 0.7521 (ppp) cc_final: 0.7252 (ppp) REVERT: D 943 LEU cc_start: 0.9168 (mt) cc_final: 0.8846 (mt) REVERT: D 983 LEU cc_start: 0.8520 (mm) cc_final: 0.8218 (mm) REVERT: D 995 MET cc_start: 0.8104 (tmm) cc_final: 0.7539 (tmm) REVERT: D 2150 MET cc_start: 0.8404 (mtp) cc_final: 0.8203 (mtp) REVERT: D 2538 THR cc_start: 0.8223 (OUTLIER) cc_final: 0.7962 (t) REVERT: D 2627 TRP cc_start: 0.8465 (OUTLIER) cc_final: 0.7653 (m-10) REVERT: D 2939 TYR cc_start: 0.7955 (m-10) cc_final: 0.7603 (m-80) REVERT: D 2940 ILE cc_start: 0.8767 (OUTLIER) cc_final: 0.8452 (tt) REVERT: D 3003 MET cc_start: 0.8802 (mtm) cc_final: 0.8325 (mtm) REVERT: D 3104 MET cc_start: 0.8233 (ptm) cc_final: 0.7851 (ptt) REVERT: D 3215 MET cc_start: 0.9089 (mmt) cc_final: 0.8744 (mmm) REVERT: D 3273 MET cc_start: 0.9109 (OUTLIER) cc_final: 0.8849 (mmt) REVERT: D 3286 ASN cc_start: 0.8632 (m-40) cc_final: 0.8280 (m-40) REVERT: D 3304 GLN cc_start: 0.8916 (tp-100) cc_final: 0.8412 (tp-100) REVERT: D 3888 PHE cc_start: 0.9102 (OUTLIER) cc_final: 0.8702 (m-80) REVERT: D 4258 MET cc_start: 0.7647 (ttt) cc_final: 0.7173 (tmt) REVERT: D 4292 MET cc_start: 0.8378 (mmm) cc_final: 0.8144 (mmp) REVERT: D 4303 ARG cc_start: 0.6099 (mmp-170) cc_final: 0.5761 (mmt180) REVERT: D 4707 MET cc_start: 0.8136 (ttp) cc_final: 0.7883 (ttm) REVERT: D 4878 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.7220 (mt-10) outliers start: 110 outliers final: 45 residues processed: 981 average time/residue: 2.3418 time to fit residues: 3320.1752 Evaluate side-chains 970 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 902 time to evaluate : 11.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 1896 MET Chi-restraints excluded: chain A residue 2142 MET Chi-restraints excluded: chain A residue 2234 MET Chi-restraints excluded: chain A residue 2538 THR Chi-restraints excluded: chain A residue 2627 TRP Chi-restraints excluded: chain A residue 2940 ILE Chi-restraints excluded: chain A residue 3121 LEU Chi-restraints excluded: chain A residue 3150 ARG Chi-restraints excluded: chain A residue 3297 LYS Chi-restraints excluded: chain A residue 3653 GLU Chi-restraints excluded: chain A residue 3854 PHE Chi-restraints excluded: chain A residue 3888 PHE Chi-restraints excluded: chain A residue 4878 GLU Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 30 MET Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 30 MET Chi-restraints excluded: chain B residue 198 ASN Chi-restraints excluded: chain B residue 776 GLN Chi-restraints excluded: chain B residue 1599 MET Chi-restraints excluded: chain B residue 1896 MET Chi-restraints excluded: chain B residue 2095 ILE Chi-restraints excluded: chain B residue 2142 MET Chi-restraints excluded: chain B residue 2234 MET Chi-restraints excluded: chain B residue 2538 THR Chi-restraints excluded: chain B residue 2627 TRP Chi-restraints excluded: chain B residue 2940 ILE Chi-restraints excluded: chain B residue 3121 LEU Chi-restraints excluded: chain B residue 3201 VAL Chi-restraints excluded: chain B residue 3290 ILE Chi-restraints excluded: chain B residue 3653 GLU Chi-restraints excluded: chain B residue 3854 PHE Chi-restraints excluded: chain B residue 3888 PHE Chi-restraints excluded: chain B residue 4558 HIS Chi-restraints excluded: chain B residue 4878 GLU Chi-restraints excluded: chain C residue 776 GLN Chi-restraints excluded: chain C residue 931 TYR Chi-restraints excluded: chain C residue 1599 MET Chi-restraints excluded: chain C residue 1896 MET Chi-restraints excluded: chain C residue 2234 MET Chi-restraints excluded: chain C residue 2627 TRP Chi-restraints excluded: chain C residue 2940 ILE Chi-restraints excluded: chain C residue 3121 LEU Chi-restraints excluded: chain C residue 3150 ARG Chi-restraints excluded: chain C residue 3290 ILE Chi-restraints excluded: chain C residue 3653 GLU Chi-restraints excluded: chain C residue 3854 PHE Chi-restraints excluded: chain C residue 4878 GLU Chi-restraints excluded: chain D residue 776 GLN Chi-restraints excluded: chain D residue 1896 MET Chi-restraints excluded: chain D residue 2142 MET Chi-restraints excluded: chain D residue 2234 MET Chi-restraints excluded: chain D residue 2538 THR Chi-restraints excluded: chain D residue 2627 TRP Chi-restraints excluded: chain D residue 2844 MET Chi-restraints excluded: chain D residue 2940 ILE Chi-restraints excluded: chain D residue 3273 MET Chi-restraints excluded: chain D residue 3318 HIS Chi-restraints excluded: chain D residue 3739 MET Chi-restraints excluded: chain D residue 3854 PHE Chi-restraints excluded: chain D residue 3888 PHE Chi-restraints excluded: chain D residue 3954 MET Chi-restraints excluded: chain D residue 4485 ILE Chi-restraints excluded: chain D residue 4558 HIS Chi-restraints excluded: chain D residue 4878 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1030 optimal weight: 1.9990 chunk 665 optimal weight: 10.0000 chunk 994 optimal weight: 9.9990 chunk 501 optimal weight: 9.9990 chunk 327 optimal weight: 0.9980 chunk 322 optimal weight: 3.9990 chunk 1058 optimal weight: 6.9990 chunk 1134 optimal weight: 9.9990 chunk 823 optimal weight: 5.9990 chunk 155 optimal weight: 1.9990 chunk 1309 optimal weight: 9.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4493 ASN E 26 HIS G 26 HIS H 26 HIS B 225 GLN B 469 HIS ** B1501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4493 ASN ** C 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3318 HIS C3955 GLN C3975 GLN C4493 ASN ** C4636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3318 HIS D4493 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 141608 Z= 0.278 Angle : 0.613 18.055 191332 Z= 0.308 Chirality : 0.041 0.383 20988 Planarity : 0.004 0.089 24584 Dihedral : 5.966 178.691 19024 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.71 % Allowed : 9.42 % Favored : 89.86 % 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: 1.60 (0.07), residues: 17212 helix: 2.20 (0.06), residues: 8920 sheet: 0.01 (0.12), residues: 1868 loop : -0.20 (0.08), residues: 6424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.097 0.002 TRP A 893 HIS 0.017 0.001 HIS H 26 PHE 0.021 0.001 PHE A4660 TYR 0.031 0.001 TYR B4080 ARG 0.019 0.000 ARG H 14 *********************** 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 1025 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 917 time to evaluate : 11.575 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: A 313 ASN cc_start: 0.7924 (t0) cc_final: 0.7566 (m-40) REVERT: A 317 MET cc_start: 0.7541 (ppp) cc_final: 0.7150 (pp-130) REVERT: A 520 ARG cc_start: 0.7114 (ttp80) cc_final: 0.6890 (ttp80) REVERT: A 943 LEU cc_start: 0.9151 (mt) cc_final: 0.8906 (mt) REVERT: A 964 MET cc_start: 0.7175 (pmt) cc_final: 0.6854 (pmm) REVERT: A 995 MET cc_start: 0.8116 (tmm) cc_final: 0.7572 (tmm) REVERT: A 1057 LEU cc_start: 0.9319 (mm) cc_final: 0.9046 (mt) REVERT: A 2279 MET cc_start: 0.8040 (ttp) cc_final: 0.7806 (tmm) REVERT: A 2538 THR cc_start: 0.8111 (OUTLIER) cc_final: 0.7858 (t) REVERT: A 2627 TRP cc_start: 0.8369 (OUTLIER) cc_final: 0.7430 (m-10) REVERT: A 2939 TYR cc_start: 0.7910 (m-10) cc_final: 0.7603 (m-80) REVERT: A 2940 ILE cc_start: 0.8835 (OUTLIER) cc_final: 0.8501 (tt) REVERT: A 3104 MET cc_start: 0.8180 (mtp) cc_final: 0.7923 (ptt) REVERT: A 3121 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8541 (tp) REVERT: A 3215 MET cc_start: 0.9196 (mmt) cc_final: 0.8861 (mmm) REVERT: A 3286 ASN cc_start: 0.8439 (m-40) cc_final: 0.8078 (m-40) REVERT: A 3304 GLN cc_start: 0.8928 (tp-100) cc_final: 0.8428 (tp-100) REVERT: A 3888 PHE cc_start: 0.9110 (OUTLIER) cc_final: 0.8724 (m-80) REVERT: A 4258 MET cc_start: 0.7709 (ttt) cc_final: 0.7261 (tmt) REVERT: A 4292 MET cc_start: 0.8399 (mmm) cc_final: 0.8183 (mmp) REVERT: A 4303 ARG cc_start: 0.6203 (mmp-170) cc_final: 0.5843 (mmt90) REVERT: A 4502 MET cc_start: 0.7840 (mtm) cc_final: 0.7629 (mtp) REVERT: A 4707 MET cc_start: 0.8171 (ttp) cc_final: 0.7873 (ttm) REVERT: A 4878 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.7273 (mt-10) REVERT: G 18 LYS cc_start: 0.9077 (mppt) cc_final: 0.8823 (mttp) REVERT: G 30 MET cc_start: 0.7345 (OUTLIER) cc_final: 0.6767 (mpp) REVERT: H 30 MET cc_start: 0.7368 (OUTLIER) cc_final: 0.6879 (mpt) REVERT: B 198 ASN cc_start: 0.4756 (OUTLIER) cc_final: 0.4235 (m110) REVERT: B 313 ASN cc_start: 0.7792 (t0) cc_final: 0.7548 (m-40) REVERT: B 655 MET cc_start: 0.8587 (mmm) cc_final: 0.8367 (mmm) REVERT: B 943 LEU cc_start: 0.9115 (mt) cc_final: 0.8806 (mt) REVERT: B 964 MET cc_start: 0.7403 (pmt) cc_final: 0.7136 (pmm) REVERT: B 995 MET cc_start: 0.8142 (tmm) cc_final: 0.7566 (tmm) REVERT: B 1975 MET cc_start: 0.7577 (mtp) cc_final: 0.7292 (mtm) REVERT: B 2150 MET cc_start: 0.8174 (OUTLIER) cc_final: 0.6506 (mpp) REVERT: B 2279 MET cc_start: 0.7963 (ttp) cc_final: 0.7692 (tmm) REVERT: B 2538 THR cc_start: 0.8086 (OUTLIER) cc_final: 0.7841 (t) REVERT: B 2627 TRP cc_start: 0.8348 (OUTLIER) cc_final: 0.7503 (m-10) REVERT: B 2940 ILE cc_start: 0.8845 (OUTLIER) cc_final: 0.8508 (tt) REVERT: B 3104 MET cc_start: 0.8202 (ptm) cc_final: 0.7825 (ptt) REVERT: B 3215 MET cc_start: 0.9193 (mmt) cc_final: 0.8846 (mmm) REVERT: B 3286 ASN cc_start: 0.8484 (m-40) cc_final: 0.8171 (m-40) REVERT: B 3304 GLN cc_start: 0.8923 (tp-100) cc_final: 0.8452 (tp-100) REVERT: B 3888 PHE cc_start: 0.9116 (OUTLIER) cc_final: 0.8671 (m-80) REVERT: B 4035 TYR cc_start: 0.7752 (m-80) cc_final: 0.7531 (m-80) REVERT: B 4258 MET cc_start: 0.7728 (ttt) cc_final: 0.7328 (tmt) REVERT: B 4303 ARG cc_start: 0.6254 (mmp-170) cc_final: 0.5718 (mmt90) REVERT: B 4707 MET cc_start: 0.8175 (ttp) cc_final: 0.7872 (ttm) REVERT: B 4878 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.7259 (mt-10) REVERT: C 241 MET cc_start: 0.5549 (tpt) cc_final: 0.5310 (mmm) REVERT: C 317 MET cc_start: 0.7539 (ppp) cc_final: 0.7300 (ppp) REVERT: C 943 LEU cc_start: 0.9147 (mt) cc_final: 0.8815 (mm) REVERT: C 983 LEU cc_start: 0.8433 (mm) cc_final: 0.8018 (mm) REVERT: C 995 MET cc_start: 0.8104 (tmm) cc_final: 0.7518 (tmm) REVERT: C 2279 MET cc_start: 0.8070 (ttp) cc_final: 0.7825 (tmm) REVERT: C 2627 TRP cc_start: 0.8476 (OUTLIER) cc_final: 0.7798 (m-10) REVERT: C 2939 TYR cc_start: 0.8016 (m-10) cc_final: 0.7667 (m-80) REVERT: C 2940 ILE cc_start: 0.8810 (OUTLIER) cc_final: 0.8495 (tt) REVERT: C 3104 MET cc_start: 0.8234 (ptm) cc_final: 0.7863 (ptt) REVERT: C 3121 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8541 (tp) REVERT: C 3215 MET cc_start: 0.9151 (mmt) cc_final: 0.8806 (mmm) REVERT: C 3297 LYS cc_start: 0.7065 (mmpt) cc_final: 0.6665 (mmtt) REVERT: C 4258 MET cc_start: 0.7616 (ttt) cc_final: 0.7185 (tmt) REVERT: C 4303 ARG cc_start: 0.6296 (mmp-170) cc_final: 0.5927 (mmt180) REVERT: C 4878 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.7227 (mt-10) REVERT: D 241 MET cc_start: 0.5641 (tpt) cc_final: 0.5414 (tpp) REVERT: D 943 LEU cc_start: 0.9161 (mt) cc_final: 0.8863 (mt) REVERT: D 964 MET cc_start: 0.6683 (pmt) cc_final: 0.6185 (pmm) REVERT: D 983 LEU cc_start: 0.8529 (mm) cc_final: 0.8202 (mm) REVERT: D 995 MET cc_start: 0.8107 (tmm) cc_final: 0.7538 (tmm) REVERT: D 1057 LEU cc_start: 0.9323 (mm) cc_final: 0.9120 (mt) REVERT: D 2150 MET cc_start: 0.8406 (mtp) cc_final: 0.8204 (mtp) REVERT: D 2538 THR cc_start: 0.8178 (OUTLIER) cc_final: 0.7901 (t) REVERT: D 2627 TRP cc_start: 0.8433 (OUTLIER) cc_final: 0.7579 (m-10) REVERT: D 2939 TYR cc_start: 0.7947 (m-10) cc_final: 0.7592 (m-80) REVERT: D 2940 ILE cc_start: 0.8762 (OUTLIER) cc_final: 0.8452 (tt) REVERT: D 3003 MET cc_start: 0.8790 (mtm) cc_final: 0.8341 (mtm) REVERT: D 3104 MET cc_start: 0.8262 (ptm) cc_final: 0.7902 (ptt) REVERT: D 3273 MET cc_start: 0.9106 (OUTLIER) cc_final: 0.8847 (mmt) REVERT: D 3286 ASN cc_start: 0.8641 (m-40) cc_final: 0.8291 (m-40) REVERT: D 3304 GLN cc_start: 0.8911 (tp-100) cc_final: 0.8406 (tp-100) REVERT: D 3888 PHE cc_start: 0.9103 (OUTLIER) cc_final: 0.8699 (m-80) REVERT: D 4035 TYR cc_start: 0.7506 (m-80) cc_final: 0.7140 (t80) REVERT: D 4258 MET cc_start: 0.7644 (ttt) cc_final: 0.7195 (tmt) REVERT: D 4292 MET cc_start: 0.8381 (mmm) cc_final: 0.8147 (mmp) REVERT: D 4303 ARG cc_start: 0.6096 (mmp-170) cc_final: 0.5752 (mmt180) REVERT: D 4707 MET cc_start: 0.8134 (ttp) cc_final: 0.7873 (ttm) REVERT: D 4878 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7232 (mt-10) outliers start: 108 outliers final: 51 residues processed: 979 average time/residue: 2.1361 time to fit residues: 2967.8394 Evaluate side-chains 982 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 906 time to evaluate : 11.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 1896 MET Chi-restraints excluded: chain A residue 2142 MET Chi-restraints excluded: chain A residue 2234 MET Chi-restraints excluded: chain A residue 2538 THR Chi-restraints excluded: chain A residue 2627 TRP Chi-restraints excluded: chain A residue 2940 ILE Chi-restraints excluded: chain A residue 3121 LEU Chi-restraints excluded: chain A residue 3150 ARG Chi-restraints excluded: chain A residue 3297 LYS Chi-restraints excluded: chain A residue 3653 GLU Chi-restraints excluded: chain A residue 3854 PHE Chi-restraints excluded: chain A residue 3888 PHE Chi-restraints excluded: chain A residue 4558 HIS Chi-restraints excluded: chain A residue 4878 GLU Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain G residue 30 MET Chi-restraints excluded: chain H residue 30 MET Chi-restraints excluded: chain B residue 198 ASN Chi-restraints excluded: chain B residue 776 GLN Chi-restraints excluded: chain B residue 1599 MET Chi-restraints excluded: chain B residue 1896 MET Chi-restraints excluded: chain B residue 2095 ILE Chi-restraints excluded: chain B residue 2142 MET Chi-restraints excluded: chain B residue 2150 MET Chi-restraints excluded: chain B residue 2234 MET Chi-restraints excluded: chain B residue 2538 THR Chi-restraints excluded: chain B residue 2627 TRP Chi-restraints excluded: chain B residue 2940 ILE Chi-restraints excluded: chain B residue 3121 LEU Chi-restraints excluded: chain B residue 3150 ARG Chi-restraints excluded: chain B residue 3201 VAL Chi-restraints excluded: chain B residue 3290 ILE Chi-restraints excluded: chain B residue 3653 GLU Chi-restraints excluded: chain B residue 3854 PHE Chi-restraints excluded: chain B residue 3888 PHE Chi-restraints excluded: chain B residue 4558 HIS Chi-restraints excluded: chain B residue 4878 GLU Chi-restraints excluded: chain C residue 776 GLN Chi-restraints excluded: chain C residue 931 TYR Chi-restraints excluded: chain C residue 1599 MET Chi-restraints excluded: chain C residue 1896 MET Chi-restraints excluded: chain C residue 2234 MET Chi-restraints excluded: chain C residue 2456 MET Chi-restraints excluded: chain C residue 2627 TRP Chi-restraints excluded: chain C residue 2844 MET Chi-restraints excluded: chain C residue 2940 ILE Chi-restraints excluded: chain C residue 3121 LEU Chi-restraints excluded: chain C residue 3150 ARG Chi-restraints excluded: chain C residue 3288 LEU Chi-restraints excluded: chain C residue 3290 ILE Chi-restraints excluded: chain C residue 3310 VAL Chi-restraints excluded: chain C residue 3653 GLU Chi-restraints excluded: chain C residue 3739 MET Chi-restraints excluded: chain C residue 3854 PHE Chi-restraints excluded: chain C residue 4878 GLU Chi-restraints excluded: chain D residue 776 GLN Chi-restraints excluded: chain D residue 931 TYR Chi-restraints excluded: chain D residue 1896 MET Chi-restraints excluded: chain D residue 2142 MET Chi-restraints excluded: chain D residue 2234 MET Chi-restraints excluded: chain D residue 2538 THR Chi-restraints excluded: chain D residue 2627 TRP Chi-restraints excluded: chain D residue 2844 MET Chi-restraints excluded: chain D residue 2940 ILE Chi-restraints excluded: chain D residue 3273 MET Chi-restraints excluded: chain D residue 3318 HIS Chi-restraints excluded: chain D residue 3739 MET Chi-restraints excluded: chain D residue 3854 PHE Chi-restraints excluded: chain D residue 3888 PHE Chi-restraints excluded: chain D residue 3954 MET Chi-restraints excluded: chain D residue 4485 ILE Chi-restraints excluded: chain D residue 4558 HIS Chi-restraints excluded: chain D residue 4568 MET Chi-restraints excluded: chain D residue 4878 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1515 optimal weight: 10.0000 chunk 1595 optimal weight: 20.0000 chunk 1455 optimal weight: 5.9990 chunk 1552 optimal weight: 8.9990 chunk 934 optimal weight: 4.9990 chunk 676 optimal weight: 7.9990 chunk 1218 optimal weight: 7.9990 chunk 476 optimal weight: 8.9990 chunk 1402 optimal weight: 9.9990 chunk 1467 optimal weight: 0.0000 chunk 1546 optimal weight: 7.9990 overall best weight: 5.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 26 HIS G 26 HIS H 26 HIS B 225 GLN B 238 HIS ** B1501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1974 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2830 ASN ** B3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4493 ASN ** C 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1974 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3318 HIS C4493 ASN ** C4636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3318 HIS D4493 ASN ** D4636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 141608 Z= 0.444 Angle : 0.666 17.729 191332 Z= 0.335 Chirality : 0.044 0.333 20988 Planarity : 0.005 0.097 24584 Dihedral : 6.059 179.414 19024 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.67 % Allowed : 9.64 % Favored : 89.69 % 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: 1.47 (0.06), residues: 17212 helix: 2.10 (0.06), residues: 8920 sheet: -0.07 (0.12), residues: 1816 loop : -0.26 (0.08), residues: 6476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.101 0.002 TRP A 893 HIS 0.042 0.001 HIS D3318 PHE 0.024 0.002 PHE B2085 TYR 0.029 0.002 TYR C2801 ARG 0.021 0.001 ARG D 520 *********************** 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 1025 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 923 time to evaluate : 11.904 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: A 313 ASN cc_start: 0.7986 (t0) cc_final: 0.7581 (m-40) REVERT: A 317 MET cc_start: 0.7541 (ppp) cc_final: 0.7152 (pp-130) REVERT: A 943 LEU cc_start: 0.9203 (mt) cc_final: 0.8955 (mt) REVERT: A 995 MET cc_start: 0.8150 (tmm) cc_final: 0.7593 (tmm) REVERT: A 1057 LEU cc_start: 0.9330 (mm) cc_final: 0.9065 (mt) REVERT: A 2279 MET cc_start: 0.8061 (ttp) cc_final: 0.7820 (tmm) REVERT: A 2627 TRP cc_start: 0.8454 (OUTLIER) cc_final: 0.7612 (m-10) REVERT: A 2939 TYR cc_start: 0.7953 (m-10) cc_final: 0.7622 (m-80) REVERT: A 2940 ILE cc_start: 0.8848 (OUTLIER) cc_final: 0.8507 (tt) REVERT: A 3046 MET cc_start: 0.9151 (mmp) cc_final: 0.8909 (mmm) REVERT: A 3092 GLN cc_start: 0.7684 (tp40) cc_final: 0.7381 (tp-100) REVERT: A 3104 MET cc_start: 0.8203 (mtp) cc_final: 0.7918 (ptt) REVERT: A 3121 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8542 (tp) REVERT: A 3215 MET cc_start: 0.9199 (mmt) cc_final: 0.8863 (mmm) REVERT: A 3273 MET cc_start: 0.9130 (mmm) cc_final: 0.8894 (mmt) REVERT: A 3286 ASN cc_start: 0.8491 (m-40) cc_final: 0.8131 (m-40) REVERT: A 3304 GLN cc_start: 0.8954 (tp-100) cc_final: 0.8445 (tp-100) REVERT: A 3888 PHE cc_start: 0.9143 (OUTLIER) cc_final: 0.8697 (m-80) REVERT: A 4258 MET cc_start: 0.7748 (ttt) cc_final: 0.7286 (tmt) REVERT: A 4292 MET cc_start: 0.8411 (mmm) cc_final: 0.8192 (mmp) REVERT: A 4303 ARG cc_start: 0.6213 (mmp-170) cc_final: 0.5842 (mmt90) REVERT: A 4707 MET cc_start: 0.8179 (ttp) cc_final: 0.7884 (ttm) REVERT: A 4878 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.7231 (mt-10) REVERT: G 18 LYS cc_start: 0.9076 (mppt) cc_final: 0.8788 (mttp) REVERT: G 30 MET cc_start: 0.7415 (OUTLIER) cc_final: 0.6890 (mpt) REVERT: H 30 MET cc_start: 0.7418 (OUTLIER) cc_final: 0.6872 (mpt) REVERT: B 198 ASN cc_start: 0.4796 (OUTLIER) cc_final: 0.4456 (m-40) REVERT: B 313 ASN cc_start: 0.7900 (t0) cc_final: 0.7612 (m-40) REVERT: B 655 MET cc_start: 0.8597 (mmm) cc_final: 0.8368 (mmm) REVERT: B 943 LEU cc_start: 0.9146 (mt) cc_final: 0.8804 (mm) REVERT: B 964 MET cc_start: 0.7327 (pmt) cc_final: 0.7051 (pmm) REVERT: B 995 MET cc_start: 0.8171 (tmm) cc_final: 0.7583 (tmm) REVERT: B 2150 MET cc_start: 0.8180 (OUTLIER) cc_final: 0.6581 (mpp) REVERT: B 2279 MET cc_start: 0.7988 (ttp) cc_final: 0.7714 (tmm) REVERT: B 2627 TRP cc_start: 0.8428 (OUTLIER) cc_final: 0.7598 (m-10) REVERT: B 2940 ILE cc_start: 0.8842 (OUTLIER) cc_final: 0.8512 (tt) REVERT: B 3104 MET cc_start: 0.8257 (ptm) cc_final: 0.7892 (ptt) REVERT: B 3150 ARG cc_start: 0.7569 (tpm-80) cc_final: 0.7215 (tpm170) REVERT: B 3215 MET cc_start: 0.9215 (mmt) cc_final: 0.8894 (mmm) REVERT: B 3286 ASN cc_start: 0.8519 (m-40) cc_final: 0.8216 (m-40) REVERT: B 3888 PHE cc_start: 0.9142 (OUTLIER) cc_final: 0.8687 (m-80) REVERT: B 4258 MET cc_start: 0.7752 (ttt) cc_final: 0.7339 (tmt) REVERT: B 4303 ARG cc_start: 0.6291 (mmp-170) cc_final: 0.5804 (mmt90) REVERT: B 4707 MET cc_start: 0.8177 (ttp) cc_final: 0.7876 (ttm) REVERT: B 4878 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.7213 (mt-10) REVERT: C 317 MET cc_start: 0.7508 (ppp) cc_final: 0.7227 (ppp) REVERT: C 943 LEU cc_start: 0.9164 (mt) cc_final: 0.8834 (mm) REVERT: C 983 LEU cc_start: 0.8467 (mm) cc_final: 0.8028 (mm) REVERT: C 995 MET cc_start: 0.8144 (tmm) cc_final: 0.7599 (tmm) REVERT: C 1953 MET cc_start: 0.7977 (mmt) cc_final: 0.7740 (mpp) REVERT: C 2279 MET cc_start: 0.8070 (ttp) cc_final: 0.7808 (tmm) REVERT: C 2584 MET cc_start: 0.8724 (mmm) cc_final: 0.8447 (mtm) REVERT: C 2627 TRP cc_start: 0.8518 (OUTLIER) cc_final: 0.7928 (m-10) REVERT: C 2939 TYR cc_start: 0.8012 (m-10) cc_final: 0.7655 (m-80) REVERT: C 2940 ILE cc_start: 0.8821 (OUTLIER) cc_final: 0.8500 (tt) REVERT: C 3104 MET cc_start: 0.8272 (ptm) cc_final: 0.7918 (ptt) REVERT: C 3121 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8541 (tp) REVERT: C 3215 MET cc_start: 0.9175 (mmt) cc_final: 0.8832 (mmm) REVERT: C 3888 PHE cc_start: 0.9105 (OUTLIER) cc_final: 0.8649 (m-80) REVERT: C 4258 MET cc_start: 0.7612 (ttt) cc_final: 0.7170 (tmt) REVERT: C 4303 ARG cc_start: 0.6331 (mmp-170) cc_final: 0.5962 (mpt180) REVERT: C 4307 ARG cc_start: 0.7561 (mtt90) cc_final: 0.7321 (mtt90) REVERT: D 241 MET cc_start: 0.5705 (tpt) cc_final: 0.5485 (tpp) REVERT: D 895 MET cc_start: 0.8494 (mtt) cc_final: 0.7892 (ptp) REVERT: D 943 LEU cc_start: 0.9157 (mt) cc_final: 0.8844 (mt) REVERT: D 964 MET cc_start: 0.6518 (pmt) cc_final: 0.6017 (pmm) REVERT: D 983 LEU cc_start: 0.8569 (mm) cc_final: 0.8223 (mm) REVERT: D 995 MET cc_start: 0.8141 (tmm) cc_final: 0.7554 (tmm) REVERT: D 1057 LEU cc_start: 0.9343 (mm) cc_final: 0.9139 (mt) REVERT: D 2627 TRP cc_start: 0.8493 (OUTLIER) cc_final: 0.7726 (m-10) REVERT: D 2939 TYR cc_start: 0.8001 (m-10) cc_final: 0.7628 (m-80) REVERT: D 2940 ILE cc_start: 0.8779 (OUTLIER) cc_final: 0.8480 (tt) REVERT: D 3003 MET cc_start: 0.8824 (mtm) cc_final: 0.8352 (mtm) REVERT: D 3104 MET cc_start: 0.8292 (ptm) cc_final: 0.7937 (ptt) REVERT: D 3215 MET cc_start: 0.9107 (mmt) cc_final: 0.8767 (mmm) REVERT: D 3273 MET cc_start: 0.9125 (OUTLIER) cc_final: 0.8882 (mmt) REVERT: D 3286 ASN cc_start: 0.8661 (m-40) cc_final: 0.8320 (m-40) REVERT: D 3304 GLN cc_start: 0.8935 (tp-100) cc_final: 0.8431 (tp-100) REVERT: D 3310 VAL cc_start: 0.9439 (t) cc_final: 0.9202 (m) REVERT: D 3888 PHE cc_start: 0.9132 (OUTLIER) cc_final: 0.8669 (m-80) REVERT: D 4035 TYR cc_start: 0.7558 (m-80) cc_final: 0.7224 (t80) REVERT: D 4258 MET cc_start: 0.7673 (ttt) cc_final: 0.7219 (tmt) REVERT: D 4303 ARG cc_start: 0.6101 (mmp-170) cc_final: 0.5743 (mmt180) REVERT: D 4707 MET cc_start: 0.8141 (ttp) cc_final: 0.7883 (ttm) outliers start: 102 outliers final: 49 residues processed: 984 average time/residue: 2.1568 time to fit residues: 3035.6576 Evaluate side-chains 978 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 908 time to evaluate : 11.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 1896 MET Chi-restraints excluded: chain A residue 2142 MET Chi-restraints excluded: chain A residue 2234 MET Chi-restraints excluded: chain A residue 2627 TRP Chi-restraints excluded: chain A residue 2681 MET Chi-restraints excluded: chain A residue 2940 ILE Chi-restraints excluded: chain A residue 3121 LEU Chi-restraints excluded: chain A residue 3150 ARG Chi-restraints excluded: chain A residue 3297 LYS Chi-restraints excluded: chain A residue 3653 GLU Chi-restraints excluded: chain A residue 3854 PHE Chi-restraints excluded: chain A residue 3888 PHE Chi-restraints excluded: chain A residue 4558 HIS Chi-restraints excluded: chain A residue 4878 GLU Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain G residue 30 MET Chi-restraints excluded: chain H residue 30 MET Chi-restraints excluded: chain B residue 198 ASN Chi-restraints excluded: chain B residue 776 GLN Chi-restraints excluded: chain B residue 1599 MET Chi-restraints excluded: chain B residue 1608 VAL Chi-restraints excluded: chain B residue 1896 MET Chi-restraints excluded: chain B residue 2142 MET Chi-restraints excluded: chain B residue 2150 MET Chi-restraints excluded: chain B residue 2234 MET Chi-restraints excluded: chain B residue 2627 TRP Chi-restraints excluded: chain B residue 2940 ILE Chi-restraints excluded: chain B residue 3121 LEU Chi-restraints excluded: chain B residue 3201 VAL Chi-restraints excluded: chain B residue 3290 ILE Chi-restraints excluded: chain B residue 3310 VAL Chi-restraints excluded: chain B residue 3653 GLU Chi-restraints excluded: chain B residue 3854 PHE Chi-restraints excluded: chain B residue 3888 PHE Chi-restraints excluded: chain B residue 4558 HIS Chi-restraints excluded: chain B residue 4878 GLU Chi-restraints excluded: chain C residue 776 GLN Chi-restraints excluded: chain C residue 931 TYR Chi-restraints excluded: chain C residue 1599 MET Chi-restraints excluded: chain C residue 1896 MET Chi-restraints excluded: chain C residue 2234 MET Chi-restraints excluded: chain C residue 2627 TRP Chi-restraints excluded: chain C residue 2763 LEU Chi-restraints excluded: chain C residue 2940 ILE Chi-restraints excluded: chain C residue 3121 LEU Chi-restraints excluded: chain C residue 3150 ARG Chi-restraints excluded: chain C residue 3288 LEU Chi-restraints excluded: chain C residue 3290 ILE Chi-restraints excluded: chain C residue 3310 VAL Chi-restraints excluded: chain C residue 3653 GLU Chi-restraints excluded: chain C residue 3854 PHE Chi-restraints excluded: chain C residue 3888 PHE Chi-restraints excluded: chain C residue 4878 GLU Chi-restraints excluded: chain D residue 776 GLN Chi-restraints excluded: chain D residue 1896 MET Chi-restraints excluded: chain D residue 2142 MET Chi-restraints excluded: chain D residue 2234 MET Chi-restraints excluded: chain D residue 2627 TRP Chi-restraints excluded: chain D residue 2844 MET Chi-restraints excluded: chain D residue 2940 ILE Chi-restraints excluded: chain D residue 3273 MET Chi-restraints excluded: chain D residue 3739 MET Chi-restraints excluded: chain D residue 3854 PHE Chi-restraints excluded: chain D residue 3888 PHE Chi-restraints excluded: chain D residue 4558 HIS Chi-restraints excluded: chain D residue 4568 MET Chi-restraints excluded: chain D residue 4878 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1019 optimal weight: 0.7980 chunk 1641 optimal weight: 0.9990 chunk 1001 optimal weight: 5.9990 chunk 778 optimal weight: 6.9990 chunk 1140 optimal weight: 4.9990 chunk 1721 optimal weight: 4.9990 chunk 1584 optimal weight: 6.9990 chunk 1370 optimal weight: 0.8980 chunk 142 optimal weight: 5.9990 chunk 1058 optimal weight: 4.9990 chunk 840 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4164 GLN A4493 ASN E 26 HIS G 26 HIS G 44 ASN H 26 HIS B 225 GLN ** B1501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3318 HIS C 896 ASN ** C 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3318 HIS C3955 GLN C3975 GLN ** C4636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1974 ASN ** D3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3318 HIS ** D4057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4493 ASN ** D4636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 141608 Z= 0.239 Angle : 0.618 18.693 191332 Z= 0.309 Chirality : 0.041 0.334 20988 Planarity : 0.004 0.085 24584 Dihedral : 5.930 179.812 19024 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.52 % Allowed : 9.83 % Favored : 89.65 % 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: 1.57 (0.07), residues: 17212 helix: 2.18 (0.06), residues: 8924 sheet: -0.03 (0.12), residues: 1824 loop : -0.20 (0.08), residues: 6464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.105 0.002 TRP A 893 HIS 0.018 0.001 HIS D3318 PHE 0.025 0.001 PHE A4660 TYR 0.031 0.001 TYR B4080 ARG 0.020 0.000 ARG G 14 ********************** 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 988 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 909 time to evaluate : 10.901 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: A 313 ASN cc_start: 0.7942 (t0) cc_final: 0.7550 (m-40) REVERT: A 317 MET cc_start: 0.7563 (ppp) cc_final: 0.7166 (pp-130) REVERT: A 943 LEU cc_start: 0.9168 (mt) cc_final: 0.8906 (mt) REVERT: A 964 MET cc_start: 0.6901 (pmt) cc_final: 0.6471 (pmm) REVERT: A 995 MET cc_start: 0.8111 (tmm) cc_final: 0.7456 (tmm) REVERT: A 1057 LEU cc_start: 0.9313 (mm) cc_final: 0.9046 (mt) REVERT: A 2279 MET cc_start: 0.8011 (ttp) cc_final: 0.7783 (tmm) REVERT: A 2627 TRP cc_start: 0.8350 (OUTLIER) cc_final: 0.7466 (m-10) REVERT: A 2939 TYR cc_start: 0.7911 (m-10) cc_final: 0.7597 (m-80) REVERT: A 2940 ILE cc_start: 0.8814 (OUTLIER) cc_final: 0.8492 (tt) REVERT: A 3092 GLN cc_start: 0.7655 (tp40) cc_final: 0.7351 (tp-100) REVERT: A 3121 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8562 (tp) REVERT: A 3215 MET cc_start: 0.9164 (mmt) cc_final: 0.8856 (mmm) REVERT: A 3273 MET cc_start: 0.9099 (mmm) cc_final: 0.8894 (mmt) REVERT: A 3286 ASN cc_start: 0.8485 (m-40) cc_final: 0.8147 (m-40) REVERT: A 3297 LYS cc_start: 0.6566 (OUTLIER) cc_final: 0.5650 (mmtt) REVERT: A 3304 GLN cc_start: 0.8921 (tp-100) cc_final: 0.8416 (tp-100) REVERT: A 4258 MET cc_start: 0.7722 (ttt) cc_final: 0.7275 (tmt) REVERT: A 4292 MET cc_start: 0.8408 (mmm) cc_final: 0.8194 (mmp) REVERT: A 4303 ARG cc_start: 0.6198 (mmp-170) cc_final: 0.5840 (mmt90) REVERT: A 4707 MET cc_start: 0.8165 (ttp) cc_final: 0.7840 (ttm) REVERT: A 4878 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.7224 (mt-10) REVERT: G 18 LYS cc_start: 0.9087 (mppt) cc_final: 0.8796 (mttp) REVERT: G 30 MET cc_start: 0.7335 (OUTLIER) cc_final: 0.6755 (mpp) REVERT: H 30 MET cc_start: 0.7352 (OUTLIER) cc_final: 0.6761 (mpp) REVERT: H 44 ASN cc_start: 0.8618 (t0) cc_final: 0.8251 (t0) REVERT: B 198 ASN cc_start: 0.4607 (OUTLIER) cc_final: 0.4015 (m-40) REVERT: B 313 ASN cc_start: 0.7879 (t0) cc_final: 0.7597 (m-40) REVERT: B 655 MET cc_start: 0.8583 (mmm) cc_final: 0.8329 (mmm) REVERT: B 943 LEU cc_start: 0.9113 (mt) cc_final: 0.8835 (mt) REVERT: B 964 MET cc_start: 0.7067 (pmt) cc_final: 0.6766 (pmm) REVERT: B 995 MET cc_start: 0.8118 (tmm) cc_final: 0.7557 (tmm) REVERT: B 1975 MET cc_start: 0.7571 (mtp) cc_final: 0.7293 (mtm) REVERT: B 2150 MET cc_start: 0.8158 (OUTLIER) cc_final: 0.6498 (mpp) REVERT: B 2279 MET cc_start: 0.7951 (ttp) cc_final: 0.7692 (tmm) REVERT: B 2627 TRP cc_start: 0.8320 (OUTLIER) cc_final: 0.7457 (m-10) REVERT: B 2940 ILE cc_start: 0.8815 (OUTLIER) cc_final: 0.8488 (tt) REVERT: B 3104 MET cc_start: 0.8242 (ptm) cc_final: 0.7897 (ptt) REVERT: B 3150 ARG cc_start: 0.7394 (tpm-80) cc_final: 0.7095 (tpm170) REVERT: B 3215 MET cc_start: 0.9210 (mmt) cc_final: 0.8872 (mmm) REVERT: B 3286 ASN cc_start: 0.8473 (m-40) cc_final: 0.8154 (m-40) REVERT: B 3888 PHE cc_start: 0.9128 (OUTLIER) cc_final: 0.8703 (m-80) REVERT: B 4258 MET cc_start: 0.7730 (ttt) cc_final: 0.7311 (tmt) REVERT: B 4303 ARG cc_start: 0.6239 (mmp-170) cc_final: 0.5771 (mmt90) REVERT: B 4307 ARG cc_start: 0.7474 (mtt90) cc_final: 0.7209 (mtt90) REVERT: B 4502 MET cc_start: 0.7775 (mtm) cc_final: 0.7447 (mtm) REVERT: B 4707 MET cc_start: 0.8163 (ttp) cc_final: 0.7855 (ttm) REVERT: B 4878 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.7242 (mt-10) REVERT: C 943 LEU cc_start: 0.9144 (mt) cc_final: 0.8803 (mm) REVERT: C 983 LEU cc_start: 0.8464 (mm) cc_final: 0.8019 (mm) REVERT: C 995 MET cc_start: 0.8096 (tmm) cc_final: 0.7538 (tmm) REVERT: C 2279 MET cc_start: 0.8052 (ttp) cc_final: 0.7815 (tmm) REVERT: C 2627 TRP cc_start: 0.8410 (OUTLIER) cc_final: 0.7674 (m-10) REVERT: C 2939 TYR cc_start: 0.7990 (m-10) cc_final: 0.7638 (m-80) REVERT: C 2940 ILE cc_start: 0.8795 (OUTLIER) cc_final: 0.8500 (tt) REVERT: C 3104 MET cc_start: 0.8256 (ptm) cc_final: 0.7918 (ptt) REVERT: C 3121 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8542 (tp) REVERT: C 3215 MET cc_start: 0.9192 (mmt) cc_final: 0.8841 (mmm) REVERT: C 3297 LYS cc_start: 0.7189 (mmpt) cc_final: 0.6730 (mmtt) REVERT: C 4258 MET cc_start: 0.7589 (ttt) cc_final: 0.7146 (tmt) REVERT: C 4303 ARG cc_start: 0.6321 (mmp-170) cc_final: 0.5910 (mmt180) REVERT: C 4502 MET cc_start: 0.7772 (mtm) cc_final: 0.7501 (mtm) REVERT: C 4878 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.7224 (mt-10) REVERT: D 241 MET cc_start: 0.5620 (tpt) cc_final: 0.5406 (tpp) REVERT: D 943 LEU cc_start: 0.9135 (mt) cc_final: 0.8821 (mt) REVERT: D 964 MET cc_start: 0.6318 (pmt) cc_final: 0.5800 (pmm) REVERT: D 983 LEU cc_start: 0.8543 (mm) cc_final: 0.8286 (mm) REVERT: D 995 MET cc_start: 0.8092 (tmm) cc_final: 0.7527 (tmm) REVERT: D 1057 LEU cc_start: 0.9312 (mm) cc_final: 0.9103 (mt) REVERT: D 2939 TYR cc_start: 0.7959 (m-10) cc_final: 0.7599 (m-80) REVERT: D 2940 ILE cc_start: 0.8746 (OUTLIER) cc_final: 0.8456 (tt) REVERT: D 3003 MET cc_start: 0.8773 (mtm) cc_final: 0.8361 (mtm) REVERT: D 3104 MET cc_start: 0.8290 (ptm) cc_final: 0.7953 (ptt) REVERT: D 3215 MET cc_start: 0.9115 (mmt) cc_final: 0.8762 (mmm) REVERT: D 3273 MET cc_start: 0.9100 (OUTLIER) cc_final: 0.8852 (mmt) REVERT: D 3286 ASN cc_start: 0.8631 (m-40) cc_final: 0.8286 (m-40) REVERT: D 3304 GLN cc_start: 0.8906 (tp-100) cc_final: 0.8405 (tp-100) REVERT: D 4258 MET cc_start: 0.7643 (ttt) cc_final: 0.7192 (tmt) REVERT: D 4303 ARG cc_start: 0.6105 (mmp-170) cc_final: 0.5751 (mmt180) REVERT: D 4707 MET cc_start: 0.8125 (ttp) cc_final: 0.7883 (ttm) REVERT: D 4878 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.7193 (mt-10) outliers start: 79 outliers final: 40 residues processed: 955 average time/residue: 2.3004 time to fit residues: 3163.1068 Evaluate side-chains 963 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 903 time to evaluate : 11.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 1896 MET Chi-restraints excluded: chain A residue 2142 MET Chi-restraints excluded: chain A residue 2234 MET Chi-restraints excluded: chain A residue 2627 TRP Chi-restraints excluded: chain A residue 2940 ILE Chi-restraints excluded: chain A residue 3121 LEU Chi-restraints excluded: chain A residue 3297 LYS Chi-restraints excluded: chain A residue 3653 GLU Chi-restraints excluded: chain A residue 3854 PHE Chi-restraints excluded: chain A residue 4558 HIS Chi-restraints excluded: chain A residue 4878 GLU Chi-restraints excluded: chain G residue 30 MET Chi-restraints excluded: chain H residue 30 MET Chi-restraints excluded: chain B residue 198 ASN Chi-restraints excluded: chain B residue 776 GLN Chi-restraints excluded: chain B residue 1599 MET Chi-restraints excluded: chain B residue 1608 VAL Chi-restraints excluded: chain B residue 1896 MET Chi-restraints excluded: chain B residue 2142 MET Chi-restraints excluded: chain B residue 2150 MET Chi-restraints excluded: chain B residue 2234 MET Chi-restraints excluded: chain B residue 2627 TRP Chi-restraints excluded: chain B residue 2940 ILE Chi-restraints excluded: chain B residue 3121 LEU Chi-restraints excluded: chain B residue 3201 VAL Chi-restraints excluded: chain B residue 3290 ILE Chi-restraints excluded: chain B residue 3653 GLU Chi-restraints excluded: chain B residue 3854 PHE Chi-restraints excluded: chain B residue 3888 PHE Chi-restraints excluded: chain B residue 4558 HIS Chi-restraints excluded: chain B residue 4878 GLU Chi-restraints excluded: chain C residue 776 GLN Chi-restraints excluded: chain C residue 1599 MET Chi-restraints excluded: chain C residue 1896 MET Chi-restraints excluded: chain C residue 2234 MET Chi-restraints excluded: chain C residue 2627 TRP Chi-restraints excluded: chain C residue 2940 ILE Chi-restraints excluded: chain C residue 3121 LEU Chi-restraints excluded: chain C residue 3288 LEU Chi-restraints excluded: chain C residue 3290 ILE Chi-restraints excluded: chain C residue 3310 VAL Chi-restraints excluded: chain C residue 3318 HIS Chi-restraints excluded: chain C residue 3653 GLU Chi-restraints excluded: chain C residue 3854 PHE Chi-restraints excluded: chain C residue 4878 GLU Chi-restraints excluded: chain D residue 776 GLN Chi-restraints excluded: chain D residue 1608 VAL Chi-restraints excluded: chain D residue 1896 MET Chi-restraints excluded: chain D residue 2142 MET Chi-restraints excluded: chain D residue 2234 MET Chi-restraints excluded: chain D residue 2940 ILE Chi-restraints excluded: chain D residue 3273 MET Chi-restraints excluded: chain D residue 3318 HIS Chi-restraints excluded: chain D residue 3739 MET Chi-restraints excluded: chain D residue 3854 PHE Chi-restraints excluded: chain D residue 4558 HIS Chi-restraints excluded: chain D residue 4568 MET Chi-restraints excluded: chain D residue 4878 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1088 optimal weight: 7.9990 chunk 1460 optimal weight: 1.9990 chunk 419 optimal weight: 6.9990 chunk 1264 optimal weight: 5.9990 chunk 202 optimal weight: 4.9990 chunk 380 optimal weight: 8.9990 chunk 1373 optimal weight: 8.9990 chunk 574 optimal weight: 3.9990 chunk 1409 optimal weight: 50.0000 chunk 173 optimal weight: 2.9990 chunk 252 optimal weight: 8.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3318 HIS E 26 HIS G 26 HIS ** G 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 26 HIS B 225 GLN ** B1974 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1974 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3318 HIS C3955 GLN C3975 GLN ** C4636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1974 ASN ** D3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3318 HIS ** D4057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.053720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.039331 restraints weight = 1014728.167| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 3.51 r_work: 0.2956 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2955 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2955 r_free = 0.2955 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2955 r_free = 0.2955 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| r_final: 0.2955 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 141608 Z= 0.348 Angle : 0.644 15.857 191332 Z= 0.323 Chirality : 0.043 0.326 20988 Planarity : 0.005 0.098 24584 Dihedral : 5.954 179.750 19024 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.54 % Allowed : 9.94 % Favored : 89.52 % 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: 1.53 (0.07), residues: 17212 helix: 2.14 (0.06), residues: 8940 sheet: 0.00 (0.12), residues: 1868 loop : -0.23 (0.08), residues: 6404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.117 0.002 TRP A 893 HIS 0.029 0.001 HIS C3318 PHE 0.025 0.002 PHE C3319 TYR 0.038 0.002 TYR D4035 ARG 0.023 0.001 ARG A 520 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 47672.32 seconds wall clock time: 827 minutes 53.88 seconds (49673.88 seconds total)